Mercurial > repos > tduigou > get_sbml_model
view model.sbml @ 8:768ed7cc0978 draft
planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
| author | tduigou |
|---|---|
| date | Fri, 29 Sep 2023 09:03:09 +0000 |
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<?xml version='1.0' encoding='UTF-8'?> <sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1" sboTerm="SBO:0000624" fbc:required="false"> <model fbc:strict="true" id="iML1515"> <listOfUnitDefinitions> <unitDefinition id="mmol_per_gDW_per_hr"> <listOfUnits> <unit kind="mole" scale="-3" multiplier="1" exponent="1"/> <unit kind="gram" scale="0" multiplier="1" exponent="-1"/> <unit kind="second" scale="0" multiplier="3600" exponent="-1"/> </listOfUnits> </unitDefinition> </listOfUnitDefinitions> <fbc:listOfObjectives fbc:activeObjective="obj"> <fbc:objective fbc:id="obj" fbc:type="maximize"> <fbc:listOfFluxObjectives> <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ec_iML1515_core_75p37M" fbc:coefficient="1"/> </fbc:listOfFluxObjectives> </fbc:objective> </fbc:listOfObjectives> <listOfParameters> <parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> <parameter value="1000" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> <parameter value="0" id="cobra_0_bound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> <parameter id="R_EX_glc__D_e_lower_bound" value="-10" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> <parameter id="R_ATPM_lower_bound" value="6.86" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> </listOfParameters> <listOfCompartments> <compartment id="c" name="cytosol" constant="true"/> <compartment id="e" name="extracellular space" constant="true"/> <compartment id="p" name="periplasm" constant="true"/> </listOfCompartments> <listOfSpecies> <species id="M_octapb_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="Octanoate (protein bound)" metaid="M_octapb_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="1" fbc:chemicalFormula="C8H15O"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#M_octapb_c"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/octapb"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM147531"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> </species> <species id="M_cysi__L_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="L Cystine C6H12N2O4S2" metaid="M_cysi__L_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C6H12N2O4S2"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#M_cysi__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/cysi__L"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CYSTINE"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:6209"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:35491"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:63163"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13097"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16283"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:21278"/> <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00192"/> <rdf:li rdf:resource="http://identifiers.org/inchi_key/LEVWYRKDKASIDU-IMJSIDKUSA-N"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00491"/> <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D03636"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM927"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2060"/> <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00381"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> </species> <species id="M_dhap_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="Dihydroxyacetone phosphate" metaid="M_dhap_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C3H5O6P"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#M_dhap_c"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/dhap"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DIHYDROXY-ACETONE-PHOSPHATE"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:14341"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:5454"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16108"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:14342"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:24355"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:39571"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:57642"/> <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB11735"/> <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB01473"/> <rdf:li rdf:resource="http://identifiers.org/inchi_key/GNGACRATGGDKBX-UHFFFAOYSA-L"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00111"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM77"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/390404"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/75970"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/188451"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/28"/> <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00095"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> </species> <species id="M_prbatp_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="1-(5-Phosphoribosyl)-ATP" metaid="M_prbatp_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="-6" fbc:chemicalFormula="C15H19N5O20P4"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#M_prbatp_c"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/prbatp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PHOSPHORIBOSYL-ATP"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:73200"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:58424"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:11196"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18263"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:73183"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:8167"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18970"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:59460"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:11192"/> <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB03665"/> <rdf:li rdf:resource="http://identifiers.org/inchi_key/RKNHJBVBFHDXGR-KEOHHSTQSA-H"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C02739"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM1351"/> <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd01775"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> </species> <species id="M_10fthf_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="10-Formyltetrahydrofolate" metaid="M_10fthf_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C20H21N7O7"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#M_10fthf_c"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/10fthf"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:10-FORMYL-THF"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:19108"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15637"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:698"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:19109"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:11304"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:57454"/> <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00972"/> <rdf:li rdf:resource="http://identifiers.org/inchi_key/AUFGTPPARQZWDO-YPMHNXCESA-L"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00234"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM237"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/5389850"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/419151"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1318"/> <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00201"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> </species> <species id="M_btal_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="Butanal C4H8O" metaid="M_btal_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="0" fbc:chemicalFormula="C4H8O"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#M_btal_c"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/btal"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:BUTANAL"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:22938"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:3233"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15743"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13923"/> <rdf:li rdf:resource="http://identifiers.org/envipath/650babc9-9d68-4b73-9332-11972ca26f7b/compound/242f8a4e-2a91-4c5f-a129-d044d115b969"/> <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB03543"/> <rdf:li rdf:resource="http://identifiers.org/inchi_key/ZTQSAGDEMFDKMZ-UHFFFAOYSA-N"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C01412"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM1017"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2281"/> <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd01011"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> </species> <species id="M_6pgg_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="6-Phospho-beta-D-glucosyl-(1,4)-D-glucose" metaid="M_6pgg_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="-2" fbc:chemicalFormula="C12H21O14P"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#M_6pgg_c"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/6pgg"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM147389"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> </species> <species id="M_co2_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="CO2 CO2" metaid="M_co2_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="CO2"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#M_co2_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/co2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CARBON-DIOXIDE"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:23011"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:3283"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:48829"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16526"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13283"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13285"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13284"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13282"/> <rdf:li rdf:resource="http://identifiers.org/envipath/650babc9-9d68-4b73-9332-11972ca26f7b/compound/2ec3da94-5f50-4525-81b1-5607c5c7a3d3"/> <rdf:li rdf:resource="http://identifiers.org/envipath/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05f60af4-0a3f-4ead-9a29-33bb0f123379"/> <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB01967"/> <rdf:li rdf:resource="http://identifiers.org/inchi_key/CURLTUGMZLYLDI-UHFFFAOYSA-N"/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00011"/> <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00004"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM13"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/29376"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/5668565"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/189480"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/1132345"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/113528"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/1237009"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/159751"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/389536"/> <rdf:li rdf:resource="http://identifiers.org/reactome.compound/159942"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1266"/> <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00011"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> </species> <species id="M_akg_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="2-Oxoglutarate" metaid="M_akg_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="-2" fbc:chemicalFormula="C5H4O5"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#M_akg_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/akg"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2-KETOGLUTARATE"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:40661"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16810"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:11638"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:30916"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:19749"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:1253"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:30915"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:19748"/> <rdf:li rdf:resource="http://identifiers.org/envipath/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/5b0a94f6-d411-44fd-bcc1-fb79b4e697f5"/> <rdf:li rdf:resource="http://identifiers.org/envipath/4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/6557f3f2-0ab8-494b-a865-8ce0eae788a9"/> <rdf:li 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</bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> </species> <species id="M_gsn_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="Guanosine" metaid="M_gsn_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C10H13N5O5"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#M_gsn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/gsn"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GUANOSINE"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:14375"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16750"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42853"/> <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:24444"/> <rdf:li 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rdf:resource="http://identifiers.org/rhea/10382"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10380"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/401"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01362"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_orot5p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_orot_c" stoichiometry="1" constant="true"/> <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3642"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RBFSa" fast="false" reversible="false" name="Riboflavin synthase" metaid="R_RBFSa" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> 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<listOfProducts> <speciesReference species="M_dmlz_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0415"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACHBS" fast="false" reversible="false" name="2-aceto-2-hydroxybutanoate