Mercurial > repos > bimib > marea_2_0
changeset 215:69ffff42d658 draft
Uploaded
| author | luca_milaz |
|---|---|
| date | Sat, 06 Jul 2024 09:24:54 +0000 |
| parents | 37c343ca4448 |
| children | da5071684811 |
| files | marea_2_0/flux_sampling.py marea_2_0/flux_sampling.xml marea_2_0/local/COBRA models/ENGRO2.xml marea_2_0/model_generator.py marea_2_0/model_generator.xml marea_2_0/utils/CBS_backend.py marea_2_0/utils/flux_analysis.py marea_2_0/utils/general_utils.py |
| diffstat | 5 files changed, 11634 insertions(+), 87 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/marea_2_0/local/COBRA models/ENGRO2.xml Sat Jul 06 09:24:54 2024 +0000 @@ -0,0 +1,11558 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" metaid="meta_" sboTerm="SBO:0000624" level="3" version="1" fbc:required="false"> + <model metaid="meta_dc" id="dc" name="Empty model structure" fbc:strict="true"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit kind="mole" exponent="1" scale="-3" multiplier="1"/> + <unit kind="gram" exponent="-1" scale="0" multiplier="1"/> + <unit kind="second" exponent="-1" scale="0" multiplier="3600"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment id="C_c" name="cytosol" constant="true"/> + <compartment id="C_m" name="mitochondrium" constant="true"/> + <compartment id="C_e" name="extracellular" constant="true"/> + </listOfCompartments> + <listOfSpecies> + <species metaid="meta_M_accoa_c" sboTerm="SBO:0000299" id="M_accoa_c" name="acetylCoAc" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C23H34N7O17P3S"/> + <species metaid="meta_M_accoa_m" sboTerm="SBO:0000299" id="M_accoa_m" name="acetylCoAm" compartment="C_m" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C23H34N7O17P3S"/> + <species metaid="meta_M_pyr_m" sboTerm="SBO:0000299" id="M_pyr_m" name="pyruvatem" compartment="C_m" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C3H3O3"/> + <species metaid="meta_M_pyr_c" sboTerm="SBO:0000299" id="M_pyr_c" name="pyruvatec" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C3H3O3"/> + <species metaid="meta_M_lac__L_c" sboTerm="SBO:0000299" id="M_lac__L_c" name="lactatec" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C3H5O3"/> + <species metaid="meta_M_lac__L_e" sboTerm="SBO:0000299" id="M_lac__L_e" name="lactatex" compartment="C_e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C3H5O3"/> + <species metaid="meta_M_f6p_c" sboTerm="SBO:0000299" id="M_f6p_c" name="fructose6phosphatec" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C6H11O9P"/> + <species metaid="meta_M_fdp_c" sboTerm="SBO:0000299" id="M_fdp_c" name="fructose1_6bisphosphatec" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C6H10O12P2"/> + <species metaid="meta_M_pep_c" sboTerm="SBO:0000299" id="M_pep_c" name="PEPc" 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fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_13dpg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8896"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8898"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_DPGM" sboTerm="SBO:0000176" id="R_DPGM" name="13BPGM" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_13dpg_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_23dpg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8889"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8888"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1093"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_DPGase" sboTerm="SBO:0000176" id="R_DPGase" name="23BPGM" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_23dpg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8889"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8888"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1093"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PGM" sboTerm="SBO:0000176" id="R_PGM" name="PGM_1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8889"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8888"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1093"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ENO" sboTerm="SBO:0000176" id="R_ENO" name="ENO" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3350"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3354"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3353"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PYK" sboTerm="SBO:0000176" id="R_PYK" name="PK" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9021"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9020"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_LDH_L" sboTerm="SBO:0000176" id="R_LDH_L" name="LDH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_lac__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6541"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6535"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30866"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6544"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__28335"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21481"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_r0407" sboTerm="SBO:0000176" id="R_r0407" name="ALDO1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_HC00361_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__418"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__417"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__414"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PRPPS" sboTerm="SBO:0000176" id="R_PRPPS" name="PRPS1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9465"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9462"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9463"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_G6PDH2r" sboTerm="SBO:0000176" id="R_G6PDH2r" name="G6PD" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_6pgl_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4057"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PGL" sboTerm="SBO:0000176" id="R_PGL" name="PGLS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_6pgl_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4795"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8903"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GND" sboTerm="SBO:0000176" id="R_GND" name="6PGD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8891"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_RPI" sboTerm="SBO:0000176" id="R_RPI" name="RPI" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10297"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_TKT2" sboTerm="SBO:0000176" id="R_TKT2" name="TKT1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11835"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__25313"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11834"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_RPE" sboTerm="SBO:0000176" id="R_RPE" name="RPE" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10293"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__45241"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_TKT1" sboTerm="SBO:0000176" id="R_TKT1" name="TKT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_s7p_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11835"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__25313"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11834"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_TALA" sboTerm="SBO:0000176" id="R_TALA" name="TALDO1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_s7p_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11559"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_r0408" sboTerm="SBO:0000176" id="R_r0408" name="SBPase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_s7p_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_HC00361_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8878"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8876"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8877"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PDHm" sboTerm="SBO:0000176" id="R_PDHm" name="PDH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_accoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2898"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21350"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2896"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8808"/> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8806"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8807"/> + </fbc:or> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PCm" sboTerm="SBO:0000176" id="R_PCm" name="PC" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_hco3_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_oaa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8636"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PEPCK_re" sboTerm="SBO:0000176" id="R_PEPCK_re" name="PEPCK" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8724"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_CSm" sboTerm="SBO:0000176" id="R_CSm" name="CS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_accoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_oaa_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_cit_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2422"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ACONTm" sboTerm="SBO:0000176" id="R_ACONTm" name="mACO" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_cit_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_icit_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__118"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__117"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ICDHxm" sboTerm="SBO:0000176" id="R_ICDHxm" name="IDH3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_icit_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5386"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5385"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5384"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ICDHym" sboTerm="SBO:0000176" id="R_ICDHym" name="IDH2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_icit_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5383"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_AKGDm" sboTerm="SBO:0000176" id="R_AKGDm" name="AKGDH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_succoa_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2898"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8124"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2911"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_SUCOAS1m" sboTerm="SBO:0000176" id="R_SUCOAS1m" name="SCS" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gdp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_succoa_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_gtp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_succ_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11449"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11450"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_SUCD1m" sboTerm="SBO:0000176" id="R_SUCD1m" name="SDH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_succ_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_fum_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10680"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10681"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10682"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10683"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_FUMm" sboTerm="SBO:0000176" id="R_FUMm" name="FH1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fum_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3700"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MDHm" sboTerm="SBO:0000176" id="R_MDHm" name="MDH2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_oaa_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6971"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ME1m" sboTerm="SBO:0000176" id="R_ME1m" name="ME2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6984"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ME2m" sboTerm="SBO:0000176" id="R_ME2m" name="ME3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6985"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ME2" sboTerm="SBO:0000176" id="R_ME2" name="ME1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6983"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ACITL" sboTerm="SBO:0000176" id="R_ACITL" name="ACLY" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__115"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_FUM" sboTerm="SBO:0000176" id="R_FUM" name="FH2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3700"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MDH" sboTerm="SBO:0000176" id="R_MDH" name="MDH1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6970"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17836"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_AKGMALtm" sboTerm="SBO:0000176" id="R_AKGMALtm" name="SLC25A11" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10981"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10980"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ACONT" sboTerm="SBO:0000176" id="R_ACONT" name="cACO" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_icit_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__117"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ICDHyr" sboTerm="SBO:0000176" id="R_ICDHyr" name="IDH1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_icit_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5382"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PPA" sboTerm="SBO:0000176" id="R_PPA" name="cPPA" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="2" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30042"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9226"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_Complex1ROS" sboTerm="SBO:0000176" id="R_Complex1ROS" name="Complex1ROS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_m" stoichiometry="4.75" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_m" stoichiometry="0.05" constant="true"/> + <speciesReference