vapB5 Family assigned · medium auto-curated
H37Rv Rv0626 · MTBC0 mtbc0_000659 ·
86 aa · 721578–721838 (+) ·
RefSeq NP_215140.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB5 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system Phd/YefM family antitoxin |
| Revised (this work) | Type II toxin-antitoxin system Phd/YefM family antitoxin. Pfam: PhdYeFM_antitox (PF02604.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WF19
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative antitoxin VapB5 |
| Curated function | Probable antitoxin component of a type II toxin-antitoxin (TA) system. The cognate toxin is VapC5. |
UniProt still lists this protein as Putative antitoxin VapB5; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| eggNOG description | Antitoxin component of a toxin-antitoxin (TA) module |
| Orthologous group | COG4118 |
| Gene Ontology (9) |
GO:0003674, GO:0005488, GO:0008150, GO:0015643, GO:0040008, GO:0045927, GO:0048518, GO:0050789, GO:0065007
|
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 | 0.199 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
PhdYeFM_antitox | PF02604.27 | 1.2e-07 | 1–42 | Antitoxin Phd_YefM, type II toxin-antitoxin system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC5 (ribonuclease VapC5), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0627 vapC5 |
ribonuclease VapC5 | 999 | 1000 ctx | neighborhood:882 cooccurence:769 experimental:999 textmining:818 |
Rv0665 vapC8 |
ribonuclease VapC8 | 978 | 977 ctx | cooccurence:772 experimental:891 |
Rv0595c vapC4 |
ribonuclease VapC4 | 977 | 977 ctx | cooccurence:771 experimental:891 |
Rv3408 vapC47 |
ribonuclease VapC47 | 710 | 710 ctx | cooccurence:702 |
Rv3384c vapC46 |
ribonuclease VapC46 | 636 | 636 ctx | cooccurence:620 |
Rv3479 |
transmembrane protein | 604 | 604 ctx | cooccurence:604 |
Rv0625c |
transmembrane protein | 582 | 582 ctx | neighborhood:579 |
Rv1962c vapC35 |
ribonuclease VapC35 | 547 | 548 ctx | cooccurence:539 |
Rv3385c vapB46 |
antitoxin VapB46 | 545 | 545 ctx | cooccurence:537 |
Rv3697c vapC48 |
ribonuclease VapC48 | 541 | 541 ctx | cooccurence:530 |
Rv1953 vapC14 |
ribonuclease VapC14 | 529 | 529 | experimental:513 |
Rv2103c vapC37 |
ribonuclease VapC37 | 524 | 525 ctx | cooccurence:511 |
Rv0749 vapC31 |
ribonuclease VapC31 | 520 | 521 ctx | cooccurence:509 |
Rv1242 vapC33 |
ribonuclease VapC33 | 488 | 489 ctx | cooccurence:478 |
Rv2872 vapC43 |
ribonuclease VapC43 | 476 | 476 ctx | cooccurence:465 |
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 VapB5
- MTBC0 PGAP product: type II toxin-antitoxin system Phd/YefM family antitoxin
- Pfam (hmmscan --cut_ga): PhdYeFM_antitox PF02604.27 (E=1e-07)
- (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_215140.1)
- Domains: Pfam-A via hmmscan --cut_ga — PhdYeFM_antitox (PF02604.27)
- 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
COG4118 - Curated reference: UniProt P9WF19 (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 —
29 functional partner(s); context anchor
vapC5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000659|Rv0626|vapB5 MSEVASRELRNDTAGVLRRVRAGEDVTITVSGRPVAVLTPVRPRRRRWLSKTEFLSRLRGAQADPGLRNDLAVLAGDTTEDLGPIR