Rv0495c Family assigned · medium auto-curated
H37Rv Rv0495c · MTBC0 - ·
296 aa · 585424–586314 (-) ·
RefSeq NP_215009.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Rv0495c (PF11307.14) domain(s); putative function inferred from the domain architecture. |
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 |
P9WKU5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable redox regulatory protein Rv0495c |
| Curated function | Essential for maintaining intracellular redox homeostasis. Could help overcome various host-induced stress conditions, ensure bacterial survival within macrophages and modulate in vivo growth of M.tuberculosis for long-term disease persistence. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 28IRH |
|---|
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 | 0.426 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
Rv0495c | PF11307.14 | 2.4e-41 | 70–278 | Rv0495c-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0428c (GCN5-like N-acetyltransferase), high confidence from genomic context alone (score 738 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0499 hyp |
hypothetical protein | 745 | 746 ctx | neighborhood:744 |
Rv0428c |
GCN5-like N-acetyltransferase | 737 | 738 ctx | cooccurence:737 |
Rv0500 proC |
pyrroline-5-carboxylate reductase | 737 | 737 ctx | neighborhood:737 |
Rv2616 hyp |
hypothetical protein | 660 | 661 ctx | cooccurence:655 |
Rv3818 hyp |
hypothetical protein | 644 | 644 ctx | cooccurence:643 |
Rv0497 |
transmembrane protein | 644 | 644 ctx | neighborhood:639 |
Rv0496 ppx1 hyp |
hypothetical protein | 643 | 643 ctx | neighborhood:639 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 618 | 619 ctx | cooccurence:617 |
Rv0498 hyp |
hypothetical protein | 618 | 619 ctx | neighborhood:617 |
Rv1845c blaR |
sensor-transducer protein BlaR | 515 | 515 ctx | cooccurence:504 |
Rv0500A |
DNA-binding protein | 512 | 512 ctx | neighborhood:430 |
Rv0487 hyp |
hypothetical protein | 502 | 502 ctx | cooccurence:488 |
Rv3802c |
membrane protein | 485 | 486 ctx | cooccurence:481 |
Rv2342 hyp |
hypothetical protein | 473 | 474 ctx | cooccurence:466 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 431 | 432 ctx | cooccurence:428 |
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): hypothetical protein
- Pfam (hmmscan --cut_ga): Rv0495c PF11307.14 (E=2e-41)
- (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_215009.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv0495c (PF11307.14)
- 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
28IRH - Curated reference: UniProt P9WKU5 (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 —
25 functional partner(s); context anchor
Rv0428c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0495c| MWRPAQGARWHVPAVLGYGGIPRRASWSNVESVANSRRRPVHPGQEVELDFAREWVEFYDPDNPEHLIAADLTWLLSRWACVFGTPACQGTVAGRPNDGCCSHGAFLSDDDDRTRLADAVHKLTDDDWQFRAKGLRRKGYLELDEHDGQPQHRTRKHKGACIFLNRPGFAGGAGCALHSKALKLGVPPLTMKPDVCWQLPIRRSQEWVTRPDGTEILKTTLTEYDRRGWGSGGADLHWYCTGDPAAHVGTKQVWQSLADELTELLGEKAYGELAAMCKRRSQLGLIAVHPATRAAQ