[Annotation] interpro scan question

[Doug howe]

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