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Sunday, July 03, 2005

pattern for motif 2C

I use SSE to align 2C proteins in our statistics file.
and grab the fasta format result into GeneDoc
then use Physiochemical (H) point of view to get the alignment.
after disgards 1dr9, means I only use fold1-superfamily1-family2,
I got a pattern as follow.

P-X-[VLITAM]-X-[ILPTAV]-X(10,16)-[VLI]-X-C-X-[LMIAV]-X-X-[FILY]-X-P-X-X-[IAVL]-X-[VFTLIM]-X-[WLMF]-X(17,25)-[DNGST]-X-X-[YFW]-X(5)-[LVAT]-X-[LVFIM]-X(7,15)-[YVFIL]-X-C-X-[VAM]-X-[FH]-X(8,27)-[FLVIWAY]

I use ScanProsite to search the pattern

and use SuperFamily to check if the results are sandwich-like proteins. (click Immunoglobulin in Superfamily section)

seems like all proteins matchs this pattern are sandwich-like proteins.

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