Mercurial > repos > iuc > abricate

comparison test-data/output_db-card.txt @ 5:f9bf6a8d8547 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
author iuc
date Wed, 11 Sep 2019 23:57:17 -0400
parents 6e9aea89e388
children 1bb2ba6d3d96
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4:78c75f134c16 5:f9bf6a8d8547
1 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION 1 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT
2 NC_002952.2 40786 41547 ANT(4')-Ib 1-762/762 =============== 0/0 100.00 100.00 card NC_013342.1:26738-27500 2 MRSA0252.fna gi|49482253|ref|NC_002952.2| 40786 41547 ANT(4')-Ib 1-762/762 =============== 0/0 100.00 100.00 card GQ900432.1:26738-27500 card~~~ANT(4')-Ib~~~GQ900432.1:26738-27500 Kanamycin nucleotidyltransferase sequence from Staphylococcus aureus plasmid. Confers resistance to kanamycin neomycin and other aminoglycosides
3 NC_002952.2 44918 46925 mecA 1-2008/2008 =============== 0/0 100.00 99.90 card KC243783:1-2008 3 MRSA0252.fna gi|49482253|ref|NC_002952.2| 44919 46925 mecA 1-2007/2007 =============== 0/0 100.00 99.90 card KC243783:1-2008 card~~~mecA~~~KC243783:1-2008 A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.
4 NC_002952.2 47025 48783 mecR1 1-1759/1759 =============== 0/0 100.00 99.94 card NC_009487:40849-42607 4 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 card~~~mecR1~~~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.
5 NC_002952.2 48782 49154 mecI 1-373/373 =============== 0/0 100.00 99.73 card NC_002745:48894-49266 5 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 card~~~mecI~~~BA000018.3:48894-49266 mecI acts as a repressor of transcription of the mecA/mecR1/mecI operon.
6 NC_002952.2 55890 56622 ErmA 1-733/733 =============== 0/0 100.00 100.00 card NC_009632:49745-50477 6 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 card~~~ErmA~~~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.
7 NC_002952.2 152865 154217 tet(38) 1-1353/1353 =============== 0/0 100.00 98.52 card AY825285:1-1354 7 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 card~~~tet(38)~~~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.
8 NC_002952.2 376045 376465 mepR 1-421/421 =============== 0/0 100.00 99.05 card NC_009782:379935-380355 8 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 card~~~mepR~~~BA000017.4:379932-380352 MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon.
9 NC_002952.2 376571 377926 mepA 1-1356/1356 =============== 0/0 100.00 98.53 card AY661734.1:840-2196 9 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 card~~~mepA~~~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.
10 NC_002952.2 774312 774756 mgrA 1-445/445 =============== 0/0 100.00 99.78 card NC_013450:694853-695297 10 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 card~~~mgrA~~~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.
11 NC_002952.2 782414 783543 norA 1-1130/1165 ========/====== 7/14 96.39 76.08 card AY566250:392-1556 11 MRSA0252.fna gi|49482253|ref|NC_002952.2| 782414 783579 Staphylococcus_aureus_norA 1-1166/1167 =============== 0/0 99.91 91.51 card D90119.1:478-1645 card~~~Staphylococcus_aureus_norA~~~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.
12 NC_002952.2 1486310 1487666 arlS 1-1357/1357 =============== 0/0 100.00 98.38 card NC_007795:1360281-1361637 12 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 card~~~arlS~~~CP000253.1:1360281-1361637 ArlS is a protein histidine kinase that phosphorylates ArlR a promoter for norA expression.
13 NC_002952.2 1487662 1488322 arlR 1-661/661 =============== 0/0 100.00 99.09 card NC_009641:1461589-1462249 13 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 card~~~arlR~~~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.
14 NC_002952.2 1796513 1797245 ErmA 1-733/733 =============== 0/0 100.00 100.00 card NC_009632:49745-50477 14 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 card~~~ErmA~~~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.
15 NC_002952.2 1913826 1914672 PC1_beta-lactamase_(blaZ) 1-847/847 =============== 0/0 100.00 97.17 card NC_010066:9683-10529 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 CP000732.1:9683-10529 card~~~PC1_beta-lactamase_(blaZ)~~~CP000732.1:9683-10529 The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus.
16 NC_002952.2 2047036 2048773 sav1866 1-1738/1738 =============== 0/0 100.00 99.19 card NC_002951:1987720-1989457 16 MRSA0252.fna gi|49482253|ref|NC_002952.2| 2338959 2340402 Staphylococcys_aureus_LmrS 1-1443/1443 ========/====== 1/1 100.00 91.41 card CP000046.1:2235375-2236818 card~~~Staphylococcys_aureus_LmrS~~~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
17 MRSA0252.fna gi|49482253|ref|NC_002952.2| 2488459 2488878 Staphylococcus_aureus_FosB 1-420/420 =============== 0/0 100.00 98.81 card AHLO01000073.1:63139-63559 card~~~Staphylococcus_aureus_FosB~~~AHLO01000073.1:63139-63559 The Bacillus subtilis fosB gene encodes a fosfomycin resistance protein
18 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 card~~~DHA-1~~~BA000018.3:2517801-2518989 DHA-1 is a class C beta-lactamase found in Morganella morganii and Salmonella enterica