Mercurial > repos > iuc > gem_extract_exchange
view test-data/textbook_model_cobrapy.xml @ 0:d9893d41dd6a draft default tip
planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
| author | iuc |
|---|---|
| date | Fri, 13 Dec 2024 21:33:34 +0000 |
| parents | |
| children |
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rdf:resource="https://identifiers.org/pubchem.substance/3344"/> <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_113536"/> <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_433123"/> <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_29434"/> <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_389583"/> <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_1650769"/> <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_159939"/> <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00036"/> <rdf:li rdf:resource="https://identifiers.org/unipathway.compound/UPC00042"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="meta_M_succoa_c" id="M_succoa_c" name="Succinyl-CoA" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-5" fbc:chemicalFormula="C25H35N7O19P3S"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_M_succoa_c"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/succoa"/> <rdf:li rdf:resource="https://identifiers.org/cas/604-98-8"/> <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:15127"/> <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:15380"/> <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:57292"/> <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:26811"/> <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:9310"/> <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:45541"/> <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:10746"/> <rdf:li 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xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_M_xu5p__D_c"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/xu5p__D"/> <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00231"/> <rdf:li rdf:resource="https://identifiers.org/pubchem.substance/3530"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> </listOfSpecies> <listOfParameters> <parameter sboTerm="SBO:0000626" id="cobra_default_lb" value="-1000" constant="true"/> <parameter sboTerm="SBO:0000626" id="cobra_default_ub" value="1000" constant="true"/> <parameter sboTerm="SBO:0000626" id="cobra_0_bound" value="0" constant="true"/> <parameter sboTerm="SBO:0000626" id="minus_inf" value="-INF" constant="true"/> <parameter sboTerm="SBO:0000626" id="plus_inf" value="INF" constant="true"/> <parameter sboTerm="SBO:0000625" id="R_ATPM_lower_bound" value="8.39" units="mmol_per_gDW_per_hr" constant="true"/> <parameter sboTerm="SBO:0000625" id="R_EX_glc__D_e_lower_bound" value="-10" units="mmol_per_gDW_per_hr" constant="true"/> </listOfParameters> <listOfReactions> <reaction metaid="meta_R_ACALD" id="R_ACALD" name="acetaldehyde dehydrogenase (acetylating)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ACALD"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ACALD"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_accoa_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:or> <fbc:geneProductRef fbc:geneProduct="G_b0351"/> <fbc:geneProductRef fbc:geneProduct="G_b1241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ACALDt" id="R_ACALDt" name="R acetaldehyde reversible - transport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ACALDt"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ACALDt"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_acald_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ACKr" id="R_ACKr" name="acetate kinase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ACKr"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ACKr"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_actp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2296"/> <fbc:geneProductRef fbc:geneProduct="G_b3115"/> <fbc:geneProductRef fbc:geneProduct="G_b1849"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ACONTa" id="R_ACONTa" name="aconitase (half-reaction A, Citrate hydro-lyase)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ACONTa"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ACONTa"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acon_C_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0118"/> <fbc:geneProductRef fbc:geneProduct="G_b1276"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ACONTb" id="R_ACONTb" name="aconitase (half-reaction B, Isocitrate hydro-lyase)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ACONTb"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ACONTb"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_acon_C_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_icit_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0118"/> <fbc:geneProductRef fbc:geneProduct="G_b1276"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ACt2r" id="R_ACt2r" name="R acetate reversible transport via proton - symport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ACt2r"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ACt2r"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_ac_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction metaid="meta_R_ADK1" id="R_ADK1" name="adenylate kinase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ADK1"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ADK1"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0474"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_AKGDH" id="R_AKGDH" name="2-Oxogluterate dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_AKGDH"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/AKGDH"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0726"/> <fbc:geneProductRef fbc:geneProduct="G_b0116"/> <fbc:geneProductRef fbc:geneProduct="G_b0727"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_AKGt2r" id="R_AKGt2r" name="R 2 oxoglutarate reversible transport via - symport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_AKGt2r"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/AKGt2r"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_akg_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2587"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ALCD2x" id="R_ALCD2x" name="alcohol