This run was generated using rMAP version 1.0 performed on 2021-06-14… Thank you for using this pipeline!!


Assembly summary statistics


Field Description
SampleID Name of the sample
TrimReads Total number of reads after quality filtering
MeanReadLen Average read length after quality filtering
Contigs Number of contigs of the draft genome (>200bp)
GenomeLength Length (bp) of the draft genome
LargestContig Length (bp) of the largest contig in the genome
N50 Length of the smallest contig in the set that contains the fewest (largest) contigs whose combined length represents at least 50% of the assembly
GC-Content GC content (%) of the draft genome
Depth Number of times each nucleotide position in the draft genome has a read that aligns to that position


SampleID TrimReads MeanReadLen Contigs GenomeLength LargestContig N50 GC-Content Depth
SRR8948878 115236 164 71 3102954 545479 273671 37.22 6X
SRR8948879 114450 163 80 3010523 603711 179463 37.45 6X
SRR8948880 114295 163 102 3167039 417860 239597 37.18 5X
SRR8948881 113261 164 44 2924324 516731 202453 37.46 6X
SRR8948882 113692 164 170 2925331 107207 46219 37.69 6X
SRR8948883 112973 164 179 2963634 113751 44888 37.74 6X
SRR8948884 112646 163 56 2933495 644112 179342 37.46 6X
SRR8948885 109926 162 60 3364036 424585 243114 40.43 5X
SRR8948886 112978 163 56 2786571 344853 172313 38.08 6X
SRR8948887 113971 162 90 2988194 603711 185199 37.49 6X
SRR8948888 112312 162 55 3023079 544043 211710 37.28 6X
SRR8948889 111701 164 297 5900301 544519 66637 37.49 3X
SRR8948890 114507 162 52 3016707 544186 207384 37.27 6X
SRR8948891 113598 164 66 3038151 544195 219893 37.30 6X

Select the parameter

Number of reads

Average number of reads per sample = 113253

Average read length

Average read length per sample = 163 bp

Number of contigs

Average number of contigs per sample = 98

Genome length

Average genome length per sample = 3224596 bp

Largest contig length

Average largest contig length per sample = 464210 bp

N50

Average N50 per sample = 176563 bp

GC content

Average GC content per sample = 37.681%

Sequencing depth

Average sequencing depth = 5.643X

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SNP-variant calling


Field Description
GenomePosition Position in the genome where SNP is found
Type Nature of the SNP identified (Only ‘True’ SNPs are shown by default)
ReferenceAllele Allele found in the reference genome
AlternateAllele Allele found in the genome of interest forming the SNP
Consequence Amino acid alterations caused by the SNP
AffectedGene The tartget gene affected by the SNP
Product The outcome from the presence of the SNP


Select the sample

SRR8948878
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
295574 snp G A missense_variant c.1772G>A p.Ser591Asn tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295633 snp C T missense_variant c.1831C>T p.His611Tyr tet(M) tetracycline resistance ribosomal protection protein Tet(M)
SRR8948879
## Error in read.table("SRR8948879_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
295574 snp G A missense_variant c.1772G>A p.Ser591Asn tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295633 snp C T missense_variant c.1831C>T p.His611Tyr tet(M) tetracycline resistance ribosomal protection protein Tet(M)
SRR8948880
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
295033 snp A G missense_variant c.1231A>G p.Ile411Val tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295633 snp C T missense_variant c.1831C>T p.His611Tyr tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295651 snp C T missense_variant c.1849C>T p.Pro617Ser tet(M) tetracycline resistance ribosomal protection protein Tet(M)
SRR8948881
## Error in read.table("SRR8948881_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
295033 snp A G missense_variant c.1231A>G p.Ile411Val tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295633 snp C T missense_variant c.1831C>T p.His611Tyr tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295651 snp C T missense_variant c.1849C>T p.Pro617Ser tet(M) tetracycline resistance ribosomal protection protein Tet(M)
SRR8948882
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
419154 snp TRUE C missense_variant c.487A>G p.Lys163Glu NA tetronasin resistance protein
SRR8948883
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
419154 snp TRUE C missense_variant c.487A>G p.Lys163Glu NA tetronasin resistance protein
SRR8948884
## Error in read.table("SRR8948884_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
419154 snp TRUE C missense_variant c.487A>G p.Lys163Glu NA tetronasin resistance protein
SRR8948885
## Error in read.table("SRR8948885_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
419154 snp TRUE C missense_variant c.487A>G p.Lys163Glu NA tetronasin resistance protein
SRR8948886
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
331277 snp G A missense_variant c.34G>A p.Ala12Thr NA copper resistance protein CopZ
418068 snp A C missense_variant c.1573T>G p.Ser525Ala NA tetronasin resistance protein
418080 snp A T missense_variant c.1561T>A p.Phe521Ile NA tetronasin resistance protein
418251 snp G A missense_variant c.1390C>T p.Leu464Phe NA tetronasin resistance protein
418258 snp G C missense_variant c.1383C>G p.Ile461Met NA tetronasin resistance protein
418291 snp A C missense_variant c.1350T>G p.Ile450Met NA tetronasin resistance protein
418347 snp T G missense_variant c.1294A>C p.Met432Leu NA tetronasin resistance protein
418944 snp T A missense_variant c.697A>T p.Thr233Ser NA tetronasin resistance protein
419064 snp A C missense_variant c.577T>G p.Ser193Ala NA tetronasin resistance protein
419082 snp C A missense_variant c.559G>T p.Ala187Ser NA tetronasin resistance protein
419117 snp A G missense_variant c.524T>C p.Met175Thr NA tetronasin resistance protein
419154 snp T C missense_variant c.487A>G p.Lys163Glu NA tetronasin resistance protein
566234 snp C T missense_variant c.665G>A p.Arg222Lys NA toxic anion resistance protein
566262 snp T A missense_variant c.637A>T p.Thr213Ser NA toxic anion resistance protein
1376084 snp T A missense_variant c.1178A>T p.Lys393Ile NA tetracycline resistance MFS efflux pump
1376142 snp A C missense_variant c.1120T>G p.Phe374Val NA tetracycline resistance MFS efflux pump
1376242 snp A T missense_variant c.1020T>A p.Asp340Glu NA tetracycline resistance MFS efflux pump
1376390 snp A C missense_variant c.872T>G p.Phe291Cys NA tetracycline resistance MFS efflux pump
1376465 snp G A missense_variant c.797C>T p.Thr266Ile NA tetracycline resistance MFS efflux pump
1376526 snp C T missense_variant c.736G>A p.Ala246Thr NA tetracycline resistance MFS efflux pump
1376705 snp A T missense_variant c.557T>A p.Leu186Gln NA tetracycline resistance MFS efflux pump
1376985 snp G T missense_variant c.277C>A p.Leu93Ile NA tetracycline resistance MFS efflux pump
1377032 snp T C missense_variant c.230A>G p.His77Arg NA tetracycline resistance MFS efflux pump
1377257 snp T A missense_variant c.5A>T p.Tyr2Phe NA tetracycline resistance MFS efflux pump
1507208 snp C T missense_variant c.257C>T p.Thr86Met NA organic hydroperoxide resistance protein
SRR8948887
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
331277 snp G A missense_variant c.34G>A p.Ala12Thr NA copper resistance protein CopZ
418291 snp A C missense_variant c.1350T>G p.Ile450Met NA tetronasin resistance protein
418347 snp T G missense_variant c.1294A>C p.Met432Leu NA tetronasin resistance protein
418944 snp T A missense_variant c.697A>T p.Thr233Ser NA tetronasin resistance protein
419064 snp A C missense_variant c.577T>G p.Ser193Ala NA tetronasin resistance protein
419082 snp C A missense_variant c.559G>T p.Ala187Ser NA tetronasin resistance protein
419117 snp A G missense_variant c.524T>C p.Met175Thr NA tetronasin resistance protein
419154 snp T C missense_variant c.487A>G p.Lys163Glu NA tetronasin resistance protein
1376465 snp G A missense_variant c.797C>T p.Thr266Ile NA tetracycline resistance MFS efflux pump
1376526 snp C T missense_variant c.736G>A p.Ala246Thr NA tetracycline resistance MFS efflux pump
1376705 snp A T missense_variant c.557T>A p.Leu186Gln NA tetracycline resistance MFS efflux pump
SRR8948888
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
295033 snp A G missense_variant c.1231A>G p.Ile411Val tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295574 snp G A missense_variant c.1772G>A p.Ser591Asn tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295633 snp C T missense_variant c.1831C>T p.His611Tyr tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295651 snp C T missense_variant c.1849C>T p.Pro617Ser tet(M) tetracycline resistance ribosomal protection protein Tet(M)
SRR8948889
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
295574 snp G A missense_variant c.1772G>A p.Ser591Asn tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295633 snp C T missense_variant c.1831C>T p.His611Tyr tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295651 snp C T missense_variant c.1849C>T p.Pro617Ser tet(M) tetracycline resistance ribosomal protection protein Tet(M)
419154 snp T C missense_variant c.487A>G p.Lys163Glu tetronasin resistance protein
SRR8948890
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
295033 snp A G missense_variant c.1231A>G p.Ile411Val tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295574 snp G A missense_variant c.1772G>A p.Ser591Asn tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295633 snp C T missense_variant c.1831C>T p.His611Tyr tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295651 snp C T missense_variant c.1849C>T p.Pro617Ser tet(M) tetracycline resistance ribosomal protection protein Tet(M)
SRR8948891
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
295574 snp G A missense_variant c.1772G>A p.Ser591Asn tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295633 snp C T missense_variant c.1831C>T p.His611Tyr tet(M) tetracycline resistance ribosomal protection protein Tet(M)
295651 snp C T missense_variant c.1849C>T p.Pro617Ser tet(M) tetracycline resistance ribosomal protection protein Tet(M)


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Phylogenetic inference

Phylogenetic inference based on vcf SNPS

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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Antimicrobial Resistance Profiling


Field Description
Contig Contig name where the gene was found
Start Start position of the gene within the contig
End End position of the gene within the contig
Gene Antibiotic resistance gene
Gaps Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage Proportion (%) of the gene covered
Identity Proportion (%) of exact nucleotide matches
Accession Accesion number of the antibiotic resistance gene
Product Antibiotic resistance gene product
Resistance Antibiotic that the gene confers resistance to


