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Table 1 Selected Pareto optimal engineering designs

From: Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

Design identifiers Design criteria Design annotations Design metrics
Design Ida Cluster Idb Design goalsc Design typed Gene deletions Nutrient sourcese Organismf Acetate production rate (mmol gDW-1 hr-1) Acetate purity Biomass production rate (hr-1) Microarray consistencyg Succinate production rate (mmol gDW-1 hr-1) Succinate purity Total economic cost rate ($ hr-1)
1 8 Succinate production rate (0.99), Succinate purity (0.01) candidate edd, gnd malthx, fum, gam, pi, so4 ec 0 0 1.85 NA 195.34 0.63 19314.4
2 8 Succinate production rate (0.5), Succinate purity (0.5) candidate atpH, caiD malthx, fum, gam, pi, so4 ec 0 0 1.85 NA 181.57 0.71 19305.4
3 3 Succinate purity (1) candidate SO4417, SO3136 ac, fum, nh4, pi, so4 so 0 0 0.01 NA 20 1 3.72
4 1 Succinate production rate (0.01), Total economic cost rate (−0.99) candidate kgtP, lysP sucr, o2, gam, ppt, so4 ec 36.17 0.35 1.85 NA 51.45 0.49 4.33
5 30 Succinate purity (0.5), Total economic cost rate (−0.5) candidate YBR196C, YMR256C glc, o2, urea, pi, so4 sc 0 0 0.26 NA 14.77 0.43 0.05
6 1 Succinate production rate (0.33), Succinate purity (0.33), Total economic cost rate (−0.33) candidate SO4417, SO3136 glyclt, fum, nh4, pi, so4 so 0 0 0.06 NA 20 1 2.26
7 1 Succinate production rate (1) validated ptsG, pykFA, pfl glc, NA, nh4, pi, so4 ec 4.28 0.24 0.12 NA 9.12 0.5 0.03
8 1 Acetate production rate (1) microarray appY glc, NA, nh4, pi, so4 ec 6.76 0.24 0.17 0.46 0.06 0 0.75
9 1 Acetate purity (1) microarray arcA glc, o2, nh4, pi, so4 ec 1.1 1 0.63 0.02 0 0 2.35
10 1 Microarray consistency (1) microarray arcA glc, NA, nh4, pi, so4 ec 0 0 0.11 0.56 0.04 0 0.02
11 1 Acetate production rate (0.33), Microarray consistency (0.33), Acetate purity (0.33) microarray appY glc, NA, nh4, pi, so4 ec 6.76 0.24 0.17 0.46 0.06 0 0.75
  1. a Engineering designs are referenced in the text by this identifier. b Each engineering design is associated with an engineering phenotype cluster (meta-phenotype) and identified according to the “Clusters” shown in Figure6(A) for E. coli, Additional file1: Figure S13(A) for S. cerevisiae, and Additional file1: Figure S14(A) for S. oneidensis. c The specified engineering design goals and weights (shown in parentheses, where positive weights indicate goal maximization and negative weights indicate goal minimization) are used to determine the optimal engineering designs for the corresponding “Design type”. d “Validated” designs are designs that were experimentally validated, “microarray” designs are designs that had matching experimental microarray data, and “candidate” designs are simulated designs that are neither “validated” nor “microarray” designs. e Nutrients are ordered by nutrient type: carbon, electron acceptor, nitrogen, phosphorous, and sulfur source. “NA” indicates that no nutrient source of that type was provided. Metabolite abbreviations: ac = Acetate, fum = Fumarate, gam = D-Glucosamine, glc = D-Glucose, glu-L = L-Glutamate, glyclt = Glycolate, malthx = Maltohexoase, nh4 = Ammonium, o2 = O2, pi = Phosphate, ppt = Phosphonate, sbt-D = D-Sorbitol, so4 = Sulfate, sucr = Sucrose, urea = Urea. f Organism abbreviations: ec = Escherichia coli, sc = Saccharomyces cerevisiae, so = Shewanella oneidensis. g Engineering design simulations were compared with microarray data to compute experimental microarray consistency. “NA” indicates that no microarray data was available for the corresponding design.