annotate test-data/output_db-card.txt @ 10:c2ef298da409 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"

#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40786	41547	-	ANT(4')-Ib	1-762/762	===============	0/0	100.00	100.00	card	GQ900432.1:27499-26737	Kanamycin nucleotidyltransferase sequence from Staphylococcus aureus plasmid. Confers resistance to kanamycin neomycin and other aminoglycosides	aminoglycoside
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46925	-	mecA	1-2007/2007	===============	0/0	100.00	99.90	card	KC243783:0-2007	A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.	penam
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	47025	48782	+	mecR1	1-1758/1758	===============	0/0	100.00	99.94	card	CP000703.1:40848-42606	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.	penam
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	48782	49153	+	mecI	1-372/372	===============	0/0	100.00	99.73	card	BA000018.3:48893-49265	mecI acts as a repressor of transcription of the mecA/mecR1/mecI operon.	penam
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	55890	56621	+	ErmA	1-732/732	===============	0/0	100.00	100.00	card	X03216.1:5282-4550	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.	lincosamide;macrolide;streptogramin
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	152865	154217	+	tet(38)	1-1353/1353	===============	0/0	100.00	98.52	card	AY825285:0-1353	Tet38 is a tetracycline efflux pump found in the Gram-positive Staphylococcus aureus. It is regulated by mgrA which also regulates NorB.	tetracycline
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	376045	376464	+	mepR	1-420/420	===============	0/0	100.00	99.05	card	BA000017.4:379931-380351	MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon.	glycylcycline;tetracycline
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	376571	377926	+	mepA	1-1356/1356	===============	0/0	100.00	98.53	card	AY661734.1:839-2195	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.	glycylcycline;tetracycline
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	774312	774755	-	mgrA	1-444/444	===============	0/0	100.00	99.78	card	BA000018.3:735860-735416	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.	acridine_dye;cephalosporin;fluoroquinolone;penam;peptide;tetracycline
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	782414	783579	+	Staphylococcus_aureus_norA	1-1166/1167	===============	0/0	99.91	91.51	card	D90119.1:477-1644	NorA gene cloned from Staphylococcus aureus conferred relatively high resistance to hydrophilic quinolones such as norfloxacin enoxacin ofloxacin and ciprofloxacin in S. aureus and Escherichia coli. Had low or no resistance at all to hydrophobic ones such as nalidixic acid oxolinic acid and sparfloxacin in S. aureus and Escherichia coli.	fluoroquinolone
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1486310	1487665	-	arlS	1-1356/1356	===============	0/0	100.00	98.38	card	CP000253.1:1361636-1360280	ArlS is a protein histidine kinase that phosphorylates ArlR a promoter for norA expression.	acridine_dye;fluoroquinolone
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1487662	1488321	-	arlR	1-660/660	===============	0/0	100.00	99.09	card	CP023390.1:1462248-1461588	ArlR is a response regulator that binds to the norA promoter to activate expression. ArlR must first be phosphorylated by ArlS.	acridine_dye;fluoroquinolone
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	+	ErmA	1-732/732	===============	0/0	100.00	100.00	card	X03216.1:5282-4550	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.	lincosamide;macrolide;streptogramin
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1913827	1914672	+	PC1_beta-lactamase_(blaZ)	1-846/846	===============	0/0	100.00	97.16	card	CP000732.1:10528-9682	The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus.	penam
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2338959	2340402	-	Staphylococcys_aureus_LmrS	1-1443/1443	========/======	1/1	100.00	91.41	card	CP000046.1:2236817-2235374	MFS transporters are secondary active transporters with single-polypeptide chains containing 400-600 amino acids that transport small solutes across the membrane by using electrochemical gradients. LmrS has 14 transmembrane helices and when expressed in E. coli is capable of extruding a variety of antibiotics inclinding linezolid trimethoprim florfenicol chlorampheniocol erythromycin streptomycin kanamycin and fusidic acid	aminoglycoside;diaminopyrimidine;macrolide;oxazolidinone;phenicol
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2488459	2488878	+	Staphylococcus_aureus_FosB	1-420/420	===============	0/0	100.00	98.81	card	AHLO01000073.1:63138-63558	The Bacillus subtilis fosB gene encodes a fosfomycin resistance protein	fosfomycin