vapB2 Resolved · high auto-curated
H37Rv Rv0300 · MTBC0 mtbc0_000319 ·
73 aa · 367165–367386 (+) ·
RefSeq NP_214814.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB2 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system antitoxin VapB2 |
| Revised (this work) | Type II toxin-antitoxin system antitoxin VapB2. Pfam: RHH_1 (PF01402.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07227
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB2 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin VapC2. The C-terminal helix of the antitoxin may obstruct the toxin's RNA-binding groove, blocking access to the active sites. Additionally, the C-terminal arginine of the antitoxin may remove Mg(2+) ions from the toxin active sites. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2EI9R |
|---|---|
| Gene Ontology (53) |
GO:0006417, GO:0008150, GO:0009889, GO:0009891, GO:0009892, GO:0009893, GO:0010468, GO:0010556, GO:0010557, GO:0010604, GO:0010605, GO:0010608 +41 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.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.178 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RHH_1 | PF01402.28 | 2.9e-05 | 9–37 | Ribbon-helix-helix protein, copG family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC2 (ribonuclease VapC2), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0301 vapC2 |
ribonuclease VapC2 | 999 | 1000 ctx | neighborhood:882 experimental:999 textmining:870 |
Rv0299 |
toxin | 781 | 781 ctx | neighborhood:667 |
Rv0298 |
antitoxin | 681 | 681 ctx | neighborhood:667 |
Rv0302 |
transcriptional regulator | 532 | 532 ctx | neighborhood:520 |
Rv0303 |
dehydrogenase/reductase | 504 | 504 ctx | neighborhood:504 |
Rv2010 vapC15 |
ribonuclease VapC15 | 814 | 454 | experimental:412 textmining:674 |
Rv0627 vapC5 |
ribonuclease VapC5 | 925 | 449 | experimental:412 textmining:870 |
Rv0229c vapC51 hyp |
hypothetical protein | 444 | 445 | experimental:412 |
Rv1561 vapC11 |
ribonuclease VapC11 | 438 | 439 | experimental:412 |
Rv1397c vapC10 |
ribonuclease VapC10 | 435 | 436 | experimental:412 |
Rv0665 vapC8 |
ribonuclease VapC8 | 435 | 435 | experimental:412 |
Rv0656c vapC6 |
ribonuclease VapC6 | 434 | 435 | experimental:412 |
Rv0595c vapC4 |
ribonuclease VapC4 | 520 | 434 | experimental:412 |
Rv2527 vapC17 |
ribonuclease VapC17 | 433 | 434 | experimental:412 |
Rv1114 vapC32 |
ribonuclease VapC32 | 433 | 434 | experimental:412 |
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 VapB2
- MTBC0 PGAP product: type II toxin-antitoxin system antitoxin VapB2
- Pfam (hmmscan --cut_ga): RHH_1 PF01402.28 (E=3e-05)
- (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_214814.1)
- Domains: Pfam-A via hmmscan --cut_ga — RHH_1 (PF01402.28)
- 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
2EI9R - Curated reference: UniProt O07227 (SwissProt, reviewed; Evidence at protein level)
- 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 —
26 functional partner(s); context anchor
vapC2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000319|Rv0300|vapB2 MSDVLIRDIPDDVLASLDAIAARLGLSRTEYIRRRLAQDAQTARVTVTAADLRRLRGAVAGLGDPELMRQAWR