species="M_q10_m" stoichiometry="0.95" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_c" stoichiometry="3.8" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2s_m" stoichiometry="0.05" constant="true"/> + <speciesReference species="M_q10h2_m" stoichiometry="0.95" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7694"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7707"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7699"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7697"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7702"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7705"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7715"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7714"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7698"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7692"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7683"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7688"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7684"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7685"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7700"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7693"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7696"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20372"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7704"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7706"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7708"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7701"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7703"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7716"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7712"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7686"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20371"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7717"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7695"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7690"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17194"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7462"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7456"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7461"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7458"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7459"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7455"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7460"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7710"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_FADH2ETC" sboTerm="SBO:0000176" id="R_FADH2ETC" name="Complex2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_q10_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_q10h2_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3483"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3482"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3481"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_CYOR_u10mi" sboTerm="SBO:0000176" id="R_CYOR_u10mi" name="Complex3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ficytC_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_q10h2_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_focytC_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> + <speciesReference species="M_q10_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12585"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30862"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12586"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12582"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29594"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12587"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12590"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2579"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30863"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7427"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_CYOOm2i" sboTerm="SBO:0000176" id="R_CYOOm2i" name="Complex4" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_focytC_m" stoichiometry="4" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="8" constant="true"/> + <speciesReference species="M_o2_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_ficytC_m" stoichiometry="4" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2292"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2269"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2285"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2267"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7421"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7419"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7422"/> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2277"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2279"/> + </fbc:or> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2288"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2287"/> + </fbc:or> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2280"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__24380"/> + </fbc:or> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__16232"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2265"/> + </fbc:or> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2291"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__24381"/> + </fbc:or> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2294"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__24382"/> + </fbc:or> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ATPS4mi" sboTerm="SBO:0000176" id="R_ATPS4mi" name="ATPsynthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="3" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__837"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__830"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__840"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__838"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__823"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__847"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__833"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14247"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__845"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__846"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7414"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7415"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__848"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__850"/> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__842"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__843"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__841"/> + </fbc:or> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLUCYS" sboTerm="SBO:0000176" id="R_GLUCYS" name="GCL" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glucys_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4311"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4312"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GTHS" sboTerm="SBO:0000176" id="R_GTHS" name="GSS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glucys_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4624"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_SPODMm" sboTerm="SBO:0000176" id="R_SPODMm" name="SOD2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_o2s_m" stoichiometry="2" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h2o2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11180"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GTHPi" sboTerm="SBO:0000176" id="R_GTHPi" name="GPcit" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9352"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4556"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9353"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4554"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4553"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GTHPm" sboTerm="SBO:0000176" id="R_GTHPm" name="GPmit" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gthrd_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_h2o2_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gthox_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="2" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9354"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4556"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4553"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GDR" sboTerm="SBO:0000176" id="R_GDR" name="cGSRnadh" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4623"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GTHOr" sboTerm="SBO:0000176" id="R_GTHOr" name="cGSRnadph" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4623"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GDRm" sboTerm="SBO:0000176" id="R_GDRm" name="mGSRnadh" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gthox_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gthrd_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4623"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GTHOm" sboTerm="SBO:0000176" id="R_GTHOm" name="mGSRnadph" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gthox_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gthrd_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4623"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_r0885" sboTerm="SBO:0000176" id="R_r0885" name="TrasportGSH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gthrd_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10980"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PYRt2m" sboTerm="SBO:0000176" id="R_PYRt2m" name="MPC" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21606"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__24515"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10922"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_4964" sboTerm="SBO:0000176" id="R_HMR_4964" name="SLC25A1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_cit_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10979"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_r2420" sboTerm="SBO:0000176" id="R_r2420" name="SLC25A2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10989"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ATPtm" sboTerm="SBO:0000176" id="R_ATPtm" name="ANT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10991"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10990"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10992"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_FUMtm" sboTerm="SBO:0000176" id="R_FUMtm" name="SLC25A10" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_fum_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10980"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_CO2tm" sboTerm="SBO:0000176" id="R_CO2tm" name="TransportCO2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_O2tm" sboTerm="SBO:0000176" id="R_O2tm" name="TransportO2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_o2_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_r0801" sboTerm="SBO:0000176" id="R_r0801" name="GNT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gtp_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gdp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10992"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_THD1m" sboTerm="SBO:0000176" id="R_THD1m" name="NNT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7863"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_H2Otm" sboTerm="SBO:0000176" id="R_H2Otm" name="AQP8" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__642"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_NH4tm" sboTerm="SBO:0000176" id="R_NH4tm" name="TransportNH3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_nh4_