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pstjohn/becker_results_recreation.ipynb

Last active October 12, 2017 13:38
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Recreate results from Becker et al (10.1002/bit.24963)
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becker_results_recreation.ipynb
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sbml_version.xml
<?xml version='1.0' encoding='UTF-8'?>
<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" sboTerm="SBO:0000624" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false">
<model fbc:strict="true" id="basfia" name="b. Succiniciproducens">
<listOfUnitDefinitions>
<unitDefinition id="mmol_per_gDW_per_hr">
<listOfUnits>
<unit exponent="1" kind="mole" multiplier="1" scale="-3"/>
<unit exponent="-1" kind="gram" multiplier="1" scale="0"/>
<unit exponent="-1" kind="second" multiplier="3600" scale="0"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<fbc:listOfObjectives fbc:activeObjective="obj">
<fbc:objective fbc:id="obj" fbc:type="maximize">
<fbc:listOfFluxObjectives>
<fbc:fluxObjective fbc:reaction="R_biomass" fbc:coefficient="1"/>
</fbc:listOfFluxObjectives>
</fbc:objective>
</fbc:listOfObjectives>
<listOfParameters>
<parameter constant="true" id="cobra_default_lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-1000"/>
<parameter constant="true" id="cobra_default_ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="1000"/>
<parameter constant="true" id="cobra_0_bound" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="0"/>
<parameter constant="true" id="R_ATPM_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.55"/>
<parameter constant="true" id="R_EX_glc__D_e_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="-7.7"/>
</listOfParameters>
<listOfCompartments>
<compartment constant="true" id="c" name=""/>
<compartment constant="true" id="e" name=""/>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_13dpg_c" compartment="c" fbc:charge="-4" fbc:chemicalFormula="C3H4O10P2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_2pg_c" compartment="c" fbc:charge="-3" fbc:chemicalFormula="C3H4O7P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_3pg_c" compartment="c" fbc:charge="-3" fbc:chemicalFormula="C3H4O7P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_6pgc_c" compartment="c" fbc:charge="-3" fbc:chemicalFormula="C6H10O10P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_H2S_c" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_MKH2_c" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_MK_c" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_SO4_c" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_SUCC-CoA_c" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_ac_c" compartment="c" fbc:charge="-1" fbc:chemicalFormula="C2H3O2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_ac_e" compartment="e" fbc:charge="-1" fbc:chemicalFormula="C2H3O2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_acald_c" compartment="c" fbc:charge="0" fbc:chemicalFormula="C2H4O"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_accoa_c" compartment="c" fbc:charge="-4" fbc:chemicalFormula="C23H34N7O17P3S"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_actp_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C2H3O5P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_adp_c" compartment="c" fbc:charge="-3" fbc:chemicalFormula="C10H12N5O10P2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_akg_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C5H4O5"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_atp_c" compartment="c" fbc:charge="-4" fbc:chemicalFormula="C10H12N5O13P3"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_atpm_e" compartment="e"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_biomass_e" compartment="e"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_cit_c" compartment="c" fbc:charge="-3" fbc:chemicalFormula="C6H5O7"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_co2_c" compartment="c" fbc:charge="0" fbc:chemicalFormula="CO2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_coa_c" compartment="c" fbc:charge="-4" fbc:chemicalFormula="C21H32N7O16P3S"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_dhap_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C3H5O6P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_e4p_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C4H7O7P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_etoh_c" compartment="c" fbc:charge="0" fbc:chemicalFormula="C2H6O"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_etoh_e" compartment="e" fbc:charge="0" fbc:chemicalFormula="C2H6O"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_f6p_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C6H11O9P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_fdp_c" compartment="c" fbc:charge="-4" fbc:chemicalFormula="C6H10O12P2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_for_c" compartment="c" fbc:charge="-1" fbc:chemicalFormula="CH1O2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_for_e" compartment="e" fbc:charge="-1" fbc:chemicalFormula="CH1O2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_fum_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C4H2O4"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_g3p_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C3H5O6P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_g6p_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C6H11O9P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_glc__D_c" compartment="c" fbc:charge="0" fbc:chemicalFormula="C6H12O6"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_glc__D_e" compartment="e" fbc:charge="0" fbc:chemicalFormula="C6H12O6"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_icit_c" compartment="c" fbc:charge="-3" fbc:chemicalFormula="C6H5O7"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_lac__D_c" compartment="c" fbc:charge="-1" fbc:chemicalFormula="C3H5O3"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_lac__D_e" compartment="e" fbc:charge="-1" fbc:chemicalFormula="C3H5O3"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_mal__D_c" compartment="c" fbc:charge="-2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_nad_c" compartment="c" fbc:charge="-1" fbc:chemicalFormula="C21H26N7O14P2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_nadh_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C21H27N7O14P2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_nadp_c" compartment="c" fbc:charge="-3" fbc:chemicalFormula="C21H25N7O17P3"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_nadph_c" compartment="c" fbc:charge="-4" fbc:chemicalFormula="C21H26N7O17P3"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_nh4_c" compartment="c" fbc:charge="1" fbc:chemicalFormula="H4N"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_oaa_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C4H2O5"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_pep_c" compartment="c" fbc:charge="-3" fbc:chemicalFormula="C3H2O6P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_pyr_c" compartment="c" fbc:charge="-1" fbc:chemicalFormula="C3H3O3"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_r5p_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C5H9O8P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_ru5p_c" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_s7p_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C7H13O10P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_succ_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C4H4O4"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_succ_e" compartment="e" fbc:charge="-2" fbc:chemicalFormula="C4H4O4"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_xu5p__D_c" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C5H9O8P"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_xu_c" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_xyl_c" compartment="c" fbc:charge="0" fbc:chemicalFormula="C5H10O5"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_xyl_e" compartment="e"/>
</listOfSpecies>
<listOfReactions>
<reaction fast="false" id="R_ATPM" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="R_ATPM_lower_bound">
