vapB21 Family assigned · medium auto-curated
H37Rv Rv2758c · MTBC0 mtbc0_002935 ·
88 aa · 3092998–3093264 (-) ·
RefSeq NP_217274.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB21 |
|---|---|
| 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 |
P9WJ43
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB21 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin VapC21. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | positive regulation of growth |
| Orthologous group | COG5450 |
| Gene Ontology (6) |
GO:0008150, GO:0040008, GO:0045927, GO:0048518, GO:0050789, GO:0065007
|
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 | 0.674 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
VapB_antitoxin | PF09957.16 | 7.2e-09 | 16–56 | Bacterial antitoxin of type II TA system, VapB |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC21 (ribonuclease VapC21), high confidence from genomic context alone (score 980 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2757c vapC21 |
ribonuclease VapC21 | 979 | 980 ctx | neighborhood:882 coexpression:804 |
Rv2759c vapC42 |
ribonuclease VapC42 | 756 | 756 ctx | neighborhood:753 |
Rv2760c vapB42 |
antitoxin VapB42 | 755 | 755 ctx | neighborhood:753 |
Rv2761c hsdS |
type I restriction/modification system specificity determinant HsdS | 735 | 735 ctx | neighborhood:731 |
Rv2762c hyp |
hypothetical protein | 710 | 710 ctx | neighborhood:707 |
Rv2756c hsdM |
type I restriction/modification system DNA methylase HsdM | 618 | 618 ctx | neighborhood:598 |
Rv2755c hsdS.1 |
Rv2755c, (MTV002.20c), len: 91 aa. Possible hsdS.1,fragment of type I restriction/modification system specificity determinant (S protein), s | 586 | 587 ctx | neighborhood:572 |
Rv2763c dfrA |
dihydrofolate reductase | 530 | 530 ctx | neighborhood:523 |
Rv2764c thyA |
thymidylate synthase ThyA | 403 | 403 ctx | neighborhood:400 |
Rv2494 vapC38 |
ribonuclease VapC38 | 683 | 47 | textmining:682 |
Rv0960 vapC9 |
ribonuclease VapC9 | 521 | 47 | textmining:518 |
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 VapB21
- MTBC0 PGAP product: type II toxin-antitoxin system VapB family antitoxin
- Pfam (hmmscan --cut_ga): VapB_antitoxin PF09957.16 (E=7e-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_217274.1)
- 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 P9WJ43 (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 —
11 functional partner(s); context anchor
vapC21 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002935|Rv2758c|vapB21 MHRGYALVVCSPGVTRTMIDIDDDLLARAAKELGTTTKKDTVHAALRAALRASAARSLMNRMAENATGTQDEALVNAMWRDGHPENTA