Display 'binding and ' active site' from UniPRot

[ValWood]

This is quite hidden unt her the function section in a subsection 'features' So this is different from the "PTM-type" features

It seemed to include only: binding site and catalytic site, but there may be more

These could be 1 track or 2 tracks

eg

need to acknowledge UniProt as source in the pop-up

[ValWood]

Sorry!. Now I can't remember what that was. Here is a different one https://www.uniprot.org/uniprotkb/Q9P376/entry#function

[ValWood]

This ticket is related to website https://github.com/pombase/website/issues/2159

[ValWood]

Also related, although a different datatype https://github.com/pombase/pombase-chado/issues/1172

[kimrutherford]

See also:

• https://github.com/pombase/pombase-chado/issues/52

[kimrutherford]

I've had a look at the data from the UniProt file (https://github.com/pombase/pombase-chado/issues/52).

For binding site we get:

• position: 123 or can be a range 138..146
• /evidence="ECO:0000250" or /evidence="ECO:0000250|UniProtKB:G0SHW7"
• /ligand="1,2-diacylglycero-3-phosphoethanolamine" or /ligand="DNA"
• /ligand_id="ChEBI:CHEBI:29991"
• notes, for example: /note="in chain C" or /note="Nucleophile"

For active sites we get:

• position: always a point not a range
• /evidence="ECO:0000250|UniProtKB:O22317"
  • a few have multiple evidence: /evidence="ECO:0000250|UniProtKB:P15731, ECO:0000255|PROSITE-ProRule:PRU00388"
• notes

We need to decide which of these qualifiers we want to display.

[kimrutherford]

Also related, although a different datatype https://github.com/pombase/pombase-chado/issues/1172

1172 is this issue?

[kimrutherford]

I've added the code for binding sites and active sites in time for the current load. Here's how it looks:

Let me know if we should change the formatting of the text in the mouse-over for binding sites.

The new display is on my desktop for now: https://desktop.kmr.nz/gene/SPAC11E3.13c It should be on the main site in the morning.

[kimrutherford]

It should be on the main site in the morning.

That's live now: https://www.pombase.org/gene_protein_features/SPBC1105.02c

[kimrutherford]

I forgot to say: for now the binding and active sites are only shown on the full view, not in the widget on the gene pages.

[ValWood]

That's live now:

nice!

[ValWood]

I think full view is OK.

[kimrutherford]

I'll add something to the docs before closing: https://www.pombase.org/documentation/gene-page-protein-features-widget

[kimrutherford]

I'll add something to the docs before closing: https://www.pombase.org/documentation/gene-page-protein-features-widget

I've added this documentation by copy and pasting from the UniProt track descriptions. Is this OK?

• Signal peptide N-terminal signal peptide position, imported from UniProt
• Transit peptide Transit peptide position, imported from UniProt
• Active sites Amino acid(s) directly involved in the activity of an enzyme, imported from UniProt
• Binding sites Binding site for any chemical group (co-enzyme, prosthetic group, etc.), imported from UniProt
• Beta strands Experimentally determined beta strands, imported from UniProt
• Helices Experimentally determined helical regions, imported from UniProt

[ValWood]

Sounds good except Signal peptide N-terminal signal peptide position, imported from UniProt should be a mixture of imported, curated, and running signal peptide locally

[kimrutherford]

I think all the signal peptides in the protein feature viewer are from UniProt, because they have positions.

[ValWood]

I think all the signal peptides in the protein feature viewer are from UniProt, because they have positions.

yes they seem to be. I think we need to get the others from phobius to fil in the gaps.

[ValWood]

I think this can close?