vapC10 Family assigned · medium auto-curated
H37Rv Rv1397c · MTBC0 mtbc0_001498 ·
133 aa · 1583456–1583857 (-) ·
RefSeq NP_215913.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC10 |
|---|---|
| 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 |
P9WFA7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC10 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. The cognate antitoxin is VapB10 (By similarity). |
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 | COG1487 |
| 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 | 0.701 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
PIN | PF01850.28 | 1.8e-12 | 2–109 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB10 (antitoxin VapB10), high confidence from genomic context alone (score 889 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1398c vapB10 |
antitoxin VapB10 | 889 | 889 ctx | neighborhood:882 |
Rv1399c nlhH |
carboxylesterase NlhH | 605 | 605 ctx | neighborhood:604 |
Rv1400c lipI |
lipase | 543 | 543 ctx | neighborhood:543 |
Rv0611c hyp |
hypothetical protein | 514 | 514 ctx | cooccurence:511 |
Rv2549c vapC20 |
ribonuclease VapC20 | 680 | 484 ctx | cooccurence:475 textmining:406 |
Rv1396c PE_PGRS25 |
PE-PGRS family protein PE_PGRS25 | 452 | 452 ctx | neighborhood:452 |
Rv0277c vapC25 |
ribonuclease VapC25 | 665 | 449 ctx | cooccurence:439 textmining:419 |
Rv0749 vapC31 |
ribonuclease VapC31 | 765 | 441 ctx | cooccurence:435 textmining:598 |
Rv0300 vapB2 |
antitoxin VapB2 | 435 | 436 | experimental:412 |
Rv2063A mazF7 |
mRNA interferase MazF7 | 791 | 418 ctx | cooccurence:414 textmining:657 |
Rv2601A vapB41 |
antitoxin VapB41 | 432 | 410 | |
Rv1952 vapB14 |
antitoxin VapB14 | 432 | 410 | |
Rv0626 vapB5 |
antitoxin VapB5 | 408 | 408 | |
Rv2103c vapC37 |
ribonuclease VapC37 | 625 | 400 | textmining:401 |
Rv3697c vapC48 |
ribonuclease VapC48 | 412 | 400 |
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 VapC10
- MTBC0 PGAP product: type II toxin-antitoxin system VapC family toxin
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=2e-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_215913.1)
- 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
COG1487 - Curated reference: UniProt P9WFA7 (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 —
31 functional partner(s); context anchor
vapB10 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001498|Rv1397c|vapC10 MILVDSDVLIAHLRGVVAARDWLVSARKDGPLAISVVSTAELIGGMRTAERREVWRLLASFRVQPATEVIARRAGDMMRRYRRSHNRIGLGDYLIAATADVQGLQLATLNVWHFPMFEQLKPPFAVPGHRPRA