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PMID: 31575748 Xanthomonas translucens commandeers the host rate-limiting step in ABA biosynthesis for disease susceptibility #97

Closed CuzickA closed 4 weeks ago

CuzickA commented 3 years ago

First host target paper suggested by Kim Hammond-Kosack for curation

CuzickA commented 2 years ago

Current link https://canto.phi-base.org/curs/2c927ce951d0944f

Note: session currently contains dummy entry UniProt for Fg TRI5 as I was testing out the PHI-Canto email templates.

CuzickA commented 2 years ago

Hi @smvelasquez, I started entering the PMID for this publication into PHI-Canto but have now just reassigned this session to you. You should have an email with the session link. Please let me know if there are any issues.

smvelasquez commented 2 years ago

I'll let you know (this is also my trial putting a comment)

CuzickA commented 2 years ago

Thanks. Your trial comment has worked :-)

smvelasquez commented 2 years ago

I am having issues finding the Uniprot code for TAL8 from Xanthomonas translucens pv. undulosa. I have the protein sequence and I've blasted in Uniprot and I get matches to Xanthomonas oryzae pv. oryzae. However, when I go to BLAST itself, it does find the correct protein (NCBI Accession AKK68514). Any clues how should I go about it?

ValWood commented 2 years ago

@jseager7 it might be worth mailing UniProt helpdesk to see e why this isn't available (NCBI should exchange data with ENA/EMBL and from here it should get into UniPRot Trembl).

ValWood commented 2 years ago

@smvelasquez first which UniProt blast option did you use?

smvelasquez commented 2 years ago

@ValWood On the main page, the BLAST symbol on the top left corner

jseager7 commented 2 years ago

I found this entry in UniParc, which seems to match the accession number from NCBI GenBank:

https://www.uniprot.org/uniparc/UPI000641D658

Based on the history for the accession, it seems it was deleted from UniProtKB on 16 January 2019.

jseager7 commented 2 years ago

I'm just running BLAST on this accession now to see what the closest active entry in UniProtKB is.

jseager7 commented 2 years ago

@smvelasquez Here's a link to the query results:

https://www.uniprot.org/blast/uniprot/B20220411F248CABF64506F29A91F8037F07B67D10387A5F

The closest match based on identity is A0A1C3TJJ8. You can see the sequence alignment here.

Unfortunately, the above accession is on pv. translucens, not pv. undulosa, and UniProtKB seems to refer to the gene as talCU1 instead of TAL8.

ValWood commented 2 years ago

Hi Alex, Can you put is in contact with the person in the UniProt software team who can tell us why this entry has been deleted from UniProt? @alexsign

Thanks! Val

alexsign commented 2 years ago

@ValWood Hi Val, I've sent the message to UniProt production team, hopefully they can comment on it soon.

alexsign commented 2 years ago

UniProt production needs to know which accession is deleted

jseager7 commented 2 years ago

@alexsign The deleted accession is A0A0G3LPK9 (https://www.uniprot.org/uniprot/A0A0G3LPK9)

Here's the corresponding entry in UniParc: https://www.uniprot.org/uniparc/UPI000641D658

CuzickA commented 1 year ago

Has there been any progress on identifying an active UniProt ID for TAL8 from Xanthomonas translucens pv. undulosa?