Rv0431 Resolved · high auto-curated
H37Rv Rv0431 · MTBC0 - ·
164 aa · 519073–519567 (+) ·
RefSeq NP_214945.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tuberculin-like peptide |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Tuberculin-like peptide. Pfam: LytR_C (PF13399.12). |
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 |
P96277
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Vesiculogenesis and immune response regulator |
| Curated function | Virulence factor that regulates vesiculogenesis. Acts by regulating the production of mycobacterial membrane vesicles (MV) bearing Toll-like receptor 2 (TLR2) ligands, including the lipoproteins LpqH, a major host TLR2 agonist, and SodC. By restraining the release of most of the material that activates host cells through TLR2, VirR reduces the immunostimulant potential of M.tuberculosis and increases its virulence. May contribute to cell envelope integrity..; FUNCTION: When overexpressed in M.smegmatis, it modulates the production of IL-10, IL-12 p40 and TNF by RAW264.7 macrophages and it decr. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | LytR cell envelope-related transcriptional attenuator |
| Orthologous group | 2DP6P |
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 | 1.211 · diversifying/relaxed |
|---|---|
| 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
LytR_C | PF13399.12 | 4.4e-14 | 77–162 | LytR cell envelope-related transcriptional attenuator |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0433 (carboxylate-amine ligase), high confidence from genomic context alone (score 835 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0430 hyp |
hypothetical protein | 856 | 856 ctx | neighborhood:835 |
Rv0433 |
carboxylate-amine ligase | 835 | 835 ctx | neighborhood:833 |
Rv0432 sodC |
superoxide dismutase | 835 | 835 ctx | neighborhood:833 |
Rv0434 hyp |
hypothetical protein | 760 | 760 ctx | neighborhood:758 |
Rv2732c |
transmembrane protein | 760 | 760 ctx | cooccurence:757 |
Rv2138 lppL |
lipoprotein LppL | 759 | 759 ctx | cooccurence:758 |
Rv1109c hyp |
hypothetical protein | 751 | 752 ctx | cooccurence:749 |
Rv1632c hyp |
hypothetical protein | 750 | 751 ctx | cooccurence:739 |
Rv3212 hyp |
hypothetical protein | 747 | 748 ctx | cooccurence:745 |
Rv0556 |
transmembrane protein | 744 | 745 ctx | cooccurence:741 |
Rv0996 |
transmembrane protein | 740 | 740 ctx | cooccurence:732 |
Rv0250c hyp |
hypothetical protein | 737 | 738 ctx | cooccurence:736 |
Rv0882 |
transmembrane protein | 733 | 733 ctx | cooccurence:732 |
Rv2743c hyp |
hypothetical protein | 728 | 728 ctx | cooccurence:725 |
Rv1486c hyp |
hypothetical protein | 711 | 712 ctx | cooccurence:711 |
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): tuberculin-like peptide
- Pfam (hmmscan --cut_ga): LytR_C PF13399.12 (E=4e-14)
- (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_214945.1)
- Domains: Pfam-A via hmmscan --cut_ga — LytR_C (PF13399.12)
- 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
2DP6P - Curated reference: UniProt P96277 (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 —
121 functional partner(s); context anchor
Rv0433 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0431| MLVTVGSMNERVPDSSGLPLRAMVMVLLFLGVVFLLLVWQALGSSPNSEDDSSAISTMTTTTAAPTSTSVKPAAPRAEVRVYNISGTEGAAARTADRLKAAGFTVTDVGNLSLPDVAATTVYYTEVEGERATADAVGRTLGAAVELRLPELSDQPPGVIVVVTG