synthase" metaid="R_ACHBS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACHBS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACHBS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACETOOHBUTSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.2.1.6"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R08648"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95260"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27657"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27655"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27654"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27656"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/6688"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2obut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2ahbut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3670"/> <fbc:geneProductRef fbc:geneProduct="G_b3671"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0077"/> <fbc:geneProductRef fbc:geneProduct="G_b0078"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PFK_3" fast="false" reversible="false" name="Phosphofructokinase (s7p)" metaid="R_PFK_3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PFK_3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PFK_3"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6541"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.11"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01843"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102510"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31445"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31446"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31444"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31443"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/41"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01343"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_s7p_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_s17bp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3916"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHAD2" fast="false" reversible="false" name="Dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate)" metaid="R_DHAD2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHAD2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHAD2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DIHYDROXYMETVALDEHYDRAT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.9"/> <rdf:li 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<fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2243"/> <fbc:geneProductRef fbc:geneProduct="G_b2242"/> <fbc:geneProductRef fbc:geneProduct="G_b2241"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3426"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_G1PP" fast="false" reversible="false" name="Glucose-1-phosphatase" metaid="R_G1PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G1PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G1PP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUCOSE-1-PHOSPHAT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-17330"/> <rdf:li 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species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2293"/> <fbc:geneProductRef fbc:geneProduct="G_b3885"/> <fbc:geneProductRef fbc:geneProduct="G_b3697"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PFL" fast="false" reversible="false" name="Pyruvate formate lyase" metaid="R_PFL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PFL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PFL"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRUVFORMLY-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.54"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00212"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102514"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11847"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11845"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11844"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11846"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/146"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00157"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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_b0903"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0902"/> <fbc:geneProductRef fbc:geneProduct="G_b3114"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3951"/> <fbc:geneProductRef fbc:geneProduct="G_b3952"/> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0902"/> <fbc:geneProductRef fbc:geneProduct="G_b0903"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2579"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_acgam_e" fast="false" reversible="false" name="N-Acetyl-D-glucosamine exchange" metaid="R_EX_acgam_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_acgam_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_acgam_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95252"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08042"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgam_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ANS" fast="false" reversible="false" name="Anthranilate synthase" metaid="R_ANS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ANS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ANS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ANTHRANSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00986"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95843"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21734"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21733"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21735"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21732"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1280"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00727"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_chor_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_anth_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1263"/> <fbc:geneProductRef fbc:geneProduct="G_b1264"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRD2" fast="false" reversible="false" name="Fumarate reductase" metaid="R_FRD2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRD2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRD2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99637"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29216"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29215"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29218"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29217"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08527"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4152"/> <fbc:geneProductRef fbc:geneProduct="G_b4151"/> <fbc:geneProductRef fbc:geneProduct="G_b4153"/> <fbc:geneProductRef fbc:geneProduct="G_b4154"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRD3" fast="false" reversible="false" name="Fumarate reductase" metaid="R_FRD3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRD3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRD3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99639"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08528"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2dmmq8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4152"/> <fbc:geneProductRef fbc:geneProduct="G_b4151"/> <fbc:geneProductRef fbc:geneProduct="G_b4153"/> <fbc:geneProductRef fbc:geneProduct="G_b4154"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ANPRT" fast="false" reversible="false" name="Anthranilate phosphoribosyltransferase" metaid="R_ANPRT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ANPRT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ANPRT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PRTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.18"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01073"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95842"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11771"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11770"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11768"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11769"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00791"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anth_c" stoichiometry="1" constant="true"/> <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pran_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1263"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_POX" fast="false" reversible="false" name="Pyruvate oxidase" metaid="R_POX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_POX"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/POX"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103067"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29168"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29170"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29167"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29169"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09167"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0871"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CHORM" fast="false" reversible="false" name="Chorismate mutase" metaid="R_CHORM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CHORM"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHORM"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CHORISMATEMUT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.99.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01715"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96708"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13897"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13899"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13898"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13900"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1827"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01256"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_chor_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pphn_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2599"/> <fbc:geneProductRef fbc:geneProduct="G_b2600"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PTAr" fast="false" reversible="true" name="Phosphotransacetylase" metaid="R_PTAr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PTAr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PTAr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PHOSACETYLTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.8"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00230"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103319"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19521"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19523"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19522"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19524"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/72"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00173"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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 id="R_CHORS" fast="false" reversible="false" name="Chorismate synthase" metaid="R_CHORS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CHORS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHORS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CHORISMATE-SYNTHASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.3.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01714"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96709"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21020"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21023"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21022"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21021"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1826"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01255"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3psme_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_chor_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2329"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_IGPS" fast="false" reversible="false" name="Indole-3-glycerol-phosphate synthase" metaid="R_IGPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_IGPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/IGPS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:IGPSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.48"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03508"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100814"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23476"/> <rdf:li 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<speciesReference species="M_arg__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_asp__L_e" fast="false" reversible="false" name="L-Aspartate exchange" metaid="R_EX_asp__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_asp__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_asp__L_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-554"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96107"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10906"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08170"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13232"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asp__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_pyr_e" fast="false" reversible="false" name="Pyruvate exchange" metaid="R_EX_pyr_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_pyr_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pyr_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-506"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-570"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103384"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12168"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10929"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09218"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pyr_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_succ_e" fast="false" reversible="false" name="Succinate exchange" metaid="R_EX_succ_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_succ_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_succ_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-552"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104619"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10952"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09271"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_succ_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_thymd_e" fast="false" reversible="false" name="Thymidine