possible additional modifications

[ValWood]

• Lipidation IMPORTED??? - edit: done 2024-09-24
• 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]

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 #52)

[kimrutherford]

• 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]

We're not loading the Lipidation data.

Moved to #1220 and now done.

[kimrutherford]

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

I think we can close this now. We're loading the modifications with positions from UniProt (see #1216) and the "Post-translational modification" data are notes without positions.