Select the samples and the database

SRR8948878
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00007 82257 82754 dfrG_1 0/0 100 100.0 AB205645 dfrG Trimethoprim
contig00027 2694 3456 erm(B)_18 1/1 100 99.1 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00004 172990 174486 lsa(A)_1 0/0 100 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00002 31907 33826 tet(M)_10 0/0 100 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00027 2719 3464 ErmB 1/1 99.9 99.5 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB 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 ErmB. lincosamide, macrolide, streptogramin
contig00001 78017 78511 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00007 82257 82754 dfrG 0/0 100.0 100.0 AB205645:1012-1510 dfrG is a plasmid-encoded dihydrofolate reductase found in Staphylococcus aureus diaminopyrimidine
contig00008 24880 26607 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00008 23268 24321 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 519193 520347 emeA 1/27 97.7 97.1 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00004 172990 174486 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00002 31907 33826 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00027 2719 3456 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00004 172990 174486 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00006 213113 213946 (MLS)mph(D) 0/0 100 99.8 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 31907 33826 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 78017 78511 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
contig00007 82257 82754 (Tmt)dfrG 0/0 100 100.0 AB205645:1013-1510 (Tmt)dfrG NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 78017 78511 dfrE 0/0 100 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00007 82257 82754 dfrG 0/0 100 100.0 NG_047756.1 trimethoprim-resistant dihydrofolate reductase DfrG TRIMETHOPRIM
contig00027 2719 3456 erm(B) 0/0 100 100.0 NG_047794.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00004 172990 174486 lsa(A) 0/0 100 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00002 31907 33826 tet(M) 0/0 100 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 78017 78511 dfrE 0/0 100 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00007 82257 82754 dfrG 0/0 100 100.0 NG_047756.1 trimethoprim-resistant dihydrofolate reductase DfrG TRIMETHOPRIM
contig00027 2719 3456 erm(B) 0/0 100 100.0 NG_047794.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00004 172990 174486 lsa(A) 0/0 100 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00002 31907 33826 tet(M) 0/0 100 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
SRR8948879
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00033 2093 4699 VanHAX_2 0/0 100 100.0 M97297 VanHAX Vancomycin, Teicoplanin
contig00028 3187 3834 cat(pC221)_1 0/0 100 97.7 X02529 cat(pC221) Chloramphenicol
contig00011 56585 58081 lsa(A)_1 0/0 100 99.4 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00007 124979 126898 tet(M)_13 0/0 100 99.9 AM990992 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 3187 3834 Enterococcus_faecalis_chloramphenicol_acetyltransferase 0/0 100.0 100.0 X92945.2:9582-8934 A chloramphenicol acetyltransferase and resistance determinant described in Enterococcus faecalis phenicol
contig00001 182045 182539 dfrE 0/0 100.0 97.6 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00013 25119 26846 efrA 0/0 100.0 99.3 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00013 23507 24560 efrB 6/6 96.7 97.6 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00006 173315 174469 emeA 1/27 97.7 97.0 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00011 56585 58081 lsaA 0/0 100.0 99.4 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00007 124979 126898 tetM 0/0 100.0 99.9 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
contig00044 728 1045 tetU 0/0 100.0 99.4 U01917.1:412-730 Tetracycline-resistant determinant encoded on the plasmid pKQ10 in Enterococcus faecium tetracycline
contig00033 3054 4085 vanA 0/0 100.0 100.0 M97297:6979-8010 VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance. glycopeptide
contig00033 2093 3061 vanHA 0/0 100.0 100.0 M97297:6018-6986 vanHA also known as vanH is a vanH variant in the vanA gene cluster glycopeptide
contig00033 51 746 vanRA 0/0 100.0 100.0 M97297:3976-4671 vanRA also known as vanR is a vanR variant found in the vanA gene cluster glycopeptide
contig00033 724 1878 vanSA 0/0 100.0 100.0 M97297:4649-5803 vanSA also known as vanS is a vanS variant found in the vanA gene cluster glycopeptide
contig00033 4091 4699 vanXA 0/0 100.0 100.0 M97297:8016-8624 vanXA also known as vanX is a vanX variant found in the vanA gene cluster glycopeptide
contig00028 9615 10100 vanZA 0/0 100.0 100.0 M97297:10116-10601 vanZA also known as vanZ is a vanZ variant found in the vanA gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00033 3054 4085 (Gly)vanA-A 0/0 100 100.0 M97297:6979-8010 (Gly)vanA-A NA
contig00033 2093 3061 (Gly)vanH-A 0/0 100 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00033 51 746 (Gly)vanR-A 0/0 100 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00033 724 1878 (Gly)vanS-A 0/0 100 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00033 4091 4699 (Gly)vanX-A 0/0 100 100.0 M97297:8016-8624 (Gly)vanX-A NA
contig00028 9615 10100 (Gly)vanZ-A 0/0 100 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00011 56585 58081 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00001 490345 491178 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00028 3187 3834 (Phe)cat-pC221 0/0 100 97.7 X02529:2267-2914 (Phe)cat-pC221 NA
contig00007 124979 126898 (Tet)tetM 0/0 100 99.2 DQ534550:1451-3370 (Tet)tetM NA
contig00044 728 1045 (Tet)tetU 0/0 100 99.4 U01917:413-730 (Tet)tetU NA
contig00001 182045 182539 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 3187 3834 catA7 0/0 100 100.0 NG_047568.1 type A-7 chloramphenicol O-acetyltransferase CHLORAMPHENICOL
contig00001 182045 182539 dfrE 0/0 100 97.6 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00011 56585 58081 lsa(A) 0/0 100 99.4 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00007 124979 126898 tet(M) 0/0 100 99.8 NG_048213.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
contig00033 3054 4085 vanA 0/0 100 100.0 NG_048323.1 D-alanine–(R)-lactate ligase VanA VANCOMYCIN
contig00033 2093 3061 vanH-A 0/0 100 100.0 NG_048372.1 D-lactate dehydrogenase VanH-A VANCOMYCIN
contig00033 51 746 vanR-A 0/0 100 100.0 NG_048399.1 VanA-type vancomycin resistance DNA-binding response regulator VanR VANCOMYCIN
contig00033 724 1878 vanS-A 0/0 100 100.0 NG_048425.1 VanA-type vancomycin resistance histidine kinase VanS VANCOMYCIN
contig00033 4091 4699 vanX-A 0/0 100 100.0 NG_048477.1 D-Ala-D-Ala dipeptidase VanX-A VANCOMYCIN
contig00028 9615 10100 vanZ-A 0/0 100 100.0 NG_048534.1 glycopeptide resistance protein VanZ-A VANCOMYCIN
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 3187 3834 catA7 0/0 100 100.0 NG_047568.1 type A-7 chloramphenicol O-acetyltransferase CHLORAMPHENICOL
contig00001 182045 182539 dfrE 0/0 100 97.6 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00011 56585 58081 lsa(A) 0/0 100 99.4 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00007 124979 126898 tet(M) 0/0 100 99.8 NG_048213.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
contig00033 3054 4085 vanA 0/0 100 100.0 NG_048323.1 D-alanine–(R)-lactate ligase VanA VANCOMYCIN
contig00033 2093 3061 vanH-A 0/0 100 100.0 NG_048372.1 D-lactate dehydrogenase VanH-A VANCOMYCIN
contig00033 51 746 vanR-A 0/0 100 100.0 NG_048399.1 VanA-type vancomycin resistance DNA-binding response regulator VanR VANCOMYCIN
contig00033 724 1878 vanS-A 0/0 100 100.0 NG_048425.1 VanA-type vancomycin resistance histidine kinase VanS VANCOMYCIN
contig00033 4091 4699 vanX-A 0/0 100 100.0 NG_048477.1 D-Ala-D-Ala dipeptidase VanX-A VANCOMYCIN
contig00028 9615 10100 vanZ-A 0/0 100 100.0 NG_048534.1 glycopeptide resistance protein VanZ-A VANCOMYCIN
SRR8948880
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00040 1 2558 VanHAX_2 0/0 98.1 100.0 M97297 VanHAX Vancomycin, Teicoplanin
contig00062 1 881 ant(6)-Ia_1 0/0 96.9 100.0 AF330699 ant(6)-Ia Streptomycin
contig00039 1557 2204 cat(pC221)_1 0/0 100.0 97.7 X02529 cat(pC221) Chloramphenicol
contig00008 82257 82754 dfrG_1 0/0 100.0 100.0 AB205645 dfrG Trimethoprim
contig00031 2694 3456 erm(B)_18 1/1 100.0 99.1 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00004 172990 174486 lsa(A)_1 0/0 100.0 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00002 32394 34313 tet(M)_10 0/0 100.0 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00039 1557 2204 Enterococcus_faecalis_chloramphenicol_acetyltransferase 0/0 100.0 100.0 X92945.2:9582-8934 A chloramphenicol acetyltransferase and resistance determinant described in Enterococcus faecalis phenicol
contig00031 2719 3464 ErmB 1/1 99.9 99.5 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB 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 ErmB. lincosamide, macrolide, streptogramin
contig00062 51 881 aad(6) 0/0 100.0 100.0 AY712687:0-831 aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis aminoglycoside
contig00009 78017 78511 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00008 82257 82754 dfrG 0/0 100.0 100.0 AB205645:1012-1510 dfrG is a plasmid-encoded dihydrofolate reductase found in Staphylococcus aureus diaminopyrimidine
contig00003 24880 26607 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00003 23268 24321 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 25016 26170 emeA 1/27 97.7 97.1 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00004 172990 174486 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00002 32394 34313 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
contig00046 728 1045 tetU 0/0 100.0 99.4 U01917.1:412-730 Tetracycline-resistant determinant encoded on the plasmid pKQ10 in Enterococcus faecium tetracycline
contig00040 913 1944 vanA 0/0 100.0 100.0 M97297:6979-8010 VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance. glycopeptide
contig00040 1 920 vanHA 0/0 94.9 100.0 M97297:6018-6986 vanHA also known as vanH is a vanH variant in the vanA gene cluster glycopeptide
contig00040 1950 2558 vanXA 0/0 100.0 100.0 M97297:8016-8624 vanXA also known as vanX is a vanX variant found in the vanA gene cluster glycopeptide
contig00057 380 1291 vanYA 0/0 100.0 100.0 M97297:9052-9963 vanYA also known as vanY is a vanY variant found in the vanA gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00062 1 881 (AGly)ant6-Ia 0/0 96.9 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00040 913 1944 (Gly)vanA-A 0/0 100.0 100.0 M97297:6979-8010 (Gly)vanA-A NA
contig00040 1 920 (Gly)vanH-A 0/0 94.9 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00040 1950 2558 (Gly)vanX-A 0/0 100.0 100.0 M97297:8016-8624 (Gly)vanX-A NA
contig00057 380 1291 (Gly)vanY-A 0/0 100.0 100.0 M97297:9052-9963 (Gly)vanY-A NA
contig00031 2719 3456 (MLS)erm(B) 0/0 100.0 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00004 172990 174486 (MLS)lsa(A) 0/0 100.0 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00005 213113 213946 (MLS)mph(D) 0/0 100.0 99.8 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00039 1557 2204 (Phe)cat-pC221 0/0 100.0 97.7 X02529:2267-2914 (Phe)cat-pC221 NA
contig00002 32394 34313 (Tet)tetM 0/0 100.0 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00046 728 1045 (Tet)tetU 0/0 100.0 99.4 U01917:413-730 (Tet)tetU NA
contig00009 78017 78511 (Tmt)dfrE 0/0 100.0 97.4 NG_055770:101-595 (Tmt)dfrE NA
contig00008 82257 82754 (Tmt)dfrG 0/0 100.0 100.0 AB205645:1013-1510 (Tmt)dfrG NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00062 1 881 ant(6)-Ia 0/0 96.9 100.0 NG_047393.1 aminoglycoside nucleotidyltransferase ANT(6)-Ia STREPTOMYCIN
contig00039 1557 2204 catA7 0/0 100.0 100.0 NG_047568.1 type A-7 chloramphenicol O-acetyltransferase CHLORAMPHENICOL
contig00009 78017 78511 dfrE 0/0 100.0 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00008 82257 82754 dfrG 0/0 100.0 100.0 NG_047756.1 trimethoprim-resistant dihydrofolate reductase DfrG TRIMETHOPRIM
contig00031 2719 3456 erm(B) 0/0 100.0 100.0 NG_047794.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00004 172990 174486 lsa(A) 0/0 100.0 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00002 32394 34313 tet(M) 0/0 100.0 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
contig00040 913 1944 vanA 0/0 100.0 100.0 NG_048323.1 D-alanine–(R)-lactate ligase VanA VANCOMYCIN
contig00040 1 920 vanH-A 0/0 94.9 100.0 NG_048372.1 D-lactate dehydrogenase VanH-A VANCOMYCIN
contig00040 1950 2558 vanX-A 0/0 100.0 100.0 NG_048477.1 D-Ala-D-Ala dipeptidase VanX-A VANCOMYCIN
contig00057 380 1291 vanY-A 0/0 100.0 100.0 NG_048516.1 D-Ala-D-Ala carboxypeptidase VanY-A VANCOMYCIN
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00062 1 881 ant(6)-Ia 0/0 96.9 100.0 NG_047393.1 aminoglycoside nucleotidyltransferase ANT(6)-Ia STREPTOMYCIN
contig00039 1557 2204 catA7 0/0 100.0 100.0 NG_047568.1 type A-7 chloramphenicol O-acetyltransferase CHLORAMPHENICOL
contig00009 78017 78511 dfrE 0/0 100.0 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00008 82257 82754 dfrG 0/0 100.0 100.0 NG_047756.1 trimethoprim-resistant dihydrofolate reductase DfrG TRIMETHOPRIM
contig00031 2719 3456 erm(B) 0/0 100.0 100.0 NG_047794.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00004 172990 174486 lsa(A) 0/0 100.0 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00002 32394 34313 tet(M) 0/0 100.0 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
contig00040 913 1944 vanA 0/0 100.0 100.0 NG_048323.1 D-alanine–(R)-lactate ligase VanA VANCOMYCIN
contig00040 1 920 vanH-A 0/0 94.9 100.0 NG_048372.1 D-lactate dehydrogenase VanH-A VANCOMYCIN
contig00040 1950 2558 vanX-A 0/0 100.0 100.0 NG_048477.1 D-Ala-D-Ala dipeptidase VanX-A VANCOMYCIN
