parE2 Family assigned · medium auto-curated
H37Rv Rv2142c · MTBC0 mtbc0_002277 ·
105 aa · 2429572–2429889 (-) ·
RefSeq NP_216658.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | toxin ParE2 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system RelE/ParE family toxin |
| Revised (this work) | Type II toxin-antitoxin system RelE/ParE family toxin. Pfam: ParE_toxin (PF05016.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHG5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Toxin ParE2 |
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. Upon expression in E.coli inhibits cell growth and colony formation. Its toxic effect is neutralized by coexpression with cognate antitoxin ParD2. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| eggNOG description | Plasmid stabilization system |
| Orthologous group | COG3668 |
| KEGG orthology |
K19093
|
| Gene Ontology (6) |
GO:0008150, GO:0040008, GO:0045926, GO:0048519, 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 0 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.21% of strains (302) · clonal |
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 |
|---|---|---|---|---|
ParE_toxin | PF05016.22 | 4.9e-07 | 6–91 | ParE toxin of type II toxin-antitoxin system, parDE |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: parD2 (antitoxin ParD2), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2142A parD2 |
antitoxin ParD2 | 976 | 882 ctx | neighborhood:882 textmining:806 |
Rv2143 hyp |
hypothetical protein | 470 | 470 ctx | neighborhood:467 |
Rv1959c parE1 |
toxin ParE1 | 876 | 87 | textmining:870 |
Rv1960c parD1 |
antitoxin ParD1 | 804 | 50 | textmining:803 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 654 | 47 | textmining:652 |
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: toxin ParE2
- MTBC0 PGAP product: type II toxin-antitoxin system RelE/ParE family toxin
- Pfam (hmmscan --cut_ga): ParE_toxin PF05016.22 (E=5e-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_216658.1)
- Domains: Pfam-A via hmmscan --cut_ga — ParE_toxin (PF05016.22)
- 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
COG3668 - Curated reference: UniProt P9WHG5 (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 —
5 functional partner(s); context anchor
parD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002277|Rv2142c|parE2 MTRRLRVHNGVEDDLFEAFSYYADAAPDQIDRLYNLFVDAVTKRIPQAPNAFAPLFKHYRHIYLRPFRYYVAYRTTDEAIDILAVRHGMENPNAVEAEISGRTFE