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uniprot protein information about reactions

I am interested in retrieving the information for proteins and understand which ones are enzyme and which ones are not. Is there an easy way to do it for a large number of genes ? using uniprot ?

gene
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written by Learner Learner

How about retrieving all UniProtKB entries with an EC number? You can use a query like ec:* AND organism:"Homo sapiens (Human) [9606]" for that.

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written by vkkodali_ncbi vkkodali_ncbi

@vkkodali I don't mind doing that but it does not give anything :-) I am more looking to find something programing rather than try and error

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written by Learner Learner

@vkkodali so you mean those 15000 hit are the enzymes proteins ? if so, it would be easy then to match and find those that are not. let me know If that is the right thing :-)

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written by Learner Learner

The assumption I am making here is that the protein is an enzyme if there is an EC number assigned to it. Out of the ~15000 hits, less than 5000 are UniProt Reviewed records; which would be the only ones I'd bother to look at. Beyond that, it depends on your use case. If you need to include absolutely all enzymes then this will surely miss a few. Along the same lines, this list may include a few that are actually not enzymes. But that's some QC work you will have to do.

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written by vkkodali_ncbi vkkodali_ncbi

@vkkodali Thank you . how can I extract the EC number too? I want to know how to QC it !

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written by Learner Learner

Have you used the UniProt REST API before? One of the options there is to specify which columns you want. In your case, you should have ec in addition to other columns such as id and entry name. Read up on their API at the link shown above and post your code here that I can review.

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written by vkkodali_ncbi vkkodali_ncbi

@vkkodali This is how I am trying to do it but I get error over url 

import urllib,urllib2
    url = 'https://www.uniprot.org/uploadlists/'
    params = {
    'query': 'gene_exact:mapk1 AND organism:homo_sapiens AND reviewed:yes', 
    'format': 'tab', 
    'columns': 'id,ec,entry_name,genes'}

    data = urllib.urlencode(params)
    request = urllib2.Request(url, data)
    contact = "xxxx@outlook.com" 
    request.add_header('User-Agent', 'Python %s' % contact)
    response = urllib2.urlopen(request)
    header = response.readline()
    entries=response.read()

    id_list=[]
    new_entries=entries.split("\n")
    for element in new_entries:
        if element=="":
            continue
        else:
            element=element.split("\t")
            if "_HUMAN" in element[1]:
                id_list.append(element[1])
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written by Learner Learner

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