exchange" metaid="R_EX_thymd_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_thymd_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_thymd_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104821"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10916"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09299"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_thymd_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_rib__D_e" fast="false" reversible="false" name="D-Ribose exchange" metaid="R_EX_rib__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_rib__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_rib__D_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104036"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09228"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_rib__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_tyr__L_e" fast="false" reversible="false" name="L-Tyrosine exchange" metaid="R_EX_tyr__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_tyr__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tyr__L_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-446"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105002"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13471"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09339"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10974"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tyr__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_cytd_e" fast="false" reversible="false" name="Cytidine exchange" metaid="R_EX_cytd_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cytd_e"> 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xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOAT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:KDOTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.99.12"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04658"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101683"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28067"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28068"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28066"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28069"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03182"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ckdo_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lipidA_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> 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rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99715"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08544"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11013"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fum_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_sbt__D_e" fast="false" reversible="false" name="D-Sorbitol exchange" metaid="R_EX_sbt__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_sbt__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_sbt__D_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104288"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09243"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09662"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sbt__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_glu__L_e" fast="false" reversible="false" name="L-Glutamate exchange" metaid="R_EX_glu__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_glu__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glu__L_e"/> <rdf:li 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<speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1850"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_spmd_e" fast="false" reversible="false" name="Spermidine exchange" metaid="R_EX_spmd_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_spmd_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_spmd_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104495"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35040"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35039"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35042"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35041"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13767"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13397"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09266"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_spmd_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_thym_e" fast="false" reversible="false" name="Thymine exchange" metaid="R_EX_thym_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_thym_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_thym_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-524"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104853"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09309"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_thym_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_xtsn_e" fast="false" reversible="false" name="Xanthosine exchange" metaid="R_EX_xtsn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_xtsn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_xtsn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105247"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09382"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_xtsn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_NTPP1" fast="false" reversible="false" name="Nucleoside triphosphate pyrophosphorylase (dgtp)" metaid="R_NTPP1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTPP1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPP1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-385"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.19"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01855"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102049"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28364"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28363"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28362"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28365"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/302"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01351"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dgtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dgmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0099"/> <fbc:geneProductRef fbc:geneProduct="G_b2781"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_URIK1" fast="false" reversible="false" name="Uridine kinase ATPUridine " metaid="R_URIK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_URIK1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URIK1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:URIDINEKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.48"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.213"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00964"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105162"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16828"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16826"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16825"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16827"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/85"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00709"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uri_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_ump_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2066"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_URIK2" fast="false" reversible="false" name="Uridine kinase (GTP:Uridine)" metaid="R_URIK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_URIK2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URIK2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:URKI-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.48"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00968"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105163"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27650"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27651"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27652"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27653"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00713"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2066"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTPP2" fast="false" reversible="false" name="Nucleoside triphosphate pyrophosphorylase (gtp)" metaid="R_NTPP2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTPP2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPP2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14140"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00426"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102052"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29391"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29392"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29393"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29394"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/301"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00301"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0099"/> <fbc:geneProductRef fbc:geneProduct="G_b2781"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGL" fast="false" reversible="false" name="6-phosphogluconolactonase" metaid="R_PGL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGL"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:6PGLUCONOLACT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.31"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02035"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102539"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71296"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-71296"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12559"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12556"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12557"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12558"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/109"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01476"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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 id="R_NTPTP1" fast="false" reversible="false" name="Nucleoside triphosphate tripolyhydrolase" metaid="R_NTPTP1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTPTP1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPTP1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DGTPTRIPHYDRO-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.5.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01856"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102057"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15196"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15195"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15193"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15194"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/232"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01352"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dgtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dgsn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0160"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTPTP2" fast="false" reversible="false" name="Nucleoside triphosphate tripolyhydrolase" metaid="R_NTPTP2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTPTP2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPTP2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102058"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30562"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30559"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30561"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30560"/> 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xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNDR4"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDPREDUCT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.17.4.