(441a) Reaction/Metabolite Standardization and Congruency Across Databases and Genome-Scale Metabolic Models
AIChE Annual Meeting
Wednesday, November 10, 2010 - 12:30pm to 12:50pm
Databases and genome-scale models account for a rapidly expanding list of biotransformations occurring in nature. Available information can vary significantly but generally includes reactant and product designation, stoichiometric coefficients, organism assignment, compartment localization and associated genes. Unfortunately, both databases and metabolic models suffer by a number of shortcomings that complicates their use in metabolic model reconstruction, gap filling, and strain optimization efforts. Many inadvertently include reactions that may be elementally and/or charge unbalanced and the presence of multiple synonyms for the same metabolite and/or reactions among databases and models further complicates the sharing of information from multiple sources. In this talk, we describe how we used naming synonyms and molecular geometry comparisons to generate a reconciled database that encompasses BRENDA, KEGG, MetaCyc and existing genome-scale metabolic models. All reactions in the database are charge and elementally balanced, allowing for their direct use in simulations. We discuss the challenges involved with stereochemistry, non-specific side-chains, polymerization, and the identification of lumped reactions. We examine the use of the database in bioinformatic applications, including gap-filling and elucidating shared pathways among organisms, and its impacts on the metabolic engineering efforts of flux simulations, enabled engineering interventions, and the choice of host organism selection for recombinant pathways.