possible additional modifications

ValWood commented 1 week ago

Lipidation IMPORTED???
Modified residue What does this provide??? how does it differ from Post-translational modification **- Post-translational modification What does this provide??? how does it differ from Modified residue

It would be good to know what these include so we can see if they are useful

kimrutherford commented 1 week ago

Lipidation IMPORTED???

We're not loading the Lipidation data. Here's a sample of what it looks like. There are only 51 genes from UniProt that have this field:

 LIPID 485; /note="GPI-anchor amidated serine"; /evidence="ECO:0000255"                                                                     
 LIPID 202; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000250|UniProtKB:P62745"
 LIPID 404; /note="S-farnesyl cysteine"; /evidence="ECO:0000250"
 LIPID 116; /note="Phosphatidylethanolamine amidated glycine"; /evidence="ECO:0000250|UniProtKB:P38182"
 LIPID 182; /note="S-farnesyl cysteine"; /evidence="ECO:0000250"
 LIPID 203; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000250|UniProtKB:P36586"; LIPID 205; /note="S-geranylgeranyl cysteine"; /evi…
 LIPID 216; /note="S-farnesyl cysteine"; /evidence="ECO:0000250"
 LIPID 202; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000269|PubMed:1597466"; LIPID 203; /note="S-geranylgeranyl cysteine"; /evide…
 LIPID 199; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000250"; LIPID 201; /note="S-geranylgeranyl cysteine"; /evidence="ECO:000025…
 LIPID 213; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000269|PubMed:1597466"; LIPID 214; /note="S-geranylgeranyl cysteine"; /evide…
 LIPID 2; /note="N-myristoyl glycine"; /evidence="ECO:0000250"; LIPID 3; /note="S-palmitoyl cysteine"; /evidence="ECO:0000250"
 LIPID 189; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000250"
 LIPID 2; /note="N-myristoyl glycine"; /evidence="ECO:0000269|PubMed:14722091"
 LIPID 199; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000250"
 LIPID 197; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000250"
 LIPID 200; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000250"
 LIPID 199; /note="GPI-anchor amidated serine"; /evidence="ECO:0000255"
 LIPID 206; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000250|UniProtKB:P36586"; LIPID 208; /note="S-geranylgeranyl cysteine"; /evi…
 LIPID 516; /note="GPI-anchor amidated serine"; /evidence="ECO:0000255"

(Moved from https://github.com/pombase/pombase-chado/issues/52)

kimrutherford commented 1 week ago

Modified residue What does this provide??? how does it differ from Post-translational modification

Post-translational modification What does this provide??? how does it differ from Modified residue

Here is a sample of the "Modified residue" data:

 SPAC144.13c;   │ MOD_RES 62; /note="Phosphoserine"; /evidence="ECO:0000269|PubMed:10921878"
 SPBC428.11;    │ MOD_RES 210; /note="N6-(pyridoxal phosphate)lysine"; /evidence="ECO:0000250|UniProtKB:P06721"
 SPAC22A12.07c; │ MOD_RES 451; /note="Phosphothreonine"; /evidence="ECO:0000269|PubMed:18257517"
 SPAC23C4.08;   │ MOD_RES 202; /note="Cysteine methyl ester"; /evidence="ECO:0000250|UniProtKB:P62745"
 SPAC2F3.09;    │ MOD_RES 377; /note="N6-(pyridoxal phosphate)lysine"; /evidence="ECO:0000250|UniProtKB:P18079"
 SPAC31G5.15;   │ MOD_RES 912; /note="Pyruvic acid (Ser); by autocatalysis"; /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
 SPBC428.02c;   │ MOD_RES 256; /note="N6-(pyridoxal phosphate)lysine"; /evidence="ECO:0000250"
 SPAC10F6.09c;  │ MOD_RES 105; /note="N6-acetyllysine"; /evidence="ECO:0000250"

And here is a sample of the "Post-translational modification" data. It seems to be free text notes. Some are quite long:

 SPBP16F5.04;            │ PTM: Autoubiquitinated at Cys-90; undergoes 'Lys-48'-linked polyubiquitination, which leads to proteasome-dependent protein degradation. {ECO:0000250|UniProtKB:Q02159}.
 SPAC144.13c;            │ PTM: Phosphorylated by cdc2-cdc13-CDK complex. This targets srw1 for proteolysis which in turn promotes cdc13 turnover. Dephosphorylated during G1 arrest. {ECO:0000269|PubMed:10921878, ECO:0000269|PubMed:18257517}.
 SPAC11E3.13c;           │ PTM: The GPI-anchor is attached to the protein in the endoplasmic reticulum and serves to target the protein to the cell surface. There, the glucosamine-inositol phospholipid moiety is cleaved off and the GPI-modified mannoprotein is covalently attached via its lipidless GPI glycan remnant to the 1,6-beta-glucan of the outer cell wall layer.
 SPAC14C4.09;            │ PTM: Not glycosylated.
 SPAC17A5.04c;           │ PTM: Glycosylated. {ECO:0000269|PubMed:14871934}.
 SPAC17G6.12;            │ PTM: Neddylated; enhancing the ubiquitin-ligase activity. {ECO:0000250|UniProtKB:P47050}.
 SPAC19G12.14;           │ PTM: Phosphorylated by casein kinase I. Phosphorylation inactivates the enzyme. {ECO:0000269|PubMed:9873063}.                                                                                                                                                                                                                                                                                                                                   
 SPAC20G4.03c;           │ PTM: Autophosphorylated.
 SPAC22A12.08c;          │ PTM: [Isoform 1]: Proteolytically cleaved, presumably during its import into the mitochondrion by mitochondrial processing peptidase. {ECO:0000269|PubMed:29958934}.
 SPAC23C4.08;            │ PTM: Palmitoylated by the erf2-erf4 complex. {ECO:0000269|PubMed:23843742}.
 SPCC962.02c;            │ PTM: Phosphorylated by ark1. {ECO:0000269|PubMed:11950927}.
 SPAC31G5.15;            │ PTM: Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the c…
 SPAC31G5.18c;           │ PTM: The N-terminal UBL (ubiquitin-like) propeptide is cleaved at Gly-84 by the deubiquitinating enzymes ubp5 and ubp15; the resulting mature sde2 associates with spliceosomes. {ECO:0000269|PubMed:28947618, ECO:0000269|PubMed:36095128}.; PTM: Polyubiquitinated; ubiquitination is partially dependent on ubr11. {ECO:0000269|PubMed:28947618}.
 SPAC3A11.08;            │ PTM: Neddylated; enhancing the ubiquitin-ligase activity. {ECO:0000250|UniProtKB:P47050}.
 SPAC56E4.06c;           │ PTM: Cleaved by autocatalysis into a large and a small subunit. {ECO:0000250}.
 SPAC6B12.11;            │ PTM: Phosphorylated by cdc2 at the onset of S-phase. {ECO:0000269|PubMed:11937031, ECO:0000269|PubMed:18257517}.
 SPAC9E9.11;             │ PTM: The N-terminus is blocked. {ECO:0000269|PubMed:10438489}.
 SPBC16E9.18;            │ PTM: Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the c…
 SPBC30D10.10c;          │ PTM: Phosphorylation at Thr-1972 in the ATP-binding region by AKT1 strongly reduces kinase activity. {ECO:0000269|PubMed:24247430}.

(Moved from #52)

kimrutherford commented 6 days ago

We're not loading the Lipidation data.

Moved to pombase/pombase-chado#1220 and now done.

pombase / pombase-chado

possible additional modifications #1213