vapB8 Resolved · medium auto-curated
H37Rv Rv0664 · MTBC0 - ·
90 aa · 758532–758804 (+) ·
RefSeq NP_215178.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB8 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Antitoxin VapB8. |
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 |
O06775
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Putative antitoxin VapB8 |
| Curated function | Antitoxin component of a possible type II toxin-antitoxin (TA) system. The cognate toxin is VapC8. |
UniProt still lists this protein as Putative antitoxin VapB8; the revised annotation above is ahead of the current UniProt record.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.37 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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: vapC8 (ribonuclease VapC8), high confidence from genomic context alone (score 888 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0665 vapC8 |
ribonuclease VapC8 | 888 | 888 ctx | neighborhood:882 |
Rv0666 |
membrane protein | 787 | 788 ctx | neighborhood:781 |
Rv0663 atsD |
arylsulfatase AtsD | 707 | 708 ctx | neighborhood:700 |
Rv0662c vapB7 |
antitoxin VapB7 | 475 | 476 ctx | neighborhood:473 |
Rv0661c vapC7 |
ribonuclease VapC7 | 736 | 474 ctx | neighborhood:473 textmining:520 |
Rv1440 secG |
protein-export membrane protein SecG | 444 | 50 | textmining:439 |
Rv2760c vapB42 |
antitoxin VapB42 | 624 | 44 | textmining:623 |
Rv0581 vapB26 |
antitoxin VapB26 | 544 | 41 | textmining:544 |
Rv3155 nuoK |
NADH-quinone oxidoreductase subunit K | 510 | 41 | textmining:510 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 432 | 41 | textmining:432 |
Rv1458c |
antibiotic ABC transporter ATP-binding protein | 410 | 41 | textmining:411 |
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 VapB8
- (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_215178.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt O06775 (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 —
11 functional partner(s); context anchor
vapC8 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0664|vapB8 MEKSRCHAVAHGGGCAGSAKSHKSGGRCGQGRGAGDSHGTRGAGRRYRAASAPHPLAVGAHLRDELAKRSADPRLTDELNDLAGHTLDDL