rphB

Accession ARO:3003992
CARD Short NamerphB
DefinitionrphB is a rifampin phosphotransferase protein found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to rifamycin antibiotics, specifically rifampin, through rifampin inactivation. Described by Pawlowski et al. 2016.
AMR Gene Familyrifampin phosphotransferase
Drug Classrifamycin antibiotic
Resistance Mechanismantibiotic inactivation
Classification9 ontology terms | Show
Parent Term(s)5 ontology terms | Show
+ rifampin phosphotransferase [AMR Gene Family]
+ confers_resistance_to_antibiotic rifampin [Antibiotic]
+ confers_resistance_to_antibiotic rifaximin [Antibiotic]
+ confers_resistance_to_antibiotic rifabutin [Antibiotic]
+ confers_resistance_to_antibiotic rifapentine [Antibiotic]
Publications

Pawlowski AC, et al. 2016. Nat Commun 7:13803 A diverse intrinsic antibiotic resistome from a cave bacterium. (PMID 27929110)

Resistomes

Prevalence of rphB among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 413 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

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
No prevalence data


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): 1500

Type of Antibiotic Resistance: Intrinsic or chromosomally-encoded


>gb|APB03222.1|+|rphB [Paenibacillus sp. LC231]
MRSLVLDFQEMDKKQLGLVGGKGLHLGELSKIEGIRVPEGFCVTTIGYQRAIEQNETYQAMLNRLTMLSAEDRDQMVEISRKIRQTIMEV
EIPSDVVTAVTRYLSRFGEEQAYAVRSSATAEDLPHASFAGQQDTYLNIIGVDAILQHISKCWASLFTDRAVIYRMQNGFDHRQVYLSVV
VQRMVFPEASGILFTADPMTSNRKLLSIDAGFGLGEALVSGLVSADGYKVREGEIIEKRIAAKTLAIYGRKEGGTETKQIDPDQQKSQTL
TDEQILQLARIGRQIEAHFGQPQDIEWCLAQDTFYIVQSRPITTLYPIPEANDQENHVYVSVGHQQMMTDPMKPLGLSFFLLTTPAPMRT
AGGRLFVDTTAMLASPVSRENVLNTLGQSDPLIKDALMTILERGDFIKSLPIAENEQTPGKNNISSAGYQTPIDHDPTIVSDLMERTQSS
IEVLKQNIQTKSGSDLFDFILEDIQELKKNLFDPQSSAVIMAAMNASTWINEKMNEWLGEKNAADTLSQSVPGNVTSEMGLALLDVADVI
RPYPEIIDYLEQAKDDHFLDKLLTFDGGQQAQDAILDFLDKYGMRCAGEIDLTRTRWSEKPIALVPLILGNIKNFEPNASHRKFEQGRQE
ALKKEQELLDRLKQLPDGEGKAQETKRMIDLIRNFMGYREYPKYGMVNRYFIYKQALLKEAERLVQAGVIHHKEDIYYLTFEELDEVVRT
NKLDNPGSMVEQQAKLAIRQMISKRKEEYNVFEKLTPPRVITSDGEIIAGEYKRENIPAEAIVGLPVSSGTVEGRARVILNMKDADLEEG
DILVTAFTDPSWTPLFVSIKGLVTEVGGLMTHGAVIAREYGLPAVVGVENATKRIKDGQRIRVHGSEGYIEILS


