pgsA1 Resolved · high auto-curated
H37Rv Rv2612c · MTBC0 - ·
217 aa · 2939959–2940612 (-) ·
RefSeq YP_177894.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | CDP-diacylglycerol--inositol 3-phosphatidyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | CDP-diacylglycerol--inositol 3-phosphatidyltransferase. Pfam: CDP-OH_P_transf (PF01066.27). |
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 |
P9WPG7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphatidylinositol phosphate synthase |
| EC (curated) |
EC 2.7.8.-
|
| Curated function | Catalyzes the conjugation of the 1'-hydroxyl group of D-myo-inositol-3-phosphate (also named L-myo-inositol-1-phosphate) with a lipid tail of cytidine diphosphate diacylglycerol (CDP-DAG), forming phosphatidylinositol phosphate (PIP) and CMP. PIP is a precursor of phosphatidylinositol (PI) which is an essential lipid for mycobacteria required for formation of their cell wall. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | pgsA1 |
| eggNOG description | Belongs to the CDP-alcohol phosphatidyltransferase class-I family |
| Orthologous group | COG0558 |
| EC number |
EC 2.7.8.11, EC 2.7.8.5
|
| KEGG orthology |
K00995, K00999
|
| KEGG pathways |
map00562, map00564, map01100, map04070
|
| Gene Ontology (40) |
GO:0003674, GO:0003824, GO:0003881, GO:0003882, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0006629, GO:0006644, GO:0006650 +28 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 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 |
|---|---|---|---|---|
CDP-OH_P_transf | PF01066.27 | 4.5e-12 | 29–135 | CDP-alcohol phosphatidyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2611c (phosphatidylinositol mannoside acyltransferase), high confidence from genomic context alone (score 969 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2611c |
phosphatidylinositol mannoside acyltransferase | 992 | 969 ctx | neighborhood:882 fusion:463 cooccurence:448 textmining:753 |
Rv2610c pimA |
alpha-(1-2)-phosphatidylinositol mannosyltransferase | 963 | 952 ctx | neighborhood:879 cooccurence:510 |
Rv2613c |
AP-4-A phosphorylase | 964 | 922 ctx | neighborhood:882 textmining:565 |
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 981 | 914 | database:900 textmining:793 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 971 | 906 | database:900 textmining:708 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 958 | 906 | database:900 textmining:582 |
Rv2289 cdh |
CDP-diacylglycerol pyrophosphatase | 900 | 901 | database:900 |
Rv2746c pgsA3 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 987 | 900 | database:900 textmining:876 |
Rv2614c thrS |
threonine--tRNA ligase | 929 | 888 ctx | neighborhood:881 textmining:400 |
Rv0046c ino1 |
inositol-3-phosphate synthase | 896 | 861 ctx | cooccurence:712 database:500 |
Rv2609c |
membrane protein | 884 | 814 ctx | neighborhood:798 textmining:402 |
Rv1901 cinA |
competence damage-inducible protein CinA | 823 | 769 | coexpression:736 |
Rv2614A hyp |
hypothetical protein | 552 | 553 ctx | neighborhood:550 |
Rv2606c snzP |
pyridoxine biosynthesis protein | 506 | 507 ctx | neighborhood:498 |
Rv3310 sapM |
acid phosphatase | 499 | 500 | database:500 |
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): CDP-diacylglycerol--inositol 3-phosphatidyltransferase
- Pfam (hmmscan --cut_ga): CDP-OH_P_transf PF01066.27 (E=4e-12)
- (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_177894.1)
- Domains: Pfam-A via hmmscan --cut_ga — CDP-OH_P_transf (PF01066.27)
- 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
COG0558 - Curated reference: UniProt P9WPG7 (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 —
34 functional partner(s); context anchor
Rv2611c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2612c|pgsA1 MSKLPFLSRAAFARITTPIARGLLRVGLTPDVVTILGTTASVAGALTLFPMGKLFAGACVVWFFVLFDMLDGAMARERGGGTRFGAVLDATCDRISDGAVFCGLLWWIAFHMRDRPLVIATLICLVTSQVISYIKARAEASGLRGDGGFIERPERLIIVLTGAGVSDFPFVPWPPALSVGMWLLAVASVITCVQRLHTVWTSPGAIDRMAIPGKGDR