[Annotation] [Gohelp] GO term for "anti-adaptor" protein

[Valerie Wood]

Hi Ingrid,

I don't know much about E. coli but I annotated something similar for 
pombe last week (a gene which negatively regulates a transcription 
factor by promoting its degradation).
I did not annotate a molecular function for this, but the mechanism is 
unknown (even interaction has not yet been demonstrated). The general 
rule I use  is, that if you do not know the mechanism, then you do not 
use a function term (i.e transcriptiional regulator, or enzyme regulator 
or one of its children), but make only a process term.  Here you seem to 
have more information
 
transcription repressor activity
http://www.ebi.ac.uk/ego/GTerm?id=GO:0016564
Any transcription regulator activity that prevents or downregulates 
transcription.

Val




Eurie Hong wrote:
> Hi Ingrid,
>
> I'm cc'ing your question to the annotation mailing list.  There are  
> many GO curators who annotate a wide range of species on this mailing  
> list so this is probably the best list for you to email regarding  
> annotation questions.
>
> Here is information to subscribe to the mailing list if you are not  
> already on it:
> http://fafner.stanford.edu/mailman/listinfo/annotation
>
> Cheers,
> Eurie
>
> On Apr 30, 2008, at 2:27 PM, Ingrid Keseler wrote:
>
>   
>> Hi everyone,
>>
>> I'm having a difficult time identifying an appropriate GO function  
>> term
>> to annotate a set of small so-called "anti-adaptor" proteins in E.
>> coli.  Here's what they do: under normal conditions, a protein called
>> RssB binds to the alternative sigma factor, sigmaS, and targets it for
>> degradation by the ClpXP protease.  Under certain environmental
>> conditions, e.g. phosphate starvation, DNA damage etc., certain small
>> proteins (IraP, IraD, IraM) are expressed; they bind to RssB, thus
>> (maybe just by competition) preventing it from binding to sigmaS, and
>> therefore sigmaS accumulates.  For illustration, see Fig. 6 in PMID
>> 18383615 or Fig. 6 in PMID 16600914 (free access).  What would you  
>> call
>> that function?  I already have GO:0005515 protein binding for the
>> interaction with RssB, but that doesn't convey the actual function.   
>> For
>> process, I am using GO:0042177, negative regulation of protein  
>> catabolic
>> process.
>>
>> Any ideas?  Thanks!
>>
>> -Ingrid
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-- 
---------------------------------------------------------------------------
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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