Get the Protein-Accession - GO-ids mapping for every Protein in e.coli K12

Question

[Benni]

I only found the annotation file for e.coli from EcoCyc: "gene_association.ecocyc" But I can´t open the file. I just need a simple text file, that maps ProteinAccession to all GO-ids.

SOLVED: I just renamed the file to .gaf since it already is in the .gaf format.

Answer 1

[Elisabeth Gasteiger]

Glad you managed to get your data. Alternatively, you could also query UniProtKB, e.g.

http://www.uniprot.org/uniprot/?query=organism:83333 http://www.uniprot.org/uniprot/?query=proteome:UP000000625

and then customize your output to include a column for GO identifers, optionally remove all other columns, and download the file in tab-separated format (http://www.uniprot.org/help/customize)

This results in (preview of first 10 entries in the list): http://www.uniprot.org/uniprot/?sort=score&desc=&compress=no&query=organism:%22Escherichia%20coli%20%28strain%20K12%29%20[83333]%22&fil=&limit=10&force=no&preview=true&format=tab&columns=id,go-id