>gb|KX531052.1|+|1-2655|rphB [Paenibacillus sp. LC231]
ATGCGTTCGTTGGTTCTCGATTTTCAGGAAATGGACAAAAAGCAGCTTGGGCTCGTTGGTGGAAAAGGGCTCCATTTAGGGGAATTATCA
AAAATTGAGGGAATACGAGTTCCCGAAGGATTTTGCGTGACAACCATAGGATATCAAAGAGCCATCGAACAAAACGAAACGTATCAAGCT
ATGCTCAATCGACTAACCATGCTATCAGCAGAGGATCGAGATCAAATGGTTGAAATCAGCAGGAAGATCAGACAAACCATTATGGAGGTA
GAAATTCCATCCGATGTAGTGACAGCAGTAACTCGCTATCTCTCCCGGTTTGGCGAGGAACAGGCTTATGCCGTACGATCCAGTGCAACT
GCTGAAGATTTACCGCATGCCTCTTTTGCGGGTCAACAAGACACCTATCTAAACATCATCGGCGTCGATGCCATCTTGCAGCATATCAGC
AAATGCTGGGCTTCCTTGTTTACAGATCGCGCGGTGATCTATCGCATGCAAAATGGATTTGACCATCGTCAAGTTTATTTATCCGTAGTC
GTTCAAAGGATGGTTTTCCCCGAGGCTTCAGGGATATTATTCACCGCTGATCCGATGACTTCTAATCGAAAGCTGCTATCCATCGATGCC
GGTTTCGGACTTGGAGAAGCACTGGTCTCTGGCTTGGTATCTGCCGATGGTTACAAAGTACGGGAAGGAGAAATCATCGAGAAGCGGATA
GCAGCCAAAACATTGGCGATCTACGGACGAAAAGAAGGCGGAACAGAAACAAAGCAAATCGATCCCGATCAGCAAAAGTCACAAACACTT
ACGGATGAGCAAATTTTACAACTGGCACGCATCGGGAGACAGATTGAGGCTCATTTTGGCCAACCCCAAGATATCGAGTGGTGTTTGGCC
CAGGATACCTTTTATATTGTCCAGAGTCGGCCAATCACGACGCTATACCCGATACCTGAAGCGAATGATCAAGAAAATCACGTATACGTA
TCTGTCGGTCATCAACAAATGATGACGGATCCCATGAAACCGCTGGGATTGTCTTTTTTCCTGCTAACGACTCCTGCACCCATGCGTACA
GCTGGCGGAAGGTTGTTTGTTGATACTACGGCTATGCTGGCTTCACCGGTTAGCAGAGAAAATGTATTAAATACCCTGGGACAATCCGAT
CCACTCATCAAAGACGCTCTTATGACCATCTTAGAGCGAGGAGATTTTATAAAATCGCTACCCATCGCTGAAAATGAACAGACTCCCGGA
AAAAACAATATATCGTCTGCGGGTTATCAAACGCCAATCGACCACGATCCGACAATCGTTTCTGATTTAATGGAACGTACTCAATCATCG
ATCGAAGTGTTGAAACAAAACATCCAAACGAAATCCGGATCCGATTTATTTGATTTTATATTGGAAGATATCCAGGAACTGAAGAAGAAT
TTATTTGACCCACAAAGCTCGGCTGTCATCATGGCTGCAATGAATGCTTCAACCTGGATCAACGAAAAAATGAATGAATGGTTAGGCGAA
AAAAACGCAGCCGACACGCTTTCTCAATCCGTACCGGGCAATGTTACTTCGGAAATGGGTCTGGCGCTGCTGGATGTTGCAGACGTCATT
CGTCCTTATCCGGAAATCATTGATTATTTGGAGCAAGCAAAAGATGATCACTTTTTGGATAAGCTGCTTACATTTGATGGCGGGCAGCAA
GCTCAAGACGCGATCCTAGATTTTCTTGACAAATATGGCATGCGATGTGCTGGAGAAATCGATTTAACAAGAACTCGTTGGAGTGAAAAA
CCAATTGCGCTTGTTCCGTTGATTCTGGGTAACATCAAAAACTTCGAGCCTAATGCCAGCCATCGGAAATTCGAGCAAGGGCGGCAGGAA
GCTTTGAAAAAAGAACAAGAGCTATTAGATCGATTGAAACAATTGCCGGACGGTGAAGGAAAAGCCCAAGAAACCAAACGAATGATTGAC
CTCATTCGGAATTTCATGGGTTATCGGGAATACCCGAAATACGGTATGGTGAATCGTTACTTTATTTATAAGCAGGCTTTACTGAAAGAG
GCTGAACGACTCGTACAAGCGGGCGTTATTCATCATAAGGAAGATATATATTATCTCACTTTTGAAGAGCTTGACGAGGTCGTACGCACA
AATAAACTGGATAACCCGGGTTCCATGGTCGAGCAGCAAGCAAAGCTTGCGATCAGACAGATGATCAGCAAACGAAAAGAGGAGTACAAC
GTATTTGAAAAACTAACTCCTCCGCGCGTGATCACGTCGGATGGTGAAATCATCGCAGGGGAGTACAAACGAGAAAATATCCCAGCCGAA
GCTATTGTCGGCCTGCCTGTTTCTTCCGGAACGGTCGAAGGACGAGCGCGTGTCATCTTAAACATGAAAGACGCCGATCTCGAGGAAGGA
GATATATTAGTCACCGCTTTTACCGACCCTAGCTGGACGCCTCTGTTTGTATCCATTAAGGGCTTGGTCACCGAAGTGGGCGGACTGATG
ACCCATGGAGCCGTTATCGCGCGTGAATATGGCTTACCGGCCGTTGTCGGCGTTGAGAATGCTACCAAACGGATAAAGGACGGGCAGCGC
ATTCGCGTACATGGGTCCGAAGGCTATATTGAAATATTGTCATAG