MTBC Gene Atlas

Rv0273c Family assigned · medium auto-curated

H37Rv Rv0273c · MTBC0 mtbc0_000290 · 206 aa · 330087–330707 (-) · RefSeq NP_214787.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)transcriptional regulator
MTBC0 PGAP re-annotationTetR/AcrR family transcriptional regulator
Revised (this work)TetR/AcrR family transcriptional regulator. Pfam: TetR_N (PF00440.30).

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

Curated reference (UniProt)

UniProt O86342 TrEMBL · unreviewed · Evidence at protein level
UniProt namePossible transcriptional regulatory protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category K Transcription
eggNOG descriptiontranscriptional
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 0.303 · purifying
Polymorphic sites (≥ 0.1% of strains) 4 synonymous, 4 missense, 0 nonsense, 1 frameshift
Disruption 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (172) · clonal

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 9.9e-1018–60 Bacterial regulatory proteins, tetR family

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv0272c hyp hypothetical protein 969 970 ctx neighborhood:881 cooccurence:751
Rv0274 hyp hypothetical protein 900 900 ctx neighborhood:773 cooccurence:575
Rv0691c mftR mycofactocin biosynthesis transcriptional regulator MftR 861 858 coexpression:804
Rv0674 hyp hypothetical protein 842 843 coexpression:770
Rv1033c trcR two component transcriptional regulator TrcR 831 831 coexpression:831
Rv3164c moxR3 methanol dehydrogenase transcriptional regulator MoxR 827 827 coexpression:827
Rv2488c LuxR family transcriptional regulator 829 821 coexpression:820
Rv3736 AraC/XylS family transcriptional regulator 822 820 coexpression:819
Rv1027c kdpE transcriptional regulator KdpE 819 819 coexpression:819
Rv1725c hyp hypothetical protein 817 813 coexpression:813
Rv1151c cobB NAD-dependent protein deacylase 817 810 coexpression:810
Rv2788 sirR transcriptional repressor SirR 810 807 coexpression:806
Rv1267c embR transcriptional regulator EmbR 810 806 coexpression:806
Rv0339c iniR transcriptional regulator 805 805 coexpression:805
Rv1773c transcriptional regulator 810 803 coexpression:803

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: TetR/AcrR family transcriptional regulator
  • Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=1e-09)
  • (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_214787.1)
  • Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30)
  • 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 O86342 (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 — 106 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000290|Rv0273c|
MPDFPTQRGRRTQAAIDAAARTVVVRNGILATTVADITAEAGRSAASFYNYYDSKEAMVRQWALRFRDDANQRALSVIRHGLSDRERAYEAAAAHWYTYRNRLAEAISVSQLAMVSDDFAQYWSEICQIPISFITETVKRAQAHGYCVGDDPQLMAEAIVAMFNQFCYLQLSGKRSRRGQPDDQACIQTLANIYYRAIYSKEDSSN