vapB22 Family assigned · medium auto-curated
H37Rv Rv2830c · MTBC0 mtbc0_003009 ·
71 aa · 3157675–3157890 (-) ·
RefSeq NP_217346.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB22 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system prevent-host-death family antitoxin |
| Revised (this work) | Type II toxin-antitoxin system prevent-host-death family antitoxin. Pfam: PhdYeFM_antitox (PF02604.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71622
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB22 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin VapC22. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| eggNOG description | positive regulation of growth |
| Orthologous group | COG4118 |
| Gene Ontology (34) |
GO:0006417, GO:0008150, GO:0009889, GO:0009891, GO:0009893, GO:0010468, GO:0010556, GO:0010557, GO:0010604, GO:0010608, GO:0010628, GO:0019222 +22 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 | 1.366 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 |
|---|---|---|---|---|
PhdYeFM_antitox | PF02604.27 | 4.1e-08 | 2–38 | Antitoxin Phd_YefM, type II toxin-antitoxin system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC22 (ribonuclease VapC22), high confidence from genomic context alone (score 889 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2829c vapC22 |
ribonuclease VapC22 | 921 | 889 ctx | neighborhood:882 |
Rv2828A hyp |
hypothetical protein | 786 | 787 ctx | neighborhood:787 |
Rv2828c hyp |
hypothetical protein | 753 | 753 ctx | neighborhood:751 |
Rv2831 echA16 |
enoyl-CoA hydratase EchA16 | 833 | 648 ctx | neighborhood:647 textmining:546 |
Rv2826c hyp |
hypothetical protein | 401 | 401 | |
Rv2827c hyp |
hypothetical protein | 401 | 401 | |
Rv1397c vapC10 |
ribonuclease VapC10 | 620 | 255 | textmining:511 |
Rv2601A vapB41 |
antitoxin VapB41 | 478 | 54 | textmining:471 |
Rv1638A hyp |
hypothetical protein | 529 | 45 | textmining:528 |
Rv2063A mazF7 |
mRNA interferase MazF7 | 434 | 43 | textmining:433 |
Rv2017 |
transcriptional regulator | 410 | 42 | textmining:410 |
Rv0959A vapB9 |
antitoxin VapB9 | 511 | 41 | textmining:511 |
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 VapB22
- MTBC0 PGAP product: type II toxin-antitoxin system prevent-host-death family antitoxin
- Pfam (hmmscan --cut_ga): PhdYeFM_antitox PF02604.27 (E=4e-08)
- (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_217346.1)
- Domains: Pfam-A via hmmscan --cut_ga — PhdYeFM_antitox (PF02604.27)
- 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
COG4118 - Curated reference: UniProt P71622 (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 —
12 functional partner(s); context anchor
vapC22 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003009|Rv2830c|vapB22 MTATEVKAKILSLLDEVAQGEEIEITKHGRTVARLVAATGPHALKGRFSGVAMAAVDDDELFTTGVSWNVS