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_HCO3E" sboTerm="SBO:0000176" id="R_HCO3E" name="cCA" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_hco3_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1371"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1373"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1383"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1372"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1380"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1368"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1374"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1375"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1381"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14914"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HCO3Em" sboTerm="SBO:0000176" id="R_HCO3Em" name="mCA" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_hco3_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1378"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1377"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLUN" sboTerm="SBO:0000176" id="R_GLUN" name="cGLS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4331"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLNS" sboTerm="SBO:0000176" id="R_GLNS" name="GS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4341"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21016"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLUt2m" sboTerm="SBO:0000176" id="R_GLUt2m" name="GluCarrier" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__19954"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10988"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLNtm_1" sboTerm="SBO:0000176" id="R_GLNtm_1" name="GlnCarrier" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gln__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_GLUNm" sboTerm="SBO:0000176" id="R_GLUNm" name="mGLS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gln__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4331"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29570"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLUPRT" sboTerm="SBO:0000176" id="R_GLUPRT" name="PPAT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pram_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9238"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PRAGSr" sboTerm="SBO:0000176" id="R_PRAGSr" name="GART1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pram_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gar_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4163"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GARFT" sboTerm="SBO:0000176" id="R_GARFT" name="GART2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gar_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_fgam_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4163"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PRFGS" sboTerm="SBO:0000176" id="R_PRFGS" name="PFAS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_fgam_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_fpram_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8863"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PRAIS" sboTerm="SBO:0000176" id="R_PRAIS" name="GART3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_fpram_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_air_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference 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reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_5aizc_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_25aics_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8587"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ADSL2r" sboTerm="SBO:0000176" id="R_ADSL2r" name="PAICS3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" 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stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__794"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_IMPC" sboTerm="SBO:0000176" id="R_IMPC" name="ATIC2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fprica_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__794"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ADSS" sboTerm="SBO:0000176" id="R_ADSS" name="ADSS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dcamp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__292"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20093"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ADSL1r" sboTerm="SBO:0000176" id="R_ADSL1r" name="ADSL" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_dcamp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__291"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_IMPDH2" sboTerm="SBO:0000176" id="R_IMPDH2" name="IMPDH2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_xmp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6052"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6053"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GMPS" sboTerm="SBO:0000176" id="R_GMPS" name="GMPS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_xmp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4378"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GMPS2" sboTerm="SBO:0000176" id="R_GMPS2" name="GMPS2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_xmp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4378"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GK1" sboTerm="SBO:0000176" id="R_GK1" name="GUK1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> + 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<speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dadp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10451"/> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17296"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10452"/> + </fbc:or> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_CBPS" sboTerm="SBO:0000176" id="R_CBPS" name="CAD1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_hco3_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_cbp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1424"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ASPCT" sboTerm="SBO:0000176" id="R_ASPCT" name="CAD2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_cbp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_cbasp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1424"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_DHORTS" sboTerm="SBO:0000176" id="R_DHORTS" name="CAD3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_cbasp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dhor__S_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1424"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_DHORD9" sboTerm="SBO:0000176" id="R_DHORD9" name="DHODH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_dhor__S_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_q10_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_orot_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_q10h2_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2867"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ORPT" sboTerm="SBO:0000176" id="R_ORPT" name="UMPS1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_orot_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_orot5p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12563"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_OMPDC" sboTerm="SBO:0000176" id="R_OMPDC" name="UMPS2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_orot5p_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12563"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_UMPK" sboTerm="SBO:0000176" id="R_UMPK" name="CMPK1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18170"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_RNDR4" sboTerm="SBO:0000176" id="R_RNDR4" name="RRM2B3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dudp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10451"/> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17296"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10452"/> + </fbc:or> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_TMDS" sboTerm="SBO:0000176" id="R_TMDS" name="TYMS" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_dump_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dhf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_dtmp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12441"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_URIDK2r" sboTerm="SBO:0000176" id="R_URIDK2r" name="CMPK2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_dudp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_dump_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3061"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_NDPK2" sboTerm="SBO:0000176" id="R_NDPK2" name="NME1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7851"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20461"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20567"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7849"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7850"/> + </fbc:and> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_NDPK3" sboTerm="SBO:0000176" id="R_NDPK3" name="NME2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_cdp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7851"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20461"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20567"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7849"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7850"/> + </fbc:and> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_CTPS1" sboTerm="SBO:0000176" id="R_CTPS1" name="CTPS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2520"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2519"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_RNDR3" sboTerm="SBO:0000176" id="R_RNDR3" name="RRM2B4" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_cdp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dcdp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10451"/> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17296"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10452"/> + </fbc:or> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GDHm" sboTerm="SBO:0000176" id="R_GDHm" name="GLUDnadh" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4335"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4336"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLUDym" sboTerm="SBO:0000176" id="R_GLUDym" name="GLUDnadph" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4335"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4336"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ASPTA" sboTerm="SBO:0000176" id="R_ASPTA" name="cGOT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4432"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ASPTAm" sboTerm="SBO:0000176" id="R_ASPTAm" name="mGOT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_oaa_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_asp__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4433"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ASPGLUm" sboTerm="SBO:0000176" id="R_ASPGLUm" name="GLAST" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_asp__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10983"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10982"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ASPT" sboTerm="SBO:0000176" id="R_ASPT" name="FH3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3700"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_CBPSam" sboTerm="SBO:0000176" id="R_CBPSam" name="CPS1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_hco3_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_cbp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2323"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_OCBTm" sboTerm="SBO:0000176" id="R_OCBTm" name="OTC" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_cbp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_orn_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_citr__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8512"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ORNt4m" sboTerm="SBO:0000176" id="R_ORNt4m" name="ORNT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_citr__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_citr__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_orn_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10985"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__22921"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ARGSS" sboTerm="SBO:0000176" id="R_ARGSS" name="ASS1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_citr__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_argsuc_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__758"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ARGSL" sboTerm="SBO:0000176" id="R_ARGSL" name="ASL" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_argsuc_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__746"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ARGN" sboTerm="SBO:0000176" id="R_ARGN" name="ARG1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_urea_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__663"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ORNDC" sboTerm="SBO:0000176" id="R_ORNDC" name="ODC1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8109"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_SPMS" sboTerm="SBO:0000176" id="R_SPMS" name="SpermidineSynthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ametam_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_5mta_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11296"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_SPRMS" sboTerm="SBO:0000176" id="R_SPRMS" name="SpermineSynthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ametam_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_5mta_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_sprm_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11123"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11296"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ADMDC" sboTerm="SBO:0000176" id="R_ADMDC" name="AMD1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_ametam_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__457"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MTAP" sboTerm="SBO:0000176" id="R_MTAP" name="MTAP" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_5mta_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_5mdr1p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7413"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ADPT" sboTerm="SBO:0000176" id="R_ADPT" name="APRT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__626"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MTRI" sboTerm="SBO:0000176" id="R_MTRI" name="MRI1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_5mdr1p_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_5mdru1p_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_MDRPD" sboTerm="SBO:0000176" id="R_MDRPD" name="MTRUD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_5mdru1p_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dkmpp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__642"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7103"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__638"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__634"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__637"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__633"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_DKMPPD" sboTerm="SBO:0000176" id="R_DKMPPD" name="dkmppDegradation" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_dkmpp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_2kmb_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_SPMDtex2" sboTerm="SBO:0000176" id="R_SPMDtex2" name="DMspermidine" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_spmd_e" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_SPRMti" sboTerm="SBO:0000176" id="R_SPRMti" name="DMspermine" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_sprm_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_sprm_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10963"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLYAMDTRc" sboTerm="SBO:0000176" id="R_GLYAMDTRc" name="AGAT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gudac_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4175"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ARGDr" sboTerm="SBO:0000176" id="R_ARGDr" name="ARGAH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_citr__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_r0074" sboTerm="SBO:0000176" id="R_r0074" name="ALDH18A1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_glu5sa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__406"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLU5SAtmc" sboTerm="SBO:0000176" id="R_GLU5SAtmc" name="TransportGLU5SA" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_glu5sa_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_glu5sa_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_G5SADs" sboTerm="SBO:0000176" id="R_G5SADs" name="ALDH4A1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_glu5sa_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__406"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PRO1x" sboTerm="SBO:0000176" id="R_PRO1x" name="P5CR2nadh" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30262"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_P5CR" sboTerm="SBO:0000176" id="R_P5CR" name="P5CR2nadph" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30262"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PROD2" sboTerm="SBO:0000176" id="R_PROD2" name="PRODH2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17325"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_TransportFAD" sboTerm="SBO:0000176" id="R_TransportFAD" name="TransportFAD" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_ASNS1" sboTerm="SBO:0000176" id="R_ASNS1" name="ASNS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_asn__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__753"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ASNN" sboTerm="SBO:0000176" id="R_ASNN" name="ASRGL1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_asn__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__16448"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20123"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_METS" sboTerm="SBO:0000176" id="R_METS" name="MTR" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_5mthf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7468"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_METAT" sboTerm="SBO:0000176" id="R_METAT" name="MAT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6903"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6905"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6904"/> + </fbc:and> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_3915" sboTerm="SBO:0000176" id="R_HMR_3915" name="HNMT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_5mthf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5028"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_AHCi" sboTerm="SBO:0000176" id="R_AHCi" name="AHCY" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adn_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__642"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7103"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__638"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__634"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__637"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__633"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ADNK1" sboTerm="SBO:0000176" id="R_ADNK1" name="ADK" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_adn_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__257"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_CYSTS" sboTerm="SBO:0000176" id="R_CYSTS" name="CBS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_cyst__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1550"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_CYSTGL" sboTerm="SBO:0000176" id="R_CYSTGL" name="CTH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_cyst__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_2obut_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2501"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MTHFR3" sboTerm="SBO:0000176" id="R_MTHFR3" name="MTHFR" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_5mthf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7436"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_UNK2" sboTerm="SBO:0000176" id="R_UNK2" name="MetSynthesis" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_2kmb_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_UNK3" sboTerm="SBO:0000176" id="R_UNK3" name="TAT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_2kmb_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_5MTHFt" sboTerm="SBO:0000176" id="R_5MTHFt" name="Dm5methylTHF" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_5mthf_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_5mthf_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3791"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3795"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ILETA" sboTerm="SBO:0000176" id="R_ILETA" name="cBCAT1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3mop_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__976"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_3MOPt2im" sboTerm="SBO:0000176" id="R_3MOPt2im" name="Transport3mop" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3mop_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3mop_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_ILETAm" sboTerm="SBO:0000176" id="R_ILETAm" name="mBCAT1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_ile__L_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3mop_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__977"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_LEUTA" sboTerm="SBO:0000176" id="R_LEUTA" name="cBCAT2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_4mop_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__976"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_4MOPt2im" sboTerm="SBO:0000176" id="R_4MOPt2im" name="Transport4mop" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_4mop_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_4mop_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_LEUTAm" sboTerm="SBO:0000176" id="R_LEUTAm" name="mBCAT2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_leu__L_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_4mop_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__977"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_OIVD1m" sboTerm="SBO:0000176" id="R_OIVD1m" name="BCKD1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_4mop_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_ivcoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__987"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2898"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2698"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__986"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ACOAD8m" sboTerm="SBO:0000176" id="R_ACOAD8m" name="IVD" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_ivcoa_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3mb2coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6186"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MCCCrm" sboTerm="SBO:0000176" id="R_MCCCrm" name="MCC" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3mb2coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_hco3_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3mgcoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6936"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6937"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MGCHrm" sboTerm="SBO:0000176" id="R_MGCHrm" name="MGCoAH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3mgcoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_hmgcoa_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__890"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMGCOAtm" sboTerm="SBO:0000176" id="R_HMGCOAtm" name="TransportHMGCoA" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_hmgcoa_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_hmgcoa_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_VALTA" sboTerm="SBO:0000176" id="R_VALTA" name="cBCAT3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3mob_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__976"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_3MOBt2im" sboTerm="SBO:0000176" id="R_3MOBt2im" name="Transport3mob" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3mob_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3mob_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_VALTAim" sboTerm="SBO:0000176" id="R_VALTAim" name="mBCAT3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_val__L_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3mob_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__977"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_OIVD2m" sboTerm="SBO:0000176" id="R_OIVD2m" name="BCKD2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3mob_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_ibcoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__987"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2898"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2698"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__986"