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02018"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104066"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn06075"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dudp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3781"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2234"/> <fbc:geneProductRef fbc:geneProduct="G_b2235"/> </fbc:and> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2234"/> <fbc:geneProductRef fbc:geneProduct="G_b2235"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2582"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALDD2y" fast="false" reversible="false" name="Aldehyde dehydrogenase (acetaldehyde, NADP)" metaid="R_ALDD2y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALDD2y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALDD2y"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-3962"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00711"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95750"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25298"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25300"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25301"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25299"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/541"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00507"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acald_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_ac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3588"/> <fbc:geneProductRef fbc:geneProduct="G_b3011"/> <fbc:geneProductRef fbc:geneProduct="G_b3003"/> <fbc:geneProductRef fbc:geneProduct="G_b0493"/> <fbc:geneProductRef fbc:geneProduct="G_b4269"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TMDS" fast="false" reversible="false" name="Thymidylate synthase" metaid="R_TMDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TMDS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TMDS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.45"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02101"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104889"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12106"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12104"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12107"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12105"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dump_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhf_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dtmp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2827"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RMI" fast="false" reversible="true" name="L-rhamnose isomerase" metaid="R_RMI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RMI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RMI"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.14"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02437"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104038"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23161"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23163"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23160"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23162"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2372"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01761"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_rmn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_rml_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3903"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TMDK1" fast="false" reversible="false" name="Thymidine kinase (ATP:thymidine)" metaid="R_TMDK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TMDK1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TMDK1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THYKI-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.145"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.21"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01567"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104885"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-73632"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-73632"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19130"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19132"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19131"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19129"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/90"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01143"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thymd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dtmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1238"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LYSAM" fast="false" reversible="true" name="Lysine 2,3-aminomutase" metaid="R_LYSAM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" 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</rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_36dahx_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4146"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPCDC" fast="false" reversible="false" name="Phosphopantothenoylcysteine decarboxylase" metaid="R_PPCDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPCDC"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPCDC"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:P-PANTOCYSDECARB-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.36"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03269"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103098"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-196840"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-196840"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16793"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16796"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16794"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16795"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/3090"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02341"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4ppcys_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pan4p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3639"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FTHFD" fast="false" reversible="false" name="Formyltetrahydrofolate deformylase" metaid="R_FTHFD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FTHFD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FTHFD"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.10"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00944"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99669"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19833"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19835"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19834"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19836"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1259"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> 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constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3771"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_IPPMIa" fast="false" reversible="true" name="3-isopropylmalate dehydratase" metaid="R_IPPMIa" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_IPPMIa"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/IPPMIa"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-8991"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.33"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04001"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100827"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b1851"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_ura_e" fast="false" reversible="false" name="Uracil exchange" metaid="R_EX_ura_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ura_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ura_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-560"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105147"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27320"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28622"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27319"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b1109"/> <fbc:geneProductRef fbc:geneProduct="G_b1004"/> <fbc:geneProductRef fbc:geneProduct="G_b0046"/> <fbc:geneProductRef fbc:geneProduct="G_b3713"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_val__L_e" fast="false" reversible="false" name="L-Valine exchange" metaid="R_EX_val__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_val__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_val__L_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-269"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105190"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29706"/> 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constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1109"/> <fbc:geneProductRef fbc:geneProduct="G_b3713"/> <fbc:geneProductRef fbc:geneProduct="G_b0046"/> <fbc:geneProductRef fbc:geneProduct="G_b1004"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADK4" fast="false" reversible="true" name="Adentylate kinase (ITP)" metaid="R_ADK4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADK4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADK4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95453"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29868"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b2103"/> <fbc:geneProductRef fbc:geneProduct="G_b2418"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_KARA2" fast="false" reversible="true" name="Ketol-acid reductoisomerase (2-Acetolactate)" metaid="R_KARA2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_KARA2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/KARA2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACETOOHBUTREDUCTOISOM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100902"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13496"/> <rdf:li 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constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1208"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EDTXS2" fast="false" reversible="false" name="Endotoxin Synthesis (myristoyl transferase)" metaid="R_EDTXS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EDTXS2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EDTXS2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.243"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97901"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> 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<speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3091"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MECDPS" fast="false" reversible="false" name="2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase" metaid="R_MECDPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MECDPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MECDPS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-302"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.6.1.12"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05637"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101424"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23864"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23867"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23866"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23865"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03910"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2p4c2me_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2mecdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2746"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GUI1" fast="false" reversible="true" name="Glucuronate isomerase (D-glucuronate)" metaid="R_GUI1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GUI1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GUI1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.12"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01482"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100468"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13051"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13050"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13049"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13052"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01080"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glcur_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fruur_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3092"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EDTXS3" fast="false" reversible="false" name="Endotoxin Synthesis (palmitoleoyl ACP)" metaid="R_EDTXS3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EDTXS3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EDTXS3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97903"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_kdo2lipid4_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_kdo2lipid4p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2378"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGAMT" fast="false" reversible="true" name="Phosphoglucosamine mutase" metaid="R_PGAMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGAMT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> 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constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3176"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DDGLK" fast="false" reversible="false" name="2-dehydro-3-deoxygluconokinase" metaid="R_DDGLK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DDGLK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DDGLK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DEOXYGLUCONOKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.45"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.178"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01541"/> <rdf:li 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</reaction> <reaction id="R_EDTXS4" fast="false" reversible="false" name="Endotoxin Synthesis (myristoyl transferase)" metaid="R_EDTXS4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EDTXS4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EDTXS4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97904"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_kdo2lipid4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> 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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_melib_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_melib_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138589"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_melib_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_MACPD" fast="false" reversible="false" name="Malonyl-ACP decarboxylase" metaid="R_MACPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MACPD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MACPD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALONYL-ACPDECARBOX-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.87"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09482"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101327"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08861"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DMQMT" fast="false" reversible="false" name="3-Dimethylubiquinonol 3-methyltransferase" metaid="R_DMQMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DMQMT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DMQMT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DHHB-METHYLTRANSFER-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.64"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97527"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28682"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28680"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28679"/> <rdf:li 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<bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYLI1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:XYLISOM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01432"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105253"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22818"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22816"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22819"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22817"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01044"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_xyl__D_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_xylu__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3565"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPC" fast="false" reversible="false" name="Phosphoenolpyruvate carboxylase" metaid="R_PPC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPC"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPC"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.31"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00345"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103096"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23073"/> <rdf:li 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<reaction id="R_ICHORS_copy1" fast="false" reversible="false" name="Isochorismate synthase" metaid="R_ICHORS_copy1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ICHORS_copy1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ICHORS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ISOCHORSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.4.