[Annotation] interpro scan question

[Rama Balakrishnan]

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
>
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