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ACOAD9m" sboTerm="SBO:0000176" id="R_ACOAD9m" name="ACOAD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_ibcoa_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_2mp2coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__89"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__87"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ECOAH12m" sboTerm="SBO:0000176" id="R_ECOAH12m" name="ECoAH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_2mp2coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3hibutcoa_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3151"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4801"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4803"/> + </fbc:and> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_3HBCOAHLm" sboTerm="SBO:0000176" id="R_3HBCOAHLm" name="HIBCH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3hibutcoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3hmp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_HIBDm" sboTerm="SBO:0000176" id="R_HIBDm" name="HIBD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3hmp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_2mop_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4907"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_r0643" sboTerm="SBO:0000176" id="R_r0643" name="HIBADH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_2mop_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_HC00900_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__403"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__404"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__407"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__412"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__877"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MMSAD1m" sboTerm="SBO:0000176" id="R_MMSAD1m" name="MMAL1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_2mop_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppcoa_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7179"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MMTSADm" sboTerm="SBO:0000176" id="R_MMTSADm" name="MMAL2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_2mop_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_mmcoa__R_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_PCC" sboTerm="SBO:0000176" id="R_PCC" name="PCC" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_hco3_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppcoa_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_mmcoa__S_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_MMALH" sboTerm="SBO:0000176" id="R_MMALH" name="MMALH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_HC00900_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_mmcoa__S_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_MMEm" sboTerm="SBO:0000176" id="R_MMEm" name="MCM1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_mmcoa__S_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_mmcoa__R_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__16732"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MMMm" sboTerm="SBO:0000176" id="R_MMMm" name="MCM2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_mmcoa__R_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_succoa_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7526"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ILEtmi" sboTerm="SBO:0000176" id="R_ILEtmi" name="TransportIle" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_ile__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_LEUt5m" sboTerm="SBO:0000176" id="R_LEUt5m" name="TransportLeu" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_leu__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_VALt5m" sboTerm="SBO:0000176" id="R_VALt5m" name="TransportVal" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_val__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_PGCD" sboTerm="SBO:0000176" id="R_PGCD" name="PHGDH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3php_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8923"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PSERT" sboTerm="SBO:0000176" id="R_PSERT" name="PSAT1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3php_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pser__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__19129"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PSP_L" sboTerm="SBO:0000176" id="R_PSP_L" name="PSPH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pser__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9577"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GHMT2r" sboTerm="SBO:0000176" id="R_GHMT2r" name="cSHMT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10850"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_SERD_L" sboTerm="SBO:0000176" id="R_SERD_L" name="SDS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10691"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30404"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ALATA_L" sboTerm="SBO:0000176" id="R_ALATA_L" name="GPT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18062"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4552"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_r1435" sboTerm="SBO:0000176" id="R_r1435" name="TransportSer" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_ser__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_GLYtm" sboTerm="SBO:0000176" id="R_GLYtm" name="TransportGly" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gly_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_GHMT2rm" sboTerm="SBO:0000176" id="R_GHMT2rm" name="mSHMT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ser__L_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_thf_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gly_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_mlthf_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10852"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MLTHFtm" sboTerm="SBO:0000176" id="R_MLTHFtm" name="mlthf Transport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_mlthf_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_r0962" sboTerm="SBO:0000176" id="R_r0962" name="Transport_folate" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fol_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_fol_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29683"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_FORtm" sboTerm="SBO:0000176" id="R_FORtm" name="TransportFormate" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_for_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_r0514" sboTerm="SBO:0000176" id="R_r0514" name="DHFRL1_DHFR_5" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fol_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dhf_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2861"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_DHFRim" sboTerm="SBO:0000176" id="R_DHFRim" name="DHFRL1_DHFR_6" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_dhf_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_thf_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2861"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_FTHFLmi" sboTerm="SBO:0000176" id="R_FTHFLmi" name="mMTHFD1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_for_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_thf_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_10fthf_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7432"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21055"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MTHFCm" sboTerm="SBO:0000176" id="R_MTHFCm" name="mMTHFD2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_10fthf_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_methf_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7434"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MTHFDm" sboTerm="SBO:0000176" id="R_MTHFDm" name="mMTHFD3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_methf_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_mlthf_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7434"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7432"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_FOLR2" sboTerm="SBO:0000176" id="R_FOLR2" name="cDHFR1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dhf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2861"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_DHFR" sboTerm="SBO:0000176" id="R_DHFR" name="cDHFR2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_dhf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2861"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_FTHFLi" sboTerm="SBO:0000176" id="R_FTHFLi" name="cMTHFD1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7432"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_FTHFDH" sboTerm="SBO:0000176" id="R_FTHFDH" name="cMTHFD2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26777"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3978"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MTHFC" sboTerm="SBO:0000176" id="R_MTHFC" name="cMTHFD3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7432"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MTHFD" sboTerm="SBO:0000176" id="R_MTHFD" name="cMTHFD4" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7432"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7436"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MTHFD2i" sboTerm="SBO:0000176" id="R_MTHFD2i" name="cMTHFD5" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7434"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__31865"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_ACACT1r" sboTerm="SBO:0000176" id="R_ACACT1r" name="cACAT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_accoa_c" stoichiometry="2" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_aacoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__94"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMGCOAS" sboTerm="SBO:0000176" id="R_HMGCOAS" name="cHMGCS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_aacoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_hmgcoa_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5007"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMGCOAR" sboTerm="SBO:0000176" id="R_HMGCOAR" name="Hydroxymethylglutaryl CoA reductase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_hmgcoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="2" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_mev__R_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="2" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5006"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_MEVK1" sboTerm="SBO:0000176" id="R_MEVK1" name="Mevalonate kinase atp" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_mev__R_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_5pmev_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7530"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_PMEVK" sboTerm="SBO:0000176" id="R_PMEVK" name="Phosphomevalonate kinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_5pmev_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_5dpmev_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9141"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_IPDDI" sboTerm="SBO:0000176" id="R_IPDDI" name="Isopentenyl-diphosphate D-isomerase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ipdp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dmpp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5387"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23487"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_DPMVD" sboTerm="SBO:0000176" id="R_DPMVD" name="Diphosphomevalonate decarboxylase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_5dpmev_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ipdp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7529"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_DMATT" sboTerm="SBO:0000176" id="R_DMATT" name="Dimethylallyltranstransferase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_dmpp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ipdp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_grdp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4249"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GRTT" sboTerm="SBO:0000176" id="R_GRTT" name="Geranyltranstransferase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_grdp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ipdp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_frdp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4249"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1465" sboTerm="SBO:0000176" id="R_HMR_1465" name="Farnesyl-Diphosphate:Farnesyl-Diphosphate