vanR gene in vanA cluster

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Accession	ARO:3002919
Synonym(s)	vanR-A vanRA
CARD Short Name	vanR_in_vanA_cl
Definition	Also known as vanRA, is a vanR variant found in the vanA gene cluster.
AMR Gene Family	glycopeptide resistance gene cluster, vanR
Drug Class	glycopeptide antibiotic
Resistance Mechanism	antibiotic target alteration
Resistomes with Perfect Matches	Enterococcus avium^p, Enterococcus faecalis^p+wgs, Enterococcus faecium^g+p+wgs, Klebsiella pneumoniae^wgs, Staphylococcus aureus^g+p+wgs, Streptococcus gallolyticus^wgs
Resistomes with Sequence Variants	Bacillus anthracis^g+wgs, Bacillus cereus^g+p+wgs+gi, Bacillus thuringiensis^g+p+wgs, Brevibacillus laterosporus^g+wgs+gi, Enterococcus avium^p, Enterococcus faecalis^p+wgs, Enterococcus faecium^g+p+wgs, Klebsiella pneumoniae^wgs, Pseudomonas stutzeri^wgs, Staphylococcus aureus^g+p+wgs, Streptococcus gallolyticus^wgs
Classification	14 ontology terms \| Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + antibiotic target alteration [Resistance Mechanism] + restructuring of bacterial cell wall conferring antibiotic resistance + determinant of antibiotic resistance + protein(s) conferring antibiotic resistance via molecular bypass + antibiotic molecule + gene(s) or protein(s) associated with a glycopeptide resistance cluster + glycopeptide antibiotic [Drug Class] + antibiotic resistance gene cluster, cassette, or operon + VanS-VanR two-component regulatory system + glycopeptide resistance gene cluster [AMR Gene Family] + teicoplanin [Antibiotic] + vancomycin [Antibiotic]
Parent Term(s)	2 ontology terms \| Show + part_of glycopeptide resistance gene cluster VanA + vanR [AMR Gene Family]
Publications	Courvalin P. 2005. Clin Infect Dis 42(SUPPL 1): S25-S34. Vancomycin resistance in gram-positive cocci. (PMID 16323116) Arthur M, et al. 1993. J Bacteriol 175(1): 117-127. Characterization of Tn1546, a Tn3-related transposon conferring glycopeptide resistance by synthesis of depsipeptide peptidoglycan precursors in Enterococcus faecium BM4147. (PMID 8380148)

Resistomes

Prevalence of vanR gene in vanA 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)

Species	NCBI Chromosome	NCBI Plasmid	NCBI WGS	NCBI GI	GRDI-AMR2
Bacillus anthracis	0%	0%	0%	0%	0%
Bacillus anthracis	1.64%	0%	2.19%	0%	0%
Bacillus cereus	0%	0%	0%	0%	0%
Bacillus cereus	13.98%	2.74%	26.22%	50%	0%
Bacillus thuringiensis	0%	0%	0%	0%	0%
Bacillus thuringiensis	8.75%	0.2%	14.66%	0%	0%
Brevibacillus laterosporus	0%	0%	0%	0%	0%
Brevibacillus laterosporus	16.67%	0%	17.65%	100%	0%
Enterococcus avium	0%	33.33%	0%	0%	0%
Enterococcus avium	0%	33.33%	0%	0%	0%
Enterococcus faecalis	0%	2.46%	8.12%	0%	0%
Enterococcus faecalis	0%	1.72%	8.12%	0%	0%
Enterococcus faecium	1.59%	9.39%	47.88%	0%	0%
Enterococcus faecium	1.59%	9.65%	48.05%	0%	0%
Klebsiella pneumoniae	0%	0%	0.01%	0%	0%
Klebsiella pneumoniae	0%	0%	0.01%	0%	0%
Pseudomonas stutzeri	0%	0%	0.76%	0%	0%
Pseudomonas stutzeri	0%	0%	0%	0%	0%
Staphylococcus aureus	0.7%	0.19%	0.1%	0%	0%
Staphylococcus aureus	0.7%	0.19%	0.09%	0%	0%
Streptococcus gallolyticus	0%	0%	2.27%	0%	0%
Streptococcus gallolyticus	0%	0%	2.27%	0%	0%

Show Perfect Only

Detection Models

protein homolog model

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): 400

Protein
DNA

>gb|AAA65953.1|+|vanR gene in vanA cluster [Enterococcus faecium]
MSDKILIVDDEHEIADLVELYLKNENYTVFKYYTAKEALECIDKSEIDLAILDIMLPGTSGLTICQKIRDKHTYPIIMLTGKDTEVDKIT
GLTIGADDYITKPFRPLELIARVKAQLRRYKKFSGVKEQNENVIVHSGLVINVNTHECYLNEKQLSLTPTEFSILRILCENKGNVVSSEL
LFHEIWGDEYFSKSNNTITVHIRHLREKMNDTIDNPKYIKTVWGVGYKIEK

>gb|M97297.1|+|3976-4671|vanR gene in vanA cluster [Enterococcus faecium]
ATGAGCGATAAAATACTTATTGTGGATGATGAACATGAAATTGCCGATTTGGTTGAATTATACTTAAAAAACGAGAATTATACGGTTTTC
AAATACTATACCGCCAAAGAAGCATTGGAATGTATAGACAAGTCTGAGATTGACCTTGCCATATTGGACATCATGCTTCCCGGCACAAGC
GGCCTTACTATCTGTCAAAAAATAAGGGACAAGCACACCTATCCGATTATCATGCTGACCGGGAAAGATACAGAGGTAGATAAAATTACA
GGGTTAACAATCGGCGCGGATGATTATATAACGAAGCCCTTTCGCCCACTGGAGTTAATTGCTCGGGTAAAGGCCCAGTTGCGCCGATAC
AAAAAATTCAGTGGAGTAAAGGAGCAGAACGAAAATGTTATCGTCCACTCCGGCCTTGTCATTAATGTTAACACCCATGAGTGTTATCTG
AACGAGAAGCAGTTATCCCTTACTCCCACCGAGTTTTCAATACTGCGAATCCTCTGTGAAAACAAGGGGAATGTGGTTAGCTCCGAGCTG
CTATTTCATGAGATATGGGGCGACGAATATTTCAGCAAGAGCAACAACACCATCACCGTGCATATCCGGCATTTGCGCGAAAAAATGAAC
GACACCATTGATAATCCGAAATATATAAAAACGGTATGGGGGGTTGGTTATAAAATTGAAAAATAA

Curator Acknowledgements

Curator	Description	Most Recent Edit

vanR gene in vanA cluster

Prevalence: protein homolog model (view sequences)

Graph