vapB44 Family assigned · low auto-curated
H37Rv Rv3321c · MTBC0 mtbc0_003531 ·
80 aa · 3730212–3730454 (-) ·
RefSeq NP_217838.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB44 |
|---|---|
| MTBC0 PGAP re-annotation | CopG family transcriptional regulator |
| Revised (this work) | CopG family transcriptional regulator. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ17
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Putative antitoxin VapB44 |
| Curated function | Possibly the antitoxin component of a type II toxin-antitoxin (TA) system. Its cognate toxin is VapC44. |
UniProt still lists this protein as Putative antitoxin VapB44; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2DSQK |
|---|---|
| Gene Ontology (15) |
GO:0008150, GO:0009605, GO:0009607, GO:0043207, GO:0044403, GO:0044419, GO:0050896, GO:0051701, GO:0051704, GO:0051707, GO:0052173, GO:0052200 +3 more
|
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: vapC44 (ribonuclease VapC44), high confidence from genomic context alone (score 911 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3320c vapC44 |
ribonuclease VapC44 | 911 | 911 ctx | neighborhood:882 |
Rv3323c moaX |
MoaD-MoaE fusion protein MoaX | 566 | 567 ctx | neighborhood:564 |
Rv3322c |
methyltransferase | 565 | 565 ctx | neighborhood:564 |
Rv3324c moaC3 |
cyclic pyranopterin monophosphate synthase accessory protein | 521 | 522 ctx | neighborhood:519 |
Rv3324A |
Rv3324A, len: 44 aa. Probable pseudogene moaB3,fragment of pterin-4-alpha-carbinolamine dehydratase,equivalent to C-terminus of MT3426|Q8VJ3 | 521 | 521 ctx | neighborhood:519 |
Rv2494 vapC38 |
ribonuclease VapC38 | 426 | 68 | textmining:410 |
Rv2547 vapB19 |
antitoxin VapB19 | 807 | 64 | textmining:803 |
Rv2493 vapB38 |
antitoxin VapB38 | 662 | 55 | textmining:658 |
Rv0301 vapC2 |
ribonuclease VapC2 | 527 | 55 | textmining:520 |
Rv1494 mazE4 |
antitoxin MazE4 | 527 | 53 | textmining:522 |
Rv2601A vapB41 |
antitoxin VapB41 | 551 | 51 | textmining:547 |
Rv0608 vapB28 |
antitoxin VapB28 | 626 | 47 | textmining:624 |
Rv1114 vapC32 |
ribonuclease VapC32 | 544 | 47 | textmining:542 |
Rv2545 vapB18 |
antitoxin VapB18 | 676 | 46 | textmining:675 |
Rv0623 vapB30 |
antitoxin VapB30 | 550 | 46 | textmining:548 |
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 VapB44
- MTBC0 PGAP product: CopG family transcriptional regulator
- (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_217838.1)
- 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
2DSQK - Curated reference: UniProt P9WJ17 (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 —
22 functional partner(s); context anchor
vapC44 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003531|Rv3321c|vapB44 MRTTLSIDDDVLLAVKERARREKRTAGEILSDLARQALTNQNPQPAASQEDAFHGFEPLPHRGGAVSNALIDRLRDEEAV