vapB18 Family assigned · medium auto-curated
H37Rv Rv2545 · MTBC0 mtbc0_002712 ·
92 aa · 2891328–2891606 (+) ·
RefSeq NP_217061.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB18 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system VapB family antitoxin |
| Revised (this work) | Type II toxin-antitoxin system VapB family antitoxin. 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.
Curated reference (UniProt)
| UniProt |
P9WJ47
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Putative antitoxin VapB18 |
| Curated function | Putative antitoxin component of a possible type II toxin-antitoxin (TA) system. The cognate toxin is VapC18. |
UniProt still lists this protein as Putative antitoxin VapB18; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | positive regulation of growth |
| Orthologous group | COG5450 |
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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 25.77% of strains (37424) · clonal |
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 |
|---|---|---|---|---|
VapB_antitoxin | PF09957.16 | 2.6e-05 | 57–89 | Bacterial antitoxin of type II TA system, VapB |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC18 (ribonuclease VapC18), high confidence from genomic context alone (score 817 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2546 vapC18 |
ribonuclease VapC18 | 816 | 817 ctx | neighborhood:768 |
Rv2544 lppB |
lipoprotein LppB | 810 | 810 ctx | neighborhood:801 |
Rv2543 lppA |
lipoprotein LppA | 783 | 783 ctx | neighborhood:781 |
Rv2548 vapC19 |
ribonuclease VapC19 | 588 | 589 ctx | neighborhood:508 |
Rv2547 vapB19 |
antitoxin VapB19 | 811 | 511 ctx | neighborhood:508 textmining:630 |
Rv2542 hyp |
hypothetical protein | 504 | 505 ctx | neighborhood:502 |
Rv0301 vapC2 |
ribonuclease VapC2 | 718 | 217 | textmining:655 |
Rv1114 vapC32 |
ribonuclease VapC32 | 717 | 212 | textmining:656 |
Rv0960 vapC9 |
ribonuclease VapC9 | 418 | 55 | textmining:410 |
Rv3321c vapB44 |
antitoxin VapB44 | 676 | 46 | textmining:675 |
Rv1943c mazE5 |
antitoxin MazE5 | 803 | 44 | textmining:803 |
Rv2493 vapB38 |
antitoxin VapB38 | 660 | 44 | textmining:659 |
Rv1494 mazE4 |
antitoxin MazE4 | 656 | 44 | textmining:655 |
Rv2494 vapC38 |
ribonuclease VapC38 | 527 | 44 | textmining:526 |
Rv2651c |
prophage protease | 432 | 44 | textmining:431 |
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 VapB18
- MTBC0 PGAP product: type II toxin-antitoxin system VapB family antitoxin
- Pfam (hmmscan --cut_ga): VapB_antitoxin PF09957.16 (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_217061.1)
- 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 P9WJ47 (SwissProt, reviewed; Predicted)
- 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 —
17 functional partner(s); context anchor
vapC18 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002712|Rv2545|vapB18 MSTTIVAGVIQGHLPVILPTRRRARDLGHTTALFRAQTLQCIYLSIEYLYVCSMSRRTTIDIDDILLARAQAALGTTGLKDRVDAALRAAVR