vanY gene in vanB cluster

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Accession ARO:3002956
Synonym(s)vanY-B vanYB
CARD Short NamevanY_in_vanB_cl
DefinitionAlso known as vanYB, is a vanY variant found in the vanB gene cluster.
AMR Gene Familyglycopeptide resistance gene cluster, vanY
Drug Classglycopeptide antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Perfect MatchesEnterococcus faecalisg+wgs+gi, Enterococcus faeciumwgs
Resistomes with Sequence VariantsAchromobacter xylosoxidansg+wgs, Alloiococcus otitiswgs, Anaerostipes hadrusg+wgs, Bacillus amyloliquefaciensg+wgs, Bacillus anthracisg+wgs, Bacillus cereusg+wgs, Bacillus halotoleransg, Bacillus subtilisg+wgs, Bacillus tequilensisg+wgs, Bacillus thuringiensisg+p+wgs, Bacillus velezensisg+p+wgs, Bifidobacterium bifidumg+wgs, Borrelia crociduraewgs, Borrelia hermsiig, Borrelia miyamotoig, Brevibacillus brevisg+wgs, Burkholderia multivoranswgs, Clostridium botulinumg+wgs, Clostridium butyricumwgs, Clostridium perfringensg+wgs, Clostridium sporogenesg+wgs, Dysosmobacter welbionisg+wgs, Enterobacter roggenkampiiwgs, Enterocloster clostridioformiswgs, Enterococcus aviumg+wgs, Enterococcus faecalisg+wgs+gi, Enterococcus faeciumg+p+wgs+gi, Enterococcus gilvusg+wgs, Enterococcus hiraeg+wgs, Enterococcus pallenswgs, Erysipelatoclostridium ramosumg+wgs, Erysipelothrix rhusiopathiaeg+wgs, Eubacterium limosumg+wgs, Eubacterium maltosivoransg+wgs, Faecalibacterium prausnitziig+wgs, Francisella philomiragiag+wgs, Francisella tularensisg+wgs, Gemella haemolysansg+wgs, Gemella sanguinisg+wgs, Jeotgalibaca porcig, Kocuria palustrisg, Lactococcus garvieaeg+wgs, Listeria innocuag+wgs, Listeria monocytogeneswgs, Macrococcus canisg, Moraxella catarrhaliswgs, Mycolicibacterium fortuitumg+wgs, Mycolicibacterium septicumg+wgs, Nocardia asiaticawgs, Nocardia farcinicag+wgs, Nocardia terpenicag, Paeniclostridium sordelliig+wgs, Parabacteroides distasoniswgs, Pseudomonas aeruginosawgs, Pseudomonas putidawgs, Rhodococcus rhodochrouswgs, Roseburia hominiswgs, Rothia mucilaginosag+wgs, Ruthenibacterium lactatiformansg+wgs, Staphylococcus arlettaewgs, Staphylococcus aureuswgs, Staphylococcus capitiswgs, Staphylococcus epidermidisg+wgs, Staphylococcus haemolyticusg+wgs, Staphylococcus hominisg+wgs, Staphylococcus saprophyticusg+wgs, Staphylococcus warneriwgs, Streptococcus agalactiaeg+wgs, Streptococcus anginosusg+wgs, Streptococcus canisg+wgs, Streptococcus constellatusg+wgs, Streptococcus cristatuswgs, Streptococcus dysgalactiaeg+wgs, Streptococcus equig+wgs, Streptococcus gallolyticusg+wgs, Streptococcus gordoniig+wgs, Streptococcus iniaeg+wgs, Streptococcus intermediuswgs, Streptococcus lutetiensisg+wgs, Streptococcus pasteurianusg+wgs, Streptococcus pneumoniaeg+wgs, Streptococcus porcinusg+wgs, Streptococcus pseudoporcinusg+wgs, Streptococcus pyogenesg+wgs, Streptococcus sanguinisg+wgs, Streptococcus suisg+wgs, Streptococcus uberisg+wgs, Vibrio choleraewgs
Classification12 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ vanY [AMR Gene Family]
+ part_of glycopeptide resistance gene cluster VanB
Publications

Courvalin P. 2005. Clin Infect Dis 42(SUPPL 1): S25-S34. Vancomycin resistance in gram-positive cocci. (PMID 16323116)

Evers S and Courvalin P. 1996. J Bacteriol 178(5): 1302-1309. Regulation of VanB-type vancomycin resistance gene expression by the VanS(B)-VanR (B) two-component regulatory system in Enterococcus faecalis V583. (PMID 8631706)
Resistomes

Prevalence of vanY gene in vanB cluster among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 414 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, genome islands, or whole-genome shotgun assemblies that have at least one hit to the AMR detection model. Default view includes percentages calculated based on Perfect plus Strict RGI hits. Select the checkbox to view percentages based on only Perfect matches to AMR reference sequences curated in CARD (note: this excludes resistance via mutation as references in protein variant models are often wild-type, sensitive sequences).

