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use of Uniprot accession Vs GenBank Accession in With column

Emily Dimmer edimmer at ebi.ac.uk
Wed Jan 31 08:34:33 PST 2007


Hi,

Yes this is true, there is only one UniProtKB record when two proteins 
are from the same species and 100% identical.
I thought this discussion was started what type of accessions should be 
used in the 'with' column for IPI-evidenced annotations ... if the 
proteins are identical and the experiment e.g. a protein binding assay,  
is done with the protein,  how much is this a problem? Surely its more 
correct and more meaningful to the user to use a protein identifier.

For an example of two genes encoding the same protein sequence see 
Q9SW34 (S61G1_ARATH)  
(http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinId=S61G1_ARATH&pager.offset=null)
You can see the two gene name lines here:

GN   Name=SEC61G1; OrderedLocusNames=At4g24920; ORFNames=F13M23.60;
GN   and
GN   Name=SEC61G2; OrderedLocusNames=At5g50460; ORFNames=MBA10.1;

Emily

Doug Howe wrote:

> I seem to recall that identical proteins generated from distinct genes 
> are represented by a single UniProt record.  If that is still true, 
> isn't that a case where an EMBL accession would be better in the with 
> field?
> -Doug
>
> On Wed, 31 Jan 2007, Valerie Wood wrote:
>
>> Emily Dimmer wrote:
>>
>>> Hi,
>>>
>>> Just a quick note, GenBank Accessions are exactly the same as EMBL 
>>> accessions. All EMBL accessions are cross-referenced in UniProt. 
>>> Therefore if you *did* want to find a UniProtKB accession, you 
>>> should be able just to enter the  GenBank accession into the UniProt 
>>> website (or search via SRS etc...) and it will bring up the 
>>> quivalent UniProt entry (I do realize that for some groups there is 
>>> an issue of a UniProtKB accession not yet existing for an equivalent 
>>> GenBank accession).
>>>
>>
>> In the cases where there is no Uniprot ID, it may be a problem to 
>> refer to the Genbank/EMBL accession number as this will often be a 
>> cosmid or contig and contain multiple CDS- in these cases you can't 
>> refer to the gene/protein uniquely  with an EMBL ID.
>>
>> Presumably though, for the cases where there is no Swiss-Prot /Trembl 
>> ID then the likelihood that you would be using this as a dbxref in 
>> the with column for an ISS is very small (I have never come across 
>> one). Can't we all agree to track down the Uniprot ID (which is 
>> relatively straightforward), or in cases why there isn't one, contact 
>> Uniprot to work out why?
>>
>> Val
>>
>>> Cheers,
>>> Emily
>>>
>>> Midori Harris wrote:
>>>
>>>> Actually, GB or GenBank would also be acceptable, because they're 
>>>> listed as synonyms in GO.xrf_abbs (tthe filtering script allows 
>>>> anything in the 'aabbreviation' or 'synonym' fields).
>>>>
>>>> m
>>>>
>>>> On Tue, 30 Jan 2007, Karen Christie wrote:
>>>>
>>>>> Note that the abbreviation selected by GO for the IDs for GenBank, 
>>>>> DDBJ, and EMBL is EMBL, so that's the namespace that needs to be 
>>>>> used in the gene_association files for GO.
>>>>>
>>>>> -Karen
>>>>>
>>>>>
>>>>> On Tue, 30 Jan 2007, Pankaj Jaiswal wrote:
>>>>>
>>>>>> Got it. We will use the GB one.
>>>>>>
>>>>>> BTW GenBank ID is different than the GenBank Accession. GenBank 
>>>>>> ID is the ID exclusive for the GenBank database entry. One GB 
>>>>>> accession can have mappings to several GenBank IDs.
>>>>>>
>>>>>> Pankaj
>>>>>>
>>>>>> Karen Christie wrote:
