[Annotation] Fw: interpro scan question

[Sarah Hunter]

Hi all,

OK I have answered via SourceForge.  Thanks for pointing this problem out, Becky.

/Sarah

Rebecca Foulger wrote:
> 
> 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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