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 Curation: indicates possible missing reactions Development of metabolic flux models

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

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

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