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@axelvonkamp
axelvonkamp authored Aug 11, 2022
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1 change: 1 addition & 0 deletions e_coli_core_14bdo/ecc_14bdo_example_10.sdc
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{"model_id": "e_coli_core", "sd_modules": [{"module_type": "optknock", "constraints": [[{"BIOMASS_Ecoli_core_w_GAM": 1.0}, ">=", 0.5]], "inner_objective": {"BIOMASS_Ecoli_core_w_GAM": 1.0, "EX_14bdo_e": -0.001}, "inner_opt_sense": "maximize", "outer_objective": {"EX_14bdo_e": 1.0}, "outer_opt_sense": "maximize", "prod_id": null, "min_gcp": null, "skip_checks": true, "reac_ids": ["PFK", "PFL", "PGI", "PGK", "PGL", "ACALD", "AKGt2r", "PGM", "PIt2r", "ALCD2x", "ACALDt", "ACKr", "PPC", "ACONTa", "ACONTb", "ATPM", "PPCK", "ACt2r", "PPS", "ADK1", "AKGDH", "ATPS4r", "PTAr", "PYK", "BIOMASS_Ecoli_core_w_GAM", "PYRt2", "CO2t", "RPE", "CS", "RPI", "SUCCt2_2", "CYTBD", "D_LACt2", "ENO", "SUCCt3", "ETOHt2r", "SUCDi", "SUCOAS", "TALA", "THD2", "TKT1", "TKT2", "TPI", "EX_ac_e", "EX_acald_e", "EX_akg_e", "EX_co2_e", "EX_etoh_e", "EX_for_e", "EX_fru_e", "EX_fum_e", "EX_glc__D_e", "EX_gln__L_e", "EX_glu__L_e", "EX_h_e", "EX_h2o_e", "EX_lac__D_e", "EX_mal__L_e", "EX_nh4_e", "EX_o2_e", "EX_pi_e", "EX_pyr_e", "EX_succ_e", "FBA", "FBP", "FORt2", "FORt", "FRD7", "FRUpts2", "FUM", "FUMt2_2", "G6PDH2r", "GAPD", "GLCpts", "GLNS", "GLNabc", "GLUDy", "GLUN", "GLUSy", "GLUt2r", "GND", "H2Ot", "ICDHyr", "ICL", "LDH_D", "MALS", "MALt2_2", "MDH", "ME1", "ME2", "NADH16", "NADTRHD", "NH4t", "O2t", "PDH", "SSCOARx", "HBD", "HBCT", "HBDH", "HBDx", "BDOtpp", "BDOtex", "EX_14bdo_e", "AKGDC"]}], "gene_kos": true, "use_scenario": false, "max_solutions": "1", "max_cost": "30", "time_limit": "inf", "advanced": true, "solver": "gurobi", "solution_approach": "best", "reg_cost": {}, "ko_cost": {"EX_o2_e": 1.0}, "ki_cost": {"SSCOARx": 1.0, "AKGDC": 1.0}, "gko_cost": {"adhE": 1.0, "mhpF": 1.0, "purT": 1.0, "tdcD": 1.0, "ackA": 1.0, "acnA": 1.0, "acnB": 1.0, "adk": 1.0, "lpd": 1.0, "sucB": 1.0, "sucA": 1.0, "kgtP": 1.0, "frmA": 1.0, "adhP": 1.0, "atpA": 1.0, "atpG": 1.0, "atpF": 1.0, "atpE": 1.0, "atpI": 1.0, "atpB": 1.0, "atpH": 1.0, "atpC": 1.0, "atpD": 1.0, "gltA": 1.0, "cydA": 1.0, "cydB": 1.0, "cbdB": 1.0, "cbdA": 1.0, "lldP": 1.0, "glcA": 1.0, "eno": 1.0, "fbaA": 1.0, "ydjI": 1.0, "fbaB": 1.0, "glpX": 