dehydrogenase (ethanol)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ALCD2x"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ALCD2x"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_etoh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acald_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:or> <fbc:geneProductRef fbc:geneProduct="G_b1478"/> <fbc:geneProductRef fbc:geneProduct="G_b0356"/> <fbc:geneProductRef fbc:geneProduct="G_b1241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ATPM" id="R_ATPM" name="ATP maintenance requirement" reversible="false" fast="false" fbc:lowerFluxBound="R_ATPM_lower_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ATPM"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ATPM"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_atp_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_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction metaid="meta_R_ATPS4r" id="R_ATPS4r" name="ATP synthase (four protons for one ATP)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ATPS4r"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ATPS4r"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="4" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3738"/> <fbc:geneProductRef fbc:geneProduct="G_b3736"/> <fbc:geneProductRef fbc:geneProduct="G_b3737"/> <fbc:geneProductRef fbc:geneProduct="G_b3735"/> <fbc:geneProductRef fbc:geneProduct="G_b3733"/> <fbc:geneProductRef fbc:geneProduct="G_b3731"/> <fbc:geneProductRef fbc:geneProduct="G_b3732"/> <fbc:geneProductRef fbc:geneProduct="G_b3734"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3734"/> <fbc:geneProductRef fbc:geneProduct="G_b3732"/> <fbc:geneProductRef fbc:geneProduct="G_b3731"/> <fbc:geneProductRef fbc:geneProduct="G_b3733"/> <fbc:geneProductRef fbc:geneProduct="G_b3735"/> <fbc:geneProductRef fbc:geneProduct="G_b3737"/> <fbc:geneProductRef fbc:geneProduct="G_b3736"/> <fbc:geneProductRef fbc:geneProduct="G_b3738"/> <fbc:geneProductRef fbc:geneProduct="G_b3739"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_Biomass_Ecoli_core" sboTerm="SBO:0000629" id="R_Biomass_Ecoli_core" name="Biomass Objective Function with GAM" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_Biomass_Ecoli_core"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/Ecoli_core_w_GAM"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_3pg_c" stoichiometry="1.496" constant="true"/> <speciesReference species="M_accoa_c" stoichiometry="3.7478" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="59.81" constant="true"/> <speciesReference species="M_e4p_c" stoichiometry="0.361" constant="true"/> <speciesReference species="M_f6p_c" stoichiometry="0.0709" constant="true"/> <speciesReference species="M_g3p_c" stoichiometry="0.129" constant="true"/> <speciesReference species="M_g6p_c" stoichiometry="0.205" constant="true"/> <speciesReference species="M_gln__L_c" stoichiometry="0.2557" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="4.9414" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="59.81" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="3.547" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="13.0279" constant="true"/> <speciesReference species="M_oaa_c" stoichiometry="1.7867" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="0.5191" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="2.8328" constant="true"/> <speciesReference species="M_r5p_c" stoichiometry="0.8977" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="59.81" constant="true"/> <speciesReference species="M_akg_c" stoichiometry="4.1182" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="3.7478" constant="true"/> <speciesReference species="M_h_c" stoichiometry="59.81" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="3.547" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="13.0279" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="59.81" constant="true"/> </listOfProducts> </reaction> <reaction metaid="meta_R_CO2t" id="R_CO2t" name="R CO2 transporter via - diffusion" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_CO2t"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/CO2t"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_co2_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_CS" id="R_CS" name="citrate synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_CS"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/CS"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0720"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_CYTBD" id="R_CYTBD" name="cytochrome oxidase bd (ubiquinol-8: 2 protons)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_CYTBD"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/CYTBD"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="0.5" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="2" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0978"/> <fbc:geneProductRef fbc:geneProduct="G_b0979"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0733"/> <fbc:geneProductRef fbc:geneProduct="G_b0734"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_D_LACt2" id="R_D_LACt2" name="R D lactate transport via proton - symport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_D_LACt2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/D_LACt2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> <speciesReference species="M_lac__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lac__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2975"/> <fbc:geneProductRef fbc:geneProduct="G_b3603"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ENO" id="R_ENO" name="enolase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ENO"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ENO"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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:geneProductRef fbc:geneProduct="G_b2779"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ETOHt2r" id="R_ETOHt2r" name="ETOHt2r" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ETOHt2r"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ETOHt2r"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_etoh_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_etoh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction metaid="meta_R_EX_ac_e" sboTerm="SBO:0000627" id="R_EX_ac_e" name="Acetate exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_ac_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ac"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_ac_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_acald_e" sboTerm="SBO:0000627" id="R_EX_acald_e" name="Acetaldehyde exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_acald_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/acald"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_acald_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_akg_e" sboTerm="SBO:0000627" id="R_EX_akg_e" name="2-Oxoglutarate exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_akg_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/akg"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_akg_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_co2_e" sboTerm="SBO:0000627" id="R_EX_co2_e" name="CO2 exchange" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_co2_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/co2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_co2_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_etoh_e" sboTerm="SBO:0000627" id="R_EX_etoh_e" name="Ethanol exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_etoh_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/etoh"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_etoh_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_for_e" sboTerm="SBO:0000627" id="R_EX_for_e" name="Formate exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_for_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/for"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_for_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_fru_e" sboTerm="SBO:0000627" id="R_EX_fru_e" name="D-Fructose exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_fru_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/fru"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_fru_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_fum_e" sboTerm="SBO:0000627" id="R_EX_fum_e" name="Fumarate exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_fum_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/fum"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_fum_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_glc__D_e" sboTerm="SBO:0000627" id="R_EX_glc__D_e" name="D-Glucose exchange" reversible="true" fast="false" fbc:lowerFluxBound="R_EX_glc__D_e_lower_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_glc__D_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/glc"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_gln__L_e" sboTerm="SBO:0000627" id="R_EX_gln__L_e" name="L-Glutamine exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_gln__L_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/gln__L"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_gln__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_glu__L_e" sboTerm="SBO:0000627" id="R_EX_glu__L_e" name="L-Glutamate exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_glu__L_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/glu__L"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_glu__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_h_e" sboTerm="SBO:0000627" id="R_EX_h_e" name="H+ exchange" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_h_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/h"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_h2o_e" sboTerm="SBO:0000627" id="R_EX_h2o_e" name="H2O exchange" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_h2o_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/h2o"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h2o_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_lac__D_e" sboTerm="SBO:0000627" id="R_EX_lac__D_e" name="D-lactate exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_lac__D_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/lac__D"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_lac__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_mal__L_e" sboTerm="SBO:0000627" id="R_EX_mal__L_e" name="L-Malate exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_mal__L_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/mal__L"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_mal__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_nh4_e" sboTerm="SBO:0000627" id="R_EX_nh4_e" name="Ammonia exchange" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_nh4_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/nh4"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_nh4_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_o2_e" sboTerm="SBO:0000627" id="R_EX_o2_e" name="O2 exchange" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_o2_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/o2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_pi_e" sboTerm="SBO:0000627" id="R_EX_pi_e" name="Phosphate exchange" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_pi_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/pi"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_pi_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_pyr_e" sboTerm="SBO:0000627" id="R_EX_pyr_e" name="Pyruvate exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_pyr_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/pyr"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_pyr_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_EX_succ_e" sboTerm="SBO:0000627" id="R_EX_succ_e" name="Succinate exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_EX_succ_e"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/succ"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_succ_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction metaid="meta_R_FBA" id="R_FBA" name="fructose-bisphosphate aldolase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_FBA"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FBA"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1773"/> <fbc:geneProductRef fbc:geneProduct="G_b2097"/> <fbc:geneProductRef