vapB9 Resolved · medium auto-curated
H37Rv Rv0959A · MTBC0 - ·
73 aa · 1073327–1073548 (+) ·
RefSeq YP_007409620.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB9 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Antitoxin VapB9. |
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 |
P9WJ55
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Putative antitoxin VapB9 |
| Curated function | Antitoxin component of a possible type II toxin-antitoxin (TA) system. The cognate toxin is VapC9. |
UniProt still lists this protein as Putative antitoxin VapB9; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2E5R2 |
|---|
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.
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: vapC9 (ribonuclease VapC9), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0960 vapC9 |
ribonuclease VapC9 | 882 | 882 ctx | neighborhood:882 |
Rv0959 hyp |
hypothetical protein | 653 | 653 ctx | neighborhood:653 |
Rv0958 |
magnesium chelatase | 627 | 627 ctx | neighborhood:627 |
Rv0961 |
integral membrane protein | 496 | 496 ctx | neighborhood:496 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 440 | 440 ctx | neighborhood:440 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 440 | 440 ctx | neighborhood:440 |
Rv2601A vapB41 |
antitoxin VapB41 | 806 | 41 | textmining:806 |
Rv1952 vapB14 |
antitoxin VapB14 | 653 | 41 | textmining:653 |
Rv0662c vapB7 |
antitoxin VapB7 | 624 | 41 | textmining:624 |
Rv0277A vapB25 |
Rv0277A, len: 85 aa. Possible vapB25, antitoxin,part of toxin-antitoxin (TA) operon with Rv0277c, see Arcus et al. 2005. Has in-frame stop c | 570 | 41 | textmining:570 |
Rv2871 vapB43 |
antitoxin VapB43 | 512 | 41 | textmining:512 |
Rv2830c vapB22 |
antitoxin VapB22 | 511 | 41 | textmining:511 |
Rv1721c vapB12 |
antitoxin VapB12 | 511 | 41 | textmining:511 |
Rv3167c |
TetR family transcriptional regulator | 510 | 41 | textmining:510 |
Rv1960c parD1 |
antitoxin ParD1 | 510 | 41 | textmining:510 |
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 VapB9
- (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_007409620.1)
- 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
2E5R2 - Curated reference: UniProt P9WJ55 (SwissProt, reviewed; Predicted)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
18 functional partner(s); context anchor
vapC9 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0959A|vapB9 MKTLYLRNVPDDVVERLERLAELAKTSVSAVAVRELTEASRRADNPALLGDLPDIGIDTTELIGGIDAERAGR