1. Dead-End Metabolites by
Markus Krummenacker
Q4 2013

2. Dead-End Metabolites
Knowledge of cellular metabolism is incomplete, so some metabolites can be dead-ends in the reaction network.
Either only consumed, or only produced by their reactions
Affects whether some reactions in FBA can carry flux. Dead-ends can block flux.
EcoCyc Example: spermidine biosynthesis. S- methyl-5-thio-D-ribose had to be listed in the secretions set.

3. Dead-End Metabolite Finder
Command under Tools menu
Choice whether to ignore reactions of unknown direction, or to treat them as reversible
Resulting dead-end metabolites are shown on Cellular Overview
Report file written to *cyc/version/reports/

4. Remedies
More curation: create missing metabolic or transport reactions
Shortcut: Add to secretions (or nutrients) set in .fba file
In MILP mode, the keyword all-compounds can used for the try-secretions parameter. The try-secretion-weight should be set to a negative value, or else too many compounds are added.