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 |
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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)
Change History (4)
by , 4 years ago
Attachment: | Screen Shot 2021-09-09 at 2.38.45 AM.png added |
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comment:1 by , 4 years ago
comment:3 by , 4 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
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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
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".