Add Lipidation data from UniProt

[kimrutherford]

From:

• Uniprot data to ingest #52 (comment)

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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]

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

[kimrutherford]

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]

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]

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

What do you mean by modification viewer?

[ValWood]

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

[kimrutherford]

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

[ValWood]

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

[kimrutherford]

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:

• Possible modifications to import #1216

[ValWood]

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

ok that's why!

[kimrutherford]

This is done.