Prevalence: protein homolog model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GIGRDI-AMR2
Achromobacter xylosoxidans8.7%0%2.29%0%0%
Alloiococcus otitis0%0%100%0%0%
Anaerostipes hadrus33.33%0%32.76%0%0%
Bacillus amyloliquefaciens100%0%97.75%0%0%
Bacillus anthracis100%0%100%0%0%
Bacillus cereus100%0%101.2%0%0%
Bacillus halotolerans9.09%0%0%0%0%
Bacillus subtilis3.23%0%0.58%0%0%
Bacillus tequilensis100%0%66.67%0%0%
Bacillus thuringiensis100%0.72%100.35%0%0%
Bacillus velezensis100%0.9%98.9%0%0%
Bifidobacterium bifidum100%0%99.5%0%0%
Borrelia crocidurae0%0%100%0%0%
Borrelia hermsii100%0%0%0%0%
Borrelia miyamotoi100%0%0%0%0%
Brevibacillus brevis100%0%100%0%0%
Burkholderia multivorans0%0%0.24%0%0%
Clostridium botulinum83.58%0%61.68%0%0%
Clostridium butyricum0%0%3.92%0%0%
Clostridium perfringens97.5%0%95.11%0%0%
Clostridium sporogenes100%0%100.85%0%0%
Dysosmobacter welbionis100%0%100%0%0%
Enterobacter roggenkampii0%0%0.36%0%0%
Enterocloster clostridioformis0%0%4.65%0%0%
Enterococcus avium100%0%100%0%0%
Enterococcus faecalis29.55%0%35.08%16.67%0%
Enterococcus faecium98.73%0.52%100.1%15.69%0%
Enterococcus gilvus100%0%100%0%0%
Enterococcus hirae100%0%99.54%0%0%
Enterococcus pallens0%0%100%0%0%
Erysipelatoclostridium ramosum100%0%103.49%0%0%
Erysipelothrix rhusiopathiae100%0%100%0%0%
Escherichia coli0%0%0%0%0%
Eubacterium limosum100%0%100%0%0%
Eubacterium maltosivorans100%0%100%0%0%
Faecalibacterium prausnitzii100%0%105.83%0%0%
Francisella philomiragia100%0%100%0%0%
Francisella tularensis100%0%100%0%0%
Gemella haemolysans100%0%87.5%0%0%
Gemella sanguinis100%0%83.33%0%0%
Jeotgalibaca porci100%0%0%0%0%
Kocuria palustris100%0%0%0%0%
Lactococcus garvieae100%0%86.67%0%0%
Listeria innocua88.24%0%90.23%0%0%
Listeria monocytogenes0%0%0.24%0%0%
Macrococcus canis42.86%0%0%0%0%
Moraxella catarrhalis0%0%17.62%0%0%
Mycolicibacterium fortuitum100%0%100%0%0%
Mycolicibacterium septicum100%0%100%0%0%
Nocardia asiatica0%0%100%0%0%
Nocardia farcinica100%0%98.28%0%0%
Nocardia terpenica50%0%0%0%0%
Paeniclostridium sordellii50%0%94.92%0%0%
Parabacteroides distasonis0%0%0.47%0%0%
Pseudomonas aeruginosa0%0%0.01%0%0%
Pseudomonas putida0%0%0.53%0%0%
Rhodococcus rhodochrous0%0%11.11%0%0%
Roseburia hominis0%0%33.33%0%0%
Rothia mucilaginosa20%0%21.05%0%0%
Ruthenibacterium lactatiformans100%0%100%0%0%
Staphylococcus arlettae0%0%17.5%0%0%
Staphylococcus aureus0%0%0.05%0%0%
Staphylococcus capitis0%0%8.23%0%0%
Staphylococcus epidermidis0.65%0%6.28%0%0%
Staphylococcus haemolyticus31.03%0%18.46%0%0%
Staphylococcus hominis6.25%0%6.83%0%0%
Staphylococcus saprophyticus23.53%0%15.38%0%0%
Staphylococcus warneri0%0%3.28%0%0%
Streptococcus agalactiae97.2%0%98.9%0%0%
Streptococcus anginosus76.47%0%53.8%0%0%
Streptococcus canis100%0%100%0%0%
Streptococcus constellatus100%0%95.45%0%0%
Streptococcus cristatus0%0%2.86%0%0%
Streptococcus dysgalactiae98%0%100%0%0%
Streptococcus equi100%0%99.77%0%0%
Streptococcus gallolyticus100%0%100%0%0%
Streptococcus gordonii7.14%0%8.97%0%0%
Streptococcus iniae100%0%98.84%0%0%
Streptococcus intermedius0%0%36.36%0%0%
Streptococcus lutetiensis100%0%100%0%0%
Streptococcus pasteurianus100%0%100%0%0%
Streptococcus pneumoniae24.27%0%28.72%0%0%
Streptococcus porcinus100%0%100%0%0%
Streptococcus pseudoporcinus100%0%100%0%0%
Streptococcus pyogenes100%0%99.74%0%0%
Streptococcus sanguinis57.14%0%52.58%0%0%
Streptococcus suis88%0%91.61%0%0%
Streptococcus uberis75%0%98.21%0%0%
Vibrio cholerae0%0%0.06%0%0%
Show Perfect Only