fbc:geneProduct="G_b2925"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_FBP" id="R_FBP" name="fructose-bisphosphatase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_FBP"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FBP"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3925"/> <fbc:geneProductRef fbc:geneProduct="G_b4232"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_FORt2" id="R_FORt2" name="formate transport in via proton symport" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_FORt2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FORt2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_for_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0904"/> <fbc:geneProductRef fbc:geneProduct="G_b2492"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_FORti" id="R_FORti" name="formate transport via diffusion" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_FORti"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FORti"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_for_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0904"/> <fbc:geneProductRef fbc:geneProduct="G_b2492"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_FRD7" id="R_FRD7" name="fumarate reductase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_FRD7"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FRD7"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4153"/> <fbc:geneProductRef fbc:geneProduct="G_b4151"/> <fbc:geneProductRef fbc:geneProduct="G_b4152"/> <fbc:geneProductRef fbc:geneProduct="G_b4154"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_FRUpts2" id="R_FRUpts2" name="R Fructose transport via PEPPyr PTS-f6p - generating" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_FRUpts2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FRUpts2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_fru_e" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b1818"/> <fbc:geneProductRef fbc:geneProduct="G_b1817"/> <fbc:geneProductRef fbc:geneProduct="G_b1819"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_FUM" id="R_FUM" name="fumarase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_FUM"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FUM"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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:or> <fbc:geneProductRef fbc:geneProduct="G_b4122"/> <fbc:geneProductRef fbc:geneProduct="G_b1612"/> <fbc:geneProductRef fbc:geneProduct="G_b1611"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_FUMt2_2" id="R_FUMt2_2" name="R Fumarate transport via proton symport-2 - H" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_FUMt2_2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/FUMt2_2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_fum_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3528"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_G6PDH2r" id="R_G6PDH2r" name="glucose 6-phosphate dehydrogenase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_G6PDH2r"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/G6PDH2r"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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_b1852"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_GAPD" id="R_GAPD" name="glyceraldehyde-3-phosphate dehydrogenase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_GAPD"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GAPD"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_13dpg_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_b1779"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_GLCpts" id="R_GLCpts" name="D-glucose transport via PEP:Pyr PTS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_GLCpts"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GLCpts"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b1818"/> <fbc:geneProductRef fbc:geneProduct="G_b1817"/> <fbc:geneProductRef fbc:geneProduct="G_b1819"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b2417"/> <fbc:geneProductRef fbc:geneProduct="G_b1101"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b2417"/> <fbc:geneProductRef fbc:geneProduct="G_b1621"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_GLNS" id="R_GLNS" name="glutamine synthetase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_GLNS"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GLNS"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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_b3870"/> <fbc:geneProductRef fbc:geneProduct="G_b1297"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_GLNabc" id="R_GLNabc" name="GLNabc" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_GLNabc"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GLNabc"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gln__L_e" 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_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:and> <fbc:geneProductRef fbc:geneProduct="G_b0810"/> <fbc:geneProductRef fbc:geneProduct="G_b0811"/> <fbc:geneProductRef fbc:geneProduct="G_b0809"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_GLUDy" id="R_GLUDy" name="glutamate dehydrogenase (NADP)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_GLUDy"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GLUDy"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_glu__L_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_akg_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_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1761"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_GLUN" id="R_GLUN" name="glutaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_GLUN"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GLUN"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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:or> <fbc:geneProductRef fbc:geneProduct="G_b0485"/> <fbc:geneProductRef fbc:geneProduct="G_b1812"/> <fbc:geneProductRef fbc:geneProduct="G_b1524"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_GLUSy" id="R_GLUSy" name="glutamate synthase (NADPH)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_GLUSy"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GLUSy"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_akg_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_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glu__L_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3212"/> <fbc:geneProductRef