vapB38 Resolved · medium auto-curated
H37Rv Rv2493 · MTBC0 mtbc0_002655 ·
73 aa · 2830973–2831194 (+) ·
RefSeq NP_217009.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB38 |
|---|---|
| MTBC0 PGAP re-annotation | antitoxin |
| Revised (this work) | Antitoxin. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ25
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative antitoxin VapB38 |
| Curated function | Probable antitoxin component of a type II toxin-antitoxin (TA) system. Its putative cognate toxin is VapC38. |
UniProt still lists this protein as Putative antitoxin VapB38; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2DPH3 |
|---|
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, 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC38 (ribonuclease VapC38), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2494 vapC38 |
ribonuclease VapC38 | 931 | 884 ctx | neighborhood:881 textmining:432 |
Rv2492 hyp |
hypothetical protein | 619 | 619 ctx | neighborhood:619 |
Rv2491 hyp |
hypothetical protein | 619 | 619 ctx | neighborhood:619 |
Rv3321c vapB44 |
antitoxin VapB44 | 662 | 55 | textmining:658 |
Rv2547 vapB19 |
antitoxin VapB19 | 635 | 55 | textmining:630 |
Rv1494 mazE4 |
antitoxin MazE4 | 550 | 55 | textmining:544 |
Rv2550c vapB20 |
antitoxin VapB20 | 548 | 55 | textmining:542 |
Rv2009 vapB15 |
antitoxin VapB15 | 522 | 55 | textmining:515 |
Rv2063 mazE7 |
antitoxin MazE7 | 656 | 46 | textmining:655 |
Rv1247c relB |
antitoxin RelB | 435 | 46 | textmining:433 |
Rv2549c vapC20 |
ribonuclease VapC20 | 434 | 46 | textmining:432 |
Rv2545 vapB18 |
antitoxin VapB18 | 660 | 44 | textmining:659 |
Rv0301 vapC2 |
ribonuclease VapC2 | 544 | 44 | textmining:543 |
Rv1943c mazE5 |
antitoxin MazE5 | 653 | 41 | textmining:653 |
Rv1114 vapC32 |
ribonuclease VapC32 | 547 | 41 | textmining:547 |
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 VapB38
- MTBC0 PGAP product: antitoxin
- (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_217009.1)
- 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
2DPH3 - Curated reference: UniProt P9WJ25 (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 —
18 functional partner(s); context anchor
vapC38 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002655|Rv2493|vapB38 MRTTLDLDDDVIAAARELASSQRRSLGSVISELARRGLMPGRVEADDGLPVIRVPAGTPPITPEMVRRALDED