vapB12 Resolved · high auto-curated
H37Rv Rv1721c · MTBC0 mtbc0_001833 ·
75 aa · 1959431–1959658 (-) ·
RefSeq NP_216237.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB12 |
|---|---|
| MTBC0 PGAP re-annotation | antitoxin |
| Revised (this work) | Antitoxin. 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.
Curated reference (UniProt)
| UniProt |
P9WJ53
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative antitoxin VapB12 |
| Curated function | Putative antitoxin component of a possible type II toxin-antitoxin (TA) system. The cognate toxin is VapC12. |
UniProt still lists this protein as Putative antitoxin VapB12; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2DG55 |
|---|
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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
FitA-like_RHH | PF22513.3 | 3.6e-07 | 3–39 | Antitoxin FitA-like, ribbon-helix-helix |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC12 (ribonuclease VapC12), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1720c vapC12 |
ribonuclease VapC12 | 944 | 884 ctx | neighborhood:882 textmining:540 |
Rv1722 |
carboxylase | 515 | 515 ctx | neighborhood:512 |
Rv1723 |
hydrolase | 512 | 512 ctx | neighborhood:512 |
Rv2871 vapB43 |
antitoxin VapB43 | 441 | 50 | textmining:436 |
Rv1585c |
phage protein | 543 | 47 | textmining:541 |
Rv0662c vapB7 |
antitoxin VapB7 | 522 | 47 | textmining:519 |
Rv1802 PPE30 |
PPE family protein PPE30 | 431 | 46 | textmining:429 |
Rv1584c |
phage protein | 513 | 45 | textmining:511 |
Rv0370c |
oxidoreductase | 550 | 44 | textmining:549 |
Rv2250A |
Possible flavoprotein; Rv2250A, len: 139 aa. Conserved hypothetical protein, possibly flavoprotein. Similar to N-terminus of SCF91.28c|AL132 | 550 | 44 | textmining:549 |
Rv2601A vapB41 |
antitoxin VapB41 | 511 | 44 | textmining:510 |
Rv1960c parD1 |
antitoxin ParD1 | 433 | 44 | textmining:432 |
Rv3167c |
TetR family transcriptional regulator | 432 | 44 | textmining:431 |
Rv0665 vapC8 |
ribonuclease VapC8 | 422 | 44 | textmining:421 |
Rv2251 |
flavoprotein | 549 | 42 | textmining:549 |
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
- Legacy H37Rv annotation: antitoxin VapB12
- MTBC0 PGAP product: antitoxin
- Pfam (hmmscan --cut_ga): FitA-like_RHH PF22513.3 (E=4e-07)
- (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_216237.2)
- 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
2DG55 - Curated reference: UniProt P9WJ53 (SwissProt, reviewed; Evidence at protein level)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
23 functional partner(s); context anchor
vapC12 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001833|Rv1721c|vapB12 MSAMVQIRNVPDELLHELKARAAAQRMSLSDFLLARLAEIAEEPALDDVLDRLAALPRRDLGASAAELVDEARSE