vapB34 Family assigned · medium auto-curated
H37Rv Rv1740 · MTBC0 mtbc0_001853 ·
70 aa · 1979777–1979989 (+) ·
RefSeq NP_216256.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB34 |
|---|---|
| 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 |
P9WJ31
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Putative antitoxin VapB34 |
| Curated function | Antitoxin component of a possible type II toxin-antitoxin (TA) system. The cognate toxin is VapC34. |
UniProt still lists this protein as Putative antitoxin VapB34; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | vapB30 |
| eggNOG description | positive regulation of growth |
| Orthologous group | COG4423 |
| KEGG orthology |
K19687
|
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, 3 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 |
|---|---|---|---|---|
PSK_trans_fac | PF07704.18 | 4.5e-18 | 2–69 | Rv0623-like transcription factor |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC34 (ribonuclease VapC34), high confidence from genomic context alone (score 970 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1741 vapC34 |
ribonuclease VapC34 | 972 | 970 ctx | neighborhood:801 experimental:853 |
Rv0624 vapC30 |
ribonuclease VapC30 | 943 | 898 | experimental:853 textmining:467 |
Rv3291c lrpA |
transcriptional regulator LrpA | 797 | 797 | coexpression:797 |
Rv1742 hyp |
hypothetical protein | 786 | 785 ctx | neighborhood:780 |
Rv0273c |
transcriptional regulator | 783 | 783 | coexpression:783 |
Rv2759c vapC42 |
ribonuclease VapC42 | 792 | 769 | experimental:754 |
Rv0609 vapC28 |
ribonuclease VapC28 | 785 | 763 | experimental:754 |
Rv1982c vapC36 |
ribonuclease VapC36 | 784 | 762 | experimental:754 |
Rv3488 hyp |
hypothetical protein | 761 | 761 | coexpression:761 |
Rv2788 sirR |
transcriptional repressor SirR | 744 | 744 | coexpression:744 |
Rv1267c embR |
transcriptional regulator EmbR | 738 | 738 | coexpression:738 |
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 734 | 734 | coexpression:734 |
Rv1960c parD1 |
antitoxin ParD1 | 751 | 733 | coexpression:733 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 733 | 733 | coexpression:733 |
Rv1033c trcR |
two component transcriptional regulator TrcR | 732 | 732 | coexpression:732 |
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 VapB34
- MTBC0 PGAP product: type II toxin-antitoxin system VapB family antitoxin
- Pfam (hmmscan --cut_ga): PSK_trans_fac PF07704.18 (E=4e-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_216256.1)
- 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 P9WJ31 (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 —
55 functional partner(s); context anchor
vapC34 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001853|Rv1740|vapB34 MELAARMGETLTQAVVVAVREQLARRTGRTRSISLREELAAIGRRCAALPVLDTRAADTILGYDERGLPA