vapB3 Family assigned · medium auto-curated
H37Rv Rv0550c · MTBC0 mtbc0_000579 ·
88 aa · 644189–644455 (-) ·
RefSeq NP_215064.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB3 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system CcdA family antitoxin |
| Revised (this work) | Type II toxin-antitoxin system CcdA family antitoxin. Pfam: CcdA (PF07362.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ59
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB3 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin VapC3. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Post-segregation antitoxin CcdA |
| Orthologous group | COG5302 |
| Gene Ontology (16) |
GO:0008150, GO:0009605, GO:0009607, GO:0040008, GO:0043207, GO:0044403, GO:0044419, GO:0045926, GO:0048519, GO:0050789, GO:0050896, GO:0051701 +4 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 | 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 |
|---|---|---|---|---|
CcdA | PF07362.19 | 2.8e-06 | 19–61 | Post-segregation antitoxin CcdA |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC3 (ribonuclease VapC3), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0549c vapC3 |
ribonuclease VapC3 | 933 | 887 ctx | neighborhood:882 textmining:436 |
Rv0551c fadD8 |
fatty-acid--CoA ligase FadD8 | 468 | 468 ctx | neighborhood:466 |
Rv0548c menB |
1,4-dihydroxy-2-naphthoyl-CoA synthase | 417 | 417 ctx | neighborhood:415 |
Rv0918 hyp |
hypothetical protein | 444 | 55 | textmining:436 |
Rv3188 hyp |
hypothetical protein | 443 | 50 | textmining:438 |
Rv2278 |
Rv2278, (MTCY339.32c), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase s | 549 | 47 | textmining:547 |
Rv3189 hyp |
hypothetical protein | 482 | 47 | textmining:479 |
Rv0581 vapB26 |
antitoxin VapB26 | 439 | 46 | textmining:437 |
Rv2656c |
prophage protein | 511 | 44 | textmining:510 |
Rv2355 |
Probable transposase; Rv2355, (MTCY98.24), len: 328 aa. Probable IS6110 transposase. Identical to many other M. tuberculosis IS6110 transpos | 547 | 42 | textmining:547 |
Rv1398c vapB10 |
antitoxin VapB10 | 515 | 41 | textmining:515 |
Rv0718 rpsH |
30S ribosomal protein S8 | 510 | 41 | textmining:510 |
Rv0661c vapC7 |
ribonuclease VapC7 | 433 | 41 | textmining:433 |
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 VapB3
- MTBC0 PGAP product: type II toxin-antitoxin system CcdA family antitoxin
- Pfam (hmmscan --cut_ga): CcdA PF07362.19 (E=3e-06)
- (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_215064.1)
- Domains: Pfam-A via hmmscan --cut_ga — CcdA (PF07362.19)
- 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
COG5302 - Curated reference: UniProt P9WJ59 (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 —
13 functional partner(s); context anchor
vapC3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000579|Rv0550c|vapB3 MLSRRTKTIVVCTLVCMARLNVYVPDELAERARARGLNVSALTQAAISAELENSATDAWLEGLEPRSTGARHDDVLGAIDAARDEFEA