fbc:geneProduct="G_b3213"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_GLUt2r" id="R_GLUt2r" name="R L glutamate transport via proton - symport-reversible" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_GLUt2r"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GLUt2r"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_glu__L_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4077"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_GND" id="R_GND" name="phosphogluconate dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_GND"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GND"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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_b2029"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_H2Ot" id="R_H2Ot" name="R H2O transport via - diffusion" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_H2Ot"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/H2Ot"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h2o_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0875"/> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ICDHyr" id="R_ICDHyr" name="isocitrate dehydrogenase (NADP)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ICDHyr"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ICDHyr"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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_b1136"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ICL" id="R_ICL" name="Isocitrate lyase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ICL"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ICL"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_icit_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glx_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4015"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_LDH_D" id="R_LDH_D" name="D-lactate dehydrogenase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_LDH_D"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/LDH_D"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_lac__D_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_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2133"/> <fbc:geneProductRef fbc:geneProduct="G_b1380"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_MALS" id="R_MALS" name="malate synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_MALS"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/MALS"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glx_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_mal__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4014"/> <fbc:geneProductRef fbc:geneProduct="G_b2976"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_MALt2_2" id="R_MALt2_2" name="R Malate transport via proton symport-2 - H" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_MALt2_2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/MALt2_2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h_e" stoichiometry="2" constant="true"/> <speciesReference species="M_mal__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3528"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_MDH" id="R_MDH" name="malate dehydrogenase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_MDH"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/MDH"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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:geneProductRef fbc:geneProduct="G_b3236"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ME1" id="R_ME1" name="malic enzyme (NAD)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ME1"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ME1"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1479"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_ME2" id="R_ME2" name="malic enzyme (NADP)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_ME2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/ME2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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_b2463"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_NADH16" id="R_NADH16" name="NADH dehydrogenase (ubiquinone-8 & 3 protons)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_NADH16"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/NADH16"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_e" stoichiometry="3" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2287"/> <fbc:geneProductRef fbc:geneProduct="G_b2285"/> <fbc:geneProductRef fbc:geneProduct="G_b2283"/> <fbc:geneProductRef fbc:geneProduct="G_b2281"/> <fbc:geneProductRef fbc:geneProduct="G_b2279"/> <fbc:geneProductRef fbc:geneProduct="G_b2277"/> <fbc:geneProductRef fbc:geneProduct="G_b2276"/> <fbc:geneProductRef fbc:geneProduct="G_b2278"/> <fbc:geneProductRef fbc:geneProduct="G_b2280"/> <fbc:geneProductRef fbc:geneProduct="G_b2282"/> <fbc:geneProductRef fbc:geneProduct="G_b2284"/> <fbc:geneProductRef fbc:geneProduct="G_b2286"/> <fbc:geneProductRef fbc:geneProduct="G_b2288"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_NADTRHD" id="R_NADTRHD" name="NAD transhydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_NADTRHD"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/NADTRHD"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3962"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1602"/> <fbc:geneProductRef fbc:geneProduct="G_b1603"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_NH4t" id="R_NH4t" name="R ammonia reversible - transport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_NH4t"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/NH4t"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_nh4_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> <fbc:geneProductRef fbc:geneProduct="G_b0451"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_O2t" id="R_O2t" name="R o2 - transport-diffusion" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_O2t"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/O2t"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PDH" id="R_PDH" name="pyruvate dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PDH"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PDH"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0115"/> <fbc:geneProductRef