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Abundant protein domains occur in proportion to proteome size

Joel A Malek

Author Affiliations

Agencourt Bioscience Corporation, 100 Cummings Center, Suite 107J, Beverly, MA 01915, USA

Genome Biology 2001, 2:research0039-research0039.5  doi:10.1186/gb-2001-2-9-research0039

A previous version of this manuscript was made available before peer review at

Published: 24 August 2001



Conserved domains in proteins have crucial roles in protein interactions, DNA binding, enzyme activity and other important cellular processes. It will be of interest to determine the proportions of genes containing such domains in the proteomes of different eukaryotes.


The average proportion of conserved domains in each of five eukaryote genomes was calculated. In pairwise genome comparisons, the ratio of genes containing a given conserved domain in the two genomes on average reflected the ratio of the predicted total gene numbers of the two genomes. These ratios have been verified using a repository of databases and one of its subdivisions of conserved domains.


Many conserved domains occur as a constant proportion of proteome size across the five sequenced eukaryotic genomes. This raises the possibility that this proportion is maintained because of functional constraints on interacting domains. The universality of the ratio in the five eukaryotic genomes attests to its potential importance.