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01717"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100784"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18986"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18985"/> <rdf:li 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rdf:resource="http://identifiers.org/seed.reaction/rxn02175"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pan4p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dpcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3634"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HEX7" fast="false" reversible="false" name="Hexokinase (D-fructose:ATP)" metaid="R_HEX7" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HEX7"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HEX7"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00867"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100614"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fru_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0394"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DXPRIi" fast="false" reversible="false" name="1-deoxy-D-xylulose reductoisomerase" metaid="R_DXPRIi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DXPRIi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DXPRIi"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DXPREDISOM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.267"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05688"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97830"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13720"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13717"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13718"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13719"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/5284"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03958"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dxyl5p_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_2me4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0173"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GTPCII2" fast="false" reversible="false" name="GTP cyclohydrolase II (25drapp)" metaid="R_GTPCII2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GTPCII2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GTPCII2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GTP-CYCLOHYDRO-II-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.25"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00425"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100455"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23707"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23705"/> <rdf:li 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fbc:geneProduct="G_b2752"/> <fbc:geneProductRef fbc:geneProduct="G_b2751"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_OPHBDC" fast="false" reversible="false" name="Octaprenyl-hydroxybenzoate decarboxylase" metaid="R_OPHBDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OPHBDC"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OPHBDC"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.98"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04986"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102201"/> <rdf:li 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sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AACPS1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AACPS1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.20"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95138"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> 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constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2232"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GHMT2r" fast="false" reversible="true" name="Glycine hydroxymethyltransferase, reversible" metaid="R_GHMT2r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GHMT2r"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GHMT2r"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.2.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00945"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100142"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15481"/> <rdf:li 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rdf:resource="http://identifiers.org/ec-code/1.1.1.77"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02258"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95714"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15936"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15935"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15933"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15934"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lald__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12ppd__S_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2799"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALCD19" fast="false" reversible="true" name="Alcohol dehydrogenase (glycerol)" metaid="R_ALCD19" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALCD19"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALCD19"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.72"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.21"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01036"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95709"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30029"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30027"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30028"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30030"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00763"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1478"/> <fbc:geneProductRef fbc:geneProduct="G_b1241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_RMPA" fast="false" reversible="true" name="Rhamnulose-1-phosphate aldolase" metaid="R_RMPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RMPA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RMPA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RHAMNULPALDOL-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.19"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02263"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104043"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19689"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19691"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19690"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19692"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01621"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_rml1p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lald__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3902"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SBTPD" fast="false" reversible="true" name="Sorbitol-6-phosphate dehydrogenase" metaid="R_SBTPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SBTPD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SBTPD"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.140"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05607"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104285"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19840"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19839"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19838"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19837"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sbt6p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_f6p_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_b2705"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PFK_2" fast="false" reversible="false" name="Phosphofructokinase" metaid="R_PFK_2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PFK_2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PFK_2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TAGAKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.11"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.144"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.56"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03236"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102509"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12420"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12421"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12423"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12422"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/3059"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02314"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tag6p__D_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_tagdp__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3916"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLTPD" fast="false" reversible="true" name="Galactitol-1-phosphate dehydrogenase" metaid="R_GLTPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLTPD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLTPD"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.251"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.M6"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05571"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100275"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03856"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galt1p_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_tag6p__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2091"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_hdcea_e" fast="false" reversible="false" name="Hexadecenoate (n-C16:1) exchange" metaid="R_EX_hdcea_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_hdcea_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_hdcea_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99102"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hdcea_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ACACCT" fast="false" reversible="false" name="Acetyl-CoA:acetoacetyl-CoA transferase" metaid="R_ACACCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description 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<speciesReference species="M_acac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_aacoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2222"/> <fbc:geneProductRef fbc:geneProduct="G_b2221"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1694"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SDPDS" fast="false" reversible="false" name="Succinyl-diaminopimelate desuccinylase" metaid="R_SDPDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SDPDS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SDPDS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUCCDIAMINOPIMDESUCC-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.18"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02734"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104300"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22611"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22608"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22610"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22609"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2621"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01973"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sl26da_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_26dap_LL_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2472"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_BUTCT" fast="false" reversible="false" name="Acetyl-CoA:butyrate-CoA transferase" metaid="R_BUTCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BUTCT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BUTCT"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.8.3.8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96217"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_but_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2222"/> <fbc:geneProductRef fbc:geneProduct="G_b2221"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_TGBPA" fast="false" reversible="true" name="Tagatose-bisphosphate aldolase" metaid="R_TGBPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TGBPA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TGBPA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TAGAALDOL-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.40"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01069"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104798"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22949"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22950"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22951"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22948"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1339"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00787"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tagdp__D_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:and> <fbc:geneProductRef fbc:geneProduct="G_b3132"/> <fbc:geneProductRef fbc:geneProduct="G_b3137"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2095"/> <fbc:geneProductRef