<listOfReactants>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_atpm_e" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_EX_SO4_c" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_SO4_c" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_ac_e" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_ac_e" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_atpm_e" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_atpm_e" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_biomass_e" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_biomass_e" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_co2_c" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_co2_c" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_coa_c" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_etoh_e" reversible="false" fbc:upperFluxBound="cobra_0_bound" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_etoh_e" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_for_e" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_for_e" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_glc__D_e" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="R_EX_glc__D_e_lower_bound">
<listOfReactants>
<speciesReference constant="true" species="M_glc__D_e" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_lac__D_e" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_lac__D_e" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_nh4_c" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_nh4_c" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_succ_e" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_succ_e" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_EX_xyl_e" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_xyl_e" stoichiometry="1"/>
</listOfReactants>
</reaction>
<reaction fast="false" id="R_biomass" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_3pg_c" stoichiometry="1.221"/>
<speciesReference constant="true" species="M_H2S_c" stoichiometry="0.091"/>
<speciesReference constant="true" species="M_accoa_c" stoichiometry="2.887"/>
<speciesReference constant="true" species="M_akg_c" stoichiometry="1.186"/>
<speciesReference constant="true" species="M_atp_c" stoichiometry="36.655"/>
<speciesReference constant="true" species="M_e4p_c" stoichiometry="0.223"/>
<speciesReference constant="true" species="M_f6p_c" stoichiometry="0.071"/>
<speciesReference constant="true" species="M_g3p_c" stoichiometry="0.129"/>
<speciesReference constant="true" species="M_g6p_c" stoichiometry="0.205"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="3.094"/>
<speciesReference constant="true" species="M_nadph_c" stoichiometry="15.754"/>
<speciesReference constant="true" species="M_nh4_c" stoichiometry="9.284"/>
<speciesReference constant="true" species="M_oaa_c" stoichiometry="1.724"/>
<speciesReference constant="true" species="M_pep_c" stoichiometry="0.495"/>
<speciesReference constant="true" species="M_pyr_c" stoichiometry="2.745"/>
<speciesReference constant="true" species="M_ru5p_c" stoichiometry="0.853"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_adp_c" stoichiometry="36.655"/>
<speciesReference constant="true" species="M_biomass_e" stoichiometry="1"/>
<speciesReference constant="true" species="M_co2_c" stoichiometry="1.381"/>
<speciesReference constant="true" species="M_coa_c" stoichiometry="2.887"/>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="3.094"/>
<speciesReference constant="true" species="M_nadp_c" stoichiometry="15.754"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn13" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_glc__D_e" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_glc__D_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn14" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_glc__D_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_g6p_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn15" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_SO4_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_atp_c" stoichiometry="4"/>
<speciesReference constant="true" species="M_nadph_c" stoichiometry="3"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_H2S_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_adp_c" stoichiometry="4"/>
<speciesReference constant="true" species="M_nadp_c" stoichiometry="3"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn16" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_g6p_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_6pgc_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadph_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn17" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_6pgc_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_co2_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadph_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_r5p_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn18" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_r5p_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn19" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_r5p_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_ru5p_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn20" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_g3p_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_s7p_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_ru5p_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn21" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_g3p_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_s7p_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_e4p_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_f6p_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn22" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_f6p_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_g3p_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_e4p_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn23" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_g6p_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_f6p_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn24" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_f6p_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_fdp_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn25" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_fdp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_f6p_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn26" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_fdp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_dhap_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_g3p_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn27" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_dhap_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_g3p_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn28" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_g3p_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_13dpg_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn29" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_13dpg_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_3pg_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn30" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_3pg_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_2pg_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn31" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_2pg_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_pep_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn32" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_pep_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_pyr_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn33" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_pyr_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_accoa_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_co2_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn34" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_accoa_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_oaa_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_cit_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn35" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_cit_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