MTBC Gene Atlas

rfbD Family assigned · medium auto-curated

H37Rv Rv3783 · MTBC0 mtbc0_004011 · 280 aa · 4253379–4254221 (+) · RefSeq NP_218300.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)O-antigen/lipopolysaccharide ABC transporter permease RfbD
MTBC0 PGAP re-annotationABC transporter permease
Revised (this work)ABC transporter permease. Pfam: ABC2_membrane (PF01061.30).

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

Curated reference (UniProt)

UniProt P72049 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category G Carbohydrate transport and metabolism
M Cell wall / membrane / envelope biogenesis
Preferred namerfbD
eggNOG descriptionTransporter
Orthologous groupCOG1682
KEGG orthology K01992
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 0.847 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 5 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
ABC2_membranePF01061.30 2.3e-1734–240 ABC-2 type transporter

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

Closest characterised functional partner: rfbE (O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE), high confidence from genomic context alone (score 1000 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv3781 rfbE O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE 999 1000 ctx neighborhood:881 cooccurence:772 coexpression:864 experimental:928 database:900 textmining:917
Rv3782 glfT1 galactofuranosyl transferase GlfT 998 994 ctx neighborhood:881 cooccurence:640 coexpression:876 textmining:815
Rv3780 bpa hyp hypothetical protein 962 882 ctx neighborhood:881 textmining:694
Rv3779 transmembrane protein 930 881 ctx neighborhood:881 textmining:434
Rv3809c glf UDP-galactopyranose mutase 885 762 coexpression:667 textmining:539
Rv0014c pknB serine/threonine-protein kinase PknB 741 741 coexpression:733
Rv3265c wbbL1 N-acetylglucosaminyl-diphospho-decaprenol L-rhamnosyltransferase 900 710 ctx cooccurence:483 textmining:672
Rv3778c aminotransferase 701 701 ctx neighborhood:636
Rv3808c glfT2 galactofuranosyl transferase GlfT 924 613 textmining:813
Rv3311 hyp hypothetical protein 577 577 ctx cooccurence:573
Rv3806c ubiA decaprenyl-phosphate phosphoribosyltransferase 551 551
Rv3212 hyp hypothetical protein 545 546 ctx cooccurence:524
Rv3784 dTDP-glucose 4,6-dehydratase 568 518 ctx neighborhood:511
Rv3148 nuoD NADH-quinone oxidoreductase subunit D 514 514 coexpression:514
Rv2744c 35kd_ag hyp hypothetical protein 493 493 ctx cooccurence:486

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: O-antigen/lipopolysaccharide ABC transporter permease RfbD
  • MTBC0 PGAP product: ABC transporter permease
  • Pfam (hmmscan --cut_ga): ABC2_membrane PF01061.30 (E=2e-17)
  • (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_218300.1)
  • Domains: Pfam-A via hmmscan --cut_ga — ABC2_membrane (PF01061.30)
  • 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 COG1682
  • Curated reference: UniProt P72049 (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 — 38 functional partner(s); context anchor rfbE
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_004011|Rv3783|rfbD
MTFMDAQASFQTQSRTLARVRGDLVDGFRRHELWLHLGWQDIKQRYRRSVLGPFWITIATGTTAVAMGGLYSKLFRLELSEHLPYVTLGLIVWNLINAAILDGAEVFVANEGLIKQLPAPLSVHVYRLVWRQMIFFAHNIVIYFVIAIIFPKPWSWADLSFLPALALIFLNCVWVSLCFGILATRYRDIGPLLFSVVQLLFFMTPIIWNDETLRRQGAGRWSSIVELNPLLHYLDIVRAPLLGAHQELRHWLVVLVLTVVGWMLAAFAMRQYRARVPYWV