vapC14 Resolved · medium auto-curated
H37Rv Rv1953 · MTBC0 - ·
103 aa · 2200938–2201249 (+) ·
RefSeq NP_216469.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC14 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Ribonuclease VapC14. |
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 |
P9WF99
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Ribonuclease VapC14 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. The cognate antitoxin is VapB14 (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | vapC |
| eggNOG description | nuclease activity |
| Orthologous group | COG1487 |
| KEGG orthology |
K07062
|
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 | 0.168 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB14 (antitoxin VapB14), high confidence from genomic context alone (score 926 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1952 vapB14 |
antitoxin VapB14 | 928 | 926 ctx | neighborhood:882 |
Rv0596c vapB4 |
antitoxin VapB4 | 529 | 529 | experimental:513 |
Rv0626 vapB5 |
antitoxin VapB5 | 529 | 529 | experimental:513 |
Rv1949c |
Rv1949c, (MTCY09F9.15), len: 319 aa. Conserved hypothetical protein, partial ORF. Rv1949c and Rv1950c|MTCY09F9.14 are similar but frameshift | 472 | 473 ctx | neighborhood:466 |
Rv1950c hyp |
hypothetical protein | 471 | 471 ctx | neighborhood:463 |
Rv1951c hyp |
hypothetical protein | 465 | 465 ctx | neighborhood:463 |
Rv1948c hyp |
hypothetical protein | 464 | 465 ctx | neighborhood:463 |
Rv2063A mazF7 |
mRNA interferase MazF7 | 462 | 461 ctx | cooccurence:458 |
Rv0300 vapB2 |
antitoxin VapB2 | 433 | 433 | experimental:412 |
Rv2601A vapB41 |
antitoxin VapB41 | 429 | 407 |
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): ribonuclease VapC14
- (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_216469.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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 P9WF99 (SwissProt, reviewed; Inferred from homology)
- 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 —
10 functional partner(s); context anchor
vapB14 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1953|vapC14 MTYVLDTNVVSALRVPGRHPAVAAWADSVQVAEQFVVAITLAEIERGVIAKERTDPTQSEHLRRWFDDKVLRIFVFARRGTNLIMQPLAGHIGYSLYSGISWF