Rv1931c Family assigned · medium auto-curated
H37Rv Rv1931c · MTBC0 - ·
259 aa · 2182460–2183239 (-) ·
RefSeq NP_216447.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator. Pfam: DJ-1_PfpI (PF01965.31), HTH_18 (PF12833.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P95283
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator Rv1931c |
| Curated function | Controls the expression of genes important for virulence. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG4977 |
| Gene Ontology (22) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0009405, GO:0010468, GO:0010565, GO:0016020, GO:0019216, GO:0019217, GO:0019222, GO:0031323 +10 more
|
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 | 1.89 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DJ-1_PfpI | PF01965.31 | 8.4e-07 | 11–62 | DJ-1/PfpI family |
HTH_18 | PF12833.14 | 4.9e-23 | 178–256 | Helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sigI (ECF RNA polymerase sigma factor SigI), high confidence from genomic context alone (score 905 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1930c hyp |
hypothetical protein | 935 | 935 ctx | neighborhood:863 cooccurence:539 |
Rv1725c hyp |
hypothetical protein | 910 | 911 | coexpression:860 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 908 | 905 ctx | cooccurence:489 coexpression:822 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 888 | 883 | coexpression:831 |
Rv2488c |
LuxR family transcriptional regulator | 885 | 879 | coexpression:857 |
Rv3736 |
AraC/XylS family transcriptional regulator | 884 | 879 | coexpression:831 |
Rv3167c |
TetR family transcriptional regulator | 877 | 878 | coexpression:860 |
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 880 | 876 ctx | cooccurence:524 coexpression:751 |
Rv0212c nadR |
transcriptional regulator NadR | 865 | 866 | coexpression:846 |
Rv1674c |
transcriptional regulator | 864 | 864 | coexpression:862 |
Rv1190 hyp |
hypothetical protein | 863 | 864 | coexpression:841 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 865 | 860 | coexpression:860 |
Rv1267c embR |
transcriptional regulator EmbR | 862 | 860 | coexpression:860 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 861 | 860 | coexpression:860 |
Rv0494 |
HTH-type transcriptional regulator | 860 | 860 | coexpression:827 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): transcriptional regulator
- Pfam (hmmscan --cut_ga): DJ-1_PfpI PF01965.31 (E=8e-07), HTH_18 PF12833.14 (E=5e-23)
- (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_216447.1)
- Domains: Pfam-A via hmmscan --cut_ga — DJ-1_PfpI (PF01965.31), HTH_18 (PF12833.14)
- 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
COG4977 - Curated reference: UniProt P95283 (SwissProt, reviewed; Evidence at transcript 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 —
93 functional partner(s); context anchor
sigI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1931c| MVIVGFPGDPVDTVILPGGAGVDAARSEPALIDWVKAVSGTARRVVTVCTGAFLAAEAGLLGRTPSDDALGLCRTFRPRISGRSGRCRPDLHAQFAEGVDRGWSHRRHRPRAGTGRRRPRHRDCPDGCPLARPVSAPTRWADPVRGSGVDATRQTDLDPPGAGGHRGRAGGAHRIGELAQRAAMSPRHFTRVFSDEVGEAPGRYVERIRTEAARRQLEETHDTVVAIAARCGFGTAETMRRSFIRRVGISPDQYRKAFA