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annotate test-data/SAMN11840202-abricate_report_full.tsv @ 4:22247b1a59d5 draft default tip

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
author public-health-bioinformatics
date Fri, 03 Jan 2020 14:30:22 -0500
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22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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1 #FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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2 SAMN11840202 contig00001 43895 45142 + mdtA 1-1248/1248 =============== 0/0 100.00 98.00 card U00096:2154016-2155264 MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC. antibacterial_free_fatty_acids/aminoglycoside/diaminopyrimidine/carbapenem/aminocoumarin/phenicol/glycylcycline/monobactam/penam/fluoroquinolone/macrolide/acridine_dye/triclosan/tetracycline
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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3 SAMN11840202 contig00001 45142 48264 + mdtB 1-3123/3123 =============== 0/0 100.00 99.84 card U00096:2155263-2158386 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. aminocoumarin/aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide/phenicol/glycylcycline/monobactam
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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4 SAMN11840202 contig00001 48265 51342 + mdtC 1-3078/3078 =============== 0/0 100.00 99.84 card U00096:2158386-2161464 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. diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin/glycylcycline/monobactam/phenicol/acridine_dye/triclosan/tetracycline/macrolide/fluoroquinolone/penam
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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5 SAMN11840202 contig00001 52755 54158 + baeS 1-1404/1404 =============== 0/0 100.00 99.93 card AP009048:2165013-2166417 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. aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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6 SAMN11840202 contig00001 54155 54877 + baeR 1-723/723 =============== 0/0 100.00 99.45 card AP009048.1:2166413-2167136 BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes. phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/penam/fluoroquinolone/macrolide/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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7 SAMN11840202 contig00001 197758 199401 - yojI 1-1644/1644 =============== 0/0 100.00 97.51 card U00096.3:2306972-2308616 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. peptide/nitroimidazole/rifamycin/pleuromutilin/penam/fluoroquinolone/cephalosporin/macrolide/tetracycline/acridine_dye
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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8 SAMN11840202 contig00001 257738 258706 + pmrF 1-969/969 =============== 0/0 100.00 100.00 card U00096:2367071-2368040 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. peptide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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9 SAMN11840202 contig00002 125167 126915 - msbA 1-1749/1749 =============== 0/0 100.00 100.00 card U00096.3:966621-968370 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. peptide/rifamycin/pleuromutilin/nitroimidazole/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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10 SAMN11840202 contig00002 208622 209854 - Escherichia_coli_mdfA 1-1233/1233 =============== 0/0 100.00 98.38 card JQ394987:1-1234 Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter. antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride/rifamycin/nitroimidazole/nucleoside/macrolide/penam/rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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11 SAMN11840202 contig00003 180544 180902 + Klebsiella_pneumoniae_KpnE 5-363/363 ========/====== 2/2 98.62 75.83 card AP006725.1:2483890-2484253 KpnE subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/benzalkonium_chloride/isoniazid/lincosamide/nucleoside/nitroimidazole/rifamycin/penam/macrolide/aminoglycoside/peptide/rhodamine/phenicol/glycylcycline/fosfomycin/oxazolidinone/acridine_dye/tetracycline/fluoroquinolone/cephalosporin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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12 SAMN11840202 contig00003 180894 181218 + Klebsiella_pneumoniae_KpnF 6-330/330 =============== 0/0 98.48 75.39 card AP006725.1:2484239-2484569 KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan. fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/aminoglycoside/rhodamine/peptide/rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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13 SAMN11840202 contig00003 213611 213994 - marA 1-384/384 =============== 0/0 100.00 100.00 card AP009048.1:1621288-1621672 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. antibacterial_free_fatty_acids/penem/diaminopyrimidine/macrolide/penam/rifamycin/cephamycin/aminocoumarin/carbapenem/aminoglycoside/cephalosporin/fluoroquinolone/tetracycline/triclosan/acridine_dye/monobactam/glycylcycline/phenicol
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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14 SAMN11840202 contig00004 202570 203978 - mdtK 1-1409/1425 ========/====== 2/4 98.74 75.34 card CP014358.1:2161326-2162751 A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine. glycylcycline/fluoroquinolone/tetracycline/acridine_dye
