Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design

Table 3 (Information on resulting strains after running the algorithm for the lycopene model.

	Equal-Weighted			Thermodynamically-Weighted
Fitness function^a	Lycopene	Biomass	Lycopene × Biomass	Lycopene	Biomass	Lycopene × Biomass
Number of reactions removed	17	14	13	10	12	10
Number of associated genes (or gene clusters) ^b	21	15	12	9	9	10
Gene list	aceA adhE atpABCDEFGHI cyoABCD eda fbp fdhF frdABCD fumABC glpX hycBCDEFG ldhA maeB ndh aceEF pflB ppc pps pykAF sfcA tdcE	ackAB adhE adhP frdABCD lpdA maeB ndh aceAB pckA pgi poxB sfcA sucAB sucCD talAB	ackAB adhE adhP adk fbp fdhF glpX hycBCDEFG ldhA pckA ppc pta	adk eda frdABCD gnd ndh aceB rpe sucCD tktAB	aceA adhE adhP fbaAB ldhA maeB ndh rpe sfcA	aceAB adhE atpABCDEFGHI cyoABCD ldhA pgmA pgml poxB pta ytjC
Total number of EMs	18	21	80	174	35	86
Biomass yield (fraction of theoretical)	0.000	0.900	0.272	0.000	0.842	0.410
Lycopene yield (fraction of theoretical)	0.968	0.015	0.698	0.646	0.001	0.418

^a Fitness functions are defined in the Methods section. ^b Enzymes with multiple subunits encoded by different genes in the same operon are only counted once.)

ISSN: 1752-0509