vapC24 Family assigned · medium auto-curated
H37Rv Rv0240 · MTBC0 mtbc0_000256 ·
145 aa · 289726–290163 (+) ·
RefSeq NP_214754.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC24 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system VapC family toxin |
| Revised (this work) | Type II toxin-antitoxin system VapC family toxin. 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 |
P9WF87
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC24 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. Its cognate antitoxin is VapB24 (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | vapC |
| eggNOG description | Toxic component of a toxin-antitoxin (TA) module. An RNase |
| Orthologous group | COG1848 |
| KEGG orthology |
K07064
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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, 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 |
|---|---|---|---|---|
PIN | PF01850.28 | 1.3e-07 | 4–126 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB24 (antitoxin VapB24), high confidence from genomic context alone (score 885 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0239 vapB24 |
antitoxin VapB24 | 885 | 885 ctx | neighborhood:882 |
Rv2949c |
chorismate pyruvate-lyase | 748 | 749 ctx | cooccurence:745 |
Rv0355c PPE8 |
PPE family protein PPE8 | 684 | 685 ctx | cooccurence:683 |
Rv0918 hyp |
hypothetical protein | 682 | 682 ctx | cooccurence:681 |
Rv3350c PPE56 |
PPE family protein PPE56 | 668 | 668 ctx | cooccurence:666 |
Rv3347c PPE55 |
PPE family protein PPE55 | 667 | 667 ctx | cooccurence:665 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 660 | 660 ctx | cooccurence:660 |
Rv0304c PPE5 |
PPE family protein PPE5 | 659 | 659 ctx | cooccurence:657 |
Rv1917c PPE34 |
PPE family protein PPE34 | 656 | 656 ctx | cooccurence:655 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 655 | 655 ctx | cooccurence:655 |
Rv2209 |
integral membrane protein | 652 | 652 ctx | cooccurence:648 |
Rv3403c hyp |
hypothetical protein | 649 | 650 ctx | cooccurence:645 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 649 | 649 ctx | cooccurence:649 |
Rv0238 |
transcriptional regulator | 642 | 641 ctx | neighborhood:636 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 636 | 636 ctx | cooccurence:634 |
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 VapC24
- MTBC0 PGAP product: type II toxin-antitoxin system VapC family toxin
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=1e-07)
- (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_214754.1)
- 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
COG1848 - Curated reference: UniProt P9WF87 (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 —
89 functional partner(s); context anchor
vapB24 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000256|Rv0240|vapC24 MLSIDTNILLYAQNRDCPEHDAAAAFLVECAGRADVAVCELVLMELYQLLRNPTVVTRPLEGPEAAEVCQTFRRNRRWALLENAPVMNEVWVLAATPRIARRRLFDARLALTLRHHGVDEFATRNINGFTDFGFSRVWDPITSDG