fbc:geneProduct="G_b2096"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MANAO" fast="false" reversible="true" name="Mannonate oxidoreductase" metaid="R_MANAO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MANAO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MANAO"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MANNONOXIDOREDUCT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.57"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02454"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101389"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15729"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15732"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15731"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15730"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01775"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mana_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fruur_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_b4323"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TAGURr" fast="false" reversible="true" name="Tagaturonate reductase" metaid="R_TAGURr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TAGURr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TAGURr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ALTRO-OXIDOREDUCT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.58"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02555"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104710"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17816"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17814"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17813"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17815"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01857"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_altrn_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_tagur_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1521"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DMSOR1" fast="false" reversible="false" name="Dimethyl sulfoxide reductase (Menaquinol 8)" metaid="R_DMSOR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DMSOR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DMSOR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97529"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29206"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29203"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29204"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29205"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08354"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dmso_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dms_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1589"/> <fbc:geneProductRef fbc:geneProduct="G_b1590"/> <fbc:geneProductRef fbc:geneProduct="G_b1588"/> <fbc:geneProductRef fbc:geneProduct="G_b1587"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0895"/> <fbc:geneProductRef fbc:geneProduct="G_b0896"/> <fbc:geneProductRef fbc:geneProduct="G_b0894"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGLYCP" fast="false" reversible="false" name="Phosphoglycolate phosphatase" metaid="R_PGLYCP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGLYCP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGLYCP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GPH-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.18"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01334"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102543"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14369"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14371"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14370"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14372"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/433"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00980"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2pglyc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyclt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3385"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2DGULRx" fast="false" reversible="false" name="2-dehydro-L-gulonate reductase (NADH)" metaid="R_2DGULRx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2DGULRx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2DGULRx"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94787"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07969"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dhguln_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_idon__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3553"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DKGLCNR2y" fast="false" reversible="false" name="2,5-diketo-D-gluconate reductase (NADPH)" metaid="R_DKGLCNR2y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DKGLCNR2y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DKGLCNR2y"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:YIAE1-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.215"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R08879"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97491"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27637"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27635"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27634"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27636"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08347"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_25dkglcn_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_5dglcn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3553"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G1PTT" fast="false" reversible="false" name="Glucose-1-phosphate thymidylyltransferase" metaid="R_G1PTT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G1PTT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G1PTT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DTDPGLUCOSEPP-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.24"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02328"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99846"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15226"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15227"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15225"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15228"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2281"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01675"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dttp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dtdpglu_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2039"/> <fbc:geneProductRef fbc:geneProduct="G_b3789"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TDPGDH" fast="false" reversible="false" name="DTDPglucose 4,6-dehydratase" metaid="R_TDPGDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TDPGDH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TDPGDH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DTDPGLUCDEHYDRAT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.46"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06513"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104761"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17221"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17222"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17224"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17223"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2648"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01997"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dtdpglu_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dtdp4d6dg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3788"/> <fbc:geneProductRef fbc:geneProduct="G_b2041"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADCS" fast="false" reversible="false" name="4-amino-4-deoxychorismate synthase" metaid="R_ADCS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADCS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADCS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PABASYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.85"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01716"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95440"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11672"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11675"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11673"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11674"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1828"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01257"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_chor_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4adcho_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1812"/> <fbc:geneProductRef fbc:geneProduct="G_b3360"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADCL" fast="false" reversible="false" name="4-aminobenzoate synthase" metaid="R_ADCL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADCL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADCL"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ADCLY-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.3.38"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05553"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95436"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16201"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16203"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16204"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16202"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03841"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4adcho_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4abz_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1096"/> <fbc:geneProductRef fbc:geneProduct="G_b4039"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_2DGULRy" fast="false" reversible="false" name="2-dehydro-L-gulonate reductase (NADPH)" metaid="R_2DGULRy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2DGULRy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2DGULRy"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94788"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07970"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dhguln_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_idon__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3553"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHAPT" fast="false" reversible="false" name="Dihydroxyacetone phosphotransferase" metaid="R_DHAPT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHAPT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHAPT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2.7.1.121-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.121"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01012"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97364"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18383"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18382"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18381"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18384"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00745"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dha_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1200"/> <fbc:geneProductRef fbc:geneProduct="G_b1198"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b1199"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_lac__D_e" fast="false" reversible="false" name="D-lactate exchange" metaid="R_EX_lac__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_lac__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_lac__D_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97840"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12471"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08351"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lac__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_UDPGALM" fast="false" reversible="false" name="UDPgalactopyranose mutase" metaid="R_UDPGALM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDPGALM"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGALM"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GALPMUT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.99.