Farnesyltransferase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_frdp_c" stoichiometry="2" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_HC01118_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3629"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1467" sboTerm="SBO:0000176" id="R_HMR_1467" name="Presqualene-Diphosphate Diphosphate-Lyase (Reducing, Squalene-Forming)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_HC01118_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_sql_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3629"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_SMO" sboTerm="SBO:0000176" id="R_SMO" name="Squalene monooxygenase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_sql_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_Ssq23epx_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11279"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_LNSTLS" sboTerm="SBO:0000176" id="R_LNSTLS" name="Lanosterol synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_Ssq23epx_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_lanost_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6708"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1477" sboTerm="SBO:0000176" id="R_HMR_1477" name="Sterol 14Alpha-Demethylase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_lanost_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_M00939_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2649"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1478" sboTerm="SBO:0000176" id="R_HMR_1478" name="Sterol 14Alpha-Demethylase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_M00939_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_M00937_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2649"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1479" sboTerm="SBO:0000176" id="R_HMR_1479" name="Sterol 14Alpha-Demethylase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_M00937_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_44mctr_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2649"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_C14STR" sboTerm="SBO:0000176" id="R_C14STR" name="C 14 sterol reductase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_44mctr_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_44mzym_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6518"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11863"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1490" sboTerm="SBO:0000176" id="R_HMR_1490" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_44mzym_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_M00961_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10545"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1334"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1493" sboTerm="SBO:0000176" id="R_HMR_1493" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_M00961_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_M00957_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10545"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1334"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1494" sboTerm="SBO:0000176" id="R_HMR_1494" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_M00957_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_4mzym_int1_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10545"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1334"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_C3STDH1" sboTerm="SBO:0000176" id="R_C3STDH1" name="C 3 sterol dehydrogenase 4 methylzymosterol" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_4mzym_int1_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_4mzym_int2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13398"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1495" sboTerm="SBO:0000176" id="R_HMR_1495" name="3Beta-Hydroxysteroid-4Alpha-Carboxylate 3-Dehydrogenase (Decarboxylating)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_4mzym_int1_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_4mzym_int2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13398"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__19340"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1500" sboTerm="SBO:0000176" id="R_HMR_1500" name="3Beta-Hydroxysteroid 3-Dehydrogenase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_4mzym_int2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_HC02110_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5215"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1502" sboTerm="SBO:0000176" id="R_HMR_1502" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_HC02110_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference 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<listOfProducts> + <speciesReference species="M_M00959_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10545"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1334"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_1504" sboTerm="SBO:0000176" id="R_HMR_1504" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_M00959_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" 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reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_chlstol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_ddsmsterol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10547"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_RE2410C" sboTerm="SBO:0000176" id="R_RE2410C" name="7-Dehydrocholesterol Reductase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_ddsmsterol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dsmsterol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_DSMSTOLR" sboTerm="SBO:0000176" id="R_DSMSTOLR" name="Desmosterol reductase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_dsmsterol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" 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fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_acACP_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_HC01587_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_r0691" sboTerm="SBO:0000176" id="R_r0691" name="r0691" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_HC01587_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + 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<fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_r0682" sboTerm="SBO:0000176" id="R_r0682" name="r0682" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_but_2_enoyl_ACP_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_butyryl_ACP_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_r0760" sboTerm="SBO:0000176" id="R_r0760" name="r0760" reversible="false" 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+ </fbc:and> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> + </fbc:and> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_r0963" sboTerm="SBO:0000176" id="R_r0963" name="ExFolate" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> + <listOfReactants> + <speciesReference species="M_fol_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_fol_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3791"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3795"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3793"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_THBPTt" sboTerm="SBO:0000176" id="R_THBPTt" name="ExTetrahydrobiopterinc" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> + <listOfReactants> + <speciesReference species="M_thbpt_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_thbpt_e" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_arg_L_t" sboTerm="SBO:0000176" id="R_arg_L_t" name="ExArg" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>gpr_old: ENSG00000003989 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000268104</p> + </html> + </notes> + <listOfReactants> + <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_arg__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11067"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11057"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11060"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11061"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11026"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11065"/> + </fbc:and> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11026"/> + </fbc:and> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_phe_L_t" sboTerm="SBO:0000176" id="R_phe_L_t" name="ExPhe" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>gpr_old: ENSG00000112394 or ENSG00000149150 or ENSG00000167703</p> + </html> + </notes> + <listOfReactants> + <speciesReference species="M_phe__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_phe__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11061"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11060"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13447"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11057"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14679"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:or> + <fbc:geneProductRef 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</notes> + <listOfReactants> + <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_ile__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> + </fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9225"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23087"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> + <fbc:geneProductRef 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xmlns="http://www.w3.org/1999/xhtml"> + <p>gpr_old: ENSG00000017483 or ENSG00000111371 or ENSG00000123643 or ENSG00000134294 or ENSG00000139209 or ENSG00000165970 or ENSG00000186335 or ENSG00000196517 or ENSG00000268104 or (ENSG00000130234 and ENSG00000174358) or (ENSG00000147003 and ENSG00000164363) or (ENSG00000147003 and ENSG00000174358)</p> + </html> + </notes> + <listOfReactants> + <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gly_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11058"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11026"/> + </fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13447"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14679"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> + </fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11056"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11056"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11051"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18070"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18762"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18761"/> + </fbc:or> + </fbc:geneProductAssociation> + 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</listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__642"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7103"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__638"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__634"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__637"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__633"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_IZPN" sboTerm="SBO:0000176" id="R_IZPN" name="IZPN" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_4izp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_forglu_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" 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<speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17366"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_AASAD3m" sboTerm="SBO:0000176" id="R_AASAD3m" name="AASAD3m" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_L2aadp6sa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_L2aadp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_r0450" sboTerm="SBO:0000176" id="R_r0450" name="AADPTA" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_L2aadp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_2oxoadp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17929"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_2OXOADOXm" sboTerm="SBO:0000176" id="R_2OXOADOXm" name="OXOADPOR" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_2oxoadp_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_glutcoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2898"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8124"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21350"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2911"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLUTCOADHm" sboTerm="SBO:0000176" id="R_GLUTCOADHm" name="GLUTCOADHm" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_glutcoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_b2coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4189"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_3HBCDm" sboTerm="SBO:0000176" id="R_3HBCDm" name="ECOAH1m" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_b2coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3hbcoa__R_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23408"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HACD1m" sboTerm="SBO:0000176" id="R_HACD1m" name="HACD1m" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3hbcoa__R_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_aacoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4799"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4800"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4801"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4803"/> + </fbc:and> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMGCOASm" sboTerm="SBO:0000176" id="R_HMGCOASm" name="mHMGCS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_aacoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_accoa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_hmgcoa_m" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5008"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_cys_L_t" sboTerm="SBO:0000176" id="R_cys_L_t" name="ExCys" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>gpr_old: