vapB20 Resolved · high auto-curated
H37Rv Rv2550c · MTBC0 mtbc0_002718 ·
81 aa · 2893664–2893909 (-) ·
RefSeq NP_217066.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB20 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system antitoxin VapB20 |
| Revised (this work) | Type II toxin-antitoxin system antitoxin VapB20. 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 |
P9WJ45
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB20 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in E.coli neutralizes the toxic effect of cognate toxin VapC20. |
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 | 5.0e-09 | 10–49 | Ribbon-helix-helix protein, copG family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC20 (ribonuclease VapC20), high confidence from genomic context alone (score 888 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2549c vapC20 |
ribonuclease VapC20 | 917 | 888 ctx | neighborhood:882 |
Rv2548A hyp |
hypothetical protein | 592 | 592 ctx | neighborhood:592 |
Rv2493 vapB38 |
antitoxin VapB38 | 548 | 55 | textmining:542 |
Rv2547 vapB19 |
antitoxin VapB19 | 634 | 53 | textmining:630 |
Rv3378c |
diterpene synthase | 514 | 50 | textmining:510 |
Rv2009 vapB15 |
antitoxin VapB15 | 513 | 47 | textmining:510 |
Rv3320c vapC44 |
ribonuclease VapC44 | 513 | 47 | textmining:510 |
Rv2103c vapC37 |
ribonuclease VapC37 | 585 | 46 | textmining:583 |
Rv3376 |
phosphatase | 545 | 46 | textmining:543 |
Rv2275 |
cyclo(L-tyrosyl-L-tyrosyl) synthase | 658 | 44 | textmining:657 |
Rv2955c hyp |
hypothetical protein | 482 | 44 | textmining:481 |
Rv3087 |
diacyglycerol O-acyltransferase | 412 | 43 | textmining:411 |
Rv1288 hyp |
hypothetical protein | 655 | 41 | textmining:655 |
Rv0064 |
transmembrane protein | 650 | 41 | textmining:650 |
Rv0240 vapC24 |
ribonuclease VapC24 | 627 | 41 | textmining:627 |
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 VapB20
- MTBC0 PGAP product: type II toxin-antitoxin system antitoxin VapB20
- Pfam (hmmscan --cut_ga): RHH_1 PF01402.28 (E=5e-09)
- (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_217066.1)
- Domains: Pfam-A via hmmscan --cut_ga — RHH_1 (PF01402.28)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt P9WJ45 (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 —
23 functional partner(s); context anchor
vapC20 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002718|Rv2550c|vapB20 MLVAYICHVKRLQIYIDEDVDRALAVEARRRRTSKAALIREYVAEHLRQPGPDPVDAFVGSFVGEADLSASVDDVVYGKHE