1. Finding Dead-end Metabolites
Mike Travers Bioinformatics Research Group
SRI International

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

5. 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 methyl-5-(beta-hydroxyethyl)thiazole
DIMETHYLBENZIMIDAZOLE ,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 hydroxypropionate
CPD a debranched limit dextrin
Methylated-methyl-acceptors a methylated methyl acceptor
NUC-5-PHOSPHATE a nucleoside-5'-phosphate
TRIMETHYLAMINE trimethylamine
URATE urate
UREA urea

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