vapB27 Resolved · high auto-curated
H37Rv Rv0599c · MTBC0 mtbc0_000629 ·
78 aa · 701116–701352 (-) ·
RefSeq NP_215113.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB27 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system antitoxin VapB27 |
| Revised (this work) | Type II toxin-antitoxin system antitoxin VapB27. Pfam: MazE_antitoxin (PF04014.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07779
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB27 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Cognate toxin is VapC27. Upon expression in E.coli partially counteracts the ribonuclease activity of non-cognate toxins MazF6 and MazF9. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | SpoVT / AbrB like domain |
| Orthologous group | COG2002 |
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 | 0.37 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
MazE_antitoxin | PF04014.24 | 2.8e-09 | 5–45 | Antidote-toxin recognition MazE, bacterial antitoxin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC27 (ribonuclease VapC27), high confidence from genomic context alone (score 909 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0598c vapC27 |
ribonuclease VapC27 | 957 | 909 ctx | neighborhood:882 textmining:546 |
Rv0600c |
two component sensor kinase HK1 | 546 | 526 ctx | neighborhood:523 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 472 | 472 | coexpression:456 |
Rv0597c hyp |
hypothetical protein | 437 | 437 ctx | neighborhood:424 |
Rv0601c |
two component sensor kinase HK2 | 413 | 387 | |
Rv0617 vapC29 |
ribonuclease VapC29 | 665 | 80 | textmining:651 |
Rv2801c mazF9 |
mRNA interferase MazF9 | 483 | 78 | textmining:463 |
Rv0065 vapC1 |
ribonuclease VapC1 | 642 | 73 | textmining:630 |
Rv2595 vapB40 |
antitoxin VapB40 | 658 | 55 | textmining:653 |
Rv2801A mazE9 |
antitoxin MazE9 | 446 | 54 | textmining:439 |
Rv2547 vapB19 |
antitoxin VapB19 | 517 | 51 | textmining:512 |
Rv2530A vapB39 |
antitoxin VapB39 | 657 | 47 | textmining:655 |
Rv0064A vapB1 |
antitoxin VapB1 | 801 | 41 | textmining:801 |
Rv0616A vapB29 |
antitoxin VapB29 | 651 | 41 | textmining:651 |
Rv0456B mazE1 |
antitoxin MazE1 | 625 | 41 | textmining:625 |
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 VapB27
- MTBC0 PGAP product: type II toxin-antitoxin system antitoxin VapB27
- Pfam (hmmscan --cut_ga): MazE_antitoxin PF04014.24 (E=3e-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_215113.1)
- Domains: Pfam-A via hmmscan --cut_ga — MazE_antitoxin (PF04014.24)
- 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
COG2002 - Curated reference: UniProt O07779 (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 —
16 functional partner(s); context anchor
vapC27 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000629|Rv0599c|vapB27 MKAVVDAAGRIVVPKPLREALGLQPGSTVEISRYGAGLHLIPTGRTARLEEENGVLVATGETTIDDEVVFGLIDSGRK