ENSG00000167703</p> + </html> + </notes> + <listOfReactants> + <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_cys__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> + </fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23087"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18070"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_CYSO" sboTerm="SBO:0000176" id="R_CYSO" name="CDO1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3sala_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1795"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_3SALATAi" sboTerm="SBO:0000176" id="R_3SALATAi" name="3SALATAc" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3sala_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3snpyr_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4432"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_3SALAASPm" sboTerm="SBO:0000176" id="R_3SALAASPm" name="Transport3SALA" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3sala_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_asp__L_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_3sala_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10983"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10982"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_3SALATAim" 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species="M_3snpyr_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_3SPYRSPm" sboTerm="SBO:0000176" id="R_3SPYRSPm" name="3SPYRSTm" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_3snpyr_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> + <speciesReference species="M_so3_m" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_HMR_3951" sboTerm="SBO:0000176" id="R_HMR_3951" name="ExSulfitec" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_so3_e" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_ExSulfitem" sboTerm="SBO:0000176" id="R_ExSulfitem" name="ExSulfitem" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_so3_m" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_so3_e" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_PHETHPTOX2" sboTerm="SBO:0000176" id="R_PHETHPTOX2" name="PHETHPTOX2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_phe__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_thbpt_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_CE2705_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8582"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_tyr_L_t" sboTerm="SBO:0000176" id="R_tyr_L_t" name="ExTyr" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>gpr_old: ENSG00000112394</p> + </html> + </notes> + <listOfReactants> + <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_tyr__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17027"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> + </fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_TYRTA" sboTerm="SBO:0000176" id="R_TYRTA" name="TYRTA" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_34hpp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4432"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11573"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_34HPPOR" sboTerm="SBO:0000176" id="R_34HPPOR" name="HPPOR" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_34hpp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_hgentis_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5147"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HGNTOR" sboTerm="SBO:0000176" id="R_HGNTOR" name="HGNTOR" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_hgentis_c" stoichiometry="1" constant="true"/> + 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metaid="meta_R_FUMAC" sboTerm="SBO:0000176" id="R_FUMAC" name="FUMAC" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_4fumacac_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_acac_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3579"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_AACOAT" sboTerm="SBO:0000176" id="R_AACOAT" name="AACOAT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference 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stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_thr__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13447"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> + </fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9225"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_THRD_L" sboTerm="SBO:0000176" id="R_THRD_L" 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fbc:upperFluxBound="cobra_0_bound"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>gpr_old: ENSG00000103257</p> + </html> + </notes> + <listOfReactants> + <speciesReference species="M_trp__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_trp__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> + </fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> + </fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__19660"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17027"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_TRPO2" sboTerm="SBO:0000176" id="R_TRPO2" name="TRPO2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_trp__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_5hoxnfkyn_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6059"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27269"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11708"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_FKYNH" sboTerm="SBO:0000176" id="R_FKYNH" name="FKYNH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_5hoxnfkyn_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_Lkynr_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20910"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_KYN" sboTerm="SBO:0000176" id="R_KYN" name="KYN" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + 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</reaction> + <reaction metaid="meta_R_KYN3OX" sboTerm="SBO:0000176" id="R_KYN3OX" name="KYN3OX" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_Lkynr_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_hLkynr_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6381"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HKYNH" sboTerm="SBO:0000176" 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fbc:geneProduct="G_HGNC__58__19288"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_AM6SAD" sboTerm="SBO:0000176" id="R_AM6SAD" name="AM6SADH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_am6sa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_amuco_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="meta_R_AMCOXO" sboTerm="SBO:0000176" id="R_AMCOXO" name="AMCOXO" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" 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+ </reaction> + <reaction metaid="meta_R_r0027" sboTerm="SBO:0000176" id="R_r0027" name="CystineReductaseNADPH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_Lcystin_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_cys__L_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18155"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12437"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_HMR_3996" sboTerm="SBO:0000176" id="R_HMR_3996" name="CystineReductaseNADH" 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<reaction metaid="meta_R_G3PD1ir" sboTerm="SBO:0000176" id="R_G3PD1ir" name="G3PD1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4455"/> + </fbc:geneProductAssociation> + </reaction> + <reaction metaid="meta_R_GLYC3Ptm" sboTerm="SBO:0000176" id="R_GLYC3Ptm" name="Transport_glycerol3P" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + 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<speciesReference species="M_thymd_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_thymd_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11003"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11004"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_EX_thymd_e" name="thymd ExchangeRxn" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> + <listOfReactants> + <speciesReference species="M_thymd_e" stoichiometry="1" constant="true"/> + </listOfReactants> + </reaction> + <reaction id="R_Transport_HC00576_c_e" name="HC00576 Transport" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_HC00576_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_HC00576_e" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_EX_HC00576_e" name="HC00576 ExchangeRxn" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_HC00576_e" stoichiometry="1" constant="true"/> + </listOfReactants> + </reaction> + <reaction id="R_Transport_4abut_c_e" name="4abut Transport" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_4abut_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_4abut_e" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_EX_4abut_e" name="4abut ExchangeRxn" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_4abut_e" stoichiometry="1" constant="true"/> + </listOfReactants> + </reaction> + <reaction id="R_GLUVESSEC" name="transporto of GLUVESSEC" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__16703"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20151"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__16704"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_EX_chsterol_e" name="Exchange of Cholesterol" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_chsterol_e" stoichiometry="1" constant="true"/> + </listOfReactants> + </reaction> + <reaction id="R_r1050" name="Vesicular Transport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_chsterol_e" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_chsterol_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_EX_gal_e" name="Exchange of D-Galactose" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gal_e" stoichiometry="1" constant="true"/> + </listOfReactants> + </reaction> + <reaction id="R_GALt1r" name="Galactose Transport (Uniport)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gal_e" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gal_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13812"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11005"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11007"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11006"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13444"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_GALK" name="Galactokinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_gal_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_gal1p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4118"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4119"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_UGLT" name="UDPglucose-Hexose-1-Phosphate Uridylyltransferase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_gal1p_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_udpgal_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4135"/> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_PGMT" name="Phosphoglucomutase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:or> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8905"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8906"/> + </fbc:or> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_UDPG4E" name="UDPglucose 