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substrates

Peter D'Eustachio eustachi at cshl.edu
Tue Apr 24 05:42:10 PDT 2007


This all makes sense - the transport vs binding vs trafficking distinction 
is good.

I'd like to join the conference call - when is it?

Peter

----- Original Message ----- 
From: "Valerie Wood" <val at sanger.ac.uk>
To: "Peter D'Eustachio" <eustachi at cshl.edu>
Cc: "J Clark" <jclark at ebi.ac.uk>; <transport at genome.stanford.edu>
Sent: Tuesday, April 24, 2007 8:07 AM
Subject: Re: substrates


>
> I wonder if anyone has used any of the substrate terms to annotate these 
> gene products to 'transporter activity' or its children though?. If so, we 
> may not be able to move them directly under "transmembrane transporter 
> activity"
>
> We had an idea that we would create some sort of 'transport chaperone' 
> under the binding terms which could have the relevent synonyms for 
> searching.
>
> I think we were possible even going to have
>
> transporter activity
> --transmembrane transorter acrtivity
> --transport chaperone (wording and def to be discussed)
>
> protein binding
> --transport chaperone
>
> But, as there is no functional relationship between these it probably 
> isn't necessary (or correct) to have the
> 'transporter activity' parentage at all?
>
> One of the probelms we have is that the def of 'transporter activity' is 
> quite vague and it doesn't restrict annotations to 'transmembrane 
> transport':
>
> Enables the directed movement of substances (such as macromolecules, small 
> molecules, ions) into, out of, within or between cells.
>
> It has been used to annotate various other things like  trafficking 
> molecules (SNAP receptors, SNAREs),  and various other things. If people 
> are agreed that it should never be used for these we could approach this 
> slightly differently.
>
> Peter, perhaps you could join the conf call when we deal with this high 
> level part?
>
> Val
>
>
>
> Peter D'Eustachio wrote:
>
>> Hi Jen
>>
>> Yes - that's how we use them. When we want to talk about the behavior of 
>> albumin, we would use a "binding" term.
>>
>> Peter
>>
>> ----- Original Message ----- From: "J Clark" <jclark at ebi.ac.uk>
>> To: "Peter D'Eustachio" <deustp01 at med.nyu.edu>
>> Cc: <transport at genome.stanford.edu>
>> Sent: Tuesday, April 24, 2007 6:40 AM
>> Subject: Re: substrates
>>
>>
>>> Hi Peter,
>>>
>>> Thanks, I see what you mean. If I move these terms under the term 
>>> 'transmembrane transporter activity' would you be happy with that?
>>>
>>> Thanks,
>>>
>>> Jen
>>>
>>> Peter D'Eustachio wrote:
>>>
>>>> Narrow answer: No.
>>>>
>>>> Broad, somewhat tangential answer: yes, maybe. Biologists certainly 
>>>> talk about serum albumin and cortisol binding globulin as 
>>>> "transporters" of the hydrophobic small molecules that bind to them in 
>>>> the blood and thus move from tissue to tissue, but this clearly amounts 
>>>> to overloading of the word "transport" as far as we are concerned.
>>>>
>>>> Peter D'Etc
>>>>
>>>> ----- Original Message ----- From: "J Clark" <jclark at ebi.ac.uk>
>>>> To: <transport at genome.stanford.edu>
>>>> Sent: Monday, April 23, 2007 10:44 AM
>>>> Subject: substrates
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> Can anybody think of any example of transport of the following
>>>>> substrates (belonging in the function ontology) that is not
>>>>> straightforward transport from one side of a membrane to another?
>>>>>
>>>>> organic acid transporter activity
>>>>> tricarboxylic acid transporter activity
>>>>> carbohydrate transporter activity
>>>>> alcohol transporter activity
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Jen
>>>>>
>>>>>
>>>>>
>>>
>>> -- 
>>> Gene Ontology Consortium
>>> EMBL-European Bioinformatics Institute
>>
>>
>>
>
>
> -- 
> ---------------------------------------------------------------------------
> 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
> 




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