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Protein Folds in the Worm Genome
M Gerstein, J Lin & H Hegyi (2000). Pac. Symp. Biocomp. (in
press). [preprint]
This site gives an analysis of protein folds in the worm genome. The
methods we used include pairwise and multiple-sequence comparison
methods (i.e. FASTA and PSI-blast). Overall, we find that ~250 folds
match ~8000 domains in ~4500 ORFs, about 32 matches per fold involving
a quarter of the total worm ORFs. We compare the folds in the worm
genome to those in other model organisms, in particular yeast and
E. coli, and find that the worm shares more folds with the
phylogenetically closer yeast than with E. coli. There appear to be 36
folds unique to the worm compared to these two model organisms, and
many of these are obviously implicated in aspects of
multicellularity. The most common fold in the worm genome is the
immunoglobulin fold, and many of the common folds are repeated in
various combinations and permutations in multidomain proteins. In
addition, an approach is presented for the identification of
“sure” and “marginal” membrane proteins. When applied to
the worm genome, this reveals a much greater relative prevalence of
proteins with seven transmembrane helices in comparison to the other
completely sequenced genomes, which are not of metazoans. Combining
these analyses with some other simple filters allows one to identify
ORFs that potentially code for soluble proteins of unknown fold, which
may be promising targets for experimental investigation in structural
genomics.
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