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annotate test-data/output_db-card.txt @ 8:b734db305578 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
author iuc
date Wed, 22 Apr 2020 18:44:06 -0400
parents 4efdca267d51
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7
4efdca267d51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6535538b7767c3bbe20ac7e89b682154b595c932"
iuc
parents: 6
diff changeset
1 #FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE
8
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
2 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
3 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
4 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
5 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
6 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
7 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
8 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
9 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
10 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
11 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
12 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
13 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
14 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
15 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
16 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
b734db305578 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
iuc
parents: 7
diff changeset
17 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