>>>>>>
>>>>>>> Hi Pankaj,
>>>>>>>
>>>>>>> GenBank IDs are already allowed in the with column. The main 
>>>>>>> requirement is that the abbreviation (or namespace) for the 
>>>>>>> source of the ID be included in the GO.xrf_abbs file. There is 
>>>>>>> already an entry for IDs coming from GenBank/DDBJ/EMBL, so these 
>>>>>>> IDs are already permissable.
>>>>>>>
>>>>>>> -Karen
>>>>>>>
>>>>>>>
>>>>>>> abbreviation: EMBL
>>>>>>> database: International Nucleotide Sequence Database 
>>>>>>> Collaboration, comprising EMBL-EBI International Nucleotide 
>>>>>>> Sequence Data Library (EMBL-Bank), DNA DataBank of Japan (DDBJ), 
>>>>>>> and NCBI GenBank
>>>>>>> object: Sequence accession number
>>>>>>> example_id: EMBL:AA816246
>>>>>>> example_id: DDBJ:AA816246
>>>>>>> example_id: GB:AA816246
>>>>>>> synonym: DDBJ
>>>>>>> synonym: GB
>>>>>>> synonym: GenBank
>>>>>>> generic_url: http://www.ebi.ac.uk/embl/
>>>>>>> generic_url: http://www.ddbj.nig.ac.jp/
>>>>>>> generic_url: http://www.ncbi.nlm.nih.gov/Genbank/
>>>>>>>
>>>>>>>
>>>>>>> On Tue, 30 Jan 2007, Pankaj Jaiswal wrote:
>>>>>>>
>>>>>>>> Hi Everyone,
>>>>>>>>
>>>>>>>> I know it is an accepted SOP to include either the Uniprot 
>>>>>>>> accession number or the individual database's own gene/protein 
>>>>>>>> ID in the WITH column of the association tables.
>>>>>>>>
>>>>>>>>
>>>>>>>> However while doing it it seems that it is too much of the work 
>>>>>>>> to find out what is the Uniprot entry, because often the DDBJ 
>>>>>>>> and GenBank do not Xref each other using the Uniprot accession. 
>>>>>>>> However the best alternative is to use the GenBank's Accession 
>>>>>>>> number. Which I see that almost all the databases including 
>>>>>>>> Uniprot, DDBJ, EMBL, PIR etc. use it to cross refer. It is also 
>>>>>>>> the most suitable ID used to find the particular 
>>>>>>>> nucleotide/protein accession that we are looking for using the 
>>>>>>>> same query, no matter which db is queried.
>>>>>>>>
>>>>>>>> I hope you would consider my request by adopting the GenBank's 
>>>>>>>> accession number, unless there is a better option.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Pankaj
>>>>>>>> -- 
>>>>>>>> Pankaj Jaiswal
>>>>>>>> G-15, Bradfield Hall
>>>>>>>> Dept. of Plant Breeding and Genetics
>>>>>>>> Cornell University
>>>>>>>> Ithaca, NY-14853, USA
>>>>>>>>
>>>>>>>> Ph. +1-607-255-3103 / 4199
>>>>>>>> fax: +1-607-255-6683
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> -- 
>>>>>> Pankaj Jaiswal
>>>>>> G-15, Bradfield Hall
>>>>>> Dept. of Plant Breeding and Genetics
>>>>>> Cornell University
>>>>>> Ithaca, NY-14853, USA
>>>>>>
>>>>>> Ph. +1-607-255-3103 / 4199
>>>>>> fax: +1-607-255-6683
>>>>>>
>>>>>
>>>
>>>
>>
>>
>> -- 
>> --------------------------------------------------------------------------- 
>>
>> Valerie Wood             Tel: 01223 496909
>> S. pombe Genome Project         Fax: 01223 494919 Wellcome Trust 
>> Sanger Institute     email: val at sanger.ac.uk
>> Wellcome Trust Genome Campus     http://www.genedb.org/genedb/pombe 
>> Hinxton, Cambridge, CB10 1HH     
>> http://www.sanger.ac.uk/Projects/S_pombe
>>


-- 
 ************************************
    Emily Dimmer
    GOA and IntAct Database Curator
    EMBL-EBI
    Wellcome Trust Genome Campus
    Hinxton
    Cambridge CB10 1SD, U.K.
    Tel:     +44 1223 494654
    Fax:    +44 1223 494468
    email:  edimmer at ebi.ac.uk
 ************************************




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