MTBC Gene Atlas

Rv1458c Family assigned · medium auto-curated

H37Rv Rv1458c · MTBC0 mtbc0_001560 · 313 aa · 1653071–1654012 (-) · RefSeq NP_215974.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)antibiotic ABC transporter ATP-binding protein
MTBC0 PGAP re-annotationABC transporter ATP-binding protein
Revised (this work)ABC transporter ATP-binding protein. Pfam: ABC_tran (PF00005.34), AAA_21 (PF13304.13).

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

Curated reference (UniProt)

UniProt O53149 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable unidentified antibiotic-transport ATP-binding protein ABC transporter

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category V Defense mechanisms
Preferred namedrrA_2
eggNOG descriptionABC transporter
Orthologous groupCOG1131
KEGG orthology K01990
KEGG modules M00254

Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.

Conservation & selection (intra-MTBC, 145 209 strains)

pN/pS 0.552 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 3 missense, 0 nonsense, 0 frameshift

pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.

Domains (Pfam, hmmscan --cut_ga)

PfamAccessioni-EvalueResiduesDescription
ABC_tranPF00005.34 1.3e-2528–166 ABC transporter
AAA_21PF13304.13 5.1e-09126–196 AAA domain, putative AbiEii toxin, Type IV TA system

Functional interaction network (STRING v12, guilt-by-association)

Closest characterised functional partner: Rv1457c (antibiotic ABC transporter permease), high confidence from genomic context alone (score 997 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv1457c antibiotic ABC transporter permease 999 997 ctx neighborhood:882 cooccurence:570 coexpression:405 database:900 textmining:814
Rv1456c antibiotic ABC transporter permease 996 978 ctx neighborhood:746 database:900 textmining:865
Rv1459c mptB alpha-(1->6)-mannopyranosyltransferase 906 795 ctx neighborhood:772 textmining:561
Rv1464 csd cysteine desulfurase 715 715 ctx neighborhood:712
Rv1465 nitrogen fixation related protein 725 712 ctx neighborhood:712
Rv1463 sufC ABC transporter ATP-binding protein 724 712 ctx neighborhood:712
Rv1460 sufR transcriptional regulator 723 712 ctx neighborhood:712
Rv1462 sufD hyp hypothetical protein 712 712 ctx neighborhood:712
Rv1466 hyp hypothetical protein 712 712 ctx neighborhood:712
Rv1349 irtB iron ABC transporter ATP-binding protein/permease IrtB 661 644 database:536
Rv0194 multidrug ABC transporter ATPase/permease 686 635 database:536
Rv1273c drug ABC transporter ATP-binding protein 689 633 database:536
Rv1272c drug ABC transporter ATP-binding protein 653 633 database:536
Rv1348 irtA iron ABC transporter ATP-binding protein/permease IrtA 635 613 database:536
Rv2938 drrC daunorubicin ABC transporter permease DrrC 652 538 coexpression:405

STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.

Evidence

  • Legacy H37Rv annotation: antibiotic ABC transporter ATP-binding protein
  • MTBC0 PGAP product: ABC transporter ATP-binding protein
  • Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=1e-25), AAA_21 PF13304.13 (E=5e-09)
  • (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)

Sources

  • Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
  • Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215974.1)
  • Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34), AAA_21 (PF13304.13)
  • Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
  • Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021, doi:10.1093/molbev/msab293), eggNOG 5.0 DB (Huerta-Cepas et al. 2019) — OG COG1131
  • Curated reference: UniProt O53149 (TrEMBL, unreviewed; Evidence at protein level)
  • Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
  • Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 48 functional partner(s); context anchor Rv1457c
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001560|Rv1458c|
MNRAPDTPEVVLRLRGVCKRYGSITAVSNLDLDVHDAEVMALLGPNGAGKTTTVEMCEGFVRPDAGSIEVLGLDPITDNARLRARIGVMLQGGGGYPAARAGEMLDLVASYAANPLDPHWLLDTLGLTEAARTTYRRLSGGQQQRLALACALVGRPQLVFLDEPTAGMDAHARVLVWELIDALRRDGVTVVLTTHHLKEAEELADRLVIIDHGVTVAAGTPAELMRSGAKDQLRFTAPPRLDLSLLASALPEGYQATELTPGEYLVEGPVDPQVLATVTAWCAQIDVLATDMRVEQRSLEDVFLDLTGRKLRQ