Automated metabolic reconstruction for Methanococcus jannaschii英文文献资料.docVIP

Archaea 1, 223–229 ? 2004 Heron Publishing—Victoria, Canada Automated metabolic reconstruction forMethanococcusjannaschii SOPHIA TSOKA,1,2 DAVID SIMON1,3 and CHRISTOS A. OUZOUNIS1 1 Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, U.K. 2 Corresponding author (tsoka@ebi.ac.uk) 3 Present address: 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 Summary We present the computational prediction and syn- genome sequence, such systems deduce a map of the entire metabolic complement of the target organism, providing an excellent basis for further computational or experimental anal- ysis of cellular metabolism. thesis 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 existenceof 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super-pathways consisting of one or more com- ponent pathways. These assignments represent significantly improvedenzymeandpathwaypredictionscomparedwithpre- vious metabolic reconstructions, and some key metabolic reac- tions, 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 mem- bers of the scientific community. The advantage of computational metabolic network synthe- sis is that the assumed “completeness” of a genome (in terms of the sequences it encodes) or biochemical pathway (in terms of the reactions it includes) may form the basis for further functional assignment beyond sequence simi