parD1 Family assigned · medium auto-curated
H37Rv Rv1960c · MTBC0 mtbc0_002075 ·
83 aa · 2223090–2223341 (-) ·
RefSeq NP_216476.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin ParD1 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system ParD family antitoxin |
| Revised (this work) | Type II toxin-antitoxin system ParD family antitoxin. Pfam: ParD_antitoxin (PF03693.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIJ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin ParD1 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in E.coli neutralizes the effect of cognate toxin ParE1. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | parD1 |
| eggNOG description | Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH |
| Orthologous group | COG3609 |
| KEGG orthology |
K07746
|
| 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 | 0.34 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
ParD_antitoxin | PF03693.21 | 6.1e-45 | 1–81 | Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: parE1 (toxin ParE1), high confidence from genomic context alone (score 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1959c parE1 |
toxin ParE1 | 999 | 995 ctx | neighborhood:882 cooccurence:774 experimental:756 textmining:815 |
Rv0624 vapC30 |
ribonuclease VapC30 | 853 | 850 | coexpression:815 |
Rv1151c cobB |
NAD-dependent protein deacylase | 803 | 803 | coexpression:803 |
Rv3291c lrpA |
transcriptional regulator LrpA | 802 | 802 | coexpression:802 |
Rv3488 hyp |
hypothetical protein | 801 | 801 | coexpression:801 |
Rv0212c nadR |
transcriptional regulator NadR | 791 | 791 | coexpression:761 |
Rv1167c |
transcriptional regulator | 791 | 791 | coexpression:791 |
Rv1395 |
HTH-type transcriptional regulator | 788 | 788 | coexpression:788 |
Rv0273c |
transcriptional regulator | 785 | 785 | coexpression:785 |
Rv3183 higA3 |
transcriptional regulator | 767 | 767 | coexpression:767 |
Rv3736 |
AraC/XylS family transcriptional regulator | 765 | 765 | coexpression:765 |
Rv3855 ethR |
HTH-type transcriptional repressor EthR | 765 | 765 | coexpression:765 |
Rv2788 sirR |
transcriptional repressor SirR | 759 | 759 | coexpression:759 |
Rv3066 |
DeoR family transcriptional regulator | 746 | 746 | coexpression:746 |
Rv1176c hyp |
hypothetical protein | 740 | 740 | coexpression:740 |
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 ParD1
- MTBC0 PGAP product: type II toxin-antitoxin system ParD family antitoxin
- Pfam (hmmscan --cut_ga): ParD_antitoxin PF03693.21 (E=6e-45)
- (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_216476.1)
- Domains: Pfam-A via hmmscan --cut_ga — ParD_antitoxin (PF03693.21)
- 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
COG3609 - Curated reference: UniProt P9WIJ7 (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 —
54 functional partner(s); context anchor
parE1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002075|Rv1960c|parD1 MGKNTSFVLDEHYSAFIDGEIAAGRYRSASEVIRSALRLLEDRETQLRALREALEAGERSGSSTPFDFDGFLGRKRADASRGR