1.0, "fbp": 1.0, "focB": 1.0, "focA": 1.0, "frdC": 1.0, "frdA": 1.0, "frdB": 1.0, "frdD": 1.0, "manZ": 1.0, "manX": 1.0, "ptsI": 1.0, "ptsH": 1.0, "manY": 1.0, "fumC": 1.0, "fumB": 1.0, "fumA": 1.0, "dctA": 1.0, "zwf": 1.0, "gapA": 1.0, "ptsG": 1.0, "crr": 1.0, "malX": 1.0, "puuA": 1.0, "glnA": 1.0, "glnQ": 1.0, "glnH": 1.0, "glnP": 1.0, "gdhA": 1.0, "glsB": 1.0, "glsA": 1.0, "pabB": 1.0, "gltD": 1.0, "gltB": 1.0, "gltP": 1.0, "gnd": 1.0, "aqpZ": 1.0, "icd": 1.0, "aceA": 1.0, "ldhA": 1.0, "dld": 1.0, "aceB": 1.0, "glcB": 1.0, "mdh": 1.0, "maeA": 1.0, "maeB": 1.0, "nuoI": 1.0, "nuoM": 1.0, "nuoJ": 1.0, "nuoC": 1.0, "nuoB": 1.0, "nuoF": 1.0, "nuoN": 1.0, "nuoH": 1.0, "nuoK": 1.0, "nuoG": 1.0, "nuoE": 1.0, "nuoA": 1.0, "nuoL": 1.0, "pntA": 1.0, "sthA": 1.0, "pntB": 1.0, "amtB": 1.0, "aceE": 1.0, "aceF": 1.0, "pfkA": 1.0, "pfkB": 1.0, "tdcE": 1.0, "grcA": 1.0, "pflD": 1.0, "pflA": 1.0, "pflC": 1.0, "pflB": 1.0, "pgi": 1.0, "pgk": 1.0, "pgl": 1.0, "gpmM": 1.0, "ytjC": 1.0, "gpmA": 1.0, "pitA": 1.0, "pitB": 1.0, "ppc": 1.0, "pck": 1.0, "ppsA": 1.0, "pta": 1.0, "eutD": 1.0, "pykF": 1.0, "pykA": 1.0, "rpe": 1.0, "sgcE": 1.0, "rpiA": 1.0, "rpiB": 1.0, "sdhC": 1.0, "sdhD": 1.0, "sdhB": 1.0, "sdhA": 1.0, "sucD": 1.0, "sucC": 1.0, "talB": 1.0, "talA": 1.0, "tktB": 1.0, "tktA": 1.0, "tpiA": 1.0}, "gki_cost": {}}
1 change: 1 addition & 0 deletions e_coli_core_14bdo/ecc_14bdo_example_12.sdc
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{"model_id": "e_coli_core", "sd_modules": [{"module_type": "robustknock", "constraints": [[{"BIOMASS_Ecoli_core_w_GAM": 1.0}, ">=", 0.5]], "inner_objective": {"BIOMASS_Ecoli_core_w_GAM": 1.0}, "inner_opt_sense": "maximize", "outer_objective": {"EX_14bdo_e": 1.0}, "outer_opt_sense": "maximize", "prod_id": null, "min_gcp": null, "skip_checks": true, "reac_ids": ["PFK", "PFL", "PGI", "PGK", "PGL", "ACALD", "AKGt2r", "PGM", "PIt2r", "ALCD2x", "ACALDt", "ACKr", "PPC", "ACONTa", "ACONTb", "ATPM", "PPCK", "ACt2r", "PPS", "ADK1", "AKGDH", "ATPS4r", "PTAr", "PYK", "BIOMASS_Ecoli_core_w_GAM", "PYRt2", "CO2t", "RPE", "CS", "RPI", "SUCCt2_2", "CYTBD", "D_LACt2", "ENO", "SUCCt3", "ETOHt2r", "SUCDi", "SUCOAS", "TALA", "THD2", "TKT1", "TKT2", "TPI", "EX_ac_e", "EX_acald_e", "EX_akg_e", "EX_co2_e", "EX_etoh_e", "EX_for_e", "EX_fru_e", "EX_fum_e", "EX_glc__D_e", "EX_gln__L_e", "EX_glu__L_e", "EX_h_e", "EX_h2o_e", "EX_lac__D_e", "EX_