vapB42 Family assigned · medium auto-curated
H37Rv Rv2760c · MTBC0 mtbc0_002937 ·
89 aa · 3093682–3093951 (-) ·
RefSeq NP_217276.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB42 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system VapB family antitoxin |
| Revised (this work) | Type II toxin-antitoxin system VapB family antitoxin. Pfam: PSK_trans_fac (PF07704.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ19
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Putative antitoxin VapB42 |
| Curated function | Possibly the antitoxin component of a type II toxin-antitoxin (TA) system. Its cognate toxin is VapC42. |
UniProt still lists this protein as Putative antitoxin VapB42; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Rv0623-like transcription factor |
| Orthologous group | COG4423 |
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 | 0.173 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 0 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.39% of strains (572) · clonal |
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 |
|---|---|---|---|---|
PSK_trans_fac | PF07704.18 | 2.1e-18 | 1–88 | Rv0623-like transcription factor |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC42 (ribonuclease VapC42), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2759c vapC42 |
ribonuclease VapC42 | 987 | 987 ctx | neighborhood:882 coexpression:834 |
Rv2761c hsdS |
type I restriction/modification system specificity determinant HsdS | 811 | 811 ctx | neighborhood:801 |
Rv2762c hyp |
hypothetical protein | 802 | 803 ctx | neighborhood:800 |
Rv0273c |
transcriptional regulator | 802 | 802 | coexpression:802 |
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 799 | 799 | coexpression:799 |
Rv3488 hyp |
hypothetical protein | 798 | 798 | coexpression:798 |
Rv0339c iniR |
transcriptional regulator | 797 | 797 | coexpression:797 |
Rv1681 moeX |
molybdopterin biosynthesis protein MoeX | 765 | 765 | coexpression:765 |
Rv2757c vapC21 |
ribonuclease VapC21 | 760 | 760 ctx | neighborhood:753 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 759 | 759 | coexpression:759 |
Rv2488c |
LuxR family transcriptional regulator | 757 | 757 | coexpression:757 |
Rv2758c vapB21 |
antitoxin VapB21 | 755 | 755 ctx | neighborhood:753 |
Rv0674 hyp |
hypothetical protein | 754 | 754 | coexpression:754 |
Rv3263 |
DNA methylase | 748 | 748 | coexpression:748 |
Rv3736 |
AraC/XylS family transcriptional regulator | 734 | 734 | coexpression:734 |
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 VapB42
- MTBC0 PGAP product: type II toxin-antitoxin system VapB family antitoxin
- Pfam (hmmscan --cut_ga): PSK_trans_fac PF07704.18 (E=2e-18)
- (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_217276.1)
- Domains: Pfam-A via hmmscan --cut_ga — PSK_trans_fac (PF07704.18)
- 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
COG4423 - Curated reference: UniProt P9WJ19 (SwissProt, reviewed; Predicted)
- 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 —
53 functional partner(s); context anchor
vapC42 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002937|Rv2760c|vapB42 MSLNIKSQRTVALVRELAARTGTNQTAAVEDAVARRLSELDREDRARAEARRAAAEQTLRDLDKLLSDDDKRLIRRHEVDLYDDSGLPR