Detection Models

Model Type: protein homolog model

Model Definition: Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.

Bit-score Cut-off (blastP): 50


>gb|AAB05624.1|+|vanY gene in vanB cluster [Enterococcus faecalis]
MEKSNYHSNVNHHKRHMKQSGEKRAFLWAFIISFTVCTLFLGWRLVSVLEATQLPPIPATHTGSGTGVAENPEENTLATAKEQGDEQEWS
LILVNRQNPIPAQYDVELEQLSNGERIDIRISPYLQDLFDAARADGVYPIVASGYRTTEKQQEIMDEKVAEYKAKGYTSAQAKAEAETWV
AVPGTSEHQLGLAVDINADGIHSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGIEAATKIYHQGLCLEEYLNTEK


>gb|U35369.1|+|2359-3165|vanY gene in vanB cluster [Enterococcus faecalis]
ATGGAAAAAAGCAACTATCATTCCAATGTGAATCATCACAAACGGCATATGAAACAATCTGGGGAAAAACGGGCTTTTCTATGGGCGTTC
ATTATCTCGTTCACAGTCTGCACGCTGTTTTTGGGGTGGAGATTGGTTTCCGTATTGGAGGCAACACAGCTACCGCCCATCCCTGCAACT
CATACAGGCAGCGGGACTGGTGTAGCGGAGAATCCAGAGGAAAACACTCTTGCCACCGCCAAAGAACAGGGAGATGAACAGGAATGGAGC
CTGATTTTAGTGAACAGGCAGAACCCCATCCCCGCCCAGTACGATGTGGAACTTGAGCAGCTGTCAAATGGTGAGCGGATAGACATTCGG
ATTTCTCCCTACCTCCAGGATTTGTTTGATGCCGCAAGAGCTGATGGAGTTTACCCGATTGTCGCATCCGGATACCGGACAACAGAAAAA
CAGCAAGAAATCATGGATGAAAAAGTCGCCGAATACAAGGCGAAAGGCTACACCTCTGCACAGGCTAAAGCGGAAGCAGAAACTTGGGTG
GCCGTGCCGGGAACAAGCGAGCATCAGCTTGGTCTTGCTGTGGATATCAATGCGGATGGAATTCATTCAACCGGCAACGAGGTTTACAGA
TGGCTGGATGAAAACAGCTATCGCTTTGGTTTTATTCGCCGCTACCCGCCAGACAAGACAGAGATAACCGGTGTGAGCAACGAGCCGTGG
CATTACCGATATGTCGGCATCGAAGCTGCCACAAAGATATACCACCAAGGGCTTTGCCTTGAGGAATATTTAAACACAGAAAAATGA

Curator Acknowledgements
Curator Description Most Recent Edit