parD2 Resolved · medium auto-curated
H37Rv Rv2142A · MTBC0 - ·
71 aa · 2402507–2402722 (-) ·
RefSeq YP_007410825.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin ParD2 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Antitoxin ParD2. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WJ75
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin ParD2 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in E.coli neutralizes the effect of cognate toxin ParE2. |
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: parE2 (toxin ParE2), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2142c parE2 |
toxin ParE2 | 976 | 882 ctx | neighborhood:882 textmining:806 |
Rv2143 hyp |
hypothetical protein | 467 | 467 ctx | neighborhood:467 |
Rv1960c parD1 |
antitoxin ParD1 | 868 | 41 | textmining:868 |
Rv1959c parE1 |
toxin ParE1 | 841 | 41 | textmining:841 |
Rv2863 vapC23 |
ribonuclease VapC23 | 627 | 41 | textmining:627 |
Rv1838c vapC13 |
ribonuclease VapC13 | 588 | 41 | textmining:588 |
Rv0616A vapB29 |
antitoxin VapB29 | 542 | 41 | textmining:542 |
Rv1991A mazE6 |
antitoxin MazE6 | 519 | 41 | textmining:519 |
Rv0598c vapC27 |
ribonuclease VapC27 | 511 | 41 | textmining:511 |
Rv3180c vapC49 |
ribonuclease VapC45 | 511 | 41 | textmining:511 |
Rv3181c vapB49 |
antitoxin VapB45 | 511 | 41 | textmining:511 |
Rv2019 vapC45 hyp |
hypothetical protein | 510 | 41 | textmining:510 |
Rv1740 vapB34 |
antitoxin VapB34 | 510 | 41 | textmining:510 |
Rv3408 vapC47 |
ribonuclease VapC47 | 510 | 41 | textmining:510 |
Rv0582 vapC26 |
ribonuclease VapC26 | 439 | 41 | textmining:439 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): antitoxin ParD2
- (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 YP_007410825.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt P9WJ75 (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 —
19 functional partner(s); context anchor
parE2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2142A|parD2 MVVNRALLASVDALSRDEQIELVEHINGNLAEGMHISEANQALIEARANDTDDAHWSTIDDFDKRIRARLG