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Updated test data for DB release 2023-09-26.1
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@evolarjun
evolarjun committed Sep 27, 2023
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3 changes: 3 additions & 0 deletions test_both.expected
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Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description
NA contig01 1 984 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 984 1176 83.67 99.80 984 NZ_CP095603.1:148777-149952 blaTEM promoter region NA NA
blaTEM-156 contig01 101 961 + blaTEM-156 class A beta-lactamase TEM-156 core AMR AMR BETA-LACTAM BETA-LACTAM ALLELEP 286 286 100.00 100.00 286 WP_061158039.1 class A beta-lactamase TEM-156 NF000531.2 TEM family class A beta-lactamase
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 extended-spectrum class C beta-lactamase EC-15 NA NA
NA contig08 1 700 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 700 1176 59.52 99.71 700 NZ_CP095603.1:148777-149952 blaTEM promoter region 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 225 267 81.27 100.00 217 WP_001082319.1 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 oxacillin-hydrolyzing 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
NA contig11 1 984 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 984 1176 83.67 96.04 984 NZ_CP095603.1:148777-149952 blaTEM promoter region 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
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3 changes: 3 additions & 0 deletions test_dna.expected
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Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description
NA contig01 1 984 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 984 1176 83.67 99.80 984 NZ_CP095603.1:148777-149952 blaTEM promoter region NA NA
NA contig01 101 958 + blaTEM-156 class A beta-lactamase TEM-156 core AMR AMR BETA-LACTAM BETA-LACTAM ALLELEX 286 286 100.00 100.00 286 WP_061158039.1 class A beta-lactamase TEM-156 NA NA
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 extended-spectrum class C beta-lactamase EC-15 NA NA
NA contig08 1 700 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 700 1176 59.52 99.71 700 NZ_CP095603.1:148777-149952 blaTEM promoter region 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 1 651 - aph(3'')-Ib aminoglycoside O-phosphotransferase APH(3'')-Ib core AMR AMR AMINOGLYCOSIDE STREPTOMYCIN PARTIAL_CONTIG_ENDX 217 267 81.27 100.00 217 WP_001082319.1 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
NA contig10 486 1307 + blaOXA OXA-9 family oxacillin-hydrolyzing 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
NA contig11 1 984 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 984 1176 83.67 96.04 984 NZ_CP095603.1:148777-149952 blaTEM promoter region NA NA
NA contig11 101 958 + blaTEM TEM family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM INTERNAL_STOP 286 286 100.00 93.01 286 WP_061158039.1 class A beta-lactamase TEM-156 NA NA
NA contig12 71 634 + qacR multidrug-binding transcriptional regulator QacR plus STRESS BIOCIDE QUATERNARY AMMONIUM QUATERNARY AMMONIUM BLASTX 188 188 100.00 99.47 188 ADK23698.1 multidrug-binding transcriptional regulator QacR NA NA
NA contig13 1 1137 + emrD3 multidrug efflux MFS transporter EmrD-3 plus AMR AMR EFFLUX EFFLUX EXACTX 379 379 100.00 100.00 379 ABQ18953.1 multidrug efflux MFS transporter EmrD-3 NA NA
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