MTBC Gene Atlas

Rv1111c Family assigned · low

H37Rv Rv1111c · MTBC0 mtbc0_001193 · 327 aa · 1245649–1246632 (-) · RefSeq NP_215627.2

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationDUF6542 domain-containing protein
Revised (this work)Polytopic integral membrane protein with 4 predicted transmembrane helices (DeepTMHMM). RefSeq leaves it 'hypothetical protein'. A topological feature consistent with a membrane transporter/permease or membrane-embedded enzyme; the transported substrate and molecular function are undetermined.

Curated reference (UniProt)

UniProt O86351 TrEMBL · unreviewed · Evidence at protein level
UniProt nameDUF6542 domain-containing protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

Orthologous group2FH0D

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 0.536 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 4 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
DUF6542PF20177.4 1.3e-3223–141 Domain of unknown function (DUF6542)

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

Closest characterised functional partner: ychF (GTP-binding protein), high confidence from genomic context alone (score 787 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.

PartnerProductScoreNo text-miningChannels (≥400)
Rv1112 ychF GTP-binding protein 786 787 ctx neighborhood:786
Rv1109c hyp hypothetical protein 769 770 ctx cooccurence:767
Rv3835 hyp hypothetical protein 766 766 ctx cooccurence:756
Rv3909 hyp hypothetical protein 760 761 ctx cooccurence:757
Rv0996 transmembrane protein 751 752 ctx cooccurence:750
Rv3212 hyp hypothetical protein 747 748 ctx cooccurence:745
Rv2732c transmembrane protein 747 747 ctx cooccurence:741
Rv3415c hyp hypothetical protein 743 743 ctx cooccurence:743
Rv0556 transmembrane protein 732 733 ctx cooccurence:731
Rv0475 hbhA heparin binding hemagglutinin HbhA 731 732 ctx cooccurence:730
Rv1083 hyp hypothetical protein 726 726 ctx cooccurence:726
Rv2164c hyp hypothetical protein 724 725 ctx cooccurence:722
Rv1222 rseA anti-sigma E factor RseA 724 724 ctx cooccurence:724
Rv2418c octT hyp hypothetical protein 719 720 ctx cooccurence:713
Rv0358 hyp hypothetical protein 719 719 ctx cooccurence:718

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

  • DeepTMHMM: 4 transmembrane helices (type TM)
  • Integral membrane topology (localisation feature, not a function)
  • DeepTMHMM topology prediction (project 'Still unknown gene function', phase8, 2026-06-10). A topological feature, not a demonstrated molecular function.

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_215627.2)
  • Domains: Pfam-A via hmmscan --cut_ga — DUF6542 (PF20177.4)
  • 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 2FH0D
  • Curated reference: UniProt O86351 (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)
  • Model confidence: ESMFold per-residue pLDDT (mean 82.5, confident)
  • Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 168 functional partner(s); context anchor ychF
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001193|Rv1111c|
MSAQRARSAVQASHRSIHPHIPGVPWWAAILIAVTATAIGYAIDAGSGHKALTLVFTGCYIAGCVGAVLAVRQSDLFTALVQPPLILFCAVPGAYWLFHGGTIGKFKDLLINCGYSLIERFPLMLGTAAGVLLIGLVRWYLGTALFDSIARKLSSLMTGDSDDDGGRRSAQRPARTRSRHARPPSEDNREPIAERRSRRRPRPQNDPHPRRNAHERPAPRSSRFDSYRSYQPSEPSGPAEPVNRYERRGARYQPYARYEPTYEPQRRRARPSEPTNPTHHPISQVRYRGSATRDARRDNYREEQRFDRRDRSRAPRRPPAESWEYDV