Supplement to: Omic Data from Evolved Strains are Consistent with Computed Optimal Growth States

A. Supplementary Figures Referenced in the Main Text .............................................. 3 Supplementary Figure 1. Parsimonious Enzyme Usage FBA. .............................. 3 Supplementary Figure 2. pFBA shows a small improvement of normal FBA. ..... 4 Supplementary Figure 3.Few less-efficient genes are up-regulated and functional in up-regulation-optimized models. ....................................................................... 5 Supplementary Figure 4. Coverage of down regulated genes and proteins in metabolic regulons. ................................................................................................ 6 Supplementary Figure 5. A flowchart for the simulation and classification of genes in pFBA........................................................................................................ 7 B. Supplementary Methods ............................................................................................ 8 AMT tag method ........................................................................................................ 8