contig00057 380 1291 vanY-A 0/0 100.0 100.0 NG_048516.1 D-Ala-D-Ala carboxypeptidase VanY-A VANCOMYCIN
SRR8948881
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00010 56301 57797 lsa(A)_1 0/0 100 99.4 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00029 524 2464 tet(S)_3 0/0 100 99.9 X92946 tet(S) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 72187 72681 dfrE 0/0 100.0 97.6 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00007 141691 143418 efrA 0/0 100.0 99.2 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00007 143977 145030 efrB 6/6 96.7 97.6 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00006 170401 171555 emeA 1/27 97.7 96.9 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00010 56301 57797 lsaA 0/0 100.0 99.4 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00029 524 2449 tetS 0/0 100.0 100.0 L09756:0-1926 Tet(S) is a ribosomal protection protein found in Gram-positive and Gram-negative strains. It is similar to tet(M) and tet(O). tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00010 56301 57797 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00001 408745 409578 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00029 524 2449 (Tet)tetS 0/0 100 100.0 L09756:447-2372 (Tet)tetS NA
contig00001 72187 72681 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 72187 72681 dfrE 0/0 100 97.6 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00010 56301 57797 lsa(A) 0/0 100 99.4 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00029 524 2449 tet(S) 0/0 100 100.0 NG_048273.1 tetracycline resistance ribosomal protection protein Tet(S) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 72187 72681 dfrE 0/0 100 97.6 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00010 56301 57797 lsa(A) 0/0 100 99.4 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00029 524 2449 tet(S) 0/0 100 100.0 NG_048273.1 tetracycline resistance ribosomal protection protein Tet(S) TETRACYCLINE
SRR8948882
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00073 4890 7496 VanHAX_2 0/0 100.0 99.9 M97297 VanHAX Vancomycin, Teicoplanin
contig00010 31434 31982 aac(6’)-Ii_1 0/0 100.0 99.6 L12710 aac(6’)-Ii Amikacin, Tobramycin
contig00126 376 1719 aac(6’)-aph(2’’)_1 0/0 93.3 99.9 M13771 aac(6’)-aph(2’’) Amikacin, Gentamicin, Tobramycin
contig00064 6660 7568 ant(6)-Ia_1 0/0 100.0 100.0 AF330699 ant(6)-Ia Streptomycin
contig00064 8200 8994 aph(3’)-III_1 0/0 100.0 100.0 M26832 aph(3’)-III Amikacin
contig00064 12761 13523 erm(B)_18 1/1 100.0 99.5 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00004 80444 81922 msr(C)_1 0/0 100.0 98.9 AY004350 msr(C) Erythromycin, Telithromycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00126 376 1719 AAC(6’)-Ie-APH(2’’)-Ia 0/0 93.3 99.9 GU565967.1:26419-24979 AAC(6’)-Ie-APH(2’’)-Ia is an aminoglycoside acetyltransferase encoded by plasmids and transposons in S. aureus E. faecalis E. faecium and Staphylococcus warneri aminoglycoside
contig00010 31434 31982 AAC(6’)-Ii 0/0 100.0 99.6 L12710:0-549 AAC(6’)-Ii is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus spp. aminoglycoside
contig00064 8200 8994 APH(3’)-IIIa 0/0 100.0 100.0 CP004067:52914-53709 APH(3’)-IIIa is a plasmid-encoded aminoglycoside phosphotransferase in S. aureus and Enterococcus spp. aminoglycoside
contig00064 12753 13498 ErmB 1/1 99.9 99.2 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB 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 ErmB. lincosamide, macrolide, streptogramin
contig00064 7565 8107 SAT-4 0/0 100.0 99.8 U01945:373-916 SAT-4 is a plasmid-mediated streptothricin acetyltransferase and streptothricin (a nucleoside antibiotic) resistant determinant. Originally described from a Campylobacter coli BE/G4 plasmid gene sequence by Jacob et al 1994. nucleoside
contig00064 6738 7568 aad(6) 0/0 100.0 100.0 AY712687:0-831 aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis aminoglycoside
contig00008 39083 40369 efmA 0/0 100.0 100.0 AB467372.1:284-1571 efmA is an MFS transporter permease in E. faecium. fluoroquinolone, macrolide
contig00004 80444 81922 msrC 0/0 100.0 94.4 AF313494:0-1479 msrC is a chromosomal-encoded ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to erythromycin and other macrolide and streptogramin B antibiotics. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00073 5504 6535 vanA 0/0 100.0 99.9 M97297:6979-8010 VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance. glycopeptide
contig00073 6528 7496 vanHA 0/0 100.0 100.0 M97297:6018-6986 vanHA also known as vanH is a vanH variant in the vanA gene cluster glycopeptide
contig00073 8843 9538 vanRA 0/0 100.0 100.0 M97297:3976-4671 vanRA also known as vanR is a vanR variant found in the vanA gene cluster glycopeptide
contig00073 7711 8865 vanSA 0/0 100.0 100.0 M97297:4649-5803 vanSA also known as vanS is a vanS variant found in the vanA gene cluster glycopeptide
contig00073 4890 5498 vanXA 0/0 100.0 99.8 M97297:8016-8624 vanXA also known as vanX is a vanX variant found in the vanA gene cluster glycopeptide
contig00073 3551 4462 vanYA 0/0 100.0 99.8 M97297:9052-9963 vanYA also known as vanY is a vanY variant found in the vanA gene cluster glycopeptide
contig00073 2913 3398 vanZA 0/0 100.0 100.0 M97297:10116-10601 vanZA also known as vanZ is a vanZ variant found in the vanA gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00126 376 1719 (AGly)aac6-Aph2 0/0 93.3 99.9 M13771:304-1743 (AGly)aac6-Aph2 NA
contig00010 31434 31982 (AGly)aac6-Ii 0/0 100.0 99.6 L12710:169-717 (AGly)aac6-Ii NA
contig00064 6660 7568 (AGly)ant6-Ia 0/0 100.0 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00064 8200 8994 (AGly)aph(3’’)-III 0/0 100.0 100.0 V01547:535-1329 (AGly)aph(3’’)-III NA
contig00064 7565 8107 (AGly)sat4A 0/0 100.0 100.0 X92945:38870-39412 (AGly)sat4A NA
contig00073 5504 6535 (Gly)vanA-A 0/0 100.0 99.9 M97297:6979-8010 (Gly)vanA-A NA
contig00073 6528 7496 (Gly)vanH-A 0/0 100.0 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00073 8843 9538 (Gly)vanR-A 0/0 100.0 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00073 7711 8865 (Gly)vanS-A 0/0 100.0 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00073 4890 5498 (Gly)vanX-A 0/0 100.0 99.8 M97297:8016-8624 (Gly)vanX-A NA
contig00073 3551 4462 (Gly)vanY-A 0/0 100.0 99.8 M97297:9052-9963 (Gly)vanY-A NA
contig00073 2913 3398 (Gly)vanZ-A 0/0 100.0 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00064 12761 13498 (MLS)erm(B) 0/0 100.0 99.9 M11180:714-1451 (MLS)erm(B) NA
contig00004 80444 81922 (MLS)msr(C) 0/0 100.0 98.9 AY004350:496-1974 (MLS)msr(C) NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00010 31434 31982 aacA-ENT1 0/0 100 100.0 NG_052371.1 aminoglycoside 6’-N-acetyltransferase AMINOGLYCOSIDE
contig00064 6660 7568 ant(6)-Ia 0/0 100 100.0 NG_047393.1 aminoglycoside nucleotidyltransferase ANT(6)-Ia STREPTOMYCIN
contig00064 8200 8994 aph(3’)-IIIa 0/0 100 100.0 NG_047418.1 aminoglycoside O-phosphotransferase APH(3’)-IIIa AMIKACIN, KANAMYCIN
contig00019 24222 25724 eat(A) 0/0 100 100.0 NG_047762.1 ABC-F type ribosomal protection protein Eat(A) PLEUROMUTILIN
contig00064 12761 13498 erm(B) 0/0 100 99.9 NG_047804.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00004 80444 81922 msr(C) 0/0 100 98.9 NG_048003.1 ABC-F type ribosomal protection protein Msr(C) MACROLIDE
contig00064 7565 8107 sat4 0/0 100 100.0 NG_048072.1 streptothricin N-acetyltransferase Sat4 STREPTOTHRICIN
contig00073 5504 6535 vanA 0/0 100 99.9 NG_048323.1 D-alanine–(R)-lactate ligase VanA VANCOMYCIN
contig00073 6528 7496 vanH-A 0/0 100 100.0 NG_048372.1 D-lactate dehydrogenase VanH-A VANCOMYCIN
contig00073 8843 9538 vanR-A 0/0 100 100.0 NG_048399.1 VanA-type vancomycin resistance DNA-binding response regulator VanR VANCOMYCIN
contig00073 7711 8865 vanS-A 0/0 100 100.0 NG_048425.1 VanA-type vancomycin resistance histidine kinase VanS VANCOMYCIN
contig00073 4890 5498 vanX-A 0/0 100 100.0 NG_048476.1 D-Ala-D-Ala dipeptidase VanX-A VANCOMYCIN
contig00073 3551 4462 vanY-A 0/0 100 99.8 NG_048516.1 D-Ala-D-Ala carboxypeptidase VanY-A VANCOMYCIN
contig00073 2913 3398 vanZ-A 0/0 100 100.0 NG_048534.1 glycopeptide resistance protein VanZ-A VANCOMYCIN
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00010 31434 31982 aacA-ENT1 0/0 100 100.0 NG_052371.1 aminoglycoside 6’-N-acetyltransferase AMINOGLYCOSIDE
contig00064 6660 7568 ant(6)-Ia 0/0 100 100.0 NG_047393.1 aminoglycoside nucleotidyltransferase ANT(6)-Ia STREPTOMYCIN
contig00064 8200 8994 aph(3’)-IIIa 0/0 100 100.0 NG_047418.1 aminoglycoside O-phosphotransferase APH(3’)-IIIa AMIKACIN, KANAMYCIN
contig00019 24222 25724 eat(A) 0/0 100 100.0 NG_047762.1 ABC-F type ribosomal protection protein Eat(A) PLEUROMUTILIN
contig00064 12761 13498 erm(B) 0/0 100 99.9 NG_047804.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00004 80444 81922 msr(C) 0/0 100 98.9 NG_048003.1 ABC-F type ribosomal protection protein Msr(C) MACROLIDE
contig00064 7565 8107 sat4 0/0 100 100.0 NG_048072.1 streptothricin N-acetyltransferase Sat4 STREPTOTHRICIN
contig00073 5504 6535 vanA 0/0 100 99.9 NG_048323.1 D-alanine–(R)-lactate ligase VanA VANCOMYCIN
contig00073 6528 7496 vanH-A 0/0 100 100.0 NG_048372.1 D-lactate dehydrogenase VanH-A VANCOMYCIN
contig00073 8843 9538 vanR-A 0/0 100 100.0 NG_048399.1 VanA-type vancomycin resistance DNA-binding response regulator VanR VANCOMYCIN
contig00073 7711 8865 vanS-A 0/0 100 100.0 NG_048425.1 VanA-type vancomycin resistance histidine kinase VanS VANCOMYCIN
contig00073 4890 5498 vanX-A 0/0 100 100.0 NG_048476.1 D-Ala-D-Ala dipeptidase VanX-A VANCOMYCIN
contig00073 3551 4462 vanY-A 0/0 100 99.8 NG_048516.1 D-Ala-D-Ala carboxypeptidase VanY-A VANCOMYCIN
contig00073 2913 3398 vanZ-A 0/0 100 100.0 NG_048534.1 glycopeptide resistance protein VanZ-A VANCOMYCIN
SRR8948883
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00097 2093 4699 VanHAX_2 0/0 100 100.0 M97297 VanHAX Vancomycin, Teicoplanin
contig00014 38383 38931 aac(6’)-Ii_1 0/0 100 98.9 L12710 aac(6’)-Ii Amikacin, Tobramycin
contig00108 2185 3093 ant(6)-Ia_1 0/0 100 100.0 AF330699 ant(6)-Ia Streptomycin
contig00080 4495 5142 cat(pC221)_1 0/0 100 97.7 X02529 cat(pC221) Chloramphenicol
contig00137 136 898 erm(B)_18 1/1 100 99.0 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00003 56772 58250 msr(C)_1 0/0 100 98.9 AY004350 msr(C) Erythromycin, Telithromycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00021 22046 23965 tet(M)_13 0/0 100 100.0 AM990992 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00014 38383 38931 AAC(6’)-Ii 0/0 100.0 98.9 L12710:0-549 AAC(6’)-Ii is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus spp. aminoglycoside
contig00080 4495 5142 Enterococcus_faecalis_chloramphenicol_acetyltransferase 0/0 100.0 100.0 X92945.2:9582-8934 A chloramphenicol acetyltransferase and resistance determinant described in Enterococcus faecalis phenicol
contig00137 161 906 ErmB 1/1 99.9 99.6 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB 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 ErmB. lincosamide, macrolide, streptogramin
contig00108 2263 3093 aad(6) 0/0 100.0 100.0 AY712687:0-831 aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis aminoglycoside
contig00070 4109 4604 dfrF 1/1 100.0 99.6 AF028812:392-887 dfrF is a chromosome-encoded dihydrofolate reductase found in Streptococcus pyogenes diaminopyrimidine
contig00006 37430 38716 efmA 0/0 100.0 100.0 AB467372.1:284-1571 efmA is an MFS transporter permease in E. faecium. fluoroquinolone, macrolide
contig00003 56772 58250 msrC 0/0 100.0 94.4 AF313494:0-1479 msrC is a chromosomal-encoded ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to erythromycin and other macrolide and streptogramin B antibiotics. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00021 22046 23965 tetM 0/0 100.0 100.0 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
contig00123 728 1045 tetU 0/0 100.0 99.4 U01917.1:412-730 Tetracycline-resistant determinant encoded on the plasmid pKQ10 in Enterococcus faecium tetracycline
contig00097 3054 4085 vanA 0/0 100.0 100.0 M97297:6979-8010 VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance. glycopeptide
contig00097 2093 3061 vanHA 0/0 100.0 100.0 M97297:6018-6986 vanHA also known as vanH is a vanH variant in the vanA gene cluster glycopeptide
contig00097 51 746 vanRA 0/0 100.0 100.0 M97297:3976-4671 vanRA also known as vanR is a vanR variant found in the vanA gene cluster glycopeptide
contig00097 724 1878 vanSA 0/0 100.0 100.0 M97297:4649-5803 vanSA also known as vanS is a vanS variant found in the vanA gene cluster glycopeptide
contig00097 4091 4699 vanXA 0/0 100.0 100.0 M97297:8016-8624 vanXA also known as vanX is a vanX variant found in the vanA gene cluster glycopeptide
contig00112 1930 2841 vanYA 0/0 100.0 100.0 M97297:9052-9963 vanYA also known as vanY is a vanY variant found in the vanA gene cluster glycopeptide
contig00112 1292 1777 vanZA 0/0 100.0 100.0 M97297:10116-10601 vanZA also known as vanZ is a vanZ variant found in the vanA gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00014 38383 38931 (AGly)aac6-Ii 0/0 100 98.9 L12710:169-717 (AGly)aac6-Ii NA
contig00108 2185 3093 (AGly)ant6-Ia 0/0 100 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00097 3054 4085 (Gly)vanA-A 0/0 100 100.0 M97297:6979-8010 (Gly)vanA-A NA
contig00097 2093 3061 (Gly)vanH-A 0/0 100 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00097 51 746 (Gly)vanR-A 0/0 100 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00097 724 1878 (Gly)vanS-A 0/0 100 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00097 4091 4699 (Gly)vanX-A 0/0 100 100.0 M97297:8016-8624 (Gly)vanX-A NA
contig00112 1930 2841 (Gly)vanY-A 0/0 100 100.0 M97297:9052-9963 (Gly)vanY-A NA
contig00112 1292 1777 (Gly)vanZ-A 0/0 100 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00137 161 898 (MLS)erm(B) 0/0 100 99.5 M11180:714-1451 (MLS)erm(B) NA
contig00003 56772 58250 (MLS)msr(C) 0/0 100 98.9 AY004350:496-1974 (MLS)msr(C) NA
