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pombase / pombase-chado

PomBase code for accessing Chado
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Add Lipidation data from UniProt #1220

Closed kimrutherford closed 2 months ago

kimrutherford commented 2 months ago

From:

We can map all of the:

LIPID 485; /note="GPI-anchor amidated serine"; /evidence="ECO:0000255" maps to N-seryl-glycosylphosphatidylinositolethanolamine https://www.pombase.org/term/MOD:00171 (currently 1 in PomBase)

LIPID 202; /note="S-geranylgeranyl cysteine"; /evidence="ECO:0000250|UniProtKB:P62745" maps to geranylgeranylated residue (All should be cysteine) https://www.pombase.org/term/MOD:00441 (currently 2 in PomBase)

LIPID 404; /note="S-farnesyl cysteine"; /evidence="ECO:0000250" maps to S-farnesyl-L-cysteine https://www.pombase.org/term/MOD:00111 (currently 3 in PomBase)

LIPID 116; /note="Phosphatidylethanolamine amidated glycine"; /evidence="ECO:0000250|UniProtKB:P38182" maps to N-glycyl-1-(phosphatidyl)ethanolamine https://www.pombase.org/term/MOD:00351 (currently 1 in PomBase)

LIPID 2; /note="N-myristoyl glycine"; /evidence="ECO:0000269|PubMed:14722091" to N-myristoylglycine https://www.pombase.org/term/MOD:00068 (currently 21 in PomBase)

The remaining mappings

SPBC13G1.11; LIPID 193; /note="S-palmitoyl cysteine"; /evidence="ECO:0000250"; maps to https://www.pombase.org/term/MOD:00115 S-palmitoyl-L-cysteine

SPBPJ4664.02; LIPID 3944; /note="GPI-anchor amidated alanine"; /evidence="ECO:0000255"0250" https://www.pombase.org/term/MOD:00818 glycosylphosphatidylinositolated residue (MOD does not have further specificity)

SPAC212.08c; LIPID 96; /note="GPI-anchor amidated glycine"; /evidence="ECO:0000255" https://www.pombase.org/term/MOD:00818 glycosylphosphatidylinositolated residue (MOD does not have further specificity)

SPCC1322.10; LIPID 242; /note="GPI-like-anchor amidated asparagine"; /evidence="ECO:0000255" Ignore

kimrutherford commented 2 months ago

I've updated pombe-embl/external_data/uniprot_data_from_api.tsv with the Lipidation data.

kimrutherford commented 2 months ago

That's all done for Wednesday morning. The lipidation sites will appear in the protein feature viewer and each site will be a PSI-MOD annotation in Chado.

I'll close this once I've checked that it looks OK on pombase.org

ValWood commented 2 months ago

thats great! note that these don't currently show in the modification viewer although they have positions at least: https://www.pombase.org/term/MOD:00171

kimrutherford commented 2 months ago

note that these don't currently show in the modification viewer although they have positions

What do you mean by modification viewer?

ValWood commented 2 months ago

In the modification track of the protein feature viewer. We can display these because we have the positional information.

kimrutherford commented 2 months ago

Currently they are in the lipidation sites track. I'll merge them into the modification track.

ValWood commented 2 months ago

Right got it. Are all of the others on the modification track?

kimrutherford commented 2 months ago

Are all of the others on the modification track?

Do you mean the PomBase curated modifications? They should all be there.

I haven't worked on the modifications from UniProt yet:

ValWood commented 2 months ago

I haven't worked on the modifications from UniProt yet:

ok that's why!

kimrutherford commented 2 months ago

This is done.