vapB14 Resolved · high auto-curated
H37Rv Rv1952 · MTBC0 mtbc0_002067 ·
71 aa · 2219842–2220057 (+) ·
RefSeq NP_216468.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB14 |
|---|---|
| MTBC0 PGAP re-annotation | antitoxin |
| Revised (this work) | Antitoxin. Pfam: FitA-like_RHH (PF22513.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95262
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Putative antitoxin VapB14 |
| Curated function | Putative antitoxin component of a possible type II toxin-antitoxin (TA) system. The cognate toxin is VapB14. |
UniProt still lists this protein as Putative antitoxin VapB14; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Plasmid stability protein |
| Orthologous group | COG4691 |
| KEGG orthology |
K21495
|
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, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.10% of strains (151) · clonal |
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 |
|---|---|---|---|---|
FitA-like_RHH | PF22513.3 | 1.8e-16 | 2–34 | Antitoxin FitA-like, ribbon-helix-helix |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC14 (ribonuclease VapC14), high confidence from genomic context alone (score 926 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1953 vapC14 |
ribonuclease VapC14 | 928 | 926 ctx | neighborhood:882 |
Rv1950c hyp |
hypothetical protein | 472 | 472 ctx | neighborhood:463 |
Rv1949c |
Rv1949c, (MTCY09F9.15), len: 319 aa. Conserved hypothetical protein, partial ORF. Rv1949c and Rv1950c|MTCY09F9.14 are similar but frameshift | 467 | 468 ctx | neighborhood:466 |
Rv1951c hyp |
hypothetical protein | 466 | 466 ctx | neighborhood:463 |
Rv1948c hyp |
hypothetical protein | 463 | 463 ctx | neighborhood:463 |
Rv0595c vapC4 |
ribonuclease VapC4 | 437 | 415 | |
Rv0665 vapC8 |
ribonuclease VapC8 | 437 | 415 | |
Rv0627 vapC5 |
ribonuclease VapC5 | 437 | 415 | |
Rv1397c vapC10 |
ribonuclease VapC10 | 432 | 410 | |
Rv0301 vapC2 |
ribonuclease VapC2 | 431 | 408 | |
Rv2527 vapC17 |
ribonuclease VapC17 | 430 | 408 | |
Rv2757c vapC21 |
ribonuclease VapC21 | 429 | 407 | |
Rv2546 vapC18 |
ribonuclease VapC18 | 429 | 407 | |
Rv1114 vapC32 |
ribonuclease VapC32 | 429 | 407 | |
Rv0656c vapC6 |
ribonuclease VapC6 | 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
- Legacy H37Rv annotation: antitoxin VapB14
- MTBC0 PGAP product: antitoxin
- Pfam (hmmscan --cut_ga): FitA-like_RHH PF22513.3 (E=2e-16)
- (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_216468.1)
- Domains: Pfam-A via hmmscan --cut_ga — FitA-like_RHH (PF22513.3)
- 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
COG4691 - Curated reference: UniProt P95262 (SwissProt, reviewed; Predicted)
- 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 —
34 functional partner(s); context anchor
vapC14 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002067|Rv1952|vapB14 MIRNLPEGTKAALRVRAARHHHSVEAEARAILTAGLLGEEVPMPVLLAADSGHDIDFEPERLGLIARTPQL