Opened 4 years ago

Closed 4 years ago

#5196 closed defect (fixed)

Blastprotein sometimes requests invalid ID from AlphaFold

Reported by: Zach Pearson Owned by: Zach Pearson
Priority: moderate Milestone: 1.3
Component: Web Services Version:
Keywords: Cc: goddard@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Screenshot attached. IDs passed to alphafold fetch are not always the 6 or 10 character format.

Attachments (1)

Screen Shot 2021-09-09 at 2.38.45 AM.png (619.8 KB ) - added by Zach Pearson 4 years ago.

Download all attachments as: .zip

Change History (4)

by Zach Pearson, 4 years ago

comment:1 by Tom Goddard, 4 years ago

In your screenshot R13P3_HUMAN is the uniprot name. The UniProt accession for that is Q6NVV1. Although some uniprot names have the accession code as the part before the underscore, very many do not and instead have a gene name. So the accession code has to come from the sequence database search, not from the uniprot name. Here's the sequence entry from the alphafold.fasta database

sp|Q6NVV1|R13P3_HUMAN Putative 60S ribosomal protein L13a protein RPL13AP3 OS=Homo sapiens OX=9606 GN=RPL13AP3 PE=5 SV=1

MLRHKTKRGHASLDCLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFALLGRQAQEVR
WKYQAVTATLEEKRKEKAKIHYWKKKQLMRLRKQAEKNVKKN

and you see the accession code is right after the ">sp|" and following that is the uniprot name. That accession code has to be parsed out of the BLAST results and used.

Actually I changed the "alphafold fetch" command a few days ago so you can give it a uniprot name. So you could use "alphafold fetch R13P3_HUMAN".

comment:2 by Zach Pearson, 4 years ago

Should be fixed in this commit.

comment:3 by Zach Pearson, 4 years ago

Resolution: fixed
Status: assignedclosed
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