MTBC Gene Atlas

Rv0876c Resolved · high auto-curated

H37Rv Rv0876c · MTBC0 mtbc0_000931 · 548 aa · 977503–979149 (-) · RefSeq NP_215391.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)transmembrane protein
MTBC0 PGAP re-annotationMFS transporter
Revised (this work)MFS transporter. Pfam: MFS_1 (PF07690.22).

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

Curated reference (UniProt)

UniProt P9WKR5 SwissProt · reviewed · Evidence at protein level
UniProt nameUncharacterized protein Rv0876c

UniProt still lists this protein as Uncharacterized protein Rv0876c; the revised annotation above is ahead of the current UniProt record.

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category E Amino acid transport and metabolism
G Carbohydrate transport and metabolism
P Inorganic ion transport and metabolism
eggNOG descriptionMajor facilitator superfamily
Orthologous groupCOG0477
Gene Ontology (7) GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944

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 0.449 · purifying
Polymorphic sites (≥ 0.1% of strains) 5 synonymous, 6 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
MFS_1PF07690.22 6.2e-12122–484 Major Facilitator Superfamily

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

Closest characterised functional partner: rseA (anti-sigma E factor RseA), high confidence from genomic context alone (score 736 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv0875c hyp hypothetical protein 968 968 ctx neighborhood:882 coexpression:740
Rv0877 hyp hypothetical protein 776 776 ctx neighborhood:774
Rv1083 hyp hypothetical protein 748 749 ctx cooccurence:747
Rv1222 rseA anti-sigma E factor RseA 735 736 ctx cooccurence:732
Rv3415c hyp hypothetical protein 684 684 ctx cooccurence:683
Rv1109c hyp hypothetical protein 670 670 ctx cooccurence:667
Rv2418c octT hyp hypothetical protein 640 640 ctx cooccurence:640
Rv0475 hbhA heparin binding hemagglutinin HbhA 636 636 ctx cooccurence:634
Rv2520c membrane protein 610 610 ctx cooccurence:610
Rv2700 cei hyp hypothetical protein 603 603 ctx cooccurence:603
Rv0854 hyp hypothetical protein 583 583 ctx cooccurence:583
Rv0902c prrB two component sensor histidine kinase PrrB 590 580 coexpression:580
Rv2091c membrane protein 574 575 ctx cooccurence:570
Rv2927c sepIVA hyp hypothetical protein 585 574 ctx cooccurence:555
Rv3277 transmembrane protein 572 572 ctx cooccurence:572

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: transmembrane protein
  • MTBC0 PGAP product: MFS transporter
  • Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=6e-12)
  • (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_215391.1)
  • Domains: Pfam-A via hmmscan --cut_ga — MFS_1 (PF07690.22)
  • 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 COG0477
  • Curated reference: UniProt P9WKR5 (SwissProt, reviewed; 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 rseA
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000931|Rv0876c|
MAPTPGRRTRNGSVNGHPGMANYPPDDANYRRSRRPPPMPSANRYLPPLGEQPEPERSRVPPRTTRAGERITVTRAAAMRSREMGSRMYLLVHRAATADGADKSGLTALTWPVMANFAVDSAMAVALANTLFFAAASGESKSRVALYLLITIAPFAVIAPLIGPALDRLQHGRRVALALSFGLRTALAVVLIMNYDGATGSFPSWVLYPCALAMMVFSKSFSVLRSAVTPRVMPPTIDLVRVNSRLTVFGLLGGTIAGGAIAAGVEFVCTHLFQLPGALFVVVAITIAGASLSMRIPRWVEVTSGEVPATLSYHRDRGRLRRRWPEEVKNLGGTLRQPLGRNIITSLWGNCTIKVMVGFLFLYPAFVAKAHEANGWVQLGMLGLIGAAAAVGNFAGNFTSARLQLGRPAVLVVRCTVLVTVLAIAAAVAGSLAATAIATLITAGSSAIAKASLDASLQHDLPEESRASGFGRSESTLQLAWVLGGAVGVLVYTELWVGFTAVSALLILGLAQTIVSFRGDSLIPGLGGNRPVMAEQETTRRGAAVAPQ