vapB46 Resolved · high auto-curated
H37Rv Rv3385c · MTBC0 - ·
102 aa · 3799635–3799943 (-) ·
RefSeq NP_217902.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB46 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Antitoxin VapB46. Pfam: PhdYeFM_antitox (PF02604.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WF13
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB46 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin VapC46. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| eggNOG description | antitoxin component of a |
| Orthologous group | COG4118 |
| 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 | 0.131 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
PhdYeFM_antitox | PF02604.27 | 7.2e-09 | 12–51 | Antitoxin Phd_YefM, type II toxin-antitoxin system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC46 (ribonuclease VapC46), high confidence from genomic context alone (score 959 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3384c vapC46 |
ribonuclease VapC46 | 959 | 959 ctx | neighborhood:780 cooccurence:766 |
Rv3408 vapC47 |
ribonuclease VapC47 | 786 | 786 ctx | cooccurence:763 |
Rv1962c vapC35 |
ribonuclease VapC35 | 766 | 766 ctx | cooccurence:741 |
Rv3407 vapB47 |
antitoxin VapB47 | 612 | 612 ctx | cooccurence:610 |
Rv0626 vapB5 |
antitoxin VapB5 | 545 | 545 ctx | cooccurence:537 |
Rv3386 |
transposase | 544 | 544 ctx | neighborhood:542 |
Rv3387 |
transposase | 542 | 542 ctx | neighborhood:542 |
Rv0665 vapC8 |
ribonuclease VapC8 | 502 | 502 | |
Rv0627 vapC5 |
ribonuclease VapC5 | 498 | 498 | |
Rv0595c vapC4 |
ribonuclease VapC4 | 443 | 443 | |
Rv2548 vapC19 |
ribonuclease VapC19 | 407 | 407 | |
Rv1720c vapC12 |
ribonuclease VapC12 | 405 | 406 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): antitoxin VapB46
- Pfam (hmmscan --cut_ga): PhdYeFM_antitox PF02604.27 (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_217902.1)
- Domains: Pfam-A via hmmscan --cut_ga — PhdYeFM_antitox (PF02604.27)
- 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
COG4118 - Curated reference: UniProt P9WF13 (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 —
12 functional partner(s); context anchor
vapC46 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3385c|vapB46 MTPTACATVSTMTSVGVRALRQRASELLRRVEAGETIEITDRGRPVALLSPLPQGGPYEQLLASGEIERATLDVVDLPEPLDLDAGVELPSVTLARLREHER