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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15 SAMN11840202 contig00007 134424 135056 - CRP 1-633/633 =============== 0/0 100.00 99.68 card AP009048.1:4153664-4154297 CRP is a global regulator that represses MdtEF multidrug efflux pump expression. tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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16 SAMN11840202 contig00008 37607 38800 + Escherichia_coli_acrA 1-1194/1194 =============== 0/0 100.00 100.00 card U00096.3:484426-485620 AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli. rifamycin/macrolide/penam/diaminopyrimidine/antibacterial_free_fatty_acids/glycylcycline/monobactam/phenicol/acridine_dye/tetracycline/triclosan/cephalosporin/fluoroquinolone/carbapenem/aminoglycoside/aminocoumarin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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17 SAMN11840202 contig00008 38823 41972 + acrB 1-3150/3150 =============== 0/0 100.00 100.00 card U00096.3:481254-484404 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. antibacterial_free_fatty_acids/diaminopyrimidine/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/phenicol/monobactam/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/triclosan/acridine_dye
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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18 SAMN11840202 contig00008 126851 128008 + Escherichia_coli_ampH 1-1158/1158 =============== 0/0 100.00 100.00 card AP012030.1:395554-396712 AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli. cephalosporin/penam
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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19 SAMN11840202 contig00010 97802 99268 - mdtP 1-1467/1467 =============== 0/0 100.00 100.00 card AP009048.1:4303043-4304510 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride benzalkonium_chloride/isoniazid/lincosamide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/penam/macrolide/nitroimidazole/rifamycin/nucleoside/rhodamine/peptide/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/fosfomycin/phenicol/glycylcycline
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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20 SAMN11840202 contig00010 99265 101316 - mdtO 1-2052/2052 =============== 0/0 100.00 99.95 card AP009048.1:4304506-4306558 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride nucleoside/rifamycin/nitroimidazole/macrolide/penam/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/isoniazid/lincosamide/benzalkonium_chloride/glycylcycline/phenicol/fosfomycin/oxazolidinone/acridine_dye/tetracycline/cephalosporin/fluoroquinolone/peptide/rhodamine
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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21 SAMN11840202 contig00010 101316 102347 - mdtN 1-1032/1032 =============== 0/0 100.00 100.00 card AP009048.1:4306557-4307589 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride. tetracycline/oxazolidinone/acridine_dye/cephalosporin/fluoroquinolone/glycylcycline/phenicol/fosfomycin/peptide/rhodamine/macrolide/penam/nucleoside/rifamycin/nitroimidazole/isoniazid/lincosamide/benzalkonium_chloride/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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22 SAMN11840202 contig00012 85775 87262 + tolC 1-1488/1488 =============== 0/0 100.00 100.00 card FJ768952:1-1489 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. rifamycin/triclosan/tetracycline/glycylcycline/cephamycin/carbapenem/aminoglycoside/macrolide/penam/pleuromutilin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/antibacterial_free_fatty_acids/bicyclomycin/penem/diaminopyrimidine/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/fosfomycin/monobactam/phenicol/rhodamine/peptide/aminocoumarin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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23 SAMN11840202 contig00013 50531 51007 - mphB 1-477/477 =============== 0/0 100.00 98.32 card AE005174.2:3397371-3397848 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. macrolide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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24 SAMN11840202 contig00013 71693 74806 - acrD 1-3114/3114 =============== 0/0 100.00 100.00 card AP009048.1:2586251-2589365 AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR. aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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25 SAMN11840202 contig00017 52034 53572 - emrY 1-1539/1539 =============== 0/0 100.00 98.83 card D78168:1592-3131 emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB. oxazolidinone/acridine_dye/tetracycline/cephalosporin/fluoroquinolone/glycylcycline/phenicol/fosfomycin/peptide/rhodamine/macrolide/penam/nucleoside/rifamycin/nitroimidazole/lincosamide/isoniazid/benzalkonium_chloride/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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26 SAMN11840202 contig00017 53572 54627 - emrK 1-1056/1056 =============== 0/0 100.00 99.72 card D78168:537-1593 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. macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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27 SAMN11840202 contig00017 55151 55765 + evgA 1-615/615 =============== 0/0 100.00 99.02 card BA000007.3:3212026-3212641 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. diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/benzalkonium_chloride/isoniazid/lincosamide/nucleoside/nitroimidazole/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/peptide/rhodamine/phenicol/monobactam/glycylcycline/fosfomycin/triclosan/tetracycline/oxazolidinone/acridine_dye/fluoroquinolone/cephalosporin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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28 SAMN11840202 contig00017 55770 59363 + evgS 1-3594/3594 =============== 0/0 100.00 99.11 card U00096:2484374-2487968 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. triclosan/tetracycline/acridine_dye/oxazolidinone/fluoroquinolone/cephalosporin/phenicol/monobactam/glycylcycline/fosfomycin/aminocoumarin/peptide/rhodamine/aminoglycoside/carbapenem/penam/macrolide/nucleoside/nitroimidazole/rifamycin/benzalkonium_chloride/isoniazid/lincosamide/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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29 SAMN11840202 contig00018 15251 16072 - bacA 1-822/822 =============== 0/0 100.00 100.00 card U00096.3:3203310-3204132 The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin. peptide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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30 SAMN11840202 contig00023 7667 9310 - eptA 1-1644/1644 =============== 0/0 100.00 99.94 card AP009048:4338625-4340269 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. peptide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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31 SAMN11840202 contig00023 51538 52671 - Escherichia_coli_ampC 1-1134/1134 =============== 0/0 100.00 97.27 card NC_000913.3:4377811-4378945 A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics. cephalosporin/penam
