MTBC Gene Atlas

rfbE Family assigned · medium auto-curated

H37Rv Rv3781 · MTBC0 mtbc0_004009 · 273 aa · 4251650–4252471 (+) · RefSeq NP_218298.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE
MTBC0 PGAP re-annotationABC transporter ATP-binding protein
Revised (this work)ABC transporter ATP-binding protein. Pfam: ABC_tran (PF00005.34).

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

Curated reference (UniProt)

UniProt P72047 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category G Carbohydrate transport and metabolism
M Cell wall / membrane / envelope biogenesis
Preferred namerfbE
eggNOG descriptionABC transporter
Orthologous groupCOG1134
KEGG orthology K01990, K09691
KEGG pathways map02010
KEGG modules M00250, 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 0.0 · strong purifying
Polymorphic sites (≥ 0.1% of strains) 1 synonymous, 0 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 2.6e-1953–183 ABC transporter

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

Closest characterised functional partner: rfbD (O-antigen/lipopolysaccharide ABC transporter permease RfbD), high confidence from genomic context alone (score 1000 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv3783 rfbD O-antigen/lipopolysaccharide ABC transporter permease RfbD 999 1000 ctx neighborhood:881 cooccurence:772 coexpression:864 experimental:928 database:900 textmining:917
Rv3782 glfT1 galactofuranosyl transferase GlfT 992 939 ctx neighborhood:882 textmining:879
Rv3780 bpa hyp hypothetical protein 964 884 ctx neighborhood:882 textmining:703
Rv3779 transmembrane protein 930 882 ctx neighborhood:881 textmining:434
Rv3242c hyp hypothetical protein 776 777 coexpression:777
Rv2894c xerC tyrosine recombinase XerC 646 646 coexpression:646
Rv3265c wbbL1 N-acetylglucosaminyl-diphospho-decaprenol L-rhamnosyltransferase 880 643 ctx cooccurence:402 textmining:678
Rv3778c aminotransferase 637 637 ctx neighborhood:636
Rv3809c glf UDP-galactopyranose mutase 791 557 coexpression:415 textmining:549
Rv3784 dTDP-glucose 4,6-dehydratase 569 518 ctx neighborhood:511
Rv2584c apt adenine phosphoribosyltransferase 495 495 coexpression:479
Rv3754 tyrA prephenate dehydrogenase TyrA 507 489 coexpression:419
Rv3226c hyp hypothetical protein 469 470
Rv3786c hyp hypothetical protein 496 469 coexpression:451
Rv1502 hyp hypothetical protein 475 456 coexpression:425

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 ATP-binding protein RfbE
  • MTBC0 PGAP product: ABC transporter ATP-binding protein
  • Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=3e-19)
  • (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_218298.1)
  • Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34)
  • 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 COG1134
  • Curated reference: UniProt P72047 (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 — 37 functional partner(s); context anchor rfbD
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_004009|Rv3781|rfbE
MSDPHHPHIQTHNAWVEFPIFDAKSRSLKKAVLGKAGGTIGRNNSNVVVIEALRDITMELNLGDRVGLVGHNGAGKSTLLRLLSGIYEPTRGWAKVTGRVAPVFDLGIGMDPEISGYENIIIRGLFLGQTRKQMQAKVDEIAEFTELGEYLSMPLRTYSTGMRVRLAMGVVTSIDPEILLLDEGIGAVDADFLRKAQSRLQNLVERSGILVFASHSNEFLARLCKTAIWIDHGVIRLAGGIEEVVRAYEGEDAARHVREVLAETQADRQNVQG