contig00080 4495 5142 (Phe)cat-pC221 0/0 100 97.7 X02529:2267-2914 (Phe)cat-pC221 NA
contig00021 22046 23965 (Tet)tetM 0/0 100 99.2 DQ534550:1451-3370 (Tet)tetM NA
contig00123 728 1045 (Tet)tetU 0/0 100 99.4 U01917:413-730 (Tet)tetU NA
contig00070 4109 4604 (Tmt)dfrF 1/1 100 99.6 NG_047755:101-595 (Tmt)dfrF NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00014 38383 38931 aacA-ENT1 0/0 100.0 99.6 NG_052140.1 aminoglycoside 6’-N-acetyltransferase AMINOGLYCOSIDE
contig00108 2185 3093 ant(6)-Ia 0/0 100.0 100.0 NG_047393.1 aminoglycoside nucleotidyltransferase ANT(6)-Ia STREPTOMYCIN
contig00080 4495 5142 catA7 0/0 100.0 100.0 NG_047568.1 type A-7 chloramphenicol O-acetyltransferase CHLORAMPHENICOL
contig00070 4109 4604 dfrF 1/1 100.0 99.6 NG_047755.1 trimethoprim-resistant dihydrofolate reductase DfrF TRIMETHOPRIM
contig00018 24280 25782 eat(A) 0/0 100.0 100.0 NG_047762.1 ABC-F type ribosomal protection protein Eat(A) PLEUROMUTILIN
contig00137 161 906 erm(B) 1/1 99.9 99.6 NG_047801.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00003 56772 58250 msr(C) 0/0 100.0 98.9 NG_048003.1 ABC-F type ribosomal protection protein Msr(C) MACROLIDE
contig00021 22046 23965 tet(M) 0/0 100.0 99.8 NG_048213.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
contig00097 3054 4085 vanA 0/0 100.0 100.0 NG_048323.1 D-alanine–(R)-lactate ligase VanA VANCOMYCIN
contig00097 2093 3061 vanH-A 0/0 100.0 100.0 NG_048372.1 D-lactate dehydrogenase VanH-A VANCOMYCIN
contig00097 51 746 vanR-A 0/0 100.0 100.0 NG_048399.1 VanA-type vancomycin resistance DNA-binding response regulator VanR VANCOMYCIN
contig00097 724 1878 vanS-A 0/0 100.0 100.0 NG_048425.1 VanA-type vancomycin resistance histidine kinase VanS VANCOMYCIN
contig00097 4091 4699 vanX-A 0/0 100.0 100.0 NG_048477.1 D-Ala-D-Ala dipeptidase VanX-A VANCOMYCIN
contig00112 1930 2841 vanY-A 0/0 100.0 100.0 NG_048516.1 D-Ala-D-Ala carboxypeptidase VanY-A VANCOMYCIN
contig00112 1292 1777 vanZ-A 0/0 100.0 100.0 NG_048534.1 glycopeptide resistance protein VanZ-A VANCOMYCIN
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00014 38383 38931 aacA-ENT1 0/0 100.0 99.6 NG_052140.1 aminoglycoside 6’-N-acetyltransferase AMINOGLYCOSIDE
contig00108 2185 3093 ant(6)-Ia 0/0 100.0 100.0 NG_047393.1 aminoglycoside nucleotidyltransferase ANT(6)-Ia STREPTOMYCIN
contig00080 4495 5142 catA7 0/0 100.0 100.0 NG_047568.1 type A-7 chloramphenicol O-acetyltransferase CHLORAMPHENICOL
contig00070 4109 4604 dfrF 1/1 100.0 99.6 NG_047755.1 trimethoprim-resistant dihydrofolate reductase DfrF TRIMETHOPRIM
contig00018 24280 25782 eat(A) 0/0 100.0 100.0 NG_047762.1 ABC-F type ribosomal protection protein Eat(A) PLEUROMUTILIN
contig00137 161 906 erm(B) 1/1 99.9 99.6 NG_047801.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00003 56772 58250 msr(C) 0/0 100.0 98.9 NG_048003.1 ABC-F type ribosomal protection protein Msr(C) MACROLIDE
contig00021 22046 23965 tet(M) 0/0 100.0 99.8 NG_048213.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
contig00097 3054 4085 vanA 0/0 100.0 100.0 NG_048323.1 D-alanine–(R)-lactate ligase VanA VANCOMYCIN
contig00097 2093 3061 vanH-A 0/0 100.0 100.0 NG_048372.1 D-lactate dehydrogenase VanH-A VANCOMYCIN
contig00097 51 746 vanR-A 0/0 100.0 100.0 NG_048399.1 VanA-type vancomycin resistance DNA-binding response regulator VanR VANCOMYCIN
contig00097 724 1878 vanS-A 0/0 100.0 100.0 NG_048425.1 VanA-type vancomycin resistance histidine kinase VanS VANCOMYCIN
contig00097 4091 4699 vanX-A 0/0 100.0 100.0 NG_048477.1 D-Ala-D-Ala dipeptidase VanX-A VANCOMYCIN
contig00112 1930 2841 vanY-A 0/0 100.0 100.0 NG_048516.1 D-Ala-D-Ala carboxypeptidase VanY-A VANCOMYCIN
contig00112 1292 1777 vanZ-A 0/0 100.0 100.0 NG_048534.1 glycopeptide resistance protein VanZ-A VANCOMYCIN
SRR8948884
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 57049 58545 lsa(A)_1 0/0 100 99.4 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00031 524 2464 tet(S)_3 0/0 100 99.9 X92946 tet(S) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00002 72187 72681 dfrE 0/0 100.0 97.6 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00013 35717 37444 efrA 0/0 100.0 99.2 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00013 38003 39056 efrB 6/6 96.7 97.6 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00004 173480 174634 emeA 1/27 97.7 96.9 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00008 57049 58545 lsaA 0/0 100.0 99.4 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00031 524 2449 tetS 0/0 100.0 100.0 L09756:0-1926 Tet(S) is a ribosomal protection protein found in Gram-positive and Gram-negative strains. It is similar to tet(M) and tet(O). tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 57049 58545 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00002 408745 409578 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00031 524 2449 (Tet)tetS 0/0 100 100.0 L09756:447-2372 (Tet)tetS NA
contig00002 72187 72681 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00002 72187 72681 dfrE 0/0 100 97.6 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00008 57049 58545 lsa(A) 0/0 100 99.4 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00031 524 2449 tet(S) 0/0 100 100.0 NG_048273.1 tetracycline resistance ribosomal protection protein Tet(S) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00002 72187 72681 dfrE 0/0 100 97.6 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00008 57049 58545 lsa(A) 0/0 100 99.4 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00031 524 2449 tet(S) 0/0 100 100.0 NG_048273.1 tetracycline resistance ribosomal protection protein Tet(S) TETRACYCLINE
SRR8948885
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00012 20441 22041 VanC1XY_1 0/0 100 99.9 AF162694 VanC1XY Vancomycin
contig00018 36401 36898 dfrG_1 0/0 100 100.0 AB205645 dfrG Trimethoprim
contig00018 43312 44074 erm(B)_18 1/1 100 99.6 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00029 796 2736 tet(S)_3 0/0 100 99.9 X92946 tet(S) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00018 43304 44049 ErmB 1/1 99.9 99.1 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB 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 ErmB. lincosamide, macrolide, streptogramin
contig00018 36401 36898 dfrG 0/0 100.0 100.0 AB205645:1012-1510 dfrG is a plasmid-encoded dihydrofolate reductase found in Staphylococcus aureus diaminopyrimidine
contig00029 796 2721 tetS 0/0 100.0 100.0 L09756:0-1926 Tet(S) is a ribosomal protection protein found in Gram-positive and Gram-negative strains. It is similar to tet(M) and tet(O). tetracycline
contig00012 21010 22041 vanC 0/0 100.0 99.8 AF162694:1410-2442 VanC is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Ser an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is specific to Enterococcus gallinarum and E. casseliflavus providing intrinsic resistance. glycopeptide
contig00012 17564 18259 vanRC 0/0 100.0 100.0 AF162694:5192-5888 vanRC is a vanR variant found in the vanC gene cluster glycopeptide
contig00012 16489 17574 vanSC 0/0 100.0 99.9 AF162694:5877-6963 vanSC is a vanS variant found in the vanC gene cluster glycopeptide
contig00012 18348 20444 vanTC 0/0 100.0 99.9 AF162694:3007-5104 vanTC is a vanT variant found in the vanC gene cluster glycopeptide
contig00012 20441 21013 vanXYC 0/0 100.0 100.0 AF162694:2438-3011 vanXYC is a vanXY variant found in the vanC gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00012 21010 22041 (Gly)vanC 0/0 100 99.8 AF162694:1411-2442 (Gly)vanC NA
contig00012 17564 18259 (Gly)vanR-C 0/0 100 100.0 AF162694:5193-5888 (Gly)vanR-C NA
contig00012 16489 17574 (Gly)vanS-C 0/0 100 99.4 DQ022190:4672-5757 (Gly)vanS-C NA
contig00012 18348 20444 (Gly)vanT 0/0 100 99.9 AF162694:3008-5104 (Gly)vanT NA
contig00012 20441 21013 (Gly)vanX-Yc 0/0 100 100.0 DQ022190:1233-1805 (Gly)vanX-Yc NA
contig00018 43312 44049 (MLS)erm(B) 0/0 100 100.0 M11180:714-1451 (MLS)erm(B) NA
contig00029 796 2721 (Tet)tetS 0/0 100 100.0 L09756:447-2372 (Tet)tetS NA
contig00018 36401 36898 (Tmt)dfrG 0/0 100 100.0 AB205645:1013-1510 (Tmt)dfrG NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00018 36401 36898 dfrG 0/0 100 100.0 NG_047756.1 trimethoprim-resistant dihydrofolate reductase DfrG TRIMETHOPRIM
contig00018 43312 44049 erm(B) 0/0 100 99.9 NG_047797.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00029 796 2721 tet(S) 0/0 100 100.0 NG_048273.1 tetracycline resistance ribosomal protection protein Tet(S) TETRACYCLINE
contig00012 21010 22041 vanC1 0/0 100 99.9 NG_048354.1 D-alanine–D-serine ligase VanC1 VANCOMYCIN
contig00012 17564 18259 vanR-C 0/0 100 100.0 NG_048404.1 VanC-type vancomycin resistance DNA-binding response regulator VanR VANCOMYCIN
contig00012 16489 17574 vanS-C 0/0 100 99.9 NG_048430.1 VanC-type vancomycin resistance histidine kinase VanS VANCOMYCIN
contig00012 18348 20444 vanT-C 0/0 100 99.9 NG_048454.1 membrane-bound serine racemase VanT-C VANCOMYCIN
contig00012 20441 21013 vanXY-C 0/0 100 100.0 NG_048503.1 D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase VanXY-C VANCOMYCIN
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00018 36401 36898 dfrG 0/0 100 100.0 NG_047756.1 trimethoprim-resistant dihydrofolate reductase DfrG TRIMETHOPRIM
contig00018 43312 44049 erm(B) 0/0 100 99.9 NG_047797.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00029 796 2721 tet(S) 0/0 100 100.0 NG_048273.1 tetracycline resistance ribosomal protection protein Tet(S) TETRACYCLINE
contig00012 21010 22041 vanC1 0/0 100 99.9 NG_048354.1 D-alanine–D-serine ligase VanC1 VANCOMYCIN
contig00012 17564 18259 vanR-C 0/0 100 100.0 NG_048404.1 VanC-type vancomycin resistance DNA-binding response regulator VanR VANCOMYCIN
contig00012 16489 17574 vanS-C 0/0 100 99.9 NG_048430.1 VanC-type vancomycin resistance histidine kinase VanS VANCOMYCIN
contig00012 18348 20444 vanT-C 0/0 100 99.9 NG_048454.1 membrane-bound serine racemase VanT-C VANCOMYCIN
contig00012 20441 21013 vanXY-C 0/0 100 100.0 NG_048503.1 D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase VanXY-C VANCOMYCIN
SRR8948886
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00011 69778 70326 aac(6’)-Ii_1 0/0 100 98.5 L12710 aac(6’)-Ii Amikacin, Tobramycin
contig00019 42610 44088 msr(C)_2 0/0 100 99.5 AF313494 msr(C) Erythromycin, Telithromycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00011 69778 70326 AAC(6’)-Ii 0/0 100 98.5 L12710:0-549 AAC(6’)-Ii is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus spp. aminoglycoside
contig00019 42610 44088 msrC 0/0 100 99.5 AF313494:0-1479 msrC is a chromosomal-encoded ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to erythromycin and other macrolide and streptogramin B antibiotics. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00011 69778 70326 (AGly)aac6-Ii 0/0 100 98.5 L12710:169-717 (AGly)aac6-Ii NA
contig00019 42610 44088 (MLS)msr(C) 0/0 100 95.3 AY004350:496-1974 (MLS)msr(C) NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00011 69778 70326 aacA-ENT1 0/0 100 100.0 NG_052140.1 aminoglycoside 6’-N-acetyltransferase AMINOGLYCOSIDE
contig00018 27508 29010 eat(A) 0/0 100 94.1 NG_047762.1 ABC-F type ribosomal protection protein Eat(A) PLEUROMUTILIN
contig00019 42610 44088 msr(C) 0/0 100 99.5 NG_048004.1 ABC-F type ribosomal protection protein Msr(C) MACROLIDE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00011 69778 70326 aacA-ENT1 0/0 100 100.0 NG_052140.1 aminoglycoside 6’-N-acetyltransferase AMINOGLYCOSIDE
contig00018 27508 29010 eat(A) 0/0 100 94.1 NG_047762.1 ABC-F type ribosomal protection protein Eat(A) PLEUROMUTILIN
contig00019 42610 44088 msr(C) 0/0 100 99.5 NG_048004.1 ABC-F type ribosomal protection protein Msr(C) MACROLIDE
SRR8948887
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 103653 105149 lsa(A)_1 0/0 100 99.4 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00006 124979 126898 tet(M)_13 0/0 100 99.9 AM990992 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 182045 182539 dfrE 0/0 100.0 97.6 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00012 25123 26850 efrA 0/0 100.0 99.3 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00012 23511 24564 efrB 6/6 96.7 97.6 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00005 173315 174469 emeA 1/27 97.7 97.0 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00008 103653 105149 lsaA 0/0 100.0 99.4 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00006 124979 126898 tetM 0/0 100.0 99.9 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 103653 105149 (MLS)lsa(A) 0/0 100 99.4 AY225127:41-1537 (MLS)lsa(A) NA
contig00001 490345 491178 (MLS)mph(D) 0/0 100 99.6 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00006 124979 126898 (Tet)tetM 0/0 100 99.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 182045 182539 (Tmt)dfrE 0/0 100 97.6 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 182045 182539 dfrE 0/0 100 97.6 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00008 103653 105149 lsa(A) 0/0 100 99.4 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00006 124979 126898 tet(M) 0/0 100 99.8 NG_048213.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 182045 182539 dfrE 0/0 100 97.6 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00008 103653 105149 lsa(A) 0/0 100 99.4 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00006 124979 126898 tet(M) 0/0 100 99.8 NG_048213.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
SRR8948888
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00026 2516 3278 erm(B)_18 1/1 100 99.2 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00003 100902 102398 lsa(A)_1 0/0 100 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00002 94435 96354 tet(M)_10 0/0 100 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00026 2541 3286 ErmB 1/1 99.9 99.5 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB 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 ErmB. lincosamide, macrolide, streptogramin
