MTBC Gene Atlas

Rv1186c Family assigned · medium auto-curated

H37Rv Rv1186c · MTBC0 mtbc0_001274 · 538 aa · 1336131–1337747 (-) · RefSeq NP_215702.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationPucR family transcriptional regulator
Revised (this work)PucR family transcriptional regulator. Pfam: HTH_30 (PF13556.13).

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

Curated reference (UniProt)

UniProt O50442 TrEMBL · unreviewed · Evidence at protein level
UniProt nameConserved protein

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

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category Q Secondary metabolites biosynthesis, transport and catabolism
T Signal transduction mechanisms
eggNOG descriptionPucR C-terminal helix-turn-helix domain
Orthologous groupCOG2508

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 0.386 · purifying
Polymorphic sites (≥ 0.1% of strains) 8 synonymous, 8 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
HTH_30PF13556.13 5.2e-21475–533 PucR C-terminal helix-turn-helix domain

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

Closest characterised functional partner: Rv1188 (proline dehydrogenase), high confidence from genomic context alone (score 840 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.

PartnerProductScoreNo text-miningChannels (≥400)
Rv1188 proline dehydrogenase 908 840 ctx neighborhood:783 textmining:451
Rv1187 rocA pyrroline-5-carboxylate dehydrogenase RocA 865 819 ctx neighborhood:783
Rv3124 moaR1 transcriptional regulator MoaR 560 561 ctx cooccurence:550
Rv3055 TetR family transcriptional regulator 498 499 ctx cooccurence:484
Rv2474c hyp hypothetical protein 497 498 ctx cooccurence:495
Rv1185c fadD21 fatty-acid--CoA ligase FadD21 489 489 ctx neighborhood:487
Rv1267c embR transcriptional regulator EmbR 484 484 ctx cooccurence:459
Rv3882c eccE1 ESX-1 secretion system protein EccE1 474 474 ctx cooccurence:474
Rv0513 transmembrane protein 462 462 ctx cooccurence:459
Rv1171 hyp hypothetical protein 459 459 ctx cooccurence:452
Rv1191 hyp hypothetical protein 456 456
Rv1871c hyp hypothetical protein 449 450 ctx cooccurence:431
Rv3071 hyp hypothetical protein 445 446 ctx cooccurence:444
Rv1748 hyp hypothetical protein 443 444 ctx cooccurence:442
Rv3824c papA1 acyltransferase 437 438 ctx cooccurence:437

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: hypothetical protein
  • MTBC0 PGAP product: PucR family transcriptional regulator
  • Pfam (hmmscan --cut_ga): HTH_30 PF13556.13 (E=5e-21)
  • (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_215702.1)
  • Domains: Pfam-A via hmmscan --cut_ga — HTH_30 (PF13556.13)
  • 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 COG2508
  • Curated reference: UniProt O50442 (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 — 24 functional partner(s); context anchor Rv1188
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001274|Rv1186c|
MRIAGVGLGQLLLALDATVVSLVDAPRGLDLPVASTALIDSDDVRLGLAAAAGSADVFFLIGVTDDEAVRWVDDQARQRAPVAIFVKHPSDSVVAGAVRAGSAVVAVEPRARWERLYHLVNHVLEHHGDRADPTDDSGTDLFGLAQSLADRIHGMISIEDAQSHVLAYSASNDEADELRRLSILGRAGPPEHLQWIGQWGIFDALRAGREVVRVAERPELGLRPRLAIGIHQPGVGALRPPVFAGTIWVQQGSQPLADDAEEMLRGAAVLAARIMSRLATQPNTHALRVQQLLGLAELNATTAPVDVSTIARELGVAAEGNATLIGFDTAENRDTAVRHVRLVDVMALSASAFRHDAQVAANGSRIYVLLPQTTTGRAVTSWVRGTISALRAELGVALRAAIAGPVAGLAEVNPARVEVDRVLESAERHPILGQVTSLAEARTTVLLDEIVTLVGTDQRLVDPRIRDLGAQDPVLAQTLRAYLDAFGDIGAAARSLQVHPNTVRYRIRRIEQLLSTSLGDPDVRLLFSLGLRAMERTA