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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32 SAMN11840202 contig00024 3696 5234 - emrB 1-1539/1539 =============== 0/0 100.00 100.00 card U00096:2812616-2814155 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. rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/rifamycin/nitroimidazole/nucleoside/macrolide/penam
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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33 SAMN11840202 contig00024 5251 6423 - emrA 1-1173/1173 =============== 0/0 100.00 99.92 card AP009048:2810083-2811256 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. benzalkonium_chloride/isoniazid/lincosamide/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/penam/macrolide/nucleoside/nitroimidazole/rifamycin/peptide/rhodamine/acridine_dye/oxazolidinone/tetracycline/fluoroquinolone/cephalosporin/phenicol/glycylcycline/fosfomycin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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34 SAMN11840202 contig00024 6550 7080 - emrR 1-531/531 =============== 0/0 100.00 99.81 card U00096.3:2810770-2811301 EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression. rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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35 SAMN11840202 contig00033 19630 20838 + mdtH 1-1209/1209 =============== 0/0 100.00 99.92 card U00096:1124118-1125327 Multidrug resistance protein MdtH nitroimidazole/rifamycin/nucleoside/penam/macrolide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/rhodamine/peptide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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36 SAMN11840202 contig00033 29467 30693 + mdtG 1-1227/1227 =============== 0/0 100.00 99.43 card CP000800.1:1191728-1192955 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. macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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37 SAMN11840202 contig00035 41010 41423 + H-NS 1-414/414 =============== 0/0 100.00 99.28 card BA000007.3:1737691-1738105 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. bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/aminoglycoside/carbapenem/rhodamine/cephamycin/aminocoumarin/peptide/fosfomycin/phenicol/glycylcycline/monobactam/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/triclosan/tetracycline
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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38 SAMN11840202 contig00043 12125 13429 - Escherichia_coli_ampC1_beta-lactamase 1-1305/1305 =============== 0/0 100.00 100.00 card FN649414.1:2765051-2766356 An ampC-like beta-lactamase identified from Escherichia coli. cephalosporin/penam
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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39 SAMN11840202 contig00044 462 1286 + gadX 1-825/825 =============== 0/0 100.00 100.00 card AP009048.1:3974605-3975430 GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/aminocoumarin/phenicol/glycylcycline/monobactam/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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40 SAMN11840202 contig00044 1654 2382 + gadW 1-729/729 =============== 0/0 100.00 94.65 card CP015085.1:2551712-2552441 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. phenicol/monobactam/glycylcycline/penam/fluoroquinolone/macrolide/triclosan/tetracycline/acridine_dye/antibacterial_free_fatty_acids/aminoglycoside/carbapenem/diaminopyrimidine/aminocoumarin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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41 SAMN11840202 contig00044 2745 5858 - mdtF 1-3114/3114 =============== 0/0 100.00 99.97 card U00096:3660414-3663528 MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex. triclosan/tetracycline/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol/aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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42 SAMN11840202 contig00044 5883 7040 - mdtE 1-1158/1158 =============== 0/0 100.00 100.00 card AP009048.1:3980026-3981184 MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA. glycylcycline/monobactam/phenicol/acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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43 SAMN11840202 contig00049 8136 8813 + kdpE 1-678/678 =============== 0/0 100.00 100.00 card U00096.3:721056-721734 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. aminoglycoside
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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44 SAMN11840202 contig00049 12775 12918 + kdpE 535-678/678 ...........==== 0/0 21.24 90.28 card U00096.3:721056-721734 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. aminoglycoside
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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45 SAMN11840202 contig00050 22680 23032 - Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2) 2980-3332/3489 ......../...=== 4/6 10.03 75.56 card AP006618.1:4835200-4838689 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. rifamycin