contig00001 77448 77942 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00015 7680 9407 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00015 9966 11019 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 518638 519792 emeA 1/27 97.7 97.4 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00003 100902 102398 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00002 94435 96354 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00026 2541 3278 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00003 100902 102398 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 94435 96354 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77448 77942 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 dfrE 0/0 100 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00026 2541 3278 erm(B) 0/0 100 100.0 NG_047794.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00003 100902 102398 lsa(A) 0/0 100 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00002 94435 96354 tet(M) 0/0 100 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 dfrE 0/0 100 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00026 2541 3278 erm(B) 0/0 100 100.0 NG_047794.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00003 100902 102398 lsa(A) 0/0 100 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00002 94435 96354 tet(M) 0/0 100 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
SRR8948889
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00115 4891 7497 VanHAX_2 0/0 100 99.9 M97297 VanHAX Vancomycin, Teicoplanin
contig00022 31437 31985 aac(6’)-Ii_1 0/0 100 99.6 L12710 aac(6’)-Ii Amikacin, Tobramycin
contig00107 6381 7289 ant(6)-Ia_1 0/0 100 100.0 AF330699 ant(6)-Ia Streptomycin
contig00107 7921 8715 aph(3’)-III_1 0/0 100 100.0 M26832 aph(3’)-III Amikacin
contig00002 100972 102468 lsa(A)_1 0/0 100 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00011 80444 81922 msr(C)_1 0/0 100 98.9 AY004350 msr(C) Erythromycin, Telithromycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00005 147681 149600 tet(M)_10 0/0 100 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00022 31437 31985 AAC(6’)-Ii 0/0 100.0 99.6 L12710:0-549 AAC(6’)-Ii is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus spp. aminoglycoside
contig00107 7921 8715 APH(3’)-IIIa 0/0 100.0 100.0 CP004067:52914-53709 APH(3’)-IIIa is a plasmid-encoded aminoglycoside phosphotransferase in S. aureus and Enterococcus spp. aminoglycoside
contig00107 7286 7828 SAT-4 0/0 100.0 99.8 U01945:373-916 SAT-4 is a plasmid-mediated streptothricin acetyltransferase and streptothricin (a nucleoside antibiotic) resistant determinant. Originally described from a Campylobacter coli BE/G4 plasmid gene sequence by Jacob et al 1994. nucleoside
contig00107 6459 7289 aad(6) 0/0 100.0 100.0 AY712687:0-831 aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis aminoglycoside
contig00001 77924 78418 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00016 38939 40225 efmA 0/0 100.0 100.0 AB467372.1:284-1571 efmA is an MFS transporter permease in E. faecium. fluoroquinolone, macrolide
contig00045 7680 9407 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00045 9966 11019 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 519114 520268 emeA 1/27 97.7 97.4 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00002 100972 102468 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00011 80444 81922 msrC 0/0 100.0 94.4 AF313494:0-1479 msrC is a chromosomal-encoded ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to erythromycin and other macrolide and streptogramin B antibiotics. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00005 147681 149600 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
contig00115 5505 6536 vanA 0/0 100.0 99.9 M97297:6979-8010 VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance. glycopeptide
contig00115 6529 7497 vanHA 0/0 100.0 100.0 M97297:6018-6986 vanHA also known as vanH is a vanH variant in the vanA gene cluster glycopeptide
contig00115 8844 9539 vanRA 0/0 100.0 100.0 M97297:3976-4671 vanRA also known as vanR is a vanR variant found in the vanA gene cluster glycopeptide
contig00115 7712 8866 vanSA 0/0 100.0 100.0 M97297:4649-5803 vanSA also known as vanS is a vanS variant found in the vanA gene cluster glycopeptide
contig00115 4891 5499 vanXA 0/0 100.0 99.8 M97297:8016-8624 vanXA also known as vanX is a vanX variant found in the vanA gene cluster glycopeptide
contig00115 3552 4463 vanYA 0/0 100.0 99.8 M97297:9052-9963 vanYA also known as vanY is a vanY variant found in the vanA gene cluster glycopeptide
contig00115 2914 3399 vanZA 0/0 100.0 100.0 M97297:10116-10601 vanZA also known as vanZ is a vanZ variant found in the vanA gene cluster glycopeptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00022 31437 31985 (AGly)aac6-Ii 0/0 100 99.6 L12710:169-717 (AGly)aac6-Ii NA
contig00107 6381 7289 (AGly)ant6-Ia 0/0 100 100.0 AF330699:22-930 (AGly)ant6-Ia NA
contig00107 7921 8715 (AGly)aph(3’’)-III 0/0 100 100.0 V01547:535-1329 (AGly)aph(3’’)-III NA
contig00107 7286 7828 (AGly)sat4A 0/0 100 100.0 X92945:38870-39412 (AGly)sat4A NA
contig00115 5505 6536 (Gly)vanA-A 0/0 100 99.9 M97297:6979-8010 (Gly)vanA-A NA
contig00115 6529 7497 (Gly)vanH-A 0/0 100 100.0 FJ866609:3762-4730 (Gly)vanH-A NA
contig00115 8844 9539 (Gly)vanR-A 0/0 100 100.0 M97297:3976-4671 (Gly)vanR-A NA
contig00115 7712 8866 (Gly)vanS-A 0/0 100 100.0 M97297:4649-5803 (Gly)vanS-A NA
contig00115 4891 5499 (Gly)vanX-A 0/0 100 99.8 M97297:8016-8624 (Gly)vanX-A NA
contig00115 3552 4463 (Gly)vanY-A 0/0 100 99.8 M97297:9052-9963 (Gly)vanY-A NA
contig00115 2914 3399 (Gly)vanZ-A 0/0 100 100.0 M97297:10116-10601 (Gly)vanZ-A NA
contig00002 100972 102468 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00011 80444 81922 (MLS)msr(C) 0/0 100 98.9 AY004350:496-1974 (MLS)msr(C) NA
contig00005 147681 149600 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77924 78418 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00022 31437 31985 aacA-ENT1 0/0 100 100.0 NG_052371.1 aminoglycoside 6’-N-acetyltransferase AMINOGLYCOSIDE
contig00107 6381 7289 ant(6)-Ia 0/0 100 100.0 NG_047393.1 aminoglycoside nucleotidyltransferase ANT(6)-Ia STREPTOMYCIN
contig00107 7921 8715 aph(3’)-IIIa 0/0 100 100.0 NG_047418.1 aminoglycoside O-phosphotransferase APH(3’)-IIIa AMIKACIN, KANAMYCIN
contig00001 77924 78418 dfrE 0/0 100 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00028 27366 28868 eat(A) 0/0 100 100.0 NG_047762.1 ABC-F type ribosomal protection protein Eat(A) PLEUROMUTILIN
contig00002 100972 102468 lsa(A) 0/0 100 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00011 80444 81922 msr(C) 0/0 100 98.9 NG_048003.1 ABC-F type ribosomal protection protein Msr(C) MACROLIDE
contig00107 7286 7828 sat4 0/0 100 100.0 NG_048072.1 streptothricin N-acetyltransferase Sat4 STREPTOTHRICIN
contig00005 147681 149600 tet(M) 0/0 100 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
contig00115 5505 6536 vanA 0/0 100 99.9 NG_048323.1 D-alanine–(R)-lactate ligase VanA VANCOMYCIN
contig00115 6529 7497 vanH-A 0/0 100 100.0 NG_048372.1 D-lactate dehydrogenase VanH-A VANCOMYCIN
contig00115 8844 9539 vanR-A 0/0 100 100.0 NG_048399.1 VanA-type vancomycin resistance DNA-binding response regulator VanR VANCOMYCIN
contig00115 7712 8866 vanS-A 0/0 100 100.0 NG_048425.1 VanA-type vancomycin resistance histidine kinase VanS VANCOMYCIN
contig00115 4891 5499 vanX-A 0/0 100 100.0 NG_048476.1 D-Ala-D-Ala dipeptidase VanX-A VANCOMYCIN
contig00115 3552 4463 vanY-A 0/0 100 99.8 NG_048516.1 D-Ala-D-Ala carboxypeptidase VanY-A VANCOMYCIN
contig00115 2914 3399 vanZ-A 0/0 100 100.0 NG_048534.1 glycopeptide resistance protein VanZ-A VANCOMYCIN
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00022 31437 31985 aacA-ENT1 0/0 100 100.0 NG_052371.1 aminoglycoside 6’-N-acetyltransferase AMINOGLYCOSIDE
contig00107 6381 7289 ant(6)-Ia 0/0 100 100.0 NG_047393.1 aminoglycoside nucleotidyltransferase ANT(6)-Ia STREPTOMYCIN
contig00107 7921 8715 aph(3’)-IIIa 0/0 100 100.0 NG_047418.1 aminoglycoside O-phosphotransferase APH(3’)-IIIa AMIKACIN, KANAMYCIN
contig00001 77924 78418 dfrE 0/0 100 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00028 27366 28868 eat(A) 0/0 100 100.0 NG_047762.1 ABC-F type ribosomal protection protein Eat(A) PLEUROMUTILIN
contig00002 100972 102468 lsa(A) 0/0 100 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00011 80444 81922 msr(C) 0/0 100 98.9 NG_048003.1 ABC-F type ribosomal protection protein Msr(C) MACROLIDE
contig00107 7286 7828 sat4 0/0 100 100.0 NG_048072.1 streptothricin N-acetyltransferase Sat4 STREPTOTHRICIN
contig00005 147681 149600 tet(M) 0/0 100 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
contig00115 5505 6536 vanA 0/0 100 99.9 NG_048323.1 D-alanine–(R)-lactate ligase VanA VANCOMYCIN
contig00115 6529 7497 vanH-A 0/0 100 100.0 NG_048372.1 D-lactate dehydrogenase VanH-A VANCOMYCIN
contig00115 8844 9539 vanR-A 0/0 100 100.0 NG_048399.1 VanA-type vancomycin resistance DNA-binding response regulator VanR VANCOMYCIN
contig00115 7712 8866 vanS-A 0/0 100 100.0 NG_048425.1 VanA-type vancomycin resistance histidine kinase VanS VANCOMYCIN
contig00115 4891 5499 vanX-A 0/0 100 100.0 NG_048476.1 D-Ala-D-Ala dipeptidase VanX-A VANCOMYCIN
contig00115 3552 4463 vanY-A 0/0 100 99.8 NG_048516.1 D-Ala-D-Ala carboxypeptidase VanY-A VANCOMYCIN
contig00115 2914 3399 vanZ-A 0/0 100 100.0 NG_048534.1 glycopeptide resistance protein VanZ-A VANCOMYCIN
SRR8948890
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 2516 3278 erm(B)_18 1/1 100 99.2 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00003 100982 102478 lsa(A)_1 0/0 100 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00002 94435 96354 tet(M)_10 0/0 100 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 2541 3286 ErmB 1/1 99.9 99.5 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB 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 ErmB. lincosamide, macrolide, streptogramin
contig00001 77448 77942 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00017 7680 9407 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00017 9966 11019 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 518638 519792 emeA 1/27 97.7 97.4 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00003 100982 102478 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00002 94435 96354 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00028 2541 3278 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00003 100982 102478 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 94435 96354 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77448 77942 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 dfrE 0/0 100 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00028 2541 3278 erm(B) 0/0 100 100.0 NG_047794.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00003 100982 102478 lsa(A) 0/0 100 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00002 94435 96354 tet(M) 0/0 100 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 dfrE 0/0 100 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00028 2541 3278 erm(B) 0/0 100 100.0 NG_047794.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00003 100982 102478 lsa(A) 0/0 100 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00002 94435 96354 tet(M) 0/0 100 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
SRR8948891
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00025 2516 3278 erm(B)_18 1/1 100 99.2 X66468 erm(B) Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00003 100981 102477 lsa(A)_1 0/0 100 98.9 AY225127 lsa(A) Lincomycin, Clindamycin, Dalfopristin, Pristinamycin_IIA, Virginiamycin_M
contig00002 92923 94842 tet(M)_10 0/0 100 100.0 EU182585 tet(M) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00025 2541 3286 ErmB 1/1 99.9 99.5 AF242872.1:2131-2878 ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB 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 ErmB. lincosamide, macrolide, streptogramin
contig00001 77448 77942 dfrE 0/0 100.0 97.4 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis diaminopyrimidine
contig00015 7680 9407 efrA 0/0 100.0 98.9 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance. fluoroquinolone, macrolide, rifamycin
contig00015 9966 11019 efrB 6/6 96.7 97.5 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance. fluoroquinolone, macrolide, rifamycin
contig00001 518638 519792 emeA 1/27 97.7 97.4 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine. acridine_dye
contig00003 100981 102477 lsaA 0/0 100.0 98.9 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00002 92923 94842 tetM 0/0 100.0 94.4 AM990992.1:1003680-1001760 TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00025 2541 3278 (MLS)erm(B) 0/0 100 99.6 M11180:714-1451 (MLS)erm(B) NA
contig00003 100981 102477 (MLS)lsa(A) 0/0 100 98.9 AY225127:41-1537 (MLS)lsa(A) NA
contig00010 40387 41220 (MLS)mph(D) 0/0 100 99.9 NC_017312:2291580-2292413 (MLS)mph(D) NA
contig00002 92923 94842 (Tet)tetM 0/0 100 94.2 DQ534550:1451-3370 (Tet)tetM NA
contig00001 77448 77942 (Tmt)dfrE 0/0 100 97.4 NG_055770:101-595 (Tmt)dfrE NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 dfrE 0/0 100 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00025 2541 3278 erm(B) 0/0 100 100.0 NG_047794.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00003 100981 102477 lsa(A) 0/0 100 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00002 92923 94842 tet(M) 0/0 100 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00001 77448 77942 dfrE 0/0 100 97.4 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE TRIMETHOPRIM
contig00025 2541 3278 erm(B) 0/0 100 100.0 NG_047794.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) MACROLIDE
contig00003 100981 102477 lsa(A) 0/0 100 98.9 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE, STREPTOGRAMIN
contig00002 92923 94842 tet(M) 0/0 100 100.0 NG_048247.1 tetracycline resistance ribosomal protection protein Tet(M) TETRACYCLINE


