Rv0494 Family assigned · medium auto-curated
H37Rv Rv0494 · MTBC0 - ·
242 aa · 584695–585423 (+) ·
RefSeq NP_215008.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | HTH-type transcriptional regulator. Pfam: GntR (PF00392.28), HTH_Crp_2 (PF13545.13), FCD (PF07729.18). |
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 |
P9WMG7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv0494 |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv0494; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | GntR family |
| Orthologous group | COG2186 |
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 | 0.367 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
GntR | PF00392.28 | 5.1e-18 | 21–82 | Bacterial regulatory proteins, gntR family |
HTH_Crp_2 | PF13545.13 | 1.2e-06 | 45–89 | Crp-like helix-turn-helix domain |
FCD | PF07729.18 | 3.8e-16 | 108–228 | FCD domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1773c (transcriptional regulator), high confidence from genomic context alone (score 869 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3167c |
TetR family transcriptional regulator | 877 | 873 | coexpression:854 |
Rv1773c |
transcriptional regulator | 875 | 869 ctx | cooccurence:581 coexpression:693 |
Rv1674c |
transcriptional regulator | 866 | 861 | coexpression:859 |
Rv1931c |
transcriptional regulator | 860 | 860 | coexpression:827 |
Rv0792c |
transcriptional regulator | 862 | 857 ctx | cooccurence:433 coexpression:757 |
Rv0602c tcrA |
two component DNA binding transcriptional regulator TcrA | 844 | 838 | coexpression:838 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 844 | 837 | coexpression:802 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 827 | 826 | coexpression:826 |
Rv3840 |
transcriptional regulator | 826 | 826 | coexpression:826 |
Rv0493c hyp |
hypothetical protein | 823 | 823 ctx | neighborhood:622 cooccurence:549 |
Rv1151c cobB |
NAD-dependent protein deacylase | 817 | 817 | coexpression:817 |
Rv0212c nadR |
transcriptional regulator NadR | 813 | 813 | coexpression:813 |
Rv1267c embR |
transcriptional regulator EmbR | 813 | 813 | coexpression:813 |
Rv0603 hyp |
hypothetical protein | 813 | 813 | coexpression:813 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 813 | 813 | coexpression:813 |
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): HTH-type transcriptional regulator
- Pfam (hmmscan --cut_ga): GntR PF00392.28 (E=5e-18), HTH_Crp_2 PF13545.13 (E=1e-06), FCD PF07729.18 (E=4e-16)
- (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_215008.2)
- Domains: Pfam-A via hmmscan --cut_ga — GntR (PF00392.28), HTH_Crp_2 (PF13545.13), FCD (PF07729.18)
- 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
COG2186 - Curated reference: UniProt P9WMG7 (SwissProt, reviewed; 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 —
83 functional partner(s); context anchor
Rv1773c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0494| MVEPMNQSSVFQPPDRQRVDERIATTIADAILDGVFPPGSTLPPERDLAERLGVNRTSLRQGLARLQQMGLIEVRHGSGSVVRDPEGLTHPAVVEALVRKLGPDFLVELLEIRAALGPLIGRLAAARSTPEDAEALCAALEVVQQADTAAARQAADLAYFRVLIHSTRNRALGLLYRWVEHAFGGREHALTGAYDDADPVLTDLRAINGAVLAGDPAAAAATVEAYLNASALRMVKSYRDRA