[Annotation] Fw: interpro scan question

[Rebecca Foulger]

Hi InterPro,

Are you able to help Doug from ZFIN with his query below?

Doug- I'll annotate those Zebrafish TrEMBL entries accordingly when the 
InterPro question has been resolved.

cheers,
Becky


----- Original Message ----- 
From: "Doug howe" <dhowe at cs.uoregon.edu>
To: <dhowe at cs.uoregon.edu>
Cc: "GO Annotation list" <annotation at genome.stanford.edu>
Sent: Friday, September 19, 2008 8:44 PM
Subject: Re: [Annotation] interpro scan question


> Furthermore..it looks like this may be a prokaryotic signature...surely 
> false positive for zebrafish then...?

>
> 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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