Rv3181c Family assigned · medium auto-curated
H37Rv Rv3181c · MTBC0 mtbc0_003382 ·
150 aa · 3574539–3574991 (-) ·
RefSeq NP_217697.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB45 |
|---|---|
| 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 |
P9WF15
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative antitoxin VapB49 |
| Curated function | Possibly the antitoxin component of a type II toxin-antitoxin (TA) system. Its cognate toxin is VapC49 (Potential). |
UniProt still lists this protein as Putative antitoxin VapB49; 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 (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 |
|---|---|---|---|---|
PhdYeFM_antitox | PF02604.27 | 4.1e-10 | 67–116 | Antitoxin Phd_YefM, type II toxin-antitoxin system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC49 (ribonuclease VapC45), high confidence from genomic context alone (score 972 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3180c vapC49 |
ribonuclease VapC45 | 995 | 972 ctx | neighborhood:882 cooccurence:773 textmining:857 |
Rv2308 hyp |
hypothetical protein | 651 | 652 ctx | cooccurence:637 |
Rv0355c PPE8 |
PPE family protein PPE8 | 646 | 646 ctx | cooccurence:646 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 637 | 637 ctx | cooccurence:637 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 634 | 634 ctx | cooccurence:634 |
Rv3347c PPE55 |
PPE family protein PPE55 | 632 | 632 ctx | cooccurence:632 |
Rv3350c PPE56 |
PPE family protein PPE56 | 628 | 628 ctx | cooccurence:628 |
Rv0613c hyp |
hypothetical protein | 627 | 627 ctx | cooccurence:627 |
Rv1917c PPE34 |
PPE family protein PPE34 | 625 | 625 ctx | cooccurence:623 |
Rv2209 |
integral membrane protein | 622 | 622 ctx | cooccurence:621 |
Rv0665 vapC8 |
ribonuclease VapC8 | 606 | 606 ctx | cooccurence:495 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 604 | 604 ctx | cooccurence:604 |
Rv0304c PPE5 |
PPE family protein PPE5 | 603 | 603 ctx | cooccurence:603 |
Rv0341 iniB |
isoniazid inducible protein IniB | 603 | 603 ctx | cooccurence:601 |
Rv1004c |
membrane protein | 603 | 603 ctx | cooccurence:601 |
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 VapB45
- MTBC0 PGAP product: type II toxin-antitoxin system Phd/YefM family antitoxin
- Pfam (hmmscan --cut_ga): PhdYeFM_antitox PF02604.27 (E=4e-10)
- (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_217697.1)
- 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 P9WF15 (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 —
86 functional partner(s); context anchor
vapC49 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003382|Rv3181c| MQLGRKVTSHHDIDRFGVASTADESVYRPLPPRLRLAQVNLSRRRCRTQSDMYKSRFSECTVQSVDVSVTELRAHLSDWLDRARAGGEVVITERGIPIARLAALDSTDTLERLTAEGVIGKATAQRPVAAGRPRPRPQRPVSDRVSDQRR