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Merge branch 'master' into dev
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@evolarjun
evolarjun committed Jun 1, 2022
2 parents 30f7689 + d9c918e commit 98c259f
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3 changes: 1 addition & 2 deletions README.md
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Expand Up @@ -35,7 +35,6 @@ Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH,
Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W.
AMRFinderPlus and the Reference Gene Catalog facilitate examination of the
genomic links among antimicrobial resistance, stress response, and virulence.
Sci Rep. 2021 Jun 16;11(1):12728. doi: 10.1038/s41598-021-91456-0. PMID:
34135355; PMCID: PMC8208984.
Sci Rep. 2021 Jun 16;11(1):12728. doi: [10.1038/s41598-021-91456-0](https://doi.org/10.1038/s41598-021-91456-0). PMID: [34135355](https://pubmed.ncbi.nlm.nih.gov/34135355/); PMCID: [PMC8208984](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8208984/).


4 changes: 2 additions & 2 deletions test_both.expected
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Expand Up @@ -3,12 +3,12 @@ blaTEM-156 contig01 101 961 + blaTEM-156 class A beta-lactamase TEM-156 core AMR
blaPDC-114_blast contig02 1 1191 + blaPDC PDC family class C beta-lactamase core AMR AMR BETA-LACTAM CEPHALOSPORIN BLASTP 397 397 100.00 99.75 397 WP_061189306.1 class C beta-lactamase PDC-114 NF000422.6 PDC family class C beta-lactamase
blaOXA-436_partial contig03 101 802 + blaOXA OXA-48 family class D beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALP 233 265 87.92 100.00 233 WP_058842180.1 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436 NF012161.0 class D beta-lactamase
vanG contig04 101 1147 + vanG D-alanine--D-serine ligase VanG core AMR AMR GLYCOPEPTIDE VANCOMYCIN EXACTP 349 349 100.00 100.00 349 WP_063856695.1 D-alanine--D-serine ligase VanG NF000091.3 D-alanine--D-serine ligase VanG
NA contig04 1261 2391 + blaEC BlaEC family class C beta-lactamase plus AMR AMR BETA-LACTAM BETA-LACTAM BLASTX 377 377 100.00 98.14 377 WP_063610930.1 class C extended-spectrum beta-lactamase EC-15 NA NA
NA contig04 1261 2391 + blaEC BlaEC family class C beta-lactamase plus AMR AMR BETA-LACTAM BETA-LACTAM BLASTX 377 377 100.00 98.14 377 WP_063610930.1 extended-spectrum class C beta-lactamase EC-15 NA NA
NA contig08 101 700 + blaTEM TEM family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIAL_CONTIG_ENDX 200 286 69.93 100.00 200 WP_061158039.1 class A beta-lactamase TEM-156 NA NA
aph3pp-Ib_partial_5p_neg contig09 1 675 - aph(3'')-Ib aminoglycoside O-phosphotransferase APH(3'')-Ib core AMR AMR AMINOGLYCOSIDE STREPTOMYCIN PARTIAL_CONTIG_ENDP 225 275 81.82 100.00 225 WP_109545041.1 aminoglycoside O-phosphotransferase APH(3'')-Ib NF032896.1 APH(3'') family aminoglycoside O-phosphotransferase
sul2_partial_3p_neg contig09 715 1377 - sul2 sulfonamide-resistant dihydropteroate synthase Sul2 core AMR AMR SULFONAMIDE SULFONAMIDE PARTIAL_CONTIG_ENDP 221 271 81.55 100.00 221 WP_001043265.1 sulfonamide-resistant dihydropteroate synthase Sul2 NA NA
NA contig10 486 1307 + blaOXA OXA-9 family class D beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM INTERNAL_STOP 274 274 100.00 99.64 274 WP_000722315.1 oxacillin-hydrolyzing class D beta-lactamase OXA-9 NA NA
blaTEM-internal_stop contig11 113 547 + blaTEM TEM family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM INTERNAL_STOP 144 286 50.35 97.22 144 WP_000027057.1 class A broad-spectrum beta-lactamase TEM-1 NA NA
blaTEM-internal_stop contig11 113 547 + blaTEM TEM family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM INTERNAL_STOP 144 286 50.35 97.22 144 WP_000027057.1 broad-spectrum class A beta-lactamase TEM-1 NA NA
qacR-curated_blast contig12 71 637 + qacR multidrug-binding transcriptional regulator QacR plus STRESS BIOCIDE QUATERNARY AMMONIUM QUATERNARY AMMONIUM BLASTP 188 188 100.00 99.47 188 ADK23698.1 multidrug-binding transcriptional regulator QacR NA NA
emrD3-suppressed-in-vibrio contig13 1 1137 + emrD3 multidrug efflux MFS transporter EmrD-3 plus AMR AMR EFFLUX EFFLUX EXACTP 379 379 100.00 100.00 379 ABQ18953.1 multidrug efflux MFS transporter EmrD-3 NA NA
