vapC26 Resolved · high auto-curated
H37Rv Rv0582 · MTBC0 mtbc0_000612 ·
135 aa · 681473–681880 (+) ·
RefSeq NP_215096.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC26 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system toxin ribonuclease C26 |
| Revised (this work) | Type II toxin-antitoxin system toxin ribonuclease C26. Pfam: PIN (PF01850.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53779
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC26 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase (By similarity). Upon expression in M.smegmatis inhibits colony formation. Its toxic effect is neutralized by coexpression with cognate antitoxin VapB26. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Toxic component of a toxin-antitoxin (TA) module. An RNase |
| Orthologous group | COG2402 |
| KEGG orthology |
K07065
|
| Gene Ontology (6) |
GO:0008150, GO:0040008, GO:0045926, GO:0048519, GO:0050789, GO:0065007
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
PIN | PF01850.28 | 6.3e-12 | 1–121 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB26 (antitoxin VapB26), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0581 vapB26 |
antitoxin VapB26 | 999 | 1000 ctx | neighborhood:882 experimental:999 textmining:437 |
Rv0580c hyp |
hypothetical protein | 601 | 602 ctx | neighborhood:599 |
Rv1034c |
Probable transposase (fragment); Rv1034c, (MTCY10G2.15), len: 129 aa. Probable IS1560 transposase fragment, similar to part of Rv3387|E12023 | 587 | 587 ctx | cooccurence:587 |
Rv3387 |
transposase | 577 | 577 ctx | cooccurence:577 |
Rv2961 |
transposase | 576 | 576 ctx | cooccurence:576 |
Rv2546 vapC18 |
ribonuclease VapC18 | 568 | 568 ctx | cooccurence:561 |
Rv2549c vapC20 |
ribonuclease VapC20 | 910 | 565 ctx | cooccurence:562 textmining:803 |
Rv3098A |
PemK-like protein | 564 | 564 ctx | cooccurence:564 |
Rv2757c vapC21 |
ribonuclease VapC21 | 595 | 547 ctx | cooccurence:538 |
Rv2018 vapB45 hyp |
hypothetical protein | 546 | 547 ctx | cooccurence:545 |
Rv2735c hyp |
hypothetical protein | 538 | 538 ctx | cooccurence:538 |
Rv3386 |
transposase | 515 | 515 ctx | cooccurence:515 |
Rv0229c vapC51 hyp |
hypothetical protein | 483 | 483 ctx | cooccurence:474 |
Rv0659c mazF2 |
toxin MazF2 | 461 | 461 ctx | cooccurence:456 |
Rv0595c vapC4 |
ribonuclease VapC4 | 887 | 439 ctx | cooccurence:429 textmining:807 |
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: ribonuclease VapC26
- MTBC0 PGAP product: type II toxin-antitoxin system toxin ribonuclease C26
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=6e-12)
- (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_215096.1)
- Domains: Pfam-A via hmmscan --cut_ga — PIN (PF01850.28)
- 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
COG2402 - Curated reference: UniProt O53779 (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 —
44 functional partner(s); context anchor
vapB26 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000612|Rv0582|vapC26 MIIDTSALLAYFDAAEPDHAAVSECIDSSADALVVSPYVVAELDYLVATRVGVDAELAVLRELAGGAWELANCGAAEIEQAARIVTKYQDQRIGIADAANVVLADRYRTRTILTLDRRHFSALRPIGGGRFTVIP