rpoB2

Accession ARO:3000501
CARD Short NamerpoB2
DefinitionDue to gene duplication, the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes, with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance.
AMR Gene Familyrifamycin-resistant beta-subunit of RNA polymerase (rpoB)
Drug Classrifamycin antibiotic
Resistance Mechanismantibiotic target alteration, antibiotic target replacement
Resistomes with Sequence VariantsNocardia farcinicag+p+wgs
Classification11 ontology terms | Show
Parent Term(s)5 ontology terms | Show
+ confers_resistance_to_antibiotic rifampin [Antibiotic]
+ rifamycin-resistant beta-subunit of RNA polymerase (rpoB) [AMR Gene Family]
+ confers_resistance_to_antibiotic rifaximin [Antibiotic]
+ confers_resistance_to_antibiotic rifabutin [Antibiotic]
+ confers_resistance_to_antibiotic rifapentine [Antibiotic]
Publications

Ishikawa J, et al. 2006. Antimicrob Agents Chemother 50(4): 1342-1346. Contribution of rpoB2 RNA polymerase beta subunit gene to rifampin resistance in Nocardia species. (PMID 16569850)

Resistomes

Prevalence of rpoB2 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 (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Nocardia farcinica75%8.33%5.17%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): 2200


>gb|BAD59497.1|+|rpoB2 [Nocardia farcinica IFM 10152]
MLEGRIVTVSSRTESPLAAPGVPGAPRRLSFARIREPLAVPGLLDIQTESFGWLIGAPDWCARAAARGTEPVAGLAEVLAEISPIEDFAG
TMSLTLSDPRFEEVKASVEECKDKDLTYAAPWFVTAEFVNNNTGEIKSQTVFMGDFPMMTAHGTFVVNGTERVVVSQLVRSPGVYFDHAI
DKGSEKDVHSARVIPSRGAWLEFDVDKRDTLGVRIDRKRRQPVTVLLKALGWSAERIAERFGFAPLIMASLAKDNVAGTDDALLEIHRKL
RPGEPPTKESAQNLLANLFFTEKRYDLARVGRYKIDKKLGLRAPGAPRVLTEDDIAATIEYLVRLHAGERTMIAPGGVEVPVEVDDIDHF
GNRRVRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQSLMNIRPVVAAMKEFFGTSQLSQFMDQRNPLASLTNKRRLSALGPGGL
SRERAGLEVRDVHYSHYGRMCPIETPEGPNIGLMGYLSVYARVNPFGFVETPYRRVVDGRVTDEVDYLTADEEDRHVVAQANEPLDAEGR
FLAARIPVRRKNSEVELVDSAAVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLIRSEAPIVGTGMELRAAVDAGDVVV
NEKAGVVEEVSADYVTVMADDGTRKSYRMRKFNRSNQGTCSNQRPIVDEGQRVEAGQVLADGPCTENGEMALGKNLLVAIMPWEGHNYED
AIILSQRLVEQDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRA
IFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDDLPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPTEDMPFLPDGTPV
DIILNTHGVPRRMNIGQILETHLGWIGKAGWKVEGNPEWAKDLPEEMWEAPADSNIATPVFDGAREEELTGLLGSTLPNRDGERMVDDNG
KAVLFDGRSGEPFPYPVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDV
VGRVKVYEAIVKGDNIPEPGVPESFKVLLKELQALCLNVEVLSAGAAVELAHGVDDDHERTAANLGINLSRAESITETELSG


