MTBC Gene Atlas

Rv0744c Family assigned · medium auto-curated

H37Rv Rv0744c · MTBC0 mtbc0_000789 · 168 aa · 838635–839141 (-) · RefSeq NP_215258.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)transcriptional regulator
MTBC0 PGAP re-annotationhelix-turn-helix domain-containing protein
Revised (this work)Helix-turn-helix domain-containing protein. Pfam: HTH_17 (PF12728.14).

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

Curated reference (UniProt)

UniProt O53807 TrEMBL · unreviewed · Evidence at protein level
UniProt namePossible transcriptional regulatory protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category K Transcription
eggNOG descriptionHelix-turn-helix domain
Orthologous group2C22B

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 0.631 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 1 synonymous, 2 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_17PF12728.14 5.4e-114–49 Helix-turn-helix domain

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv0743c hyp hypothetical protein 883 882 ctx neighborhood:882
Rv1776c transcriptional regulator 800 800 coexpression:800
Rv3167c TetR family transcriptional regulator 799 799 coexpression:799
Rv1151c cobB NAD-dependent protein deacylase 797 797 coexpression:797
Rv3830c TetR family transcriptional regulator 797 797 coexpression:797
Rv0603 hyp hypothetical protein 797 797 coexpression:797
Rv1985c lysG HTH-type transcriptional regulator 767 767 coexpression:767
Rv0602c tcrA two component DNA binding transcriptional regulator TcrA 767 767 coexpression:767
Rv1267c embR transcriptional regulator EmbR 759 759 coexpression:759
Rv1675c cmr HTH-type transcriptional regulator Cmr 744 744 coexpression:744
Rv1167c transcriptional regulator 744 744 coexpression:744
Rv3736 AraC/XylS family transcriptional regulator 733 733 coexpression:733
Rv1960c parD1 antitoxin ParD1 733 733 coexpression:733
Rv0691c mftR mycofactocin biosynthesis transcriptional regulator MftR 733 733 coexpression:733
Rv3840 transcriptional regulator 732 732 coexpression:732

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: transcriptional regulator
  • MTBC0 PGAP product: helix-turn-helix domain-containing protein
  • Pfam (hmmscan --cut_ga): HTH_17 PF12728.14 (E=5e-11)
  • (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_215258.1)
  • Domains: Pfam-A via hmmscan --cut_ga — HTH_17 (PF12728.14)
  • 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 2C22B
  • Curated reference: UniProt O53807 (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)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000789|Rv0744c|
METLLKTSEAAQILGVSRQHVVNMCDRGEMVCVHVGSHRRVPSSEVERVTSRRLTREEERSLWLHRALLSPLLTEPDTVVSAARENLRRWSGMHRRDGMAGWYFTKWQRVLNDGLDAVMHVLTSPSEDAREMRQNSPFAGILPEATRVAVLRSFKDHWDREHERAMTE