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00505"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105058"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24135"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24134"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24132"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24133"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00358"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udpgal_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_udpgalfur_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2036"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TDPDRE" fast="false" reversible="false" name="DTDP-4-dehydrorhamnose 3,5-epimerase" metaid="R_TDPDRE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TDPDRE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TDPDRE"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DTDPDEHYDRHAMEPIM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.13"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06514"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104759"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16970"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16969"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16972"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16971"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2651"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02000"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dtdp4d6dg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dtdp4d6dm_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2038"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TDPDRR" fast="false" reversible="false" name="DTDP-4-dehydrorhamnose reductase" metaid="R_TDPDRR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TDPDRR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TDPDRR"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DTDPDEHYRHAMREDUCT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.133"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02777"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104760"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21796"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21797"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21798"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21799"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02003"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dtdp4d6dm_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_dtdprmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2040"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UMPK" fast="false" reversible="true" name="UMP kinase" metaid="R_UMPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UMPK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UMPK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12002"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.22"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.14"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00158"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105118"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24400"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24402"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24401"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24403"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/201"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00119"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0910"/> <fbc:geneProductRef fbc:geneProduct="G_b0171"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_RZ5PP" fast="false" reversible="false" name="Alpha-ribazole 5-phosphate phosphatase" metaid="R_RZ5PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RZ5PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RZ5PP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-16788"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RIBAZOLEPHOSPHAT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.73"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04594"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104116"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24457"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24456"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24459"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24458"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03150"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5prdmbz_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rdmbzi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0638"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DDPGALA" fast="false" reversible="true" name="2-dehydro-3-deoxy-6-phosphogalactonate aldolase" metaid="R_DDPGALA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DDPGALA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DDPGALA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DEHYDDEOXPHOSGALACT-ALDOL-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.21"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.55"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01064"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97220"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24464"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24466"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24465"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24467"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00783"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dh3dgal6p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4477"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DURIK1" fast="false" reversible="false" name="Deoxyuridine kinase (ATP:Deoxyuridine)" metaid="R_DURIK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DURIK1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DURIK1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DURIDKI-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.145"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.21"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02099"/> <rdf:li 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fbc:geneProduct="G_b1238"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PD6" fast="false" reversible="false" name="Glycerol-3-phosphate dehydrogenase (menaquinone-8)" metaid="R_G3PD6" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PD6"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PD6"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99881"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29223"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29226"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29225"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29224"/> <rdf:li 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<fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2498"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTD9" fast="false" reversible="false" name="5'-nucleotidase (GMP)" metaid="R_NTD9" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD9"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD9"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-7609"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01227"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100381"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27715"/> <rdf:li 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</fbc:geneProductAssociation> </reaction> <reaction id="R_CTPS2" fast="false" reversible="false" name="CTP synthase (glutamine)" metaid="R_CTPS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CTPS2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CTPS2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CTPSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.4.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00573"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96945"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-504054"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b0087"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UAGPT3" fast="false" reversible="false" name="UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase" metaid="R_UAGPT3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UAGPT3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UAGPT3"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:NACGLCTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.227"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05032"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06174"/> <rdf:li 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rdf:resource="http://identifiers.org/rhea/27680"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27679"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/422"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01673"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dcdp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dctp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0474"/> <fbc:geneProductRef fbc:geneProduct="G_b2518"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_AOBUTDs" fast="false" reversible="false" name="L-2-amino-3-oxobutanoate decarboxylation (spontaneous)" metaid="R_AOBUTDs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AOBUTDs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AOBUTDs"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THREOSPON-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.381"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03758"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95851"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25654"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25655"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25653"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25656"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02666"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2aobut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_aact_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYAT" fast="false" reversible="true" name="Glycine C-acetyltransferase" metaid="R_GLYAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description 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rdf:resource="http://identifiers.org/biocyc/META:ADENOSINE-NUCLEOSIDASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.7"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01245"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95459"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18672"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18671"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18669"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18670"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00927"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0030"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GMHEPPA" fast="false" reversible="false" name="D-glycero-D-manno-heptose 1,7-bisphosphate phosphatase" metaid="R_GMHEPPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GMHEPPA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GMHEPPA"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100380"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gmhep17bp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gmhep1p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0200"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_S7PI" fast="false" reversible="false" name="Sedoheptulose 7-phosphate isomerase" metaid="R_S7PI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_S7PI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li 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</fbc:geneProductAssociation> </reaction> <reaction id="R_TRPS3" fast="false" reversible="false" name="Tryptophan synthase (indoleglycerol phosphate)" metaid="R_TRPS3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TRPS3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TRPS3"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2381"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.20"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02340"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99889"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14082"/> 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fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ttdcea_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ttdcea_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99096"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ttdcea_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_F6PA" fast="false" reversible="true" name="Fructose 6-phosphate aldolase" metaid="R_F6PA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_F6PA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/F6PA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-313"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99075"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28002"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28003"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28004"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28005"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dha_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0825"/> <fbc:geneProductRef fbc:geneProduct="G_b3946"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGMHE" fast="false" reversible="false" name="ADP-D-glycero-D-manno-heptose epimerase" metaid="R_AGMHE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGMHE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGMHE"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:5.1.3.20-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.20"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05176"/> <rdf:li 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sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNBTCT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNBTCT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-3601"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.8.3.21"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10644"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96894"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28420"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28418"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28421"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28419"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> 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<speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1033"/> <fbc:geneProductRef fbc:geneProduct="G_b3553"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NDPK4" fast="false" reversible="true" name="Nucleoside-diphosphate kinase (ATP:dTDP)" metaid="R_NDPK4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NDPK4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NDPK4"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DTDPKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.6"/> <rdf:li 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fbc:geneProduct="G_b0474"/> <fbc:geneProductRef fbc:geneProduct="G_b2518"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACODA" fast="false" reversible="false" name="Acetylornithine deacetylase" metaid="R_ACODA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACODA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACODA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACETYLORNDEACET-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.16"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.14"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00669"/> <rdf:li 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name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (dmpp)" metaid="R_DMPPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DMPPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DMPPS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.17.1.2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97524"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08352"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2mb4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dmpp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0029"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_26dap__M_e" fast="false" reversible="false" name="Meso-2,6-Diaminoheptanedioate