mal__L_e", "EX_nh4_e", "EX_o2_e", "EX_pi_e", "EX_pyr_e", "EX_succ_e", "FBA", "FBP", "FORt2", "FORt", "FRD7", "FRUpts2", "FUM", "FUMt2_2", "G6PDH2r", "GAPD", "GLCpts", "GLNS", "GLNabc", "GLUDy", "GLUN", "GLUSy", "GLUt2r", "GND", "H2Ot", "ICDHyr", "ICL", "LDH_D", "MALS", "MALt2_2", "MDH", "ME1", "ME2", "NADH16", "NADTRHD", "NH4t", "O2t", "PDH", "SSCOARx", "HBD", "HBCT", "HBDH", "HBDx", "BDOtpp", "BDOtex", "EX_14bdo_e", "AKGDC"]}], "gene_kos": true, "use_scenario": false, "max_solutions": "1", "max_cost": "30", "time_limit": "inf", "advanced": true, "solver": "gurobi", "solution_approach": "best", "reg_cost": {}, "ko_cost": {"EX_o2_e": 1.0}, "ki_cost": {"SSCOARx": 1.0, "AKGDC": 1.0}, "gko_cost": {"adhE": 1.0, "mhpF": 1.0, "purT": 1.0, "tdcD": 1.0, "ackA": 1.0, "acnA": 1.0, "acnB": 1.0, "adk": 1.0, "lpd": 1.0, "sucB": 1.0, "sucA": 1.0, "kgtP": 1.0, "frmA": 1.0, "adhP": 1.0, "atpA": 1.0, "atpG": 1.0, "atpF": 1.0, "atpE": 1.0, "atpI": 1.0, "atpB": 1.0, "atpH": 1.0, "atpC": 1.0, "atpD": 1.0, "gltA": 1.0, "cydA": 1.0, "cydB": 1.0, "cbdB": 1.0, "cbdA": 1.0, "lldP": 1.0, "glcA": 1.0, "eno": 1.0, "fbaA": 1.0, "ydjI": 1.0, "fbaB": 1.0, "glpX": 1.0, "fbp": 1.0, "focB": 1.0, "focA": 1.0, "frdC": 1.0, "frdA": 1.0, "frdB": 1.0, "frdD": 1.0, "manZ": 1.0, "manX": 1.0, "ptsI": 1.0, "ptsH": 1.0, "manY": 1.0, "fumC": 1.0, "fumB": 1.0, "fumA": 1.0, "dctA": 1.0, "zwf": 1.0, "gapA": 1.0, "ptsG": 1.0, "crr": 1.0, "malX": 1.0, "puuA": 1.0, "glnA": 1.0, "glnQ": 1.0, "glnH": 1.0, "glnP": 1.0, "gdhA": 1.0, "glsB": 1.0, "glsA": 1.0, "pabB": 1.0, "gltD": 1.0, "gltB": 1.0, "gltP": 1.0, "gnd": 1.0, "aqpZ": 1.0, "icd": 1.0, "aceA": 1.0, "ldhA": 1.0, "dld": 1.0, "aceB": 1.0, "glcB": 1.0, "mdh": 1.0, "maeA": 1.0, "maeB": 1.0, "nuoI": 1.0, "nuoM": 1.0, "nuoJ": 1.0, "nuoC": 1.0, "nuoB": 1.0, "nuoF": 1.0, "nuoN": 1.0, "nuoH": 1.0, "nuoK": 1.0, "nuoG": 1.0, "nuoE": 1.0, "nuoA": 1.0, "nuoL": 1.0, "pntA": 1.0, "sthA": 1.0, "pntB": 1.0, "amtB": 1.0, "aceE": 1.0, "aceF": 1.0, "pfkA": 1.0, "pfkB": 1.0, "tdcE": 1.0, "grcA": 1.0, "pflD": 1.0, "pflA": 1.0, "pflC": 1.0, "pflB": 1.0, "pgi": 1.0, "pgk": 1.0, "pgl": 1.0, "gpmM": 1.0, "ytjC": 1.0, "gpmA": 1.0, "pitA": 1.0, "pitB": 1.0, "ppc": 1.0, "pck": 1.0, "ppsA": 1.0, "pta": 1.0, "eutD": 1.0, "pykF": 1.0, "pykA": 1.0, "rpe": 1.0, "sgcE": 1.0, "rpiA": 1.0, "rpiB": 1.0, "sdhC": 1.0, "sdhD": 1.0, "sdhB": 1.0, "sdhA": 1.0, "sucD": 1.0, "sucC": 1.0, "talB": 1.0, "talA": 1.0, "tktB": 1.0, "tktA": 1.0, "tpiA": 1.0}, "gki_cost": {}}
