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Nucleic Acids Research 2006 34(3):1066-1080; doi:10.1093/nar/gkj494
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Published online 15 February 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space

Russell L. Marsden*, David Lee, Michael Maibaum, Corin Yeats and Christine A. Orengo

Department of Biochemistry and Molecular Biology, University College London Gower Street, London WC1E 6BT, UK

*To whom correspondence should be addressed. Tel: +44 207 679 2171; Fax: +44 207 679 7193; Email: marsden{at}biochem.ucl.ac.uk

Received September 21, 2005. Revised December 16, 2005. Accepted January 20, 2006.

We present an analysis of 203 completed genomes in the Gene3D resource (including 17 eukaryotes), which demonstrates that the number of protein families is continually expanding over time and that singleton-sequences appear to be an intrinsic part of the genomes. A significant proportion of the proteomes can be assigned to fewer than 6000 well-characterized domain families with the remaining domain-like regions belonging to a much larger number of small uncharacterized families that are largely species specific. Our comprehensive domain annotation of 203 genomes enables us to provide more accurate estimates of the number of multi-domain proteins found in the three kingdoms of life than previous calculations. We find that 67% of eukaryotic sequences are multi-domain compared with 56% of sequences in prokaryotes. By measuring the domain coverage of genome sequences, we show that the structural genomics initiatives should aim to provide structures for less than a thousand structurally uncharacterized Pfam families to achieve reasonable structural annotation of the genomes. However, in large families, additional structures should be determined as these would reveal more about the evolution of the family and enable a greater understanding of how function evolves.


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[Abstract] [Full Text] [PDF]


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