vapB11 Resolved · high auto-curated
H37Rv Rv1560 · MTBC0 - ·
72 aa · 1764755–1764973 (+) ·
RefSeq NP_216076.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB11 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Antitoxin VapB11. Pfam: VapB_antitoxin (PF09957.16). |
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 |
P9WLU3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB11 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in E.coli and M.smegmatis neutralizes the effect of cognate toxin VapC11. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Bacterial antitoxin of type II TA system, VapB |
| Orthologous group | COG5450 |
| Gene Ontology (45) |
GO:0006417, GO:0008150, GO:0009605, GO:0009607, GO:0009889, GO:0009891, GO:0009893, GO:0010468, GO:0010556, GO:0010557, GO:0010604, GO:0010608 +33 more
|
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 |
|---|---|---|---|---|
VapB_antitoxin | PF09957.16 | 1.6e-18 | 7–49 | Bacterial antitoxin of type II TA system, VapB |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC11 (ribonuclease VapC11), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1561 vapC11 |
ribonuclease VapC11 | 999 | 1000 ctx | neighborhood:882 cooccurence:703 coexpression:817 experimental:999 |
Rv2010 vapC15 |
ribonuclease VapC15 | 961 | 961 ctx | cooccurence:706 experimental:853 |
Rv1151c cobB |
NAD-dependent protein deacylase | 765 | 765 | coexpression:765 |
Rv1395 |
HTH-type transcriptional regulator | 733 | 733 | coexpression:733 |
Rv1960c parD1 |
antitoxin ParD1 | 733 | 733 | coexpression:732 |
Rv3263 |
DNA methylase | 732 | 732 | coexpression:732 |
Rv0273c |
transcriptional regulator | 731 | 731 | coexpression:731 |
Rv0624 vapC30 |
ribonuclease VapC30 | 685 | 686 ctx | cooccurence:509 |
Rv1559 ilvA |
threonine dehydratase IlvA | 667 | 667 ctx | neighborhood:659 |
Rv0158 |
transcriptional regulator | 651 | 651 | coexpression:651 |
Rv2759c vapC42 |
ribonuclease VapC42 | 623 | 624 ctx | cooccurence:529 |
Rv3488 hyp |
hypothetical protein | 615 | 615 | coexpression:615 |
Rv0603 hyp |
hypothetical protein | 580 | 580 | coexpression:580 |
Rv1558 hyp |
hypothetical protein | 566 | 565 ctx | neighborhood:563 |
Rv1557 mmpL6 |
transmembrane transport protein MmpL6 | 561 | 561 ctx | neighborhood:556 |
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 VapB11
- Pfam (hmmscan --cut_ga): VapB_antitoxin PF09957.16 (E=2e-18)
- (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_216076.1)
- Domains: Pfam-A via hmmscan --cut_ga — VapB_antitoxin (PF09957.16)
- 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
COG5450 - Curated reference: UniProt P9WLU3 (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 —
29 functional partner(s); context anchor
vapC11 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1560|vapB11 MYRWCMSRTNIDIDDELAAEVMRRFGLTTKRAAVDLALRRLVGSPLSREFLLGLEGVGWEGDLDDLRSDRPD