pgsA3 Resolved · high auto-curated
H37Rv Rv2746c · MTBC0 - ·
209 aa · 3058602–3059231 (-) ·
RefSeq NP_217262.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | CDP-diacylglycerol--glycerol-3-phosphate 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 |
P9WPG3
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable phosphatidylglycerophosphate synthase |
| EC (curated) |
EC 2.7.8.5
|
| Curated function | Probably catalyzes the synthesis of phosphatidylglycerophosphate by transferring a phosphatidyl group from CDP-diacylglycerol to glycerol 3-phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | pgsA |
| eggNOG description | Belongs to the CDP-alcohol phosphatidyltransferase class-I family |
| Orthologous group | COG0558 |
| EC number |
EC 2.7.8.41, EC 2.7.8.5
|
| KEGG orthology |
K00995, K08744
|
| KEGG pathways |
map00564, map01100
|
| Gene Ontology (36) |
GO:0003674, GO:0003824, GO:0005575, GO:0005618, GO:0005623, GO:0006629, GO:0006644, GO:0006650, GO:0006793, GO:0006796, GO:0008150, GO:0008152 +24 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 | 0.373 · 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 |
|---|---|---|---|---|
CDP-OH_P_transf | PF01066.27 | 3.9e-46 | 28–187 | CDP-alcohol phosphatidyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: argA (L-glutamate alpha-N-acetyltranferase), high confidence from genomic context alone (score 721 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 933 | 928 | database:900 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 964 | 919 | database:900 textmining:574 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 985 | 918 | database:900 textmining:825 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 987 | 900 | database:900 textmining:876 |
Rv2289 cdh |
CDP-diacylglycerol pyrophosphatase | 900 | 900 | database:900 |
Rv1901 cinA |
competence damage-inducible protein CinA | 880 | 843 | coexpression:733 |
Rv2747 argA |
L-glutamate alpha-N-acetyltranferase | 721 | 721 ctx | neighborhood:649 |
Rv2745c clgR |
transcriptional regulator ClgR | 658 | 658 ctx | neighborhood:656 |
Rv2744c 35kd_ag hyp |
hypothetical protein | 522 | 503 ctx | neighborhood:503 |
Rv2743c hyp |
hypothetical protein | 487 | 487 ctx | neighborhood:487 |
Rv2982c gpdA2 |
glycerol-3-phosphate dehydrogenase | 586 | 442 ctx | cooccurence:423 |
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase | 492 | 438 | coexpression:417 |
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 449 | 429 | coexpression:413 |
Rv0564c gpdA1 |
glycerol-3-phosphate dehydrogenase | 562 | 410 | |
Rv2483c plsC |
bifunctional L-3-phosphoserine phosphatase/1-acyl-sn-glycerol-3-phosphate acyltransferase | 419 | 363 |
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--glycerol-3-phosphate 3-phosphatidyltransferase
- Pfam (hmmscan --cut_ga): CDP-OH_P_transf PF01066.27 (E=4e-46)
- (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_217262.1)
- 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 P9WPG3 (SwissProt, reviewed; Inferred from homology)
- 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 —
30 functional partner(s); context anchor
argA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2746c|pgsA3 MSRSTRYSVAVSAQPETGQIAGRARIANLANILTLLRLVMVPVFLLALFYGGGHHSAARVVAWAIFATACITDRFDGLLARNYGMATEFGAFVDPIADKTLIGSALIGLSMLGDLPWWVTVLILTRELGVTVLRLAVIRRGVIPASWGGKLKTFVQAVAIGLFVLPLSGPLHVAAVVVMAAAILLTVITGVDYVARALRDIGGIRQTAS