vapB29 Resolved · medium auto-curated
H37Rv Rv0616A · MTBC0 - ·
75 aa · 710782–711009 (+) ·
RefSeq YP_007409270.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB29 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Antitoxin VapB29. |
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 |
P9WJ37
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative antitoxin VapB29 |
| Curated function | Possibly the antitoxic component of a type II toxin-antitoxin (TA) system. Its cognate toxin is VapC29. |
UniProt still lists this protein as Putative antitoxin VapB29; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2EM4G |
|---|
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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC29 (ribonuclease VapC29), high confidence from genomic context alone (score 801 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0617 vapC29 |
ribonuclease VapC29 | 906 | 801 ctx | neighborhood:801 textmining:548 |
Rv0616c |
Hypothetical protein; Rv0616c, (MTCY19H5.05), len: 88 aa. Hypothetical unknown protein. | 572 | 572 ctx | neighborhood:572 |
Rv0619 galTb |
Rv0619, (MTCY19H5.02c), len: 181 aa (probable partial CDS). Probable galTb, second part of galactose-1-phosphate uridylyltransferase, highly | 507 | 508 ctx | neighborhood:508 |
Rv0618 galTa |
Rv0618, (MTCY19H5.03c), len: 231 aa (probable partial CDS). Probable galTa, first part of galactose-1-phosphate uridylyltransferase, highly | 507 | 508 ctx | neighborhood:508 |
Rv0620 galK |
galactokinase | 499 | 500 ctx | neighborhood:500 |
Rv0624 vapC30 |
ribonuclease VapC30 | 586 | 190 | textmining:511 |
Rv2863 vapC23 |
ribonuclease VapC23 | 664 | 62 | textmining:657 |
Rv3180c vapC49 |
ribonuclease VapC45 | 638 | 62 | textmining:630 |
Rv3408 vapC47 |
ribonuclease VapC47 | 635 | 62 | textmining:627 |
Rv1838c vapC13 |
ribonuclease VapC13 | 553 | 62 | textmining:543 |
Rv0661c vapC7 |
ribonuclease VapC7 | 526 | 62 | textmining:516 |
Rv0064A vapB1 |
antitoxin VapB1 | 803 | 41 | textmining:803 |
Rv0582 vapC26 |
ribonuclease VapC26 | 655 | 41 | textmining:655 |
Rv0599c vapB27 |
antitoxin VapB27 | 651 | 41 | textmining:651 |
Rv3181c vapB49 |
antitoxin VapB45 | 630 | 41 | textmining:630 |
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 VapB29
- (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 YP_007409270.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2EM4G - Curated reference: UniProt P9WJ37 (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 —
26 functional partner(s); context anchor
vapC29 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0616A|vapB29 MRTTIDLPQDLHKQALAIARDTHRTLSETVADLMRRGLAANRPTALSSDPRTGLPLVSVGTVVTSEDVRSLEDEQ