NA contig14 1 1089 + pmrB_C84R Escherichia colistin resistant PmrB core AMR POINT COLISTIN COLISTIN POINTX 363 363 100.00 99.72 363 WP_001300761.1 two-component system sensor histidine kinase PmrB NA NA
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2 changes: 1 addition & 1 deletion test_dna.expected
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Expand Up @@ -3,7 +3,7 @@ NA contig01 101 958 + blaTEM-156 class A beta-lactamase TEM-156 core AMR AMR BET
NA contig02 1 1191 + blaPDC PDC family class C beta-lactamase core AMR AMR BETA-LACTAM CEPHALOSPORIN BLASTX 397 397 100.00 99.75 397 WP_061189306.1 class C beta-lactamase PDC-114 NA NA
NA contig03 101 802 + blaOXA OXA-48 family class D beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 234 265 88.30 100.00 234 WP_058842180.1 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436 NA NA
NA contig04 101 1147 + vanG D-alanine--D-serine ligase VanG core AMR AMR GLYCOPEPTIDE VANCOMYCIN EXACTX 349 349 100.00 100.00 349 WP_063856695.1 D-alanine--D-serine ligase VanG NA NA
NA contig04 1261 2391 + blaEC BlaEC family class C beta-lactamase plus AMR AMR BETA-LACTAM BETA-LACTAM BLASTX 377 377 100.00 98.14 377 WP_063610930.1 class C extended-spectrum beta-lactamase EC-15 NA NA
NA contig04 1261 2391 + blaEC BlaEC family class C beta-lactamase plus AMR AMR BETA-LACTAM BETA-LACTAM BLASTX 377 377 100.00 98.14 377 WP_063610930.1 extended-spectrum class C beta-lactamase EC-15 NA NA
NA contig08 101 700 + blaTEM TEM family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIAL_CONTIG_ENDX 200 286 69.93 100.00 200 WP_061158039.1 class A beta-lactamase TEM-156 NA NA
NA contig09 1 675 - aph(3'')-Ib aminoglycoside O-phosphotransferase APH(3'')-Ib core AMR AMR AMINOGLYCOSIDE STREPTOMYCIN PARTIAL_CONTIG_ENDX 225 275 81.82 100.00 225 WP_109545041.1 aminoglycoside O-phosphotransferase APH(3'')-Ib NA NA
NA contig09 715 1377 - sul2 sulfonamide-resistant dihydropteroate synthase Sul2 core AMR AMR SULFONAMIDE SULFONAMIDE PARTIAL_CONTIG_ENDX 221 271 81.55 100.00 221 WP_001043265.1 sulfonamide-resistant dihydropteroate synthase Sul2 NA NA
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2 changes: 1 addition & 1 deletion test_prot.expected
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Expand Up @@ -5,7 +5,7 @@ blaOXA-436_partial contig03 101 802 + blaOXA OXA-48 family class D beta-lactamas
vanG contig04 101 1147 + vanG D-alanine--D-serine ligase VanG core AMR AMR GLYCOPEPTIDE VANCOMYCIN EXACTP 349 349 100.00 100.00 349 WP_063856695.1 D-alanine--D-serine ligase VanG NF000091.3 D-alanine--D-serine ligase VanG
aph3pp-Ib_partial_5p_neg contig09 1 675 - aph(3'')-Ib aminoglycoside O-phosphotransferase APH(3'')-Ib core AMR AMR AMINOGLYCOSIDE STREPTOMYCIN PARTIAL_CONTIG_ENDP 225 275 81.82 100.00 225 WP_109545041.1 aminoglycoside O-phosphotransferase APH(3'')-Ib NF032896.1 APH(3'') family aminoglycoside O-phosphotransferase
sul2_partial_3p_neg contig09 715 1377 - sul2 sulfonamide-resistant dihydropteroate synthase Sul2 core AMR AMR SULFONAMIDE SULFONAMIDE PARTIALP 221 271 81.55 100.00 221 WP_001043265.1 sulfonamide-resistant dihydropteroate synthase Sul2 NA NA
blaTEM-internal_stop contig11 113 547 + blaTEM TEM family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALP 144 286 50.35 97.22 144 WP_000027057.1 class A broad-spectrum beta-lactamase TEM-1 NA NA
blaTEM-internal_stop contig11 113 547 + blaTEM TEM family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALP 144 286 50.35 97.22 144 WP_000027057.1 broad-spectrum class A beta-lactamase TEM-1 NA NA
qacR-curated_blast contig12 71 637 + qacR multidrug-binding transcriptional regulator QacR plus STRESS BIOCIDE QUATERNARY AMMONIUM QUATERNARY AMMONIUM BLASTP 188 188 100.00 99.47 188 ADK23698.1 multidrug-binding transcriptional regulator QacR NA NA
emrD3-suppressed-in-vibrio contig13 1 1137 + emrD3 multidrug efflux MFS transporter EmrD-3 plus AMR AMR EFFLUX EFFLUX EXACTP 379 379 100.00 100.00 379 ABQ18953.1 multidrug efflux MFS transporter EmrD-3 NA NA
pmrB_C84R contig14 1093 2181 + pmrB_C84R Escherichia colistin resistant PmrB core AMR POINT COLISTIN COLISTIN POINTP 363 363 100.00 99.72 363 WP_001300761.1 two-component system sensor histidine kinase PmrB NA NA
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