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Dead-End Metabolites. by Markus Krummenacker Q4 2011. 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

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dead end metabolites

Dead-End Metabolites

by

Markus Krummenacker

Q4 2011

dead end metabolites1
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
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
Remedies
  • More curation: create missing metabolic or transport reactions
  • Shortcut: Add to secretions (or nutrients) set in .fba file
  • In MILP mode, the new 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.