vapB1 Resolved · high auto-curated
H37Rv Rv0064A · MTBC0 - ·
79 aa · 71589–71828 (+) ·
RefSeq YP_007408701.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB1 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Antitoxin VapB1. 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.
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 |
P0CW29
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Putative antitoxin VapB1 |
| Curated function | Antitoxin component of a possible type II toxin-antitoxin (TA) system. The cognate toxin is VapC1. |
UniProt still lists this protein as Putative antitoxin VapB1; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2DF7V |
|---|
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, 3 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 |
|---|---|---|---|---|
FitA-like_RHH | PF22513.3 | 8.0e-08 | 2–36 | Antitoxin FitA-like, ribbon-helix-helix |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC1 (ribonuclease VapC1), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0065 vapC1 |
ribonuclease VapC1 | 906 | 882 ctx | neighborhood:882 |
Rv0064 |
transmembrane protein | 686 | 686 ctx | neighborhood:686 |
Rv0616A vapB29 |
antitoxin VapB29 | 803 | 41 | textmining:803 |
Rv0599c vapB27 |
antitoxin VapB27 | 801 | 41 | textmining:801 |
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 VapB1
- Pfam (hmmscan --cut_ga): FitA-like_RHH PF22513.3 (E=8e-08)
- (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 YP_007408701.1)
- 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
2DF7V - Curated reference: UniProt P0CW29 (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 —
4 functional partner(s); context anchor
vapC1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0064A|vapB1 MATIQVRDLPEDVAETYRRRATAAGQSLQTYMRTKLIEGVRGRDKAEAIEILEQALASTASPGISRETIEASRRELRGG