cdh Resolved · high auto-curated
H37Rv Rv2289 · MTBC0 mtbc0_002430 ·
260 aa · 2586422–2587204 (+) ·
RefSeq NP_216805.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | CDP-diacylglycerol pyrophosphatase |
|---|---|
| MTBC0 PGAP re-annotation | CDP-diacylglycerol diphosphatase |
| Revised (this work) | CDP-diacylglycerol diphosphatase. Pfam: CDH (PF02611.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPG9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable CDP-diacylglycerol pyrophosphatase |
| EC (curated) |
EC 3.6.1.26
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | cdh |
| eggNOG description | CDP-diacylglycerol |
| Orthologous group | COG2134 |
| EC number |
EC 3.6.1.26
|
| KEGG orthology |
K01521
|
| KEGG pathways |
map00564, map01110
|
| Gene Ontology (7) |
GO:0005575, GO:0005576, 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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.17% of strains (1694) · 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 |
|---|---|---|---|---|
CDH | PF02611.21 | 2.8e-74 | 41–257 | CDP-diacylglycerol pyrophosphatase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: yjcE (Na(+)/H(+) transporter), high confidence from genomic context alone (score 784 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2288 hyp |
hypothetical protein | 953 | 954 ctx | neighborhood:781 coexpression:798 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 903 | 903 | database:900 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 904 | 901 | database:900 |
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 901 | 901 | database:900 |
Rv2182c |
1-acylglycerol-3-phosphate O-acyltransferase | 901 | 901 | database:900 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 900 | 901 | database:900 |
Rv2252 dagK |
diacylglycerol kinase | 902 | 900 | database:900 |
Rv2746c pgsA3 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 900 | 900 | database:900 |
Rv2287 yjcE |
Na(+)/H(+) transporter | 784 | 784 ctx | neighborhood:781 |
Rv0355c PPE8 |
PPE family protein PPE8 | 595 | 596 ctx | cooccurence:594 |
Rv1956 higA |
antitoxin HigA | 600 | 592 ctx | cooccurence:591 |
Rv3347c PPE55 |
PPE family protein PPE55 | 585 | 585 ctx | cooccurence:584 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 582 | 582 ctx | cooccurence:582 |
Rv3350c PPE56 |
PPE family protein PPE56 | 582 | 582 ctx | cooccurence:581 |
Rv1004c |
membrane protein | 579 | 579 ctx | cooccurence:579 |
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: CDP-diacylglycerol pyrophosphatase
- MTBC0 PGAP product: CDP-diacylglycerol diphosphatase
- Pfam (hmmscan --cut_ga): CDH PF02611.21 (E=3e-74)
- (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_216805.1)
- Domains: Pfam-A via hmmscan --cut_ga — CDH (PF02611.21)
- 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
COG2134 - Curated reference: UniProt P9WPG9 (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 —
55 functional partner(s); context anchor
yjcE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002430|Rv2289|cdh MPKSRRAVSLSVLIGAVIAALAGALIAVTVPARPNRPEADREALWKIVHDRCEFGYRRTGAYAPCTFVDEQSGTALYKADFDPYQFLLIPLARITGIEDPALRESAGRNYLYDAWAARFLVTARLNNSLPESDVVLTINPKNARTQDQLHIHISCSSPTTSAALRNVDTSEYVGWKQLPIDLGGRRFQGLAVDTKAFESRNLFRDIYLKVTADGKKMENASIAVANVAQDQFLLLLAEGTEDQPVAAETLQDHDCSITKS