Figure 3

Comparison of reaction-based deletion strategies (OptKnock) and gene-based deletion strategies (OptORF). (A) A total of 200 optimal reaction deletion strategies (50 double, triple, quadruple, and quintuple reaction deletions each) were found by OptKnock, and the minimal number of gene deletions that are required to remove the identified reactions were found for each OptKnock strategy. The last histogram (overall) shows the overall distribution of required gene deletions across all 200 strains. (B-C) For each OptKnock strategy, an analogous strategy was then identified with OptORF which had the same number of gene deletions as the OptKnock strategy, giving 200 OptORF strains with the same overall gene deletion distribution as shown in (A). The ethanol yields and growth rates for the 200 OptKnock strains (blue triangles) and 200 OptORF strains (red circles) are shown in panels B and C, with OptORF strains having higher ethanol yields as compared to OptKnock strains for the same number of gene deletions.