1 change: 1 addition & 0 deletions e_coli_core_14bdo/ecc_14bdo_example_13.sdc
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{"model_id": "e_coli_core", "sd_modules": [{"module_type": "optcouple", "constraints": [], "inner_objective": {"BIOMASS_Ecoli_core_w_GAM": 1.0}, "inner_opt_sense": "maximize", "outer_objective": null, "outer_opt_sense": null, "prod_id": {"EX_14bdo_e": 1.0}, "min_gcp": 0.3, "skip_checks": true, "reac_ids": ["PFK", "PFL", "PGI", "PGK", "PGL", "ACALD", "AKGt2r", "PGM", "PIt2r", "ALCD2x", "ACALDt", "ACKr", "PPC", "ACONTa", "ACONTb", "ATPM", "PPCK", "ACt2r", "PPS", "ADK1", "AKGDH", "ATPS4r", "PTAr", "PYK", "BIOMASS_Ecoli_core_w_GAM", "PYRt2", "CO2t", "RPE", "CS", "RPI", "SUCCt2_2", "CYTBD", "D_LACt2", "ENO", "SUCCt3", "ETOHt2r", "SUCDi", "SUCOAS", "TALA", "THD2", "TKT1", "TKT2", "TPI", "EX_ac_e", "EX_acald_e", "EX_akg_e", "EX_co2_e", "EX_etoh_e", "EX_for_e", "EX_fru_e", "EX_fum_e", "EX_glc__D_e", "EX_gln__L_e", "EX_glu__L_e", "EX_h_e", "EX_h2o_e", "EX_lac__D_e", "EX_mal__L_e", "EX_nh4_e", "EX_o2_e", "EX_pi_e", "EX_pyr_e", "EX_succ_e", "FBA", "FBP", "FORt2", "FORt", "FRD7", "FRUpts2", "FUM", "FUMt2_2", "G6PDH2r", "GAPD", "GLCpts", "GLNS", "GLNabc", "GLUDy", "GLUN", "GLUSy", "GLUt2r", "GND", "H2Ot", "ICDHyr", "ICL", "LDH_D", "MALS", "MALt2_2", "MDH", "ME1", "ME2", "NADH16", "NADTRHD", "NH4t", "O2t", "PDH", "SSCOARx", "HBD", "HBCT", "HBDH", "HBDx", "BDOtpp", "BDOtex", "EX_14bdo_e", "AKGDC"]}], "gene_kos": true, "use_scenario": false, "max_solutions": "1", "max_cost": "15", "time_limit": "inf", "advanced": true, "solver": "gurobi", "solution_approach": "best", "reg_cost": {}, "ko_cost": {"EX_o2_e": 1.0}, "ki_cost": {"SSCOARx": 1.0, "AKGDC": 1.0}, "gko_cost": {"adhE": 1.0, "mhpF": 1.0, "purT": 1.0, "tdcD": 1.0, "ackA": 1.0, "acnA": 1.0, "acnB": 1.0, "adk": 1.0, "lpd": 1.0, "sucB": 1.0, "sucA": 1.0, "kgtP": 1.0, "frmA": 1.0, "adhP": 1.0, "atpA": 1.0, "atpG": 1.0, "atpF": 1.0, "atpE": 1.0, "atpI": 1.0, "atpB": 1.0, "atpH": 1.0, "atpC": 1.0, "atpD": 1.0, "gltA": 1.0, "cydA": 1.0, "cydB": 1.0, "cbdB": 1.0, "cbdA": 1.0, "lldP": 1.0, "glcA": 1.0, "eno": 1.0, "fbaA": 1.0, "ydjI": 1.0, "fbaB": 1.0, "glpX": 1.0, "fbp": 1.0, "focB": 1.0, "focA": 1.0, "frdC": 1.0, "frdA": 1.0, "frdB": 1.0, "frdD": 1.0, "manZ": 1.0, "manX": 1.0, "ptsI": 1.0, "ptsH": 