Dead-End Metabolites by Markus Krummenacker Q1 2013.

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Presentation transcript:

Dead-End Metabolites by Markus Krummenacker Q1 2013

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.

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/

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.