vapB48 Resolved · medium auto-curated
H37Rv Rv3697A · MTBC0 - ·
74 aa · 4140239–4140463 (-) ·
RefSeq YP_007412423.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB48 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Antitoxin VapB48. |
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 |
P9WJ15
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Putative antitoxin VapB48 |
| Curated function | Possibly the antitoxin component of a type II toxin-antitoxin (TA) system. Its cognate toxin is VapC48. |
UniProt still lists this protein as Putative antitoxin VapB48; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2A15A |
|---|
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 | 0.326 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC48 (ribonuclease VapC48), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3697c vapC48 |
ribonuclease VapC48 | 983 | 882 ctx | neighborhood:882 textmining:867 |
Rv3696c glpK |
glycerol kinase | 651 | 651 ctx | neighborhood:651 |
Rv3698 hyp |
hypothetical protein | 589 | 589 ctx | neighborhood:589 |
Rv3699 hyp |
hypothetical protein | 520 | 520 ctx | neighborhood:520 |
Rv3749c vapC50 hyp |
hypothetical protein | 803 | 41 | textmining:803 |
Rv0298 |
antitoxin | 800 | 41 | textmining:800 |
Rv0299 |
toxin | 659 | 41 | textmining:659 |
Rv3750c vapB50 |
excisionase | 657 | 41 | textmining:657 |
Rv2019 vapC45 hyp |
hypothetical protein | 655 | 41 | textmining:655 |
Rv3358 relK |
toxin RelK | 516 | 41 | textmining:516 |
Rv1246c relE |
toxin RelE | 511 | 41 | textmining:511 |
Rv1955 higB |
toxin HigB | 439 | 41 | textmining:439 |
Rv2357c glyS |
glycine--tRNA ligase | 434 | 41 | textmining:434 |
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 VapB48
- (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_007412423.1)
- 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
2A15A - Curated reference: UniProt P9WJ15 (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 —
13 functional partner(s); context anchor
vapC48 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3697A|vapB48 MRTTIDLDDDILRALKRRQREERKTLGQLASELLAQALAAEPPPNVDIRWSTADLRPRVDLDDKDAVWAILDRG