fbc:geneProduct="G_b0114"/> <fbc:geneProductRef fbc:geneProduct="G_b0116"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PFK" id="R_PFK" name="phosphofructokinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PFK"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PFK"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3916"/> <fbc:geneProductRef fbc:geneProduct="G_b1723"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PFL" id="R_PFL" name="pyruvate formate lyase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PFL"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PFL"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0902"/> <fbc:geneProductRef fbc:geneProduct="G_b3114"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0903"/> <fbc:geneProductRef fbc:geneProduct="G_b0902"/> <fbc:geneProductRef fbc:geneProduct="G_b2579"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0902"/> <fbc:geneProductRef fbc:geneProduct="G_b0903"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3951"/> <fbc:geneProductRef fbc:geneProduct="G_b3952"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PGI" id="R_PGI" name="glucose-6-phosphate isomerase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PGI"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PGI"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4025"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PGK" id="R_PGK" name="phosphoglycerate kinase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PGK"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PGK"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_13dpg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2926"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PGL" id="R_PGL" name="6-phosphogluconolactonase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PGL"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PGL"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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:geneProductRef fbc:geneProduct="G_b0767"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PGM" id="R_PGM" name="phosphoglycerate mutase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PGM"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PGM"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4395"/> <fbc:geneProductRef fbc:geneProduct="G_b3612"/> <fbc:geneProductRef fbc:geneProduct="G_b0755"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PIt2r" id="R_PIt2r" name="R phosphate reversible transport via - symport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PIt2r"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PIt2r"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <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_b2987"/> <fbc:geneProductRef fbc:geneProduct="G_b3493"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PPC" id="R_PPC" name="phosphoenolpyruvate carboxylase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PPC"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PPC"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_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_b3956"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PPCK" id="R_PPCK" name="phosphoenolpyruvate carboxykinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PPCK"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PPCK"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oaa_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_pep_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3403"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PPS" id="R_PPS" name="phosphoenolpyruvate synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PPS"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PPS"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1702"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PTAr" id="R_PTAr" name="phosphotransacetylase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PTAr"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PTAr"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_actp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2297"/> <fbc:geneProductRef fbc:geneProduct="G_b2458"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PYK" id="R_PYK" name="pyruvate kinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PYK"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PYK"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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_b1854"/> <fbc:geneProductRef fbc:geneProduct="G_b1676"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_PYRt2" id="R_PYRt2" name="R pyruvate transport in via proton - symport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_PYRt2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PYRt2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction metaid="meta_R_RPE" id="R_RPE" name="ribulose 5-phosphate 3-epimerase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_RPE"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/RPE"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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_b3386"/> <fbc:geneProductRef fbc:geneProduct="G_b4301"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_RPI" id="R_RPI" name="ribose-5-phosphate isomerase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_RPI"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/RPI"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2914"/> <fbc:geneProductRef fbc:geneProduct="G_b4090"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_SUCCt2_2" id="R_SUCCt2_2" name="R succinate transport via proton symport-2 - H" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_SUCCt2_2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/SUCCt2_2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h_e" stoichiometry="2" constant="true"/> <speciesReference species="M_succ_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3528"/> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_SUCCt3" id="R_SUCCt3" name="succinate transport out via proton antiport" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_SUCCt3"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/SUCCt3"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_e" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction