vapC13 Family assigned · medium auto-curated
H37Rv Rv1838c · MTBC0 mtbc0_001951 ·
131 aa · 2105289–2105684 (-) ·
RefSeq NP_216354.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC13 |
|---|---|
| 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 |
P9WFA1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC13 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. The cognate antitoxin is VapB13 (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Toxic component of a toxin-antitoxin (TA) module. An RNase |
| Orthologous group | COG1848 |
| KEGG orthology |
K07064
|
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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, 2 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 | 5.3e-20 | 2–125 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB13 (antitoxin VapB13), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1839c vapB13 |
antitoxin VapB13 | 884 | 884 ctx | neighborhood:882 |
Rv1840c PE_PGRS34 |
PE-PGRS family protein PE_PGRS34 | 621 | 620 ctx | neighborhood:620 |
Rv2209 |
integral membrane protein | 598 | 598 ctx | cooccurence:597 |
Rv0355c PPE8 |
PPE family protein PPE8 | 586 | 586 ctx | cooccurence:586 |
Rv3350c PPE56 |
PPE family protein PPE56 | 583 | 583 ctx | cooccurence:583 |
Rv3347c PPE55 |
PPE family protein PPE55 | 581 | 581 ctx | cooccurence:581 |
Rv3343c PPE54 |
PPE family protein PPE54 | 564 | 565 ctx | cooccurence:562 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 560 | 560 ctx | cooccurence:560 |
Rv0304c PPE5 |
PPE family protein PPE5 | 559 | 559 ctx | cooccurence:559 |
Rv1917c PPE34 |
PPE family protein PPE34 | 557 | 557 ctx | cooccurence:556 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 555 | 555 ctx | cooccurence:555 |
Rv1004c |
membrane protein | 531 | 531 ctx | cooccurence:530 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 518 | 518 ctx | cooccurence:518 |
Rv0341 iniB |
isoniazid inducible protein IniB | 516 | 516 ctx | cooccurence:516 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 516 | 516 ctx | cooccurence:514 |
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 VapC13
- MTBC0 PGAP product: type II toxin-antitoxin system VapC family toxin
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=5e-20)
- (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_216354.1)
- 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 P9WFA1 (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 —
68 functional partner(s); context anchor
vapB13 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001951|Rv1838c|vapC13 MILVDSNIPMYLVGASHPHKLDAQRLLESALSGGERLVTDAEVLQEICHRYVAIKRREAIQPAFDAIIGVVDEVLPIERTDVEHARDALLRYQTLSARDALHIAVMAHHDITRLMSFDRGFDSYPGIKRLA