[Annotation] interpro scan question

[Rama Balakrishnan]

Yes, i agree, it is spurious.

Rama

On Sep 19, 2008, at 12:54 PM, Doug howe wrote:

> If the fact that it is a fragment causes a true positive hit...but  
> we know that hit is not found in the full length proteins...perhaps  
> it isn't false positive..but isn't it at least spurious?  The result  
> is that our synaptosomal snap25a gene is annotated to have  
> 'transcription factor activity'.
>
> -Doug
>
> Rama Balakrishnan wrote:
>>
>>
>> It need not be a false-positive. My guess is, when the sequence is  
>> longer, often there are other domains for the longer part of the  
>> sequence which changes the fold of the larger protein and hence the  
>> significance of the Helix-turn-helix goes down?
>>
>> Rama
>>
>>
>> On Sep 19, 2008, at 12:32 PM, Doug howe wrote:
>>
>>> I've got two protein sequences (found below) which are 99%  
>>> identical.  Both belong to zebrafish synaptosomal protein snap25a,  
>>> but one of them is a fragment.  The fragment turns up positive for  
>>> the interpro domain IPR002197 (helix-turn-helix, Fis-type), while  
>>> the full length protein does not.  The fragment is the only  
>>> protein on the gene that is positive for this interpro domain.    
>>> It turns out that IPR002197 maps through interpro2go to  
>>> 'transcription factor activity' and 'regulation of  
>>> transcription'.  Is it possible that the protein fragment is  
>>> getting a false positive hit for the domain IPR002197?  If so, why  
>>> doesn't it also make a false positive hit on the full length  
>>> proteins?
>>>
>>> Any help welcomed...
>>>
>>> O93578
>>> LGKFCGLCSCPCNKMKSGASKAWGNNQDGVVASQPARVVDEREQMAISGGFIRRVTDDAR
>>> ENEMDENLEQVGGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKM
>>> LGSG
>>>
>>> Q693L7
>>> MAEDSDMRNELADMQQRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLERI
>>> EEGMDQINKDMKDAEKNLNDLGKFCGLCSCPCNKMKSGASKAWGNNQDGVVASQPARVVD
>>> EREQMAISGGFIRRVTDDARENEMDENLEQVGGIIGNLRHMALDMGNEIDTQNRQIDRIM
>>> EKADSNKTRFDEANQRATKMLGSG
>>>
>>>
>>> -- 
>>> Doug Howe, Ph.D.
>>> ZFIN Scientific Curator
>>> Zebrafish Nomenclature Coordinator
>>>
>>> _______________________________________________
>>> Annotation mailing list
>>> Annotation at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>
>
> -- 
> Doug Howe, Ph.D.
> ZFIN Scientific Curator
> Zebrafish Nomenclature Coordinator