exchange" metaid="R_EX_26dap__M_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_26dap__M_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_26dap__M_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94741"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07931"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_26dap__M_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_MCOATA" fast="false" reversible="true" name="Malonyl-CoA-ACP transacylase" metaid="R_MCOATA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MCOATA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MCOATA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALONYL-COA-ACP-TRANSACYL-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.0"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.39"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01626"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101421"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05465"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b1092"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_IPDPS" fast="false" reversible="false" name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (ipdp)" metaid="R_IPDPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_IPDPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/IPDPS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.17.1.2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100874"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08756"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2mb4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ipdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0029"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AST" fast="false" reversible="false" name="Arginine succinyltransferase" metaid="R_AST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AST"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AST"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ARGININE-N-SUCCINYLTRANSFERASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.109"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00832"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96115"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15185"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15187"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15186"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15188"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00601"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succoa_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_sucarg_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1747"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SGDS" fast="false" reversible="false" name="Succinylglutamate desuccinylase" metaid="R_SGDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SGDS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SGDS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUCCGLUDESUCC-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.96"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00411"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104362"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15170"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15172"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15171"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15169"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00291"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sucglu_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1744"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYNTAH" fast="false" reversible="false" name="Cyanate aminohydrolase" metaid="R_CYNTAH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYNTAH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYNTAH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12893"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.104"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10079"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138188"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11123"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11122"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11120"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11121"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08277"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cynt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_hco3_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0340"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DAPE" fast="false" reversible="true" name="Diaminopimelate epimerase" metaid="R_DAPE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAPE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAPE"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DIAMINOPIMEPIM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.1.7"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02735"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97143"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15396"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15395"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15393"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15394"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01974"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_26dap_LL_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_26dap__M_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3809"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHDPRy" fast="false" reversible="false" name="Dihydrodipicolinate reductase (NADPH)" metaid="R_DHDPRy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHDPRy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHDPRy"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.26"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR134418"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02929"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23dhdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thdp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0031"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_acnam_e" fast="false" reversible="false" name="N-Acetylneuraminate exchange" metaid="R_EX_acnam_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_acnam_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_acnam_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-15315"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-0"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95292"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28994"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28993"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28992"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28991"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08051"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acnam_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_HSK" fast="false" reversible="false" name="Homoserine kinase" metaid="R_HSK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HSK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HSK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:HOMOSERKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.39"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01771"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100737"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13985"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13987"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13986"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13988"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1866"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01300"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hom__L_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_phom_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0003"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SDPTA" fast="false" reversible="true" name="Succinyldiaminopimelate transaminase" metaid="R_SDPTA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SDPTA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SDPTA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUCCINYLDIAMINOPIMTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.17"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04475"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104301"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11960"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11961"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11963"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11962"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03087"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sl26da_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sl2a6o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3359"/> <fbc:geneProductRef fbc:geneProduct="G_b1302"/> <fbc:geneProductRef fbc:geneProduct="G_b1748"/> <fbc:geneProductRef fbc:geneProduct="G_b2662"/> <fbc:geneProductRef fbc:geneProduct="G_b0907"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GSPMDA" fast="false" reversible="false" name="Glutathionylspermidine amidase" metaid="R_GSPMDA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GSPMDA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GSPMDA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GSPAMID-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.78"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01918"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100437"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17175"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17173"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17174"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17176"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1972"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01404"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtspmd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2988"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GSPMDS" fast="false" reversible="false" name="Glutathionylspermidine synthetase" metaid="R_GSPMDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GSPMDS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GSPMDS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GSPSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.1.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.1.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01917"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100438"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21272"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21273"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21274"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21275"/> <rdf:li 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synthase" metaid="R_THRS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THRS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THRESYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.3.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01466"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104846"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10842"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10841"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10840"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10843"/> <rdf:li 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<speciesReference species="M_phpyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2599"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TMAOR1" fast="false" reversible="false" name="Trimethylamine N-oxide reductase (menaquinol 8)" metaid="R_TMAOR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TMAOR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TMAOR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104878"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29281"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29282"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29280"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29279"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09313"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tmao_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tma_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0895"/> <fbc:geneProductRef fbc:geneProduct="G_b0896"/> <fbc:geneProductRef fbc:geneProduct="G_b0894"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1589"/> <fbc:geneProductRef fbc:geneProduct="G_b1590"/> <fbc:geneProductRef fbc:geneProduct="G_b1588"/> <fbc:geneProductRef fbc:geneProduct="G_b1587"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TMAOR2" fast="false" reversible="false" name="Trimethylamine N-oxide reductase (demethylmenaquinol 8)" metaid="R_TMAOR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TMAOR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TMAOR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104880"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30583"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30586"/> <rdf:li 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</fbc:geneProductAssociation> </reaction> <reaction id="R_DDPA" fast="false" reversible="false" name="3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase" metaid="R_DDPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DDPA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DDPA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DAHPSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.54"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01826"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97218"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MTU-964912"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b1704"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NMNDA" fast="false" reversible="false" name="Nicotinamide-nucleotide amidase" metaid="R_NMNDA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NMNDA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NMNDA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:NMNAMIDOHYDRO-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.42"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02322"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101969