Nucleic Acids Research, Vol 25, Issue 9 1665-1677, Copyright © 1997 by Oxford University Press
AF Neuwald, JS Liu, DJ Lipman and CE Lawrence
Biologists often gain structural and functional insights into a protein
sequence by constructing a multiple alignment model of the family. Here a
program called Probe fully automates this process of model construction
starting from a single sequence. Central to this program is a powerful new
method to locate and align only those, often subtly, conserved patterns
essential to the family as a whole. When applied to randomly chosen
proteins, Probe found on average about four times as many relationships as
a pairwise search and yielded many new discoveries. These include: an
obscure subfamily of globins in the roundworm Caenorhabditis elegans ; two
new superfamilies of metallohydrolases; a lipoyl/biotin swinging arm domain
in bacterial membrane fusion proteins; and a DH domain in the yeast Bud3
and Fus2 proteins. By identifying distant relationships and merging
families into superfamilies in this way, this analysis further confirms the
notion that proteins evolved from relatively few ancient sequences.
Moreover, this method automatically generates models of these ancient
conserved regions for rapid and sensitive screening of sequences.
ARTICLES
Extracting protein alignment models from the sequence database
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. neuwald@ncbi.nlm.nih.gov
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