vapB15 Resolved · high auto-curated
H37Rv Rv2009 · MTBC0 - ·
80 aa · 2258030–2258272 (+) ·
RefSeq NP_216525.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB15 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Antitoxin VapB15. Pfam: VapB_antitoxin (PF09957.16). |
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 |
P9WLM7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB15 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin VapC15. Partially inhibits the RNase activity of VapC15. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | positive regulation of growth |
| Orthologous group | COG5450 |
| Gene Ontology (12) |
GO:0001666, GO:0006950, GO:0008150, GO:0009628, GO:0036293, GO:0040008, GO:0045927, GO:0048518, GO:0050789, GO:0050896, GO:0065007, GO:0070482
|
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 |
|---|---|---|---|---|
VapB_antitoxin | PF09957.16 | 5.3e-17 | 7–50 | Bacterial antitoxin of type II TA system, VapB |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC15 (ribonuclease VapC15), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2010 vapC15 |
ribonuclease VapC15 | 999 | 1000 ctx | neighborhood:882 experimental:999 textmining:888 |
Rv1561 vapC11 |
ribonuclease VapC11 | 872 | 872 | experimental:853 |
Rv2008c hyp |
hypothetical protein | 600 | 600 ctx | neighborhood:600 |
Rv0301 vapC2 |
ribonuclease VapC2 | 643 | 240 | textmining:550 |
Rv0627 vapC5 |
ribonuclease VapC5 | 717 | 224 | textmining:651 |
Rv0595c vapC4 |
ribonuclease VapC4 | 449 | 220 | |
Rv0626 vapB5 |
antitoxin VapB5 | 705 | 71 | textmining:696 |
Rv0623 vapB30 |
antitoxin VapB30 | 813 | 63 | textmining:809 |
Rv2865 relF |
antitoxin RelF | 443 | 56 | textmining:435 |
Rv0300 vapB2 |
antitoxin VapB2 | 805 | 55 | textmining:803 |
Rv2493 vapB38 |
antitoxin VapB38 | 522 | 55 | textmining:515 |
Rv1247c relB |
antitoxin RelB | 629 | 53 | textmining:625 |
Rv0624 vapC30 |
ribonuclease VapC30 | 657 | 50 | textmining:654 |
Rv0181c hyp |
hypothetical protein | 654 | 47 | textmining:652 |
Rv0912 |
transmembrane protein | 653 | 47 | textmining:651 |
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): antitoxin VapB15
- Pfam (hmmscan --cut_ga): VapB_antitoxin PF09957.16 (E=5e-17)
- (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_216525.1)
- Domains: Pfam-A via hmmscan --cut_ga — VapB_antitoxin (PF09957.16)
- 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
COG5450 - Curated reference: UniProt P9WLM7 (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 —
27 functional partner(s); context anchor
vapC15 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2009|vapB15 MYSGVVSRTNIEIDDELVAAAQRMYRLDSKRSAVDLALRRLVGEPLGRDEALALQGSGFDFSNDEIESFSDTDRKLADES