MTBC Gene Atlas

Rv0067c Family assigned · medium auto-curated

H37Rv Rv0067c · MTBC0 mtbc0_000074 · 189 aa · 74774–75343 (-) · RefSeq NP_214581.1

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: TetR_N (PF00440.30), TetR_C_43 (PF21597.3).

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

Curated reference (UniProt)

UniProt O53612 TrEMBL · unreviewed · Evidence at protein level
UniProt namePossible transcriptional regulatory protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category K Transcription
eggNOG descriptionTranscriptional regulator
Orthologous groupCOG1309

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 1.065 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 1 synonymous, 3 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
TetR_NPF00440.30 2.9e-1420–64 Bacterial regulatory proteins, tetR family
TetR_C_43PF21597.3 4.1e-3285–186 Transcriptional regulator SbtR-like, C-terminal domain

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv1725c hyp hypothetical protein 829 826 coexpression:797
Rv3055 TetR family transcriptional regulator 808 809 coexpression:754
Rv3183 higA3 transcriptional regulator 798 798 coexpression:798
Rv2488c LuxR family transcriptional regulator 800 790 coexpression:751
Rv0339c iniR transcriptional regulator 790 790 coexpression:759
Rv1931c transcriptional regulator 785 785 coexpression:732
Rv0377 HTH-type transcriptional regulator 859 784 coexpression:757
Rv3164c moxR3 methanol dehydrogenase transcriptional regulator MoxR 772 772 coexpression:772
Rv2506 TetR family transcriptional regulator 761 761 coexpression:761
Rv0691c mftR mycofactocin biosynthesis transcriptional regulator MftR 753 746 coexpression:746
Rv0212c nadR transcriptional regulator NadR 750 738 coexpression:738
Rv1359 transcriptional regulator 736 736 coexpression:687
Rv1674c transcriptional regulator 744 735 coexpression:735
Rv3263 DNA methylase 732 732 coexpression:732
Rv0624 vapC30 ribonuclease VapC30 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): TetR_N PF00440.30 (E=3e-14), TetR_C_43 PF21597.3 (E=4e-32)
  • (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_214581.1)
  • Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_43 (PF21597.3)
  • 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 COG1309
  • Curated reference: UniProt O53612 (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 — 45 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000074|Rv0067c|
MAPTDRRVRADAARNRARVLEVAYQTFAADGLSVPVDEIARRAGVGAGTVYRHFPTKEALFQAVIADRMHRIIDKGHALLKSKHPGDALFAFLRSMVLQWGATDRGLVEALAGVGIEISSAAPEAEADFLDLLTDLLRAAQRAGTVRPDVDVLEVKTLLVGCQAMQSYNAELAAKVTDVALDGLRANRK