Automated metabolic reconstruction for Methanococcus jannaschii
Open Access
- 12 August 2003
- Vol. 1 (4) , 223-229
- https://doi.org/10.1155/2004/324925
Abstract
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
Funding Information
- Medical Research Council
This publication has 45 references indexed in Scilit:
- The Phylogenetic Extent of Metabolic Enzymes and PathwaysGenome Research, 2003
- The Pathway Tools softwareBioinformatics, 2002
- Methanococcus jannaschii Uses a Pyruvoyl-dependent Arginine Decarboxylase in Polyamine BiosynthesisPublished by Elsevier ,2002
- Molecular characterization of phosphoglycerate mutase in archaeaFEMS Microbiology Letters, 2002
- Functional Versatility and Molecular Diversity of the Metabolic Map of Escherichia coliGenome Research, 2001
- Archaeal Fructose-1,6-bisphosphate Aldolases Constitute a New Family of Archaeal Type Class I AldolaseJournal of Biological Chemistry, 2001
- Archaeal Shikimate Kinase, a New Member of the GHMP-Kinase FamilyJournal of Bacteriology, 2001
- One Polypeptide with Two Aminoacyl-tRNA Synthetase ActivitiesScience, 2000
- Cysteine Biosynthesis Pathway in the Archaeon Methanosarcina barkeri Encoded by Acquired Bacterial Genes?Journal of Bacteriology, 2000
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997