_icit_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn36" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_icit_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_akg_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_co2_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadph_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn37" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_akg_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_SUCC-CoA_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_co2_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn38" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_SUCC-CoA_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_succ_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn39" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_MK_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_succ_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_MKH2_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_fum_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn40" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_fum_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_mal__D_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn41" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_mal__D_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_oaa_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn45" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_co2_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_pep_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_oaa_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn46" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_mal__D_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_co2_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadph_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_pyr_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn48" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_pyr_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_lac__D_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn49" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_pyr_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_accoa_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_for_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn50" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_for_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_co2_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn51" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_accoa_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_actp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn52" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_actp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_ac_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn54" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_accoa_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_acald_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn55" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_acald_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_etoh_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn56" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_acald_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_ac_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn57" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_lac__D_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_lac__D_e" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn58" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_ac_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_ac_e" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn59" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_succ_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_succ_e" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn60" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_for_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_for_e" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn61" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_etoh_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_etoh_e" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn63" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="3"/>
<speciesReference constant="true" species="M_nadp_c" stoichiometry="3"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="3"/>
<speciesReference constant="true" species="M_nadph_c" stoichiometry="3"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn64" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadph_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadp_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn65" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_MK_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nadh_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_MKH2_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_nad_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn68" reversible="false" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_xyl_e" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_xyl_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn69" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_xyl_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_xu_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
<reaction fast="false" id="R_rxn70" reversible="true" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_xu_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
Raw
v1_4_basfia.json
{
"compartments": {
"c": "",
"e": ""
},
"genes": [],
"id": "basfia",
"metabolites": [
{
"charge": -4,
"compartment": "c",
"formula": "C3H4O10P2",
"id": "13dpg_c",
"name": "",
"notes": {
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"display_name": "13DPG",
"flux": 14.678345296791639,
"x": 357.043223866228,
"y": 266.3584107009283
}
}
},
{
"charge": -3,
"compartment": "c",
"formula": "C3H4O7P",
"id": "2pg_c",
"name": "",
"notes": {
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"y": 361.4944779568823
}
}
},
{
"charge": -3,
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"formula": "C3H4O7P",
"id": "3pg_c",
"name": "",
"notes": {
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}
}
},
{
"charge": -3,
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"formula": "C6H10O10P",
"id": "6pgc_c",
"name": "",
"notes": {
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"display_name": "6PGC",
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"x": 225.10189728325582,
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}
}
},
{
"compartment": "c",
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"id": "H2S_c",
"name": "",
"notes": {
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"hidden": true
}
}
},
{
"compartment": "c",
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"id": "MKH2_c",
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"notes": {
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}
}
},
{
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"id": "MK_c",
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}
}
},
{
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"id": "SO4_c",
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}
}
},
{
"compartment": "c",
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"id": "SUCC-CoA_c",
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"notes": {
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}
}
},
{
"charge": -1,
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"formula": "C2H3O2",
"id": "ac_c",
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"notes": {
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}
}
},
{
"charge": -1,
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"notes": {
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}
}
},
{
"charge": 0,
"compartment": "c",
"formula": "C2H4O",
"id": "acald_c",
"name": "",
"notes": {
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"display_name": "ACALD",
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"hidden": false,
"x": 536.8326330316315,
"y": 629.6824031637002
}
}
},
{
"charge": -4,
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