Summary figures

Presence/Absence of antibiotic resistance genes (coverage and identity > 90%) on each sample

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Resfinder
CARD
ARG-ANNOT
NCBI
MEGARES


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Plasmid Profiling


Field Description
Contig Contig name where the gene was found
Start Start position of the gene within the contig
End End position of the gene within the contig
Gene Antibiotic resistance gene
Gaps Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage Proportion (%) of the gene covered
Identity Proportion (%) of exact nucleotide matches
Accession Accesion number of the antibiotic resistance gene
Product Antibiotic resistance gene product


Select sample

SRR8948878
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00026 2151 3161 rep9a_1_repA(pAD1) 0/0 100 96.0 L01794 rep9a_1_repA(pAD1)_L01794
contig00022 10809 11816 rep9b_3_repA(pMG2200) 0/0 100 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00013 55553 56554 rep9c_2_prgW(pCF10) 0/0 100 96.5 AY855841 rep9c_2_prgW(pCF10)_AY855841
contig00002 42100 43305 repUS43_1_CDS12738(DOp1) 0/0 100 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948879
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00031 5273 6129 rep11a_1_repA(pB82) 0/0 90.7 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00044 731 1744 rep14a_4_rep(AUS0004p3) 0/0 98.8 92.1 CP003354 rep14a_4_rep(AUS0004p3)_CP003354
contig00028 6614 8104 rep1_1_repE(pAMbeta) 0/0 100.0 100.0 AF007787 rep1_1_repE(pAMbeta)_AF007787
contig00029 6028 7521 rep2_1_orf1(pRE25) 0/0 100.0 100.0 X92945 rep2_1_orf1(pRE25)_X92945
contig00028 2119 3057 rep7a_8_ORF11(pRE25) 0/0 100.0 100.0 X92945 rep7a_8_ORF11(pRE25)_X92945
contig00019 6111 7121 rep9a_1_repA(pAD1) 0/0 100.0 96.0 L01794 rep9a_1_repA(pAD1)_L01794
contig00007 115500 116705 repUS43_1_CDS12738(DOp1) 0/0 100.0 99.9 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948880
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00029 5117 6061 rep11a_1_repA(pB82) 0/0 100.0 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00046 731 1744 rep14a_4_rep(AUS0004p3) 0/0 98.8 92.1 CP003354 rep14a_4_rep(AUS0004p3)_CP003354
contig00033 1494 2984 rep1_1_repE(pAMbeta) 0/0 100.0 100.0 AF007787 rep1_1_repE(pAMbeta)_AF007787
contig00039 489 1427 rep7a_8_ORF11(pRE25) 0/0 100.0 100.0 X92945 rep7a_8_ORF11(pRE25)_X92945
contig00030 2151 3161 rep9a_1_repA(pAD1) 0/0 100.0 96.0 L01794 rep9a_1_repA(pAD1)_L01794
contig00025 10809 11816 rep9b_3_repA(pMG2200) 0/0 100.0 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00014 55553 56554 rep9c_2_prgW(pCF10) 0/0 100.0 96.5 AY855841 rep9c_2_prgW(pCF10)_AY855841
contig00032 1447 2487 repUS15_2_repA(pNB2354p1) 0/0 100.0 99.8 CP004064 repUS15_2_repA(pNB2354p1)_CP004064
contig00002 42587 43792 repUS43_1_CDS12738(DOp1) 0/0 100.0 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948881
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00028 3326 4048 rep6_1_repA(pS86) 0/0 100 100.0 AJ223161 rep6_1_repA(pS86)_AJ223161
contig00018 10842 11825 rep8b_1_repA(pEJ97p1) 0/0 100 99.9 AJ49170 rep8b_1_repA(pEJ97p1)_AJ49170
SRR8948882
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00089 5317 6173 rep11a_1_repA(pB82) 0/0 90.7 100 AB178871 rep11a_1_repA(pB82)_AB178871
contig00106 2848 3798 rep14b_3_rep(pRI1) 0/0 100.0 100 EU327398 rep14b_3_rep(pRI1)_EU327398
contig00070 4699 5739 rep17_1_CDS29(pRUM) 0/0 100.0 100 AF507977 rep17_1_CDS29(pRUM)_AF507977
contig00084 4585 5322 rep29_2_EFAU085p4001(Aus0085p4)_Aus0085 0/0 100.0 100 rep29_2_EFAU085p4001(Aus0085p4)_Aus0085
contig00068 8676 10169 rep2_1_orf1(pRE25) 0/0 100.0 100 X92945 rep2_1_orf1(pRE25)_X92945
contig00083 2016 3056 repUS15_1_repA(DO3) 0/0 100.0 100 CP003586 repUS15_1_repA(DO3)_CP003586
SRR8948883
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00088 5317 6173 rep11a_1_repA(pB82) 0/0 90.7 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00123 731 1744 rep14a_4_rep(AUS0004p3) 0/0 98.8 92.1 CP003354 rep14a_4_rep(AUS0004p3)_CP003354
contig00080 225 1715 rep1_1_repE(pAMbeta) 0/0 100.0 100.0 AF007787 rep1_1_repE(pAMbeta)_AF007787
contig00075 6028 7521 rep2_1_orf1(pRE25) 0/0 100.0 100.0 X92945 rep2_1_orf1(pRE25)_X92945
contig00080 5272 6210 rep7a_8_ORF11(pRE25) 0/0 100.0 100.0 X92945 rep7a_8_ORF11(pRE25)_X92945
contig00095 2092 3132 repUS15_2_repA(pNB2354p1) 0/0 100.0 99.8 CP004064 repUS15_2_repA(pNB2354p1)_CP004064
SRR8948884
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00030 3326 4048 rep6_1_repA(pS86) 0/0 100 100.0 AJ223161 rep6_1_repA(pS86)_AJ223161
contig00019 10842 11825 rep8b_1_repA(pEJ97p1) 0/0 100 99.9 AJ49170 rep8b_1_repA(pEJ97p1)_AJ49170
SRR8948885
## [1] "NO PLASMID FOUND!!"
SRR8948886
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00033 5332 6188 rep11a_1_repA(pB82) 0/0 90.7 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00038 1065 2105 repUS15_1_repA(DO3) 0/0 100.0 99.9 CP003586 repUS15_1_repA(DO3)_CP003586
SRR8948887
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00027 5332 6188 rep11a_1_repA(pB82) 0/0 90.7 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00017 6111 7121 rep9a_1_repA(pAD1) 0/0 100.0 96.0 L01794 rep9a_1_repA(pAD1)_L01794
contig00006 115500 116705 repUS43_1_CDS12738(DOp1) 0/0 100.0 99.9 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948888
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00029 3327 4049 rep6_1_repA(pS86) 0/0 100.0 100.0 AJ223161 rep6_1_repA(pS86)_AJ223161
contig00012 54082 55089 rep9b_3_repA(pMG2200) 0/0 100.0 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00016 18859 19863 rep9c_1_repA(pTW9) 2/3 99.7 96.4 AB563188 rep9c_1_repA(pTW9)_AB563188
contig00002 104628 105833 repUS43_1_CDS12738(DOp1) 0/0 100.0 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948889
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00145 5317 6173 rep11a_1_repA(pB82) 0/0 90.7 100.0 AB178871 rep11a_1_repA(pB82)_AB178871
contig00169 2848 3798 rep14b_3_rep(pRI1) 0/0 100.0 100.0 EU327398 rep14b_3_rep(pRI1)_EU327398
contig00111 4699 5739 rep17_1_CDS29(pRUM) 0/0 100.0 100.0 AF507977 rep17_1_CDS29(pRUM)_AF507977
contig00139 4585 5322 rep29_2_EFAU085p4001(Aus0085p4)_Aus0085 0/0 100.0 100.0 rep29_2_EFAU085p4001(Aus0085p4)_Aus0085
contig00108 8676 10169 rep2_1_orf1(pRE25) 0/0 100.0 100.0 X92945 rep2_1_orf1(pRE25)_X92945
contig00157 4237 4959 rep6_1_repA(pS86) 0/0 100.0 100.0 AJ223161 rep6_1_repA(pS86)_AJ223161
contig00019 14859 15866 rep9b_3_repA(pMG2200) 0/0 100.0 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00048 12667 13671 rep9c_1_repA(pTW9) 2/3 99.7 96.4 AB563188 rep9c_1_repA(pTW9)_AB563188
contig00137 2016 3056 repUS15_1_repA(DO3) 0/0 100.0 100.0 CP003586 repUS15_1_repA(DO3)_CP003586
contig00005 138202 139407 repUS43_1_CDS12738(DOp1) 0/0 100.0 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948890
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00012 54082 55089 rep9b_3_repA(pMG2200) 0/0 100.0 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00016 19925 20929 rep9c_1_repA(pTW9) 2/3 99.7 96.4 AB563188 rep9c_1_repA(pTW9)_AB563188
contig00002 104628 105833 repUS43_1_CDS12738(DOp1) 0/0 100.0 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584
SRR8948891
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00012 54082 55089 rep9b_3_repA(pMG2200) 0/0 100.0 100.0 AB374546 rep9b_3_repA(pMG2200)_AB374546
contig00016 19026 20030 rep9c_1_repA(pTW9) 2/3 99.7 96.4 AB563188 rep9c_1_repA(pTW9)_AB563188
contig00002 103116 104321 repUS43_1_CDS12738(DOp1) 0/0 100.0 100.0 CP003584 repUS43_1_CDS12738(DOp1)_CP003584


