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Vol. 12, Issue 1, 47-56, January 2002

LETTER
Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions

Tobias Doerks,1,2,4,5 Richard R. Copley,1,4 Jörg Schultz,1,2 Chris P. Ponting,3 and Peer Bork1,2

1 European Molecular Biology Laboratory, 69114 Heidelberg, Germany; 2 Max-Delbrueck-Center, 13092 Berlin, Germany; 3 Medical Research Council Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, Oxford OX1 3QX, UK

A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic lineages, but 3 are species specific. For about 500 of the 1200 proteins that contain these new domains, nuclear localization could be inferred, and for 700, additional features could be predicted. For example, we identified a new domain, likely to have a role downstream of the unfolded protein response; a nematode-specific signalling domain; and a widespread domain, likely to be a noncatalytic homolog of ubiquitin-conjugating enzymes.

4 These authors contributed equally to this work.

5 Corresponding author.

12:47-56 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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