From GI to GO anootations

Question

[benarnon]

Hi. I have a long list of GI which I want to retrieve their GO annotations. I read that one way to do it is by converting the GI identifier into UniPortKB identifier and from there to retrieve the GO annotations. I tried to do so by using the uniprot_tools 0.4.1 where I mapped the GI into UniProtKB and then retrieved the UniProt object.

For some of the GI's it worked but for some get the following message : Sorry, no results were found. You mapped from GI number to UniProtKB. However, 1 was successfully mapped to the UniParc sequence archive. View UniParc results (1)

When I looked on the UniParc result I get the following table: http://www.uniprot.org/uniparc/?query=yourlist:M20161020F725F458AC8690F874DD868E4ED79B8896594EO&sort=yourlist:M20161020F725F458AC8690F874DD868E4ED79B8896594EO&columns=yourlist(M20161020F725F458AC8690F874DD868E4ED79B8896594EO),id,organisms,kb,first-seen,last-seen,length

First, anybody can explain me what exactly is the different between UniPARC and UniPortKB. Second, what am I suppose to do with the table and how can I get the GO annotations?

[Sej Modha]

UniParc and UniProt from Wikipedia

Answer 1

[Mahmut Uludag]

• It is likely that some of the entries that has GI numbers are not referenced by any UniProtKB entries, this could be the reason for the 'no results found' messages

• As also noted in a recent Biostars post(Question: Cannot download gi list from NCBI protein), NCBI is in the process of phasing out GI numbers. If it is possible get accession list instead of GI numbers, then you can query UniProt with the accession numbers and ask to return GO annotations, as in the following example queries

  http://www.uniprot.org/uniprot/?query=WP_048113166.1&columns=id,go&format=tab

  http://www.uniprot.org/uniprot/?query=WP_007692371.1&columns=id,go&format=tab

Answer 2

[Prasad]

try db2db from biodbnet.

Answer 3

[Elisabeth Gasteiger]

Here is some general documentation about UniProtKB and UniParc http://www.uniprot.org/help/uniprotkb http://www.uniprot.org/help/uniparc

However, since your query seems to involve bacterial entries (cf the UniParc entry in your query http://www.uniprot.org/uniparc/UPI00001B8619):

There are 65 Bordetella bronchiseptica proteomes, but only 4 of them are non-redundant: http://www.uniprot.org/proteomes/?query=organism%3A%22bordetella+bronchiseptica%22&sort=score The redundant ones (cf http://www.uniprot.org/help/proteome_redundancy_faq) can only be found in UniParc.

See also: http://www.uniprot.org/help/redundancy