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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46 SAMN11840202 contig00055 17804 19036 - mdtM 1-1233/1233 =============== 0/0 100.00 96.27 card U00096.3:4567287-4568520 Multidrug resistance protein MdtM nitroimidazole/rifamycin/nucleoside/penam/macrolide/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/lincosamide/isoniazid/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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47 SAMN11840202 contig00057 2580 3826 + tet(A) 1-1247/1275 =============== 0/0 97.80 100.00 card AF534183.1:2971-4246 TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. phenicol/glycylcycline/fosfomycin/tetracycline/oxazolidinone/acridine_dye/fluoroquinolone/cephalosporin/peptide/rhodamine/nucleoside/nitroimidazole/rifamycin/penam/macrolide/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/benzalkonium_chloride/isoniazid/lincosamide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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48 SAMN11840202 contig00063 8997 10370 - cpxA 1-1374/1374 =============== 0/0 100.00 98.98 card BA000007.3:4903689-4905063 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. acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/glycylcycline/monobactam/phenicol/aminocoumarin/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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49 SAMN11840202 contig00074 561 1373 + NDM-5 1-813/813 =============== 0/0 100.00 100.00 card JN104597:115-928 New Delhi beta-lactamase NDM-5. cephamycin/penam/cephalosporin/carbapenem
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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50 SAMN11840202 contig00074 1377 1742 + determinant_of_bleomycin_resistance 1-366/366 =============== 0/0 100.00 100.00 card KC503911.1:9884-10250 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. glycopeptide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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51 SAMN11840202 contig00074 5686 6525 - sul1 1-840/840 =============== 0/0 100.00 100.00 card JF969163:1054-1894 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. sulfonamide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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52 SAMN11840202 contig00074 7030 7809 - aadA2 1-780/780 =============== 0/0 100.00 99.87 card AF156486:5013-5793 aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp. aminoglycoside
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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53 SAMN11840202 contig00074 8229 8726 - dfrA12 1-498/498 =============== 0/0 100.00 100.00 card GU585907.1:21606-22104 dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae diaminopyrimidine
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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54 SAMN11840202 contig00074 8727 8975 - AAC(6')-Ib7 1-249/980 ====........... 0/0 25.41 98.80 card Y11946.1:1-981 AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii aminoglycoside
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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55 SAMN11840202 contig00077 5190 8294 - acrF 1-3105/3105 =============== 0/0 100.00 99.97 card U00096:3415033-3418138 AcrF is a inner membrane transporter similar to AcrB. aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin/cephamycin/phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/cephalosporin/macrolide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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56 SAMN11840202 contig00077 8306 9272 - acrE 192-1158/1158 ..============= 0/0 83.51 99.90 card U00096:3413864-3415022 AcrE is a membrane fusion protein similar to AcrA. aminocoumarin/cephamycin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/triclosan/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone/monobactam/glycylcycline/phenicol
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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57 SAMN11840202 contig00080 1250 2005 - rmtB 1-756/756 =============== 0/0 100.00 100.00 card AM886293.1:116480-117236 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. aminoglycoside
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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58 SAMN11840202 contig00080 2175 3035 - TEM-1 1-861/861 =============== 0/0 100.00 99.88 card AL513383:161911-162772 TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. penam/cephalosporin/penem/monobactam
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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59 SAMN11840202 contig00080 7165 8067 - mphA 1-903/906 =============== 0/0 99.67 100.00 card D16251.1:1626-2532 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. macrolide
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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60 SAMN11840202 contig00088 2703 3578 - CTX-M-15 1-876/876 =============== 0/0 100.00 100.00 card AY044436:1436-2312 CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family cephalosporin
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61 SAMN11840202 contig00102 130 779 + OXA-368 2072-2721/2721 ...........==== 0/0 23.89 99.08 card KT736121.1:1-2722 OXA-368 is a beta-lactamase found in Aeromonas sobria. From the Lahey list of OXA beta-lactamases. cephalosporin/penam
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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62 SAMN11840202 contig00102 844 1674 + OXA-1 1-831/831 =============== 0/0 100.00 100.00 card JN420336.1:1400-2231 OXA-1 is a beta-lactamase found in E. coli penam/cephalosporin
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63 SAMN11840202 contig00102 1812 2256 + catB3 1-445/633 ===========.... 0/0 70.30 99.78 card JX101693.1:58201-58834 catB3 is a plasmid or chromosome-encoded variant of the cat gene found in Salmonella typhimurium Acinetobacter baumannii and Escherichia coli phenicol