vapB28 Family assigned · medium auto-curated
H37Rv Rv0608 · MTBC0 mtbc0_000638 ·
81 aa · 706796–707041 (+) ·
RefSeq NP_215122.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB28 |
|---|---|
| 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 |
P9WJ39
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB28 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin VapC28. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | vapB28 |
| eggNOG description | Rv0623-like transcription factor |
| Orthologous group | COG4423 |
| KEGG orthology |
K19687
|
| Gene Ontology (6) |
GO:0008150, 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 | 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
PSK_trans_fac | PF07704.18 | 2.3e-24 | 1–80 | Rv0623-like transcription factor |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC28 (ribonuclease VapC28), high confidence from genomic context alone (score 930 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0609 vapC28 |
ribonuclease VapC28 | 932 | 930 ctx | neighborhood:882 |
Rv0609A hyp |
hypothetical protein | 803 | 803 ctx | neighborhood:801 |
Rv0607 hyp |
hypothetical protein | 675 | 675 ctx | neighborhood:675 |
Rv0605 |
IS1536 family serine type transposase | 559 | 559 ctx | neighborhood:552 |
Rv0606 |
Possible transposase (fragment); Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to | 557 | 557 ctx | neighborhood:552 |
Rv0624 vapC30 |
ribonuclease VapC30 | 465 | 443 | |
Rv2759c vapC42 |
ribonuclease VapC42 | 455 | 433 | |
Rv1741 vapC34 |
ribonuclease VapC34 | 455 | 433 | |
Rv1982c vapC36 |
ribonuclease VapC36 | 452 | 430 | |
Rv0623 vapB30 |
antitoxin VapB30 | 687 | 191 | textmining:630 |
Rv0595c vapC4 |
ribonuclease VapC4 | 621 | 139 | textmining:578 |
Rv1740 vapB34 |
antitoxin VapB34 | 619 | 55 | textmining:614 |
Rv2021c higA2 |
transcriptional regulator | 418 | 53 | textmining:411 |
Rv3321c vapB44 |
antitoxin VapB44 | 626 | 47 | textmining:624 |
Rv2547 vapB19 |
antitoxin VapB19 | 521 | 47 | textmining:518 |
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 VapB28
- MTBC0 PGAP product: type II toxin-antitoxin system VapB family antitoxin
- Pfam (hmmscan --cut_ga): PSK_trans_fac PF07704.18 (E=2e-24)
- (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_215122.1)
- 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 P9WJ39 (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 —
22 functional partner(s); context anchor
vapC28 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000638|Rv0608|vapB28 MALNIKDPSVHQAVKQIAKITGESQARAVATAVNERLARLRSDDLAARLLAIGHKTASRMSPEAKRLDHDALLYDERGLPA