protein alignment

Jean-Paul Revel revel at genbank.bio.net
Tue Sep 4 16:00:59 EST 1990



I recently isolated a new member of the connexin gene family. These 
molecules have a conserved 200 amino acid 'core' (that contains
4 transmembrane segments) but the C-termini are highly diverged and
vary in length from 20 to 150 amino acids. To improve the alignment of
our
new connexin with other members of the gene family, particularly
over the C-terminal domain, we ran all the connexins through
the PC-Gene program PROSITE which detects consensus protein
modification sites, and conserved modification sites were used to
force the
alignment. Doing this we discovered what appears to be a significant
conservation of three phophorylation sites that none of the other 
alignment programs we have tried revealed. Does anyone know of any
papers that use this approach and/or discuss the significance of the
conservation of putative modification sites? Any comments related to 
this problem would be appreciated.

Jan Hoh
jhoh at romeo.bitnet




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