4-Epimerase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_udpgal_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4116"/> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_t_Lcystin_ala__L" name="t_Lcystin_ala__L" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_Lcystin_e" stoichiometry="1" constant="true"/> + <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_Lcystin_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ala__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11067"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11025"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_t_Lcystin_glu__L" name="t_Lcystin_glu__L" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_Lcystin_e" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_Lcystin_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11059"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11026"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_t_Lcystin_leu__L" name="t_Lcystin_leu__L" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_Lcystin_e" stoichiometry="1" constant="true"/> + <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_Lcystin_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_leu__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11067"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11025"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_t_Lcystin_ser__L" name="t_Lcystin_ser__L" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_Lcystin_e" stoichiometry="1" constant="true"/> + <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_Lcystin_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ser__L_e" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:and> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11025"/> + <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11067"/> + </fbc:and> + </fbc:geneProductAssociation> + </reaction> + </listOfReactions> + <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> + <fbc:listOfGeneProducts> + <fbc:geneProduct fbc:id="G_HGNC__58__11830" fbc:name="G_HGNC:11830" fbc:label="G_HGNC__58__11830"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: TK1</p> + <p>ENSG: ENSG00000167900</p> + <p>HGNC ID: HGNC:11830</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__11831" fbc:name="G_HGNC:11831" fbc:label="G_HGNC__58__11831"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: TK2</p> + <p>ENSG: ENSG00000166548</p> + <p>HGNC ID: HGNC:11831</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__4925" fbc:name="G_HGNC:4925" fbc:label="G_HGNC__58__4925"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: HK3</p> + <p>ENSG: ENSG00000160883</p> + <p>HGNC ID: HGNC:4925</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__4195" fbc:name="G_HGNC:4195" fbc:label="G_HGNC__58__4195"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: GCK</p> + <p>ENSG: ENSG00000106633</p> + <p>HGNC ID: HGNC:4195</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__4922" fbc:name="G_HGNC:4922" fbc:label="G_HGNC__58__4922"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: HK1</p> + <p>ENSG: ENSG00000156515</p> + <p>HGNC ID: HGNC:4922</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__4923" fbc:name="G_HGNC:4923" fbc:label="G_HGNC__58__4923"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: HK2</p> + <p>ENSG: ENSG00000159399</p> + <p>HGNC ID: HGNC:4923</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__23302" fbc:name="G_HGNC:23302" fbc:label="G_HGNC__58__23302"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: HKDC1</p> + <p>ENSG: ENSG00000156510</p> + <p>HGNC ID: HGNC:23302</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__4056" fbc:name="G_HGNC:4056" fbc:label="G_HGNC__58__4056"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: G6PC1</p> + <p>ENSG: ENSG00000131482</p> + <p>HGNC ID: HGNC:4056</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__28906" fbc:name="G_HGNC:28906" fbc:label="G_HGNC__58__28906"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: G6PC2</p> + <p>ENSG: ENSG00000152254</p> + <p>HGNC ID: HGNC:28906</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__24861" fbc:name="G_HGNC:24861" fbc:label="G_HGNC__58__24861"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: G6PC3</p> + <p>ENSG: ENSG00000141349</p> + <p>HGNC ID: HGNC:24861</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__4458" fbc:name="G_HGNC:4458" fbc:label="G_HGNC__58__4458"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: GPI</p> + <p>ENSG: ENSG00000105220</p> + <p>HGNC ID: HGNC:4458</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__8877" fbc:name="G_HGNC:8877" fbc:label="G_HGNC__58__8877"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: PFKM</p> + <p>ENSG: ENSG00000152556</p> + <p>HGNC ID: HGNC:8877</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__8876" fbc:name="G_HGNC:8876" fbc:label="G_HGNC__58__8876"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: PFKL</p> + <p>ENSG: ENSG00000141959</p> + <p>HGNC ID: HGNC:8876</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__8878" fbc:name="G_HGNC:8878" fbc:label="G_HGNC__58__8878"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: PFKP</p> + <p>ENSG: ENSG00000067057</p> + <p>HGNC ID: HGNC:8878</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__3606" fbc:name="G_HGNC:3606" fbc:label="G_HGNC__58__3606"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: FBP1</p> + <p>ENSG: ENSG00000165140</p> + <p>HGNC ID: HGNC:3606</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__3607" fbc:name="G_HGNC:3607" fbc:label="G_HGNC__58__3607"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: FBP2</p> + <p>ENSG: ENSG00000130957</p> + <p>HGNC ID: HGNC:3607</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__417" fbc:name="G_HGNC:417" fbc:label="G_HGNC__58__417"> + <notes> + <html xmlns="http://www.w3.org/1999/xhtml"> + <p>HGNC symbol: ALDOB</p> + <p>ENSG: ENSG00000136872</p> + <p>HGNC ID: HGNC:417</p> + </html> + </notes> + </fbc:geneProduct> + <fbc:geneProduct fbc:id="G_HGNC__58__418" fbc:name="G_HGNC:418" 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--- a/marea_2_0/model_generator.py Fri Jul 05 16:15:30 2024 +0000 +++ b/marea_2_0/model_generator.py Sat Jul 06 09:24:54 2024 +0000 @@ -21,6 +21,16 @@ """ parser = argparse.ArgumentParser(usage = '%(prog)s [options]', description = 'process some value\'s') + + parser.add_argument( + '-ms', '--model_selector', + type = utils.Model, default = utils.Model.ENGRO2, + help = 'chose which type of model you want use') + + parser.add_argument("-mo", "--model", type = str, + help = "path to input file with custom rules, if provided") + + parser.add_argument("-mn", "--model_name", type = str, help = "custom mode name") parser.add_argument('-ol', '--out_log', help = "Output log") @@ -30,6 +40,11 @@ required = True, help = 'your tool directory') + parser.add_argument('-in', '--model', + required = True, + type=str, + help = 'input model') + parser.add_argument('-im', '--input_medium', required = True, @@ -69,6 +84,11 @@ dataset.to_csv(ARGS.output_folder + name + ".csv", sep = '\t', index = keep_index) +def generate_model(cell_name, ras, medium): + # compute FVA + pass + + ############################# main ########################################### def main() -> None: """ @@ -87,11 +107,16 @@ ARGS.output_folder = 'model_generator/' - - ras_inputs = ARGS.input_ras.split(",") ARGS.output_types = ARGS.output_type.split(",") - ras = pd.read_table(ras_inputs[0], header=0, sep=r'\s+', index_col = 0) + ras = pd.read_table(ARGS.input_ras, header=0, sep=r'\s+', index_col = 0).T + ras.replace("None", None, inplace=True) + + #medium has rows cells and columns medium reactions, not common reactions set to None + medium = pd.read_csv(ARGS.input_medium, sep = '\t', header = 0, engine='python', index_col = 0) + + for index, row in ras.iterrows(): #iterate over cells RAS + generate_model(index, row, medium.loc[index]) pass
--- a/marea_2_0/model_generator.xml Fri Jul 05 16:15:30 2024 +0000 +++ b/marea_2_0/model_generator.xml Sat Jul 06 09:24:54 2024 +0000 @@ -13,17 +13,29 @@ <command detect_errors="exit_code"> <![CDATA[ python $__tool_directory__/model_generator.py + --model_selector $cond_model.model_selector --tool_dir $__tool_directory__ - --input_medium input_medium - --input_ras "${",".join(map(str, $inputs_ras))}" + --input_medium $input_medium + --input_ras $input_ras --output_type "${",".join(map(str, $output_types))}" --out_log $log + #if $cond_model.model_selector == 'Custom' + --model $model + --model_name $model.element_identifier + #end if ]]> </command> <inputs> - <param name="inputs_ras" argument="--inputs_ras" multiple="true" type="data" format="tabular" label="RAS dataset(s):" /> + <conditional name="cond_model"> + <expand macro="options"/> + <when value="Custom"> + <param name="model" argument="--model" type="data" format="json, xml" label="Custom model" /> + </when> + </conditional> + + <param name="input_ras" argument="--input_ras" multiple="false" type="data" format="tabular, csv, tsv" label="RAS matrix:" /> <param name="input_medium" argument="--input_medium" multiple="false" type="data" format="tabular, csv, tsv" label="Medium:"/>
--- a/marea_2_0/utils/flux_analysis.py Fri Jul 05 16:15:30 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -import cobra -import utils -import pandas as pd -from scipy.stats import spearmanr, pearsonr, gaussian_kde -import numpy as np - - -def get_flux_correlation(samples:pd.DataFrame, reference_rxn:str, method:str="spearman", fillNan:bool=True) -> pd.DataFrame: - - df_result = pd.DataFrame(index = samples.columns) - - reference_rxn_data = samples[reference_rxn].values - - coefs = [] - pvals = [] - - for rxn in samples.columns: - if(method == "spearman"): - coef, pval = spearmanr(reference_rxn_data, samples[rxn].values) - elif(method == "pearson"): - coef, pval = pearsonr(reference_rxn_data, samples[rxn].values) - else: - raise utils.ValueErr(method + " is not recognized, only spearman and pearson are supported.") - coefs.append(coef) - pvals.append(pval) - - df_result["p_value"] = pvals - df_result["coefficient"] = coefs - - if(fillNan): - df_result.fillna(0, inplace = True) - - return df_result - -def compute_statistic(samples:pd.DataFrame, method:str="mean")-> pd.DataFrame: - - if(method == "dist"): - columns = [] - for rxn in samples.columns: - columns.append(rxn + "_min") - columns.append(rxn + "_1q") - columns.append(rxn + "_2q") - columns.append(rxn + "_3q") - columns.append(rxn + "_max") - - df_result = pd.DataFrame(columns = columns) - else: - df_result = pd.DataFrame(columns = samples.columns) - - stat_rxns = [] - for rxn in samples.columns: - data = samples[rxn] - if(method == "mean"): - stat_rxns.append(data.mean()) - elif(method == "median"): - stat_rxns.append(data.median()) - elif(method == "mode"): - if(len(set(data)) == 1): - stat_rxns.append(data[0]) - else: - kde = gaussian_kde(data) - x_grid = np.linspace(min(data), max(data), 100) - density = kde(x_grid) - mode_index = np.argmax(density) - stat_rxns.append(x_grid[mode_index]) - elif(method == "dist"): - stat_rxns.append(data.min()) - stat_rxns.append(data.quantile(0.25)) - stat_rxns.append(data.quantile(0.50)) - stat_rxns.append(data.quantile(0.75)) - stat_rxns.append(data.max()) - else: - raise utils.ValueErr(method + " is not recognized, only mean, median, mode and dist are supported.") - - df_result.loc[0] = stat_rxns - - return df_result - - - - \ No newline at end of file
--- a/marea_2_0/utils/general_utils.py Fri Jul 05 16:15:30 2024 +0000 +++ b/marea_2_0/utils/general_utils.py Sat Jul 06 09:24:54 2024 +0000 @@ -4,6 +4,7 @@ import csv import pickle import lxml.etree as ET +import cobra from enum import Enum from itertools import count @@ -547,5 +548,37 @@ path = customPath if self is Model.Custom else FilePath(f"{self.name}_map", FileFormat.SVG, prefix = f"{toolDir}/local/svg metabolic maps/") self.__raiseMissingPathErr(path) return readSvg(path, customErr = DataErr(path, f"custom map in wrong format")) + + def getCOBRAmodel(self, toolDir = ".", customPath :Optional[FilePath] = None, customExtension :Optional[FilePath]=None)->cobra.Model: + if(self is Model.custom): + return self.load_custom_model(customPath, customExtension) + else: + return cobra.io.read_sbml_model(FilePath(f"{self.name}", FileFormat.XML, prefix = f"{toolDir}/local/COBRA models/")) + + def load_custom_model(file_path :FilePath, ext :Optional[FileFormat] = None) -> cobra.Model: + """ + Loads a custom model from a file, either in JSON or XML format. + + Args: + file_path : The path to the file containing the custom model. + ext : explicit file extension. Necessary for standard use in galaxy because of its weird behaviour. + + Raises: + DataErr : if the file is in an invalid format or cannot be opened for whatever reason. + + Returns: + cobra.Model : the model, if successfully opened. + """ + ext = ext if ext else file_path.ext + try: + if ext is FileFormat.XML: + return cobra.io.read_sbml_model(file_path.show()) + + if ext is FileFormat.JSON: + return cobra.io.load_json_model(file_path.show()) + + except Exception as e: raise DataErr(file_path, e.__str__()) + raise DataErr(file_path, + f"Fomat \"{file_path.ext}\" is not recognized, only JSON and XML files are supported.") def __str__(self) -> str: return self.value \ No newline at end of file