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Finding Dead-end Metabolites

Finding Dead-end Metabolites. Mike Travers Bioinformatics Research Group SRI International travers@ai.sri.com. What are dead-ends?. Metabolites that are found Only as products, Or only as reactants, But not both; And are not objects of transport reactions. Uses

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Finding Dead-end Metabolites

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  1. Finding Dead-end Metabolites Mike TraversBioinformatics Research Group SRI International travers@ai.sri.com

  2. What are dead-ends? • Metabolites that are found • Only as products, • Or only as reactants, • But not both; • And are not objects of transport reactions. • Uses • Curation: indicates possible missing reactions • Development of metabolic flux models

  3. Details • Parameters • Small molecules only? • Rxns in pathways only? • Compartment • Include cofactors? • Include reactions with unknown directionality? • Outputs • Object list • Displayed on cellular overview • Report

  4. Report Dead-end metabolite report for ECOLI on 2010-10-19_17-36-29 Parameters: (SMALL-MOLS-ONLY? NIL PATHWAYS-ONLY? NIL INCLUDE-COFACTORS? NIL IGNORE-UNKNOWN-DIRECTION? T COMPARTMENT CCO-CYTOSOL) Considering 1146 initial reactions 1000 reactions remain after pruning to compartment CCO-CYTOSOL 1074 starting dead ends are substrates in those reactions 908 remain after screening them against 197 transported chemicals 813 remain after removing macromolecules, strings, classes 541 dead-ends remain after removing those that are enzyme cofactors 9 dead end reactants and 12 dead end products remain after pruning based on only-substrate/only-product Reactants which are not products: THZ 4-methyl-5-(beta-hydroxyethyl)thiazole DIMETHYLBENZIMIDAZOLE 5,6-dimethylbenzimidazole METHYLENE-THF-GLU-N a 5,10-methylene-tetrahydrofolate Demethylated-methyl-acceptors a demethylated methyl acceptor Fatty-Acyl-CoA a fatty acyl CoA Glycerophosphodiesters a glycerophosphodiester PROT-CYS a protein L-cysteine … Products which are not reactants: 3-HYDROXY-PROPIONATE 3-hydroxypropionate CPD0-1027 a debranched limit dextrin Methylated-methyl-acceptors a methylated methyl acceptor NUC-5-PHOSPHATE a nucleoside-5'-phosphate TRIMETHYLAMINE trimethylamine … URATE urate UREA urea

  5. Status • Fully functional in desktop version (15.0) • Web version working in prototype • Algorithm/parameters may be tweaked • Suggestions/feedback welcome

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