MTBC Gene Atlas

Rv1725c Family assigned · medium auto-curated

H37Rv Rv1725c · MTBC0 mtbc0_001837 · 236 aa · 1963056–1963766 (-) · RefSeq NP_216241.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationwinged helix-turn-helix transcriptional regulator
Revised (this work)Winged helix-turn-helix transcriptional regulator. Pfam: HxlR (PF01638.24).

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

Curated reference (UniProt)

UniProt P71983 TrEMBL · unreviewed · Predicted
UniProt nameHTH hxlR-type domain-containing protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category K Transcription
eggNOG descriptionHxlR-like helix-turn-helix
Orthologous groupCOG1733

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) pseudogene candidate

pN/pS 0.274 · purifying
Polymorphic sites (≥ 0.1% of strains) 4 synonymous, 3 missense, 0 nonsense, 1 frameshift
Disruption 1 distinct premature-stop/frameshift site(s); most common in 2.23% of strains (3239) · 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
HxlRPF01638.24 9.6e-2716–101 HxlR-like helix-turn-helix

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv1931c transcriptional regulator 910 911 coexpression:860
Rv1724c hyp hypothetical protein 882 882 ctx neighborhood:882
Rv1189 sigI ECF RNA polymerase sigma factor SigI 871 872 coexpression:833
Rv3055 TetR family transcriptional regulator 872 869 coexpression:850
Rv3167c TetR family transcriptional regulator 863 860 coexpression:839
Rv3328c sigJ ECF RNA polymerase sigma factor SigJ 858 859 coexpression:822
Rv1151c cobB NAD-dependent protein deacylase 858 858 coexpression:850
Rv3736 AraC/XylS family transcriptional regulator 853 853 coexpression:853
Rv0377 HTH-type transcriptional regulator 857 851 coexpression:851
Rv3263 DNA methylase 848 848 coexpression:848
Rv2488c LuxR family transcriptional regulator 851 846 coexpression:846
Rv1267c embR transcriptional regulator EmbR 846 846 coexpression:846
Rv2788 sirR transcriptional repressor SirR 844 844 coexpression:844
Rv0212c nadR transcriptional regulator NadR 840 840 coexpression:815
Rv0117 oxyS oxidative stress response regulatory protein OxyS 841 836 coexpression:835

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: winged helix-turn-helix transcriptional regulator
  • Pfam (hmmscan --cut_ga): HxlR PF01638.24 (E=1e-26)
  • (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_216241.1)
  • Domains: Pfam-A via hmmscan --cut_ga — HxlR (PF01638.24)
  • 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 COG1733
  • Curated reference: UniProt P71983 (TrEMBL, unreviewed; Predicted)
  • 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 — 87 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001837|Rv1725c|
MQPYGQYCPVARAAELLGDRWTLLIVRELLFGPLRFTEIERGLPGISRSVLAQRLRRLQHDRIIEAVPEHTGGGYRFTVAGEELRPVLQTLGDWVSRWLMADPTPAECDPELLTLWISRRVNTEALPGRRVVVEFRYHGERPLWAWLVLEPGDISVCLHDPCLPVDLTVRGHPRDLYRVYSGRSTLAAEISAERIELDGLPAMRRAFPSWMAWSPFAPAMRQAVVSVDQMPEAHGG