cdsA Resolved · high auto-curated
H37Rv Rv2881c · MTBC0 mtbc0_003063 ·
306 aa · 3211423–3212343 (-) ·
RefSeq NP_217397.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphatidate cytidylyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | phosphatidate cytidylyltransferase |
| Revised (this work) | Phosphatidate cytidylyltransferase. Pfam: CTP_transf_1 (PF01148.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPF7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphatidate cytidylyltransferase |
| EC (curated) |
EC 2.7.7.41
|
| Curated function | Transferase that catalyzes the synthesis of a CDP-diacylglycerol (CDP-DAG), the activated form of a phosphatidate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | cdsA |
| eggNOG description | Belongs to the CDS family |
| Orthologous group | COG4589 |
| EC number |
EC 2.7.7.41
|
| KEGG orthology |
K00981
|
| KEGG pathways |
map00564, map01100, map01110, map04070
|
| KEGG modules |
M00093
|
| Gene Ontology (64) |
GO:0003674, GO:0003824, GO:0004605, GO:0005575, GO:0005618, GO:0005623, GO:0006139, GO:0006220, GO:0006221, GO:0006629, GO:0006644, GO:0006650 +52 more
|
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 | 0.246 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
CTP_transf_1 | PF01148.26 | 8.2e-63 | 37–304 | Cytidylyltransferase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pyrH (uridylate kinase), high confidence from genomic context alone (score 870 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2746c pgsA3 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 964 | 919 | database:900 textmining:574 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 932 | 908 | database:900 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 958 | 906 | database:900 textmining:582 |
Rv2182c |
1-acylglycerol-3-phosphate O-acyltransferase | 960 | 905 | database:900 textmining:604 |
Rv2252 dagK |
diacylglycerol kinase | 957 | 904 | database:900 textmining:573 |
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 931 | 904 | database:900 |
Rv2289 cdh |
CDP-diacylglycerol pyrophosphatase | 903 | 903 | database:900 |
Rv2883c pyrH |
uridylate kinase | 901 | 870 ctx | neighborhood:728 cooccurence:442 |
Rv2882c frr |
ribosome recycling factor | 883 | 868 ctx | neighborhood:853 |
Rv1438 tpi |
triosephosphate isomerase | 811 | 774 | coexpression:703 |
Rv2879c rlmN |
Conserved hypothetical protein; Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs; Belong | 756 | 756 ctx | neighborhood:744 |
Rv2880c |
Rv2880c, (MTCY274.11c), len: 275 aa. Conserved hypothetical protein, highly similar in N-terminus to others e.g. O86754|SC6A9.22c hypothetic | 756 | 756 ctx | neighborhood:744 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 734 | 734 | coexpression:734 |
Rv0175 |
Mce associated membrane protein | 731 | 731 | coexpression:731 |
Rv2361c uppS |
decaprenyl diphosphate synthase | 826 | 730 | coexpression:693 |
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: phosphatidate cytidylyltransferase
- MTBC0 PGAP product: phosphatidate cytidylyltransferase
- Pfam (hmmscan --cut_ga): CTP_transf_1 PF01148.26 (E=8e-63)
- (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_217397.1)
- Domains: Pfam-A via hmmscan --cut_ga — CTP_transf_1 (PF01148.26)
- 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
COG4589 - Curated reference: UniProt P9WPF7 (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 —
71 functional partner(s); context anchor
pyrH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003063|Rv2881c|cdsA MTTNDAGTGNPAEQPARGAKQQPATETSRAGRDLRAAIVVGLSIGLVLIAVLVFVPRVWVAIVAVATLVATHEVVRRLREAGYLIPVIPLLIGGQAAVWLTWPFGAVGALAGFGGMVVVCMIWRLFMQDSVTRPTTGGAPSPGNYLSDVSATVFLAVWVPLFCSFGAMLVYPENGSGWVFCMMIAVIASDVGGYAVGVLFGKHPMVPTISPKKSWEGFAGSLVCGITATIITATFLVGKTPWIGALLGVLFVLTTALGDLVESQVKRDLGIKDMGRLLPGHGGLMDRLDGILPSAVAAWIVLTLLP