>gb|AP006618.1|+|4835200-4838688|rpoB2 [Nocardia farcinica IFM 10152]
GTGCTGGAAGGACGCATCGTGACAGTCTCGAGTCGGACCGAGTCCCCGCTCGCCGCGCCCGGAGTCCCGGGTGCGCCCCGGCGGCTCTCG
TTCGCCAGAATCCGCGAGCCCCTGGCGGTTCCGGGCCTGCTGGACATTCAGACCGAATCGTTCGGGTGGCTGATCGGCGCACCCGACTGG
TGCGCCCGCGCGGCAGCCCGCGGGACGGAACCGGTCGCCGGGCTGGCCGAGGTGCTCGCCGAGATCAGCCCCATCGAGGACTTCGCGGGC
ACGATGTCGCTGACGTTGTCCGATCCGCGGTTCGAGGAGGTCAAGGCCTCCGTCGAGGAGTGCAAGGACAAGGATCTGACCTATGCCGCG
CCGTGGTTCGTCACGGCGGAATTCGTGAACAACAACACCGGCGAGATCAAGAGCCAGACCGTTTTCATGGGTGATTTCCCCATGATGACC
GCGCACGGGACATTCGTCGTCAACGGCACCGAACGGGTGGTCGTGTCGCAACTGGTGCGCTCGCCGGGCGTGTACTTCGACCACGCGATC
GACAAGGGTTCGGAGAAGGACGTGCACAGCGCGCGGGTGATCCCGTCGCGCGGTGCCTGGCTGGAGTTCGACGTCGACAAGCGCGACACC
CTGGGCGTGCGCATCGACCGCAAGCGCCGTCAGCCGGTAACGGTGCTGCTCAAGGCGCTGGGCTGGAGTGCGGAGCGAATCGCCGAGCGA
TTCGGGTTCGCCCCGCTGATCATGGCCTCGCTGGCCAAGGACAACGTGGCGGGCACCGACGACGCTTTGCTCGAGATCCATCGCAAGCTG
CGTCCGGGCGAGCCGCCGACCAAGGAGTCGGCACAGAACCTGCTGGCAAATCTGTTCTTCACCGAGAAGCGCTACGACCTGGCGCGGGTG
GGCCGTTACAAGATCGACAAGAAGCTCGGGCTGCGCGCTCCGGGGGCACCGCGGGTGCTCACCGAGGACGACATCGCGGCCACCATCGAG
TACCTGGTGCGCCTGCACGCCGGGGAGAGGACGATGATCGCGCCCGGCGGGGTCGAGGTGCCGGTGGAGGTCGACGACATCGACCATTTC
GGTAACCGCCGGGTGCGCACCGTGGGTGAGCTGATCCAGAACCAGATCCGCGTGGGTCTGTCCCGGATGGAACGGGTGGTGCGGGAGCGC
ATGACCACCCAGGACGTCGAGGCGATCACGCCGCAGTCGCTGATGAACATCCGCCCGGTGGTCGCGGCGATGAAGGAGTTCTTCGGCACC
TCGCAGCTGTCGCAGTTCATGGACCAGCGCAACCCGCTGGCGAGCCTGACCAACAAGCGGCGGCTGTCCGCGCTCGGGCCGGGCGGGCTC
TCGCGCGAACGGGCCGGCTTGGAGGTCCGCGACGTGCACTACAGCCACTACGGCCGGATGTGCCCGATCGAGACGCCGGAGGGGCCGAAC
ATCGGCCTGATGGGGTACCTGTCGGTGTACGCGCGGGTCAACCCGTTCGGTTTCGTCGAGACCCCCTACCGGCGGGTGGTGGACGGCCGG
GTCACCGACGAGGTCGATTACCTCACCGCCGACGAGGAGGACCGGCACGTGGTGGCCCAGGCGAACGAACCGCTGGACGCCGAGGGCCGC
TTCCTGGCCGCGCGAATCCCGGTGCGCCGGAAGAACTCCGAGGTGGAACTCGTCGATTCCGCCGCGGTGGATTACATGGATGTGTCGCCG
