[Annotation] interpro scan question

[Doug howe]

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