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Archaea, 1:223–229
© 2004 Heron Publishing—Victoria, Canada
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Automated metabolic reconstruction for Methanococcus jannaschii

Sophia Tsoka (1, 2), David Simon (1, 3) and Christos A. Ouzounis (1)

1. Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, U.K. / 2. Author to whom correspondence should be addressed ([email protected]) / 3. Institut Pasteur, Génopole, Plateforme Bioinformatique, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France / Received April 8, 2003; accepted August 12, 2003; published online October 2, 2003


We present the computational prediction and synthesis of the metabolic pathways in Methanococcus jannaschii from its genomic sequence using the PathoLogic software. Metabolic reconstruction is based on a reference knowledge base of metabolic pathways and is performed with minimal manual intervention. We predict the existence of 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super-pathways consisting of one or more component pathways. These assignments represent significantly improved enzyme and pathway predictions compared with previous metabolic reconstructions, and some key metabolic reactions, previously missing, have been identified. Our results, in the form of enzymatic assignments and metabolic pathway predictions, form a database (MJCyc) that is accessible over the World Wide Web for further dissemination among members of the scientific community.

Keywords: metabolic databases, Methanocaldococcus, pathway synthesis.

 ISSN 1472-3654 (Online) ISSN 1472-3646 (Print) Copyright © 2002–2007 Heron Publishing