metaid="meta_R_SUCDi" id="R_SUCDi" name="succinate dehydrogenase (irreversible)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_SUCDi"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/SUCDi"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0723"/> <fbc:geneProductRef fbc:geneProduct="G_b0721"/> <fbc:geneProductRef fbc:geneProduct="G_b0722"/> <fbc:geneProductRef fbc:geneProduct="G_b0724"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_SUCOAS" id="R_SUCOAS" name="succinyl-CoA synthetase (ADP-forming)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_SUCOAS"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/SUCOAS"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_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_succoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0728"/> <fbc:geneProductRef fbc:geneProduct="G_b0729"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_TALA" id="R_TALA" name="transaldolase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_TALA"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/TALA"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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:or> <fbc:geneProductRef fbc:geneProduct="G_b2464"/> <fbc:geneProductRef fbc:geneProduct="G_b0008"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_THD2" id="R_THD2" name="R NAD - P-transhydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_THD2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/THD2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_h_e" stoichiometry="2" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1602"/> <fbc:geneProductRef fbc:geneProduct="G_b1603"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_TKT1" id="R_TKT1" name="transketolase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_TKT1"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/TKT1"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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_b2935"/> <fbc:geneProductRef fbc:geneProduct="G_b2465"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_TKT2" id="R_TKT2" name="transketolase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_TKT2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/TKT2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <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_b2935"/> <fbc:geneProductRef fbc:geneProduct="G_b2465"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction metaid="meta_R_TPI" id="R_TPI" name="triose-phosphate isomerase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_R_TPI"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/TPI"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfReactants> <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3919"/> </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_Ecoli_core" fbc:coefficient="1"/> </fbc:listOfFluxObjectives> </fbc:objective> </fbc:listOfObjectives> <fbc:listOfGeneProducts> <fbc:geneProduct fbc:id="G_b1241" fbc:name="adhE" fbc:label="G_b1241"/> <fbc:geneProduct fbc:id="G_b0351" fbc:name="mhpF" fbc:label="G_b0351"/> <fbc:geneProduct fbc:id="G_s0001" fbc:name="G_s0001" fbc:label="G_s0001"/> <fbc:geneProduct fbc:id="G_b3115" fbc:name="tdcD" fbc:label="G_b3115"/> <fbc:geneProduct metaid="meta_G_b1849" fbc:id="G_b1849" fbc:name="purT" fbc:label="G_b1849"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_G_b1849"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1652885"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </fbc:geneProduct> <fbc:geneProduct metaid="meta_G_b2296" fbc:id="G_b2296" fbc:name="ackA" fbc:label="G_b2296"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_G_b2296"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1652265"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </fbc:geneProduct> <fbc:geneProduct fbc:id="G_b1276" fbc:name="acnA" fbc:label="G_b1276"/> <fbc:geneProduct fbc:id="G_b0118" fbc:name="acnB" fbc:label="G_b0118"/> <fbc:geneProduct metaid="meta_G_b0474" fbc:id="G_b0474" fbc:name="adk" fbc:label="G_b0474"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_G_b0474"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1651715"/> <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1652408"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </fbc:geneProduct> <fbc:geneProduct fbc:id="G_b0116" fbc:name="lpd" fbc:label="G_b0116"/> <fbc:geneProduct fbc:id="G_b0726" fbc:name="sucA" fbc:label="G_b0726"/> <fbc:geneProduct fbc:id="G_b0727" fbc:name="sucB" fbc:label="G_b0727"/> <fbc:geneProduct fbc:id="G_b2587" fbc:name="kgtP" fbc:label="G_b2587"/> <fbc:geneProduct fbc:id="G_b0356" fbc:name="frmA" fbc:label="G_b0356"/> <fbc:geneProduct fbc:id="G_b1478" fbc:name="adhP" fbc:label="G_b1478"/> <fbc:geneProduct metaid="meta_G_b3735" fbc:id="G_b3735" fbc:name="atpH" fbc:label="G_b3735"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_G_b3735"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1651812"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </fbc:geneProduct> <fbc:geneProduct metaid="meta_G_b3733" fbc:id="G_b3733" fbc:name="atpG" fbc:label="G_b3733"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" 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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_G_b0729"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1653466"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </fbc:geneProduct> <fbc:geneProduct fbc:id="G_b2464" fbc:name="talA" fbc:label="G_b2464"/> <fbc:geneProduct metaid="meta_G_b0008" fbc:id="G_b0008" fbc:name="talB" fbc:label="G_b0008"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_G_b0008"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1651885"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </fbc:geneProduct> <fbc:geneProduct metaid="meta_G_b2935" fbc:id="G_b2935" fbc:name="tktA" fbc:label="G_b2935"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_G_b2935"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1652388"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </fbc:geneProduct> <fbc:geneProduct fbc:id="G_b2465" fbc:name="tktB" fbc:label="G_b2465"/> <fbc:geneProduct fbc:id="G_b3919" fbc:name="tpiA" fbc:label="G_b3919"/> </fbc:listOfGeneProducts> </model> </sbml>