pssA Resolved · high auto-curated
H37Rv Rv0436c · MTBC0 mtbc0_000458 ·
286 aa · 527895–528755 (-) ·
RefSeq NP_214950.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | CDP-diacylglycerol--serine O-phosphatidyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | CDP-diacylglycerol--serine O-phosphatidyltransferase |
| Revised (this work) | CDP-diacylglycerol--serine O-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.
Curated reference (UniProt)
| UniProt |
P9WPG1
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | CDP-diacylglycerol--serine O-phosphatidyltransferase |
| EC (curated) |
EC 2.7.8.8
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | pssA |
| eggNOG description | Belongs to the CDP-alcohol phosphatidyltransferase class-I family |
| Orthologous group | COG1183 |
| EC number |
EC 2.7.8.8
|
| KEGG orthology |
K17103
|
| KEGG pathways |
map00260, map00564, map01100, map01110
|
| KEGG modules |
M00093
|
| Gene Ontology (39) |
GO:0003674, GO:0003824, GO:0003882, GO:0005575, GO:0005576, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006629, GO:0006644, GO:0006650 +27 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 | 0.21 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 3 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 | 5.4e-24 | 15–165 | CDP-alcohol phosphatidyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: psd (phosphatidylserine decarboxylase), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0437c psd |
phosphatidylserine decarboxylase | 999 | 998 ctx | neighborhood:881 cooccurence:766 database:900 textmining:591 |
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 972 | 921 | database:900 textmining:672 |
Rv2746c pgsA3 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 985 | 918 | database:900 textmining:825 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 932 | 908 | database:900 |
Rv3042c serB2 |
phosphoserine phosphatase SerB | 906 | 907 | database:900 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 971 | 906 | database:900 textmining:708 |
Rv1559 ilvA |
threonine dehydratase IlvA | 904 | 905 | database:900 |
Rv0069c sdaA |
L-serine dehydratase | 901 | 902 | database:900 |
Rv1077 cbs |
cystathionine beta-synthase | 905 | 901 | database:900 |
Rv2289 cdh |
CDP-diacylglycerol pyrophosphatase | 904 | 901 | database:900 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 903 | 901 | database:900 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 903 | 901 | database:900 |
Rv1613 trpA |
tryptophan synthase subunit alpha | 900 | 901 | database:900 |
Rv1612 trpB |
tryptophan synthase subunit beta | 900 | 901 | database:900 |
Rv0435c |
ATPase | 896 | 896 ctx | neighborhood:881 |
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--serine O-phosphatidyltransferase
- MTBC0 PGAP product: CDP-diacylglycerol--serine O-phosphatidyltransferase
- Pfam (hmmscan --cut_ga): CDP-OH_P_transf PF01066.27 (E=5e-24)
- (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_214950.1)
- 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
COG1183 - Curated reference: UniProt P9WPG1 (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 —
34 functional partner(s); context anchor
psd - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000458|Rv0436c|pssA MIGKPRGRRGVNLQILPSAMTVLSICAGLTAIKFALEHQPKAAMALIAAAAILDGLDGRVARILDAQSRMGAEIDSLADAVNFGVTPALVLYVSMLSKWPVGWVVVLLYAVCVVLRLARYNALQDDGTQPAYAHEFFVGMPAPAGAVSMIGLLALKMQFGEGWWTSVWFLSFWVTGTSILLVSGIPMKKMHAVSVPPNYAAALLAVLAICAAAAVLAPYLLIWVIIIAYMCHIPFAVRSQRWLAQHPEVWDDKPKQRRAVRRASRRAHPYRPSMARLGLRKPGRRL