1.0, "manY": 1.0, "fumC": 1.0, "fumB": 1.0, "fumA": 1.0, "dctA": 1.0, "zwf": 1.0, "gapA": 1.0, "ptsG": 1.0, "crr": 1.0, "malX": 1.0, "puuA": 1.0, "glnA": 1.0, "glnQ": 1.0, "glnH": 1.0, "glnP": 1.0, "gdhA": 1.0, "glsB": 1.0, "glsA": 1.0, "pabB": 1.0, "gltD": 1.0, "gltB": 1.0, "gltP": 1.0, "gnd": 1.0, "aqpZ": 1.0, "icd": 1.0, "aceA": 1.0, "ldhA": 1.0, "dld": 1.0, "aceB": 1.0, "glcB": 1.0, "mdh": 1.0, "maeA": 1.0, "maeB": 1.0, "nuoI": 1.0, "nuoM": 1.0, "nuoJ": 1.0, "nuoC": 1.0, "nuoB": 1.0, "nuoF": 1.0, "nuoN": 1.0, "nuoH": 1.0, "nuoK": 1.0, "nuoG": 1.0, "nuoE": 1.0, "nuoA": 1.0, "nuoL": 1.0, "pntA": 1.0, "sthA": 1.0, "pntB": 1.0, "amtB": 1.0, "aceE": 1.0, "aceF": 1.0, "pfkA": 1.0, "pfkB": 1.0, "tdcE": 1.0, "grcA": 1.0, "pflD": 1.0, "pflA": 1.0, "pflC": 1.0, "pflB": 1.0, "pgi": 1.0, "pgk": 1.0, "pgl": 1.0, "gpmM": 1.0, "ytjC": 1.0, "gpmA": 1.0, "pitA": 1.0, "pitB": 1.0, "ppc": 1.0, "pck": 1.0, "ppsA": 1.0, "pta": 1.0, "eutD": 1.0, "pykF": 1.0, "pykA": 1.0, "rpe": 1.0, "sgcE": 1.0, "rpiA": 1.0, "rpiB": 1.0, "sdhC": 1.0, "sdhD": 1.0, "sdhB": 1.0, "sdhA": 1.0, "sucD": 1.0, "sucC": 1.0, "talB": 1.0, "talA": 1.0, "tktB": 1.0, "tktA": 1.0, "tpiA": 1.0}, "gki_cost": {}}
1 change: 1 addition & 0 deletions e_coli_core_14bdo/ecc_14bdo_example_9.sdc
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{"model_id": "e_coli_core", "sd_modules": [{"module_type": "optknock", "constraints": [[{"BIOMASS_Ecoli_core_w_GAM": 1.0}, ">=", 0.5]], "inner_objective": {"BIOMASS_Ecoli_core_w_GAM": 1.0}, "inner_opt_sense": "maximize", "outer_objective": {"EX_14bdo_e": 1.0}, "outer_opt_sense": "maximize", "prod_id": null, "min_gcp": null, "skip_checks": true, "reac_ids": ["PFK", "PFL", "PGI", "PGK", "PGL", "ACALD", "AKGt2r", "PGM", "PIt2r", "ALCD2x", "ACALDt", "ACKr", "PPC", "ACONTa", "ACONTb", "ATPM", "PPCK", "ACt2r", "PPS", "ADK1", "AKGDH", "ATPS4r", "PTAr", "PYK", "BIOMASS_Ecoli_core_w_GAM", "PYRt2", "CO2t", "RPE", "CS", "RPI", "SUCCt2_2", "CYTBD", "D_LACt2", "ENO", "SUCCt3", "ETOHt2r", "SUCDi", "SUCOAS", "TALA", "THD2", "TKT1", "TKT2", "TPI", "EX_ac_e", "EX_acald_e", "EX_akg_e", "EX_co2_e", "EX_etoh_e", "EX_for_e", "EX_fru_e", "EX_fum_e", "EX_glc__D_e", "EX_gln__L_e", "EX_glu__L_e", "EX_h_e", "EX_h2o_e", "EX_lac__D_e", "EX_mal__L_e", "EX_nh4_e", "EX_o2_e", "EX_pi_e", "EX_pyr_e", "EX_succ_e", "FBA", "FBP", "FORt2", "FORt", "FRD7", "FRUpts2", "FUM", "FUMt2_2", "G6PDH2r", "GAPD", "GLCpts", "GLNS", "GLNabc", "GLUDy", "GLUN", "GLUSy", "GLUt2r", "GND", "H2Ot", "ICDHyr", "ICL", "LDH_D", "MALS", "MALt2_2", "MDH", "ME1", "ME2", "NADH16", "NADTRHD", "NH4t", "O2t", "PDH", "SSCOARx", "HBD", "HBCT", "HBDH", "HBDx", "BDOtpp", "BDOtex", "EX_14bdo_e", "AKGDC"]}], "gene_kos": true, "use_scenario": false, "max_solutions": "1", "max_cost": "30", "time_limit": "inf", "advanced": true, "solver": "cplex", "solution_approach": "best", "reg_cost": {}, "ko_cost": {"EX_o2_e": 1.0}, "ki_cost": {"SSCOARx": 1.0, "AKGDC": 1.0}, "gko_cost": {"adhE": 1.0, "mhpF": 1.0, "purT": 1.0, "tdcD": 1.0, "ackA": 1.0, "acnA": 1.0, "acnB": 1.0, "adk": 1.0, "lpd": 1.0, "sucB": 1.0, "sucA": 1.0, "kgtP": 1.0, "frmA": 1.0, "adhP": 1.0, "atpA": 1.0, "atpG": 1.0, "atpF": 1.0, "atpE": 1.0, "atpI": 1.0, "atpB": 1.0, "atpH": 1.0, "atpC": 1.0, "atpD": 1.0, "gltA": 1.0, "cydA": 1.0, "cydB": 1.0, "cbdB": 1.0, "cbdA": 1.0, "lldP": 1.0, "glcA": 1.0, "eno": 1.0, "fbaA": 1.0, "ydjI": 1.0, "fbaB": 1.0, "glpX": 1.0, "fbp": 1.0, "focB": 1.0, "focA": 1.0, "frdC": 1.0, "frdA": 1.0, "frdB": 1.0, "frdD": 1.0, "manZ": 1.0, "manX": 1.0, "ptsI": 1.0, "ptsH": 1.0, "manY": 1.0, "fumC": 1.0, "fumB": 1.0, "fumA": 1.0, "dctA": 1.0, "zwf": 1.0, "gapA": 1.0, "ptsG": 1.0, "crr": 1.0, "malX": 1.0, "puuA": 1.0, "glnA": 1.0, "glnQ": 1.0, "glnH": 1.0, "glnP": 1.0, "gdhA": 1.0, "glsB": 1.0, "glsA": 1.0, "pabB": 1.0, "gltD": 1.0, "gltB": 1.0, "gltP": 1.0, "gnd": 1.0, "aqpZ": 1.0, "icd": 1.0, "aceA": 1.0, "ldhA": 1.0, "dld": 1.0, "aceB": 1.0, "glcB": 1.0, "mdh": 1.0, "maeA": 1.0, "maeB": 1.0, "nuoI": 1.0, "nuoM": 1.0, "nuoJ": 1.0, "nuoC": 1.0, "nuoB": 1.0, "nuoF": 1.0, "nuoN": 1.0, "nuoH": 1.0, "nuoK": 1.0, "nuoG": 1.0, "nuoE": 1.0, "nuoA": 1.0, "nuoL": 1.0, "pntA": 1.0, "sthA": 1.0, "pntB": 1.0, "amtB": 1.0, "aceE": 1.0, "aceF": 1.0, "pfkA": 1.0, "pfkB": 1.0, "tdcE": 1.0, "grcA": 1.0, "pflD": 1.0, "pflA": 1.0, "pflC": 1.0, "pflB": 1.0, "pgi": 1.0, "pgk": 1.0, "pgl": 1.0, "gpmM": 1.0, "ytjC": 1.0, "gpmA": 1.0, "pitA": 1.0, "pitB": 1.0, "ppc": 1.0, "pck": 1.0, "ppsA": 1.0, "pta": 1.0, "eutD": 1.0, "pykF": 1.0, "pykA": 1.0, "rpe": 1.0, "sgcE": 1.0, "rpiA": 1.0, "rpiB": 1.0, "sdhC": 1.0, "sdhD": 1.0, "sdhB": 1.0, "sdhA": 1.0, "sucD": 1.0, "sucC": 1.0, "talB": 1.0, "talA": 1.0, "tktB": 1.0, "tktA": 1.0, "tpiA": 1.0}, "gki_cost": {}}

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