pgsA2 Family assigned · medium auto-curated
H37Rv Rv1822 · MTBC0 mtbc0_001936 ·
209 aa · 2087168–2087797 (+) ·
RefSeq NP_216338.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | CDP-alcohol phosphatidyltransferase family protein |
| Revised (this work) | CDP-alcohol phosphatidyltransferase family protein. 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.
Curated reference (UniProt)
| UniProt |
P9WPG5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative cardiolipin synthase |
| EC (curated) |
EC 2.7.8.41
|
| Curated function | May catalyze the biosynthesis of cardiolipin from phosphatidylglycerol (PG) and CDP-diacylglycerol. May also catalyze the synthesis of phosphatidylinositol. |
UniProt still lists this protein as Putative cardiolipin synthase; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | pgsA2 |
| eggNOG description | CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase |
| 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 (29) |
GO:0003674, GO:0003824, GO:0006629, GO:0006644, GO:0006650, GO:0006793, GO:0006796, GO:0008150, GO:0008152, GO:0008444, GO:0008610, GO:0008654 +17 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 | 0.233 · 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 |
|---|---|---|---|---|
CDP-OH_P_transf | PF01066.27 | 6.1e-36 | 12–167 | CDP-alcohol phosphatidyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gcvH (glycine cleavage system protein H), high confidence from genomic context alone (score 794 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2746c pgsA3 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 933 | 928 | database:900 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 972 | 921 | database:900 textmining:672 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 981 | 914 | database:900 textmining:793 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 931 | 904 | database:900 |
Rv2289 cdh |
CDP-diacylglycerol pyrophosphatase | 901 | 901 | database:900 |
Rv2350c plcB |
membrane-associated phospholipase B | 900 | 901 | database:900 |
Rv2349c plcC |
phospholipase C | 900 | 900 | database:900 |
Rv1755c plcD |
Rv1755c, (MT1799, MTCY28.21c), len: 280 aa. Probable plcD, phospholipase C 4 (fragment) (see citations below),highly similar to C-terminus o | 900 | 900 | database:900 |
Rv2351c plcA |
membrane-associated phospholipase A | 900 | 900 | database:900 |
Rv1823 hyp |
hypothetical protein | 883 | 883 ctx | neighborhood:882 |
Rv1824 hyp |
hypothetical protein | 841 | 841 ctx | neighborhood:839 |
Rv1825 hyp |
hypothetical protein | 824 | 825 ctx | neighborhood:822 |
Rv1826 gcvH |
glycine cleavage system protein H | 794 | 794 ctx | neighborhood:778 |
Rv1901 cinA |
competence damage-inducible protein CinA | 823 | 769 | coexpression:736 |
Rv1821 secA2 |
accessory Sec system translocase SecA2 | 752 | 738 ctx | neighborhood:736 |
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--glycerol-3-phosphate 3-phosphatidyltransferase
- MTBC0 PGAP product: CDP-alcohol phosphatidyltransferase family protein
- Pfam (hmmscan --cut_ga): CDP-OH_P_transf PF01066.27 (E=6e-36)
- (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_216338.1)
- 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 P9WPG5 (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 —
30 functional partner(s); context anchor
gcvH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001936|Rv1822|pgsA2 MEPVLTQNRVLTVPNMLSVIRLALIPAFVYVVLSAHANGWGVAILVFSGVSDWADGKIARLLNQSSRLGALLDPAVDRLYMVTVPIVFGLSGIVPWWFVLTLLTRDALLAGTLPLLWSRGLSALPVTYVGKAATFGFMVGFPTILLGQCDPLWSHVLLACGWAFLIWGMYAYLWAFVLYAVQMTMVVRQMPKLKGRAHRPAAQNAGERG