Uniprot Database for download

Question

[SHN]

Hi All,

I am looking for a database similar to GTF file for RNA-sequence data. I 'd like to use this file to cross-reference all the protein accessions in my list with all that are available in the downloaded file and extract the protein names, gene-names and length of the peptides associated with that one.

I have downloaded a database from the UniprotKB, but non of the accession numbers that I have are in the downloaded file.

Any hint will be appreciated, SN

[GenoMax]

I have downloaded a database from the UniprotKB

Which file did you download?

but non of the accession numbers that I have are in the downloaded file.

Can you provide an example of ID's you have?

[SHN]

This is the example of an ID I used : C9J7I0

I think I downloaded the TSV file of ID mapping but I am not sure if that is the correct one. What is the correct way of downloading all the database available?

Answer 1

[GenoMax]

I assume your ID's are all human. If you get https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/UP000005640_9606.fasta.gz then you can get the protein name and gene name easily from the fasta header.

$ zgrep C9J7I0 UP000005640_9606.fasta.gz 
>sp|C9J7I0|UMAD1_HUMAN UBAP1-MVB12-associated (UMA)-domain containing protein 1 OS=Homo sapiens OX=9606 GN=UMAD1 PE=1 SV=2

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Option #2

Go to https://www.uniprot.org/uniprotkb?query=proteome:UP000005640

Click on Download and then choose All and format TSV. Check/change columns as needed. Then download. You should be able to find all entries along with length and gene/protein names.

This is the entry for your example accession: https://www.uniprot.org/uniprotkb?query=proteome%3AUP000005640+AND+C9J7I0

[Elisabeth Gasteiger]

This is the entry for your example accession: https://www.uniprot.org/uniprotkb?query=proteome%3AUP000005640+AND+C9J7I0

I would recommend this query instead, to ensure that only the entry with accession number C9J7I0 is returned, but not its interaction partners:

https://www.uniprot.org/uniprotkb?query=proteome%3AUP000005640+AND+accession%3AC9J7I0

[SHN]

Great thank you for all the information.