annotate test-data/output_db-card.txt @ 6:1bb2ba6d3d96 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"

#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	40786	41547	ANT(4')-Ib	1-762/762	===============	0/0	100.00	100.00	card	GQ900432.1:26738-27500	Kanamycin nucleotidyltransferase sequence from Staphylococcus aureus plasmid. Confers resistance to kanamycin neomycin and other aminoglycosides
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	44919	46925	mecA	1-2007/2007	===============	0/0	100.00	99.90	card	KC243783:1-2008	A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	47025	48782	mecR1	1-1758/1758	===============	0/0	100.00	99.94	card	CP000703.1:40849-42607	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.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	48782	49153	mecI	1-372/372	===============	0/0	100.00	99.73	card	BA000018.3:48894-49266	mecI acts as a repressor of transcription of the mecA/mecR1/mecI operon.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	55890	56621	ErmA	1-732/732	===============	0/0	100.00	100.00	card	X03216.1:4551-5283	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.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	152865	154217	tet(38)	1-1353/1353	===============	0/0	100.00	98.52	card	AY825285:1-1354	Tet38 is a tetracycline efflux pump found in the Gram-positive Staphylococcus aureus. It is regulated by mgrA which also regulates NorB.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	376045	376464	mepR	1-420/420	===============	0/0	100.00	99.05	card	BA000017.4:379932-380352	MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	376571	377926	mepA	1-1356/1356	===============	0/0	100.00	98.53	card	AY661734.1:840-2196	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.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	774312	774755	mgrA	1-444/444	===============	0/0	100.00	99.78	card	BA000018.3:735417-735861	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.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	782414	783579	Staphylococcus_aureus_norA	1-1166/1167	===============	0/0	99.91	91.51	card	D90119.1:478-1645	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.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1486310	1487665	arlS	1-1356/1356	===============	0/0	100.00	98.38	card	CP000253.1:1360281-1361637	ArlS is a protein histidine kinase that phosphorylates ArlR a promoter for norA expression.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1487662	1488321	arlR	1-660/660	===============	0/0	100.00	99.09	card	NC_009641.1:1461589-1462249	ArlR is a response regulator that binds to the norA promoter to activate expression. ArlR must first be phosphorylated by ArlS.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1796513	1797244	ErmA	1-732/732	===============	0/0	100.00	100.00	card	X03216.1:4551-5283	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.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	1913827	1914672	PC1_beta-lactamase_(blaZ)	1-846/846	===============	0/0	100.00	97.16	card	CP000732.1:9683-10529	The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus.
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2338959	2340402	Staphylococcys_aureus_LmrS	1-1443/1443	========/======	1/1	100.00	91.41	card	CP000046.1:2235375-2236818	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
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2488459	2488878	Staphylococcus_aureus_FosB	1-420/420	===============	0/0	100.00	98.81	card	AHLO01000073.1:63139-63559	The Bacillus subtilis fosB gene encodes a fosfomycin resistance protein
MRSA0252.fna	gi|49482253|ref|NC_002952.2|	2622988	2624175	DHA-1	1-1188/1188	===============	0/0	100.00	99.16	card	BA000018.3:2517801-2518989	DHA-1 is a class C beta-lactamase found in Morganella morganii and Salmonella enterica