CGGCAGATGGTGTCGGTGGCGACGGCGATGATTCCGTTCCTCGAGCATGATGATGCCAACCGTGCGCTGATGGGTGCGAATATGCAGCGT
CAGGCGGTGCCGTTGATTCGGTCGGAGGCGCCGATCGTGGGTACCGGTATGGAGCTGCGTGCGGCGGTGGATGCCGGTGATGTGGTGGTG
AACGAGAAGGCCGGTGTGGTCGAGGAGGTTTCGGCCGATTACGTCACGGTGATGGCCGATGACGGGACTCGTAAGTCGTATCGGATGCGG
AAGTTCAACCGGTCGAATCAGGGGACGTGTTCGAATCAGCGGCCGATCGTGGACGAGGGTCAGCGGGTCGAGGCCGGGCAGGTGTTGGCT
GATGGGCCGTGCACCGAGAACGGTGAGATGGCGCTGGGTAAGAACCTGTTGGTGGCGATCATGCCGTGGGAGGGGCACAACTACGAGGAC
GCGATCATCCTGTCGCAGCGGTTGGTGGAGCAGGATGTGTTGACCTCGATCCATATCGAGGAGCACGAGATCGATGCTCGTGACACCAAG
CTCGGTGCCGAGGAGATCACTCGCGACATTCCGAATGTCTCCGATGAGGTGTTGGCGGATCTGGACGAGCGTGGCATCGTGCGGATCGGT
GCGGAGGTGCGTGATGGTGACATCCTGGTCGGTAAGGTCACGCCCAAGGGTGAGACCGAGCTGACGCCGGAGGAGCGGTTGCTGCGGGCG
ATCTTCGGGGAGAAGGCGCGTGAGGTGCGTGATACCTCGTTGAAGGTGCCCCACGGTGAGTCGGGCAAGGTCATCGGGATCCGGGTGTTC
TCTCGGGAGGACGATGACGATCTGCCGCCCGGTGTCAACGAGTTGGTGCGGGTGTATGTGGCGCAGAAGCGCAAGATCCAAGACGGTGAC
AAGCTGGCCGGTCGGCACGGGAACAAGGGTGTGATCGGCAAGATCCTGCCCACCGAGGACATGCCGTTCCTGCCCGATGGCACCCCGGTC
GACATCATCCTCAACACCCACGGTGTGCCGCGGCGTATGAACATCGGCCAGATCCTGGAAACCCACCTCGGCTGGATCGGCAAAGCCGGC
TGGAAGGTCGAGGGCAACCCCGAGTGGGCCAAGGATCTGCCGGAGGAGATGTGGGAGGCCCCCGCGGACTCCAACATCGCGACTCCGGTG
TTCGACGGTGCCCGCGAGGAGGAGCTGACGGGTCTGCTGGGCTCGACGCTGCCCAACCGTGACGGTGAGCGGATGGTCGACGACAACGGC
AAGGCCGTGCTGTTCGACGGTCGTTCCGGTGAGCCGTTCCCGTACCCGGTGGCGGTGGGCTACATGTACATCCTGAAGCTGCACCACCTG
GTCGACGACAAGATCCACGCTCGCTCCACCGGCCCGTACTCGATGATCACCCAGCAGCCGCTCGGTGGTAAGGCCCAGTTCGGTGGCCAG
CGCTTCGGTGAGATGGAGTGCTGGGCGATGCAGGCCTACGGCGCGGCCTACACCCTGCAGGAACTGCTCACGATCAAGTCCGACGACGTC
GTCGGCCGCGTGAAGGTCTACGAGGCGATCGTCAAGGGCGACAACATCCCGGAACCCGGTGTGCCGGAATCGTTCAAGGTGTTGTTGAAG
GAACTCCAGGCACTGTGCCTCAACGTCGAGGTGCTGTCCGCCGGTGCCGCGGTCGAACTGGCGCACGGGGTCGACGACGATCACGAGCGG
ACGGCCGCGAACCTCGGCATCAACCTGTCCCGCGCCGAATCCATCACGGAGACCGAGCTGTCCGGGTGA