disordered region query

[ValWood]

Pro1 has a "disordered region" feature of 2 amino acids. This seems odd to me. I'm not sure you can call disordered for 2 amino acids.
What is the source of this (I think they come from InterPRot, but I don't see it on the InterPro website)

[kimrutherford]

The coiled coils, disordered regions and low complexity regions came from Pfam while it was still existed:

• Display TM and coiled-coil regions #1685 (comment)

That two AA region has type "IUPred" in the data from Pfam. Probably from this tool: https://iupred3.elte.hu/
(Although I tried the protein on the site just now and didn't predict anything)

[kimrutherford]

Do we have other sources of disordered region?

We don't have any other sources at the moment. I'm still trying and failing to run the InterPro pipeline locally. But I don't know if that has any disorder or complexity output.

This seems a bit flaky, (don't we also get them from InterPRo?)

They all come from Pfam (3 years ago) not from InterPro.

[kimrutherford]

If we can't locate them,

They are definitely from the data I grabbed from Pfam before it disappeared.

I will ask InterPro if they can include them in InterProscan.

InterPro does provide disordered regions in a file (but not low complexity regions). I found an old email titled "[pfam-help #751585] Pfam-N" where you asked InterPro about it. They said:

From the InterPro FTP: extra.xml.gz contains all sequence features, such as trensmembrane regions predicted by TMHMM, intrinsically disordered regions predicted by MobiDB-lite, etc. Pfam-N regions are also included in this file. There are more Pfam-N regions that the first file as it's based on UniProtKB 2024_03.

I think we talked about it and decided it was still a problem because they have out of date protein sequence so the positions will sometimes be wrong. I'm looking at installing InterPro locally.

[kimrutherford]

Pro1 has a "disordered region" feature of 2 amino acids.

InterProScan doesn't find any disordered regions in pro1

I see similar here in wee1

The 2 AA match for wee1 is gone too.

The predictions from InterProScan are quite different to the prediction from Pfam.

This is from Pfam for wee1:

Here's what we get from InterProScan, on the same scale:

A bit worrying maybe?

The screenshots are from: https://desktop.kmr.nz/gene/SPCC18B5.03

[ValWood]

I think it is OK, wee 1 is largely disordered outside of the kinase domain:

I guess InterPro have chosen the algorithm they believe performs the best. I wonder if this incorporates AlphaFold data (that would be the sensible way to do it...)

[ValWood]

I think we can close this, it's covered by [MobiDB-lite] features.
I was just going to send an announcement about that, but they aren't live yet. Which ticket is that? (That's what I was looking for when I found this.)

It seems from this ticket that the old disordered regions were from various sources that were no longer reproducible:

"That two AA region has type "IUPred" in the data from Pfam. Probably from this tool: https://iupred3.elte.hu/
(Although I tried the protein on the site just now and didn't predict anything)"

[kimrutherford]

Which ticket is that?

Mostly:

• Attempt to install and run InterProScan pombase-chado#1218

but partly:

• Integrate the 2 protein viewers #2203

[kimrutherford]

I guess the new domains panel can go together with the switch

That's what I was thinking. There are a lot of interrelated changes in various places so it's easier just to get everything done and released at once rather than bit by bit.