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Virulence Factor Determination


Field Description
Contig Contig name where the gene was found
Start Start position of the gene within the contig
End End position of the gene within the contig
Gene Antibiotic resistance gene
Coverage Proportion (%) of the gene covered
Identity Proportion (%) of exact nucleotide matches
Accession Accesion number of the antibiotic resistance gene
Product Antibiotic resistance gene product


Select the sample

SRR8948878
Contig Start End Strand Gene Coverage Identity Accession Product
contig00013 42325 46224 - EF0149 99.5 94.3 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00002 60574 61584 + bopD 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00003 383485 384300 - cpsA 100.0 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 382688 383488 - cpsB 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 381046 382215 - cpsC 100.0 99.4 NP_816139 (cpsC) teichoic acid biosynthesis protein putative [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 379561 381027 - cpsD 100.0 98.8 NP_816138 (cpsD) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 376981 379491 - cpsE 100.0 99.2 NP_816137 (cpsE) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 376106 376957 - cpsF 100.0 99.9 NP_816136 (cpsF) CpsF protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 373626 376079 - cpsG 100.0 99.4 NP_816135 (cpsG) MurB family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 373210 373608 - cpsH 100.0 99.8 NP_816134 (cpsH) lipoprotein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 372012 373151 - cpsI 100.0 100.0 NP_816133 (cpsI) UDP-galactopyranose mutase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 370643 371986 - cpsJ 100.0 100.0 NP_816132 (cpsJ) ABC transporter ATP-binding protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 369831 370643 - cpsK 100.0 99.0 NP_816131 (cpsK) ABC transporter permease protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00017 5642 6880 - cylA 100.0 99.4 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 6877 9021 - cylB 100.0 99.7 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 4658 5641 - cylI 100.0 97.2 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 12300 12506 - cylL 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 9033 12014 - cylM 100.0 99.6 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 12625 12909 + cylR1 100.0 98.6 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 12910 13110 + cylR2 100.0 99.5 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00017 12075 12266 - cylS 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 508561 511872 - ebpA 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 507127 508557 - ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 505247 507130 - ebpC 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00003 55738 56664 + efaA 100.0 99.7 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00007 116938 122901 - fss1 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00001 504309 505153 - srtC 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948879
Contig Start End Strand Gene Coverage Identity Accession Product
contig00003 16103 19117 - EF0818 100.0 99.2 NP_814561 (EF0818) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00005 42479 46597 + EF3023 100.0 98.5 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00006 150491 152515 - ace 100.0 96.9 NP_814829 (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]
contig00004 101375 102385 + bopD 100.0 99.1 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00002 99283 100098 - cpsA 100.0 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00002 98486 99286 - cpsB 100.0 99.5 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 162063 165374 - ebpA 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00006 160629 162059 - ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00006 158749 160632 - ebpC 100.0 99.0 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 557717 558643 + efaA 100.0 99.6 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00001 421437 422168 - fsrA 100.0 98.6 NP_815519 (fsrA) response regulator [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 420620 421348 - fsrB 100.0 98.8 NP_815518 (fsrB) agrBfs protein [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 419280 420623 - fsrC 100.0 99.5 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00007 2843 8806 - fss1 100.0 98.7 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00002 108314 112624 - fss2 86.7 92.5 NP_816151 (fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]
contig00001 417513 419045 - gelE 100.0 98.8 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00001 416610 417464 - sprE 100.0 98.8 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00006 157801 158655 - srtC 100.0 99.2 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948880
Contig Start End Strand Gene Coverage Identity Accession Product
contig00014 42325 46224 - EF0149 99.5 94.3 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00003 124750 128612 - EF3023 93.8 98.7 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00002 61061 62071 + bopD 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00006 191502 192317 - cpsA 100.0 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 190705 191505 - cpsB 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 189063 190232 - cpsC 100.0 99.4 NP_816139 (cpsC) teichoic acid biosynthesis protein putative [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 187578 189044 - cpsD 100.0 98.8 NP_816138 (cpsD) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 184998 187508 - cpsE 100.0 99.2 NP_816137 (cpsE) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 184123 184974 - cpsF 100.0 99.9 NP_816136 (cpsF) CpsF protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 181643 184096 - cpsG 100.0 99.4 NP_816135 (cpsG) MurB family protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 181227 181625 - cpsH 100.0 99.8 NP_816134 (cpsH) lipoprotein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 180029 181168 - cpsI 100.0 100.0 NP_816133 (cpsI) UDP-galactopyranose mutase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 178660 180003 - cpsJ 100.0 100.0 NP_816132 (cpsJ) ABC transporter ATP-binding protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 177848 178660 - cpsK 100.0 99.0 NP_816131 (cpsK) ABC transporter permease protein [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00019 5642 6880 - cylA 100.0 99.4 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 6877 9021 - cylB 100.0 99.7 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 4658 5641 - cylI 100.0 97.2 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 12300 12506 - cylL 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 9033 12014 - cylM 100.0 99.6 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 12625 12909 + cylR1 100.0 98.6 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 12910 13110 + cylR2 100.0 99.5 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00019 12075 12266 - cylS 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 33491 36802 + ebpA 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 36806 38236 + ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 38233 40116 + ebpC 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00007 56246 57172 + efaA 100.0 99.7 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00008 116938 122901 - fss1 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00001 40210 41054 + srtC 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948881
Contig Start End Strand Gene Coverage Identity Accession Product
contig00002 16103 19117 - EF0818 100.0 99.2 NP_814561 (EF0818) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00007 42444 45880 + EF3023 83.4 98.8 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00006 147577 149601 - ace 100.0 97.0 NP_814829 (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]
contig00003 140001 141011 + bopD 100.0 99.1 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00011 20269 21084 - cpsA 100.0 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00011 19472 20272 - cpsB 100.0 99.5 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 159149 162460 - ebpA 100.0 99.4 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00006 157715 159145 - ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00006 155835 157718 - ebpC 100.0 99.0 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 476710 477636 + efaA 100.0 99.6 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00001 311577 312308 - fsrA 100.0 98.6 NP_815519 (fsrA) response regulator [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 310760 311488 - fsrB 100.0 98.8 NP_815518 (fsrB) agrBfs protein [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 309420 310763 - fsrC 100.0 99.5 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00004 98319 104282 - fss1 100.0 98.7 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00011 29300 33610 - fss2 86.7 92.5 NP_816151 (fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]
contig00001 307653 309185 - gelE 100.0 98.8 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00001 306750 307604 - sprE 100.0 98.8 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00006 154887 155741 - srtC 100.0 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948882
Contig Start End Strand Gene Coverage Identity Accession Product
contig00010 18368 20533 + acm 100.0 100.0 AAN12397 (acm) collagen adhesin precursor Acm [Acm (VF0419)] [Enterococcus faecium str. TX2555]
contig00020 23250 26421 - fss3 98.3 90.7 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00007 56426 58019 + scm 80.4 96.2 ZP_00604835 (scm) collagen adhesin protein Scm [Scm (VF0418)] [Enterococcus faecium DO]
contig00048 3922 4896 + sgrA 100.0 100.0 ZP_00602747 (sgrA) cell wall anchored protein SgrA [SgrA (VF0540)] [Enterococcus faecium DO]
SRR8948883
Contig Start End Strand Gene Coverage Identity Accession Product
contig00014 49159 51324 - acm 100.0 96.9 AAN12397 (acm) collagen adhesin precursor Acm [Acm (VF0419)] [Enterococcus faecium str. TX2555]
contig00034 18672 21899 + ecbA 100.0 100.0 ZP_00603098 (ecbA) Collagen binding MSCRAMM EcbA [EcbA (VF0539)] [Enterococcus faecium DO]
contig00003 95655 98826 + fss3 98.3 90.7 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00042 3783 4757 + sgrA 100.0 100.0 ZP_00602747 (sgrA) cell wall anchored protein SgrA [SgrA (VF0540)] [Enterococcus faecium DO]
SRR8948884
Contig Start End Strand Gene Coverage Identity Accession Product
contig00001 273341 276355 - EF0818 100.0 99.2 NP_814561 (EF0818) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00007 42444 45880 + EF3023 83.4 98.8 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00004 150656 152680 - ace 100.0 97.0 NP_814829 (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]
contig00001 139741 140751 + bopD 100.0 99.1 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00010 20269 21084 - cpsA 100.0 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00010 19472 20272 - cpsB 100.0 99.5 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00004 162228 165539 - ebpA 100.0 99.4 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00004 160794 162224 - ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00004 158914 160797 - ebpC 100.0 99.0 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00002 476710 477636 + efaA 100.0 99.6 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00002 311577 312308 - fsrA 100.0 98.6 NP_815519 (fsrA) response regulator [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00002 310760 311488 - fsrB 100.0 98.8 NP_815518 (fsrB) agrBfs protein [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00002 309420 310763 - fsrC 100.0 99.5 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00005 5654 11617 - fss1 100.0 98.7 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00010 29300 33610 - fss2 86.7 92.5 NP_816151 (fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]
contig00002 307653 309185 - gelE 100.0 98.8 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00002 306750 307604 - sprE 100.0 98.8 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00004 157966 158820 - srtC 100.0 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948885
## Error in read.table("SRR8948885_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
Contig Start End Strand Gene Coverage Identity Accession Product
contig00001 273341 276355 - EF0818 100.0 99.2 NP_814561 (EF0818) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00007 42444 45880 + EF3023 83.4 98.8 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00004 150656 152680 - ace 100.0 97.0 NP_814829 (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]
contig00001 139741 140751 + bopD 100.0 99.1 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00010 20269 21084 - cpsA 100.0 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00010 19472 20272 - cpsB 100.0 99.5 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00004 162228 165539 - ebpA 100.0 99.4 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00004 160794 162224 - ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00004 158914 160797 - ebpC 100.0 99.0 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00002 476710 477636 + efaA 100.0 99.6 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00002 311577 312308 - fsrA 100.0 98.6 NP_815519 (fsrA) response regulator [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00002 310760 311488 - fsrB 100.0 98.8 NP_815518 (fsrB) agrBfs protein [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00002 309420 310763 - fsrC 100.0 99.5 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00005 5654 11617 - fss1 100.0 98.7 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00010 29300 33610 - fss2 86.7 92.5 NP_816151 (fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]
contig00002 307653 309185 - gelE 100.0 98.8 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00002 306750 307604 - sprE 100.0 98.8 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00004 157966 158820 - srtC 100.0 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948886
Contig Start End Strand Gene Coverage Identity Accession Product
contig00011 80554 82734 - acm 100.0 96.2 AAN12397 (acm) collagen adhesin precursor Acm [Acm (VF0419)] [Enterococcus faecium str. TX2555]
contig00009 34510 36109 - scm 80.5 82.9 ZP_00604835 (scm) collagen adhesin protein Scm [Scm (VF0418)] [Enterococcus faecium DO]
SRR8948887
Contig Start End Strand Gene Coverage Identity Accession Product
contig00002 234974 237988 - EF0818 100.0 99.2 NP_814561 (EF0818) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00004 42444 46562 + EF3023 100.0 98.5 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00005 150491 152515 - ace 100.0 96.9 NP_814829 (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]
contig00002 101375 102385 + bopD 100.0 99.1 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00003 99283 100098 - cpsA 100.0 99.6 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00003 98486 99286 - cpsB 100.0 99.5 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00005 162063 165374 - ebpA 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00005 160629 162059 - ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00005 158749 160632 - ebpC 100.0 99.0 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 557717 558643 + efaA 100.0 99.6 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00001 421437 422168 - fsrA 100.0 98.6 NP_815519 (fsrA) response regulator [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 420620 421348 - fsrB 100.0 98.8 NP_815518 (fsrB) agrBfs protein [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00001 419280 420623 - fsrC 100.0 99.5 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00006 2843 8806 - fss1 100.0 98.7 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00003 108314 112624 - fss2 86.7 92.5 NP_816151 (fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]
contig00001 417513 419045 - gelE 100.0 98.8 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00001 416610 417464 - sprE 100.0 98.8 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00005 157801 158655 - srtC 100.0 99.2 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948888
Contig Start End Strand Gene Coverage Identity Accession Product
contig00004 182154 186071 + EF0149 100.0 100.0 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00009 102987 106849 - EF3023 93.8 98.7 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00002 123102 124112 + bopD 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00006 194106 194921 - cpsA 100.0 99.1 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 193309 194109 - cpsB 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00021 7897 9135 - cylA 100.0 99.8 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 9132 11276 - cylB 100.0 99.8 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 6913 7896 - cylI 100.0 97.3 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 14555 14761 - cylL 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 11288 14269 - cylM 100.0 99.7 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 14880 15164 + cylR1 100.0 100.0 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 15165 15365 + cylR2 100.0 100.0 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00021 14330 14521 - cylS 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 508008 511319 - ebpA 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 506574 508004 - ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 504694 506577 - ebpC 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00011 39052 39978 - efaA 100.0 99.3 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00005 53755 54838 + fsrC 80.7 99.3 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00004 131651 137614 + fss1 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00006 203138 207225 - fss2 82.4 94.9 NP_816151 (fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]
contig00010 88814 92041 + fss3 100.0 99.4 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00005 55073 56605 + gelE 100.0 98.9 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00016 29751 33668 + prgB/asc10 100.0 94.7 NP_817031 (prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583]
contig00005 56654 57508 + sprE 100.0 98.5 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00001 503756 504600 - srtC 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948889
Contig Start End Strand Gene Coverage Identity Accession Product
contig00003 182144 186061 + EF0149 100.0 100.0 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00019 25912 29837 + EF0485 100.0 95.3 NP_814266 (EF0485) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00013 61954 65816 - EF3023 93.8 98.7 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00022 18371 20536 + acm 100.0 100.0 AAN12397 (acm) collagen adhesin precursor Acm [Acm (VF0419)] [Enterococcus faecium str. TX2555]
contig00005 119923 120933 - bopD 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00004 194106 194921 - cpsA 100.0 99.1 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00004 193309 194109 - cpsB 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00087 6895 8133 - cylA 100.0 99.8 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00087 8130 10274 - cylB 100.0 99.8 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00087 5911 6894 - cylI 100.0 97.3 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00087 13553 13759 - cylL 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00087 10286 13267 - cylM 100.0 99.7 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00087 13878 14162 + cylR1 100.0 100.0 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00087 14163 14363 + cylR2 100.0 100.0 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00087 13328 13519 - cylS 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 508484 511795 - ebpA 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 507050 508480 - ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 505170 507053 - ebpC 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00014 39052 39978 - efaA 100.0 99.3 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00044 23911 24994 - fsrC 80.7 99.3 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00003 131641 137604 + fss1 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00004 203138 207225 - fss2 82.4 94.9 NP_816151 (fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]
contig00010 88814 92041 + fss3 100.0 99.4 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00035 24478 27649 + fss3 98.3 90.7 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00044 22144 23676 - gelE 100.0 98.9 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00048 23559 27476 + prgB/asc10 100.0 94.7 NP_817031 (prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583]
contig00064 3922 4896 + sgrA 100.0 100.0 ZP_00602747 (sgrA) cell wall anchored protein SgrA [SgrA (VF0540)] [Enterococcus faecium DO]
contig00044 21241 22095 - sprE 100.0 98.5 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00001 504232 505076 - srtC 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948890
Contig Start End Strand Gene Coverage Identity Accession Product
contig00004 182154 186071 + EF0149 100.0 100.0 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00019 1 3564 - EF3023 86.5 98.9 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00002 123102 124112 + bopD 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00005 194106 194921 - cpsA 100.0 99.1 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00005 193309 194109 - cpsB 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00024 7897 9135 - cylA 100.0 99.8 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 9132 11276 - cylB 100.0 99.8 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 6913 7896 - cylI 100.0 97.3 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 14555 14761 - cylL 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 11288 14269 - cylM 100.0 99.7 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 14880 15164 + cylR1 100.0 100.0 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 15165 15365 + cylR2 100.0 100.0 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00024 14330 14521 - cylS 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 508008 511319 - ebpA 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 506574 508004 - ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 504694 506577 - ebpC 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00011 39352 40278 - efaA 100.0 99.3 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00014 23911 24994 - fsrC 80.7 99.3 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00004 131651 137614 + fss1 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00005 203138 207225 - fss2 82.4 94.9 NP_816151 (fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]
contig00010 88814 92041 + fss3 100.0 99.4 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00014 22144 23676 - gelE 100.0 98.9 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00016 30817 34734 + prgB/asc10 100.0 94.7 NP_817031 (prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583]
contig00014 21241 22095 - sprE 100.0 98.5 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00001 503756 504600 - srtC 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]
SRR8948891
Contig Start End Strand Gene Coverage Identity Accession Product
contig00004 182154 186071 + EF0149 100.0 100.0 NP_813951 (EF0149) aggregation substance [AS (VF0352)] [Enterococcus faecalis V583]
contig00009 102987 106849 - EF3023 93.8 98.7 NP_816637 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583]
contig00002 121590 122600 + bopD 100.0 98.8 NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]
contig00006 194106 194921 - cpsA 100.0 99.1 NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00006 193309 194109 - cpsB 100.0 99.2 NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]
contig00020 7897 9135 - cylA 100.0 99.8 AAM75253 (cylA) cytolysin activator [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 9132 11276 - cylB 100.0 99.8 AAM75252 (cylB) ABC-type transporter [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 6913 7896 - cylI 100.0 97.3 AAM75254 (cylI) cytolysin immunity protein [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 14555 14761 - cylL 100.0 100.0 AAM75249 (cylL) CylL; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 11288 14269 - cylM 100.0 99.7 AAM75251 (cylM) CylM; cytolysin subunit modifier [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 14880 15164 + cylR1 100.0 100.0 AAM75248 (cylR1) cytolysin regulator R1 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 15165 15365 + cylR2 100.0 100.0 AAM75247 (cylR2) cytolysin regulator R2 [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00020 14330 14521 - cylS 100.0 100.0 AAM75250 (cylS) CylS; cytolysin subunit [Cytolysin (VF0356)] [Enterococcus faecalis str. MMH594]
contig00001 508008 511319 - ebpA 100.0 99.5 NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 506574 508004 - ebpB 100.0 99.4 NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00001 504694 506577 - ebpC 100.0 99.4 NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]
contig00011 39052 39978 - efaA 100.0 99.3 NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]
contig00007 156873 157956 - fsrC 80.7 99.3 NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]
contig00004 131651 137614 + fss1 100.0 99.1 NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]
contig00006 203138 207225 - fss2 82.4 94.9 NP_816151 (fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]
contig00010 88814 92041 + fss3 100.0 99.4 NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]
contig00007 155106 156638 - gelE 100.0 98.9 NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]
contig00016 29918 33835 + prgB/asc10 100.0 94.7 NP_817031 (prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583]
contig00007 154203 155057 - sprE 100.0 98.5 NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]
contig00001 503756 504600 - srtC 98.8 99.3 NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]


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Multi-Locus Sequence Typing (MLST)


Symbol Meaning
~ novel full length allele similar to match
? partial match to known allele
- allele missing


Scheme ST 1 2 3 4 5 6 7
SRR8948878 efaecalis 16 gdh(5) gyd(1) pstS(1) gki(3) aroE(7) xpt(7) yqiL(6)
SRR8948879 efaecalis 40 gdh(3) gyd(6) pstS(23) gki(12) aroE(9) xpt(10) yqiL(7)
SRR8948880 efaecalis 16 gdh(5) gyd(1) pstS(1) gki(3) aroE(7) xpt(7) yqiL(6)
SRR8948881 efaecalis 40 gdh(3) gyd(6) pstS(23) gki(12) aroE(9) xpt(10) yqiL(7)
SRR8948882 efaecium 80 atpA(9) ddl(1) gdh(1) purK(1) gyd(12) pstS(1) adk(1)
SRR8948883 efaecium 203 atpA(15) ddl(1) gdh(1) purK(1) gyd(1) pstS(20) adk(1)
SRR8948884 efaecalis 40 gdh(3) gyd(6) pstS(23) gki(12) aroE(9) xpt(10) yqiL(7)
SRR8948885 - -
SRR8948886 efaecium 1446 atpA(11) ddl(13) gdh(18) purK(15) gyd(10) pstS(19) adk(6)
SRR8948887 efaecalis 40 gdh(3) gyd(6) pstS(23) gki(12) aroE(9) xpt(10) yqiL(7)
SRR8948888 efaecalis 179 gdh(5) gyd(1) pstS(1) gki(3) aroE(7) xpt(1) yqiL(6)
SRR8948889 efaecalis - gdh(5,92) gyd(1) pstS(1) gki(3) aroE(7) xpt(1) yqiL(6)
SRR8948890 efaecalis 179 gdh(5) gyd(1) pstS(1) gki(3) aroE(7) xpt(1) yqiL(6)
SRR8948891 efaecalis 179 gdh(5) gyd(1) pstS(1) gki(3) aroE(7) xpt(1) yqiL(6)

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Pangenome Analysis

Pangenome genes summary

Genes Description Number
Core genes (99% <= strains <= 100%) 0
Soft core genes (95% <= strains < 99%) 0
Shell genes (15% <= strains < 95%) 5570
Cloud genes (0% <= strains < 15%) 5429
Total genes (0% <= strains <= 100%) 10999

Schematic representation of genes presence (color) or absence (blank) between samples:


Pangenome tree based on presence/absence of accessory genes representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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Pangenome tree based on core genome alignment representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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Insertion sequence characterization


Field Description
Region Numeric code given to insertion sequence (IS)
Orientation The orientation of IS position: Either forward (F) or reverse (F)
X-cordinates The left coordinate of the position
Y-coordinates The right coordinate of the position
Gap The distance between the x and y coordinates
CallType Describes whether a position hit is novel (not in reference) or known (in the reference)
LeftGene Locus tag ID of the gene closest to the left side of the IS position
LeftGeneDescription Description of the gene feature from the left side of the IS position. By default this is the product position
RightGene Locus tag ID of the gene closest to the right side of the IS position
RightGeneDescription Description of the gene feature from the right side of the IS position. By default this is the product position


Select the sample

SRR8948882
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 F 2284064 2284119 55 novel* EWH22_12485 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase EWH22_12490 SIS domain-containing protein
region_1 F 29699 29704 -5 novel EWH22_00705 hypothetical protein EWH22_00705 hypothetical protein
region_2 R 2734637 2734655 18 novel* EWH22_14730 AraC family transcriptional regulator EWH22_14735 hypothetical protein
region_2 R 738427 738447 20 novel* EWH22_04390 hypothetical protein EWH22_04395 hypothetical protein
region_3 F 886707 886720 13 novel EWH22_05265 DUF3221 domain-containing protein EWH22_05270 DUF4429 domain-containing protein
region_3 F 886707 886721 14 novel EWH22_05265 DUF3221 domain-containing protein EWH22_05270 DUF4429 domain-containing protein
SRR8948883
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 F 926584 926594 10 novel EWH22_05575 IS5/IS1182 family transposase EWH22_05575 IS5/IS1182 family transposase
region_1 R 300151 300712 561 novel* EWH22_02145 protein rep EWH22_02150 IS6-like element IS1216 family transposase
region_2 R 2608633 2610173 1540 known EWH22_14015 hypothetical protein EWH22_14025 hypothetical protein
region_3 F 2781344 2781396 52 novel* EWH22_14995 ATP-binding protein EWH22_14995 ATP-binding protein
SRR8948888
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 R -1 622539 622540 novel EWH22_15635 hypothetical protein EWH22_03800 restriction endonuclease subunit S
region_2 R -1 1903126 1903127 novel EWH22_15635 hypothetical protein EWH22_10515 choloylglycine hydrolase family protein
SRR8948889
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 F 2284074 2284242 168 novel* EWH22_12485 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase EWH22_12490 SIS domain-containing protein
region_1 F 29707 29740 33 novel? EWH22_00705 hypothetical protein EWH22_00705 hypothetical protein
region_2 R 2734610 2734690 80 novel* EWH22_14730 AraC family transcriptional regulator EWH22_14735 hypothetical protein
region_2 R 300801 300927 126 novel? EWH22_02150 IS6-like element IS1216 family transposase EWH22_02155 PTS sugar transporter subunit IIA
region_3 F 886687 886779 92 novel* EWH22_05265 DUF3221 domain-containing protein EWH22_05270 DUF4429 domain-containing protein
SRR8948890
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 R -1 622539 622540 novel EWH22_15635 hypothetical protein EWH22_03800 restriction endonuclease subunit S
region_2 R -1 1903126 1903127 novel EWH22_15635 hypothetical protein EWH22_10515 choloylglycine hydrolase family protein
region_3 R -1 2751552 2751553 novel EWH22_15635 hypothetical protein EWH22_14830 IS256-like element ISEfm2 family transposase
SRR8948891
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 R -1 622539 622540 novel EWH22_15635 hypothetical protein EWH22_03800 restriction endonuclease subunit S
region_2 R -1 1903126 1903127 novel EWH22_15635 hypothetical protein EWH22_10515 choloylglycine hydrolase family protein
region_3 R -1 2751531 2751532 novel EWH22_15635 hypothetical protein EWH22_14830 IS256-like element ISEfm2 family transposase


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Citations and Bibliography

If you have used rMAP, please cite:

Sserwadda, I., & Mboowa, G. (2021). rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial genomics, 7(6), 10.1099/mgen.0.000583. https://doi.org/10.1099/mgen.0.000583


The philosophy of rMAP was built on the foundation of already pre-existing tools. As a token of gratitude to the authors of those numerous tools, please also cite:


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