Table 2

Similarity of sequences in predicted proteomes ofD. melanogaster, S. cerevisiae, and C. elegans .To be scored as a similarity, each pairwise similarity was required to extend over more than 80% of the length of the query sequence at an E value less than that indicated. For example, in “Fly proteins in Fly-yeast,” the column labeled E < 10−10 shows the number and percentage of fly proteins that match yeast proteins at this E value or less and for which more than 80% of the length of the fly protein is aligned with the yeast protein. Each set of pairs was analyzed without consideration of the third proteome. The rows labeled “Fly-worm-yeast” report the composition of an independent clustering in which only groups containing a member from all three proteomes were counted. The numbers are slightly higher for the “Fly-worm-yeast” counts than for the “Fly-yeast” or “Worm-yeast” counts because of sequence bridging; that is, not all sequences within a group necessarily have a significant match to all other members of that group. See (6) for details.

E< 10−10E < 10−20E < 10−50E < 10−100
(n)(%)(n)(%)(n)(%)(n)(%)
Fly proteins in:
Fly-yeast234516.5187713.210367.34333.1
Fly-worm499835.2421229.7244217.211067.8
Fly-worm-yeast330323.3242817.111137.84353.1
Worm proteins in:
Worm-yeast218411.817689.59335.03742.0
Fly-worm479525.8400421.6240312.910925.9
Fly-worm-yeast322917.4243913.111156.04192.3
Yeast proteins in:
Fly-yeast185629.4156724.889114.13766.0
Worm-yeast170427.0142522.680212.73355.3
Fly-worm-yeast183329.1152524.283113.23525.6