psd Resolved · high auto-curated
H37Rv Rv0437c · MTBC0 mtbc0_000459 ·
231 aa · 528752–529447 (-) ·
RefSeq NP_214951.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphatidylserine decarboxylase |
|---|---|
| MTBC0 PGAP re-annotation | phosphatidylserine decarboxylase |
| Revised (this work) | Phosphatidylserine decarboxylase. Pfam: PS_Dcarbxylase (PF02666.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHQ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphatidylserine decarboxylase proenzyme |
| EC (curated) |
EC 4.1.1.65
|
| Curated function | Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | psd |
| eggNOG description | Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer) |
| Orthologous group | COG0688 |
| EC number |
EC 4.1.1.65
|
| KEGG orthology |
K01613
|
| KEGG pathways |
map00564, map01100, map01110
|
| KEGG modules |
M00093
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.077 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 1 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 |
|---|---|---|---|---|
PS_Dcarbxylase | PF02666.21 | 4.6e-42 | 57–227 | Phosphatidylserine decarboxylase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pssA (CDP-diacylglycerol--serine O-phosphatidyltransferase), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 999 | 998 ctx | neighborhood:881 cooccurence:766 database:900 textmining:591 |
Rv2351c plcA |
membrane-associated phospholipase A | 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 |
Rv2350c plcB |
membrane-associated phospholipase B | 900 | 900 | database:900 |
Rv2349c plcC |
phospholipase C | 900 | 900 | database:900 |
Rv0435c |
ATPase | 888 | 884 ctx | neighborhood:881 |
Rv0438c moeA2 |
molybdopterin molybdenumtransferase | 807 | 807 ctx | neighborhood:802 |
Rv1279 |
GMC-type oxidoreductase | 808 | 801 | database:800 |
Rv0439c |
dehydrogenase/reductase | 632 | 618 ctx | neighborhood:613 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 605 | 605 | |
Rv0906 hyp |
hypothetical protein | 469 | 469 | |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 432 | 433 | coexpression:427 |
Rv1382 hyp |
hypothetical protein | 423 | 423 | coexpression:419 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 656 | 337 | textmining:503 |
Rv2746c pgsA3 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 712 | 335 | textmining:586 |
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: phosphatidylserine decarboxylase
- MTBC0 PGAP product: phosphatidylserine decarboxylase
- Pfam (hmmscan --cut_ga): PS_Dcarbxylase PF02666.21 (E=5e-42)
- (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_214951.1)
- Domains: Pfam-A via hmmscan --cut_ga — PS_Dcarbxylase (PF02666.21)
- 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
COG0688 - Curated reference: UniProt P9WHQ5 (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 —
18 functional partner(s); context anchor
pssA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000459|Rv0437c|psd MARRPRPDGPQHLLALVRSAVPPVHPAGRPFIAAGLAIAAVGHRYRWLRGTGLLAAAACAGFFRHPQRVPPTRPAAIVAPADGVICAIDSAAPPAELSMGDTPLPRVSIFLSILDAHVQRAPVSGEVIAVQHRPGRFGSADLPEASDDNERTSVRIRMPNGAEVVAVQIAGLVARRIVCDAHVGDKLAIGDTYGLIRFGSRLDTYLPAGAEPIVNVGQRAVAGETVLAECR