Patent Document ID: 10102335
Application ID: 14134353
Patent Flag: 1

Claim One:
1. A method for optimizing a phenotype in an actual microbial strain, the method comprising: simulating metabolic flux states by steps comprising: providing a set of reactions for a cellular phenotype; identifying a set of enzymes that participate in the set of reactions for the cellular phenotype; providing the metabolic costs associated with production of each enzyme of the set of enzymes that participates in the set of reactions for the cellular phenotype; identifying a first pool of amino acids which participate in the set of reactions for the cellular phenotype; identifying a second pool of amino acids which are constituents of the set of enzymes that participate in the set of reactions for the cellular phenotype; maximizing the cellular phenotype by obtaining a maximum flux of the first pool of amino acids through the set of reactions such that all possible fluxes corresponding to the maximized cellular phenotype are identified; obtaining a minimum-cost flux distribution of the second pool of amino acids for each of the possible fluxes corresponding to the maximized cellular phenotype based on the provided metabolic costs; whereby individual metabolic pathways that maximize the cellular phenotype while minimizing metabolic costs associated with production of the set of enzymes that participate in the set of reactions for the cellular phenotype are identified; and implementing results of the simulation by: providing an actual microbial strain and modifying the actual microbial strain to maximize the cellular phenotype of the actual microbial strain by manipulating the genome of the actual microbial strain to add or delete genes encoding specific biochemical reactions corresponding to the individual metabolic pathways that were identified to maximize the cellular phenotype while minimizing metabolic costs in the simulation.