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Nucleic Acids Research 2004 32(21):6321-6326; doi:10.1093/nar/gkh973
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Published online 1 December 2004

Nucleic Acids Research, Vol. 32 No. 21 © Oxford University Press 2004; all rights reserved

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

Tobias Doerks*, Christian von Mering and Peer Bork

EMBL, 69012 Heidelberg, Meyerhofstrasse 1 and Max-Delbrueck-Centrum, Robert-Roessle-Strasse 10, D-13092 Berlin, Germany

* To whom correspondence should be addressed. Tel: +49 6221 387456; Fax: +49 6221 387517; Email: doerks{at}embl.de
Correspondence may also be addressed to Christian von Mering. Tel: +49 6221 387534; Fax: +49 6221 387517; Email: mering{at}embl.de

Received October 6, 2004; Revised and Accepted November 11, 2004

Three integrated genomic context methods were used to annotate uncharacterized proteins in 102 bacterial genomes. Of 7853 orthologous groups with unknown function containing 45 110 proteins, 1738 groups could be linked to functionally associated partners. In many cases, those partners are uncharacterized themselves (hinting at newly identified modules) or have been described in general terms only. However, we were able to assign pathways, cellular processes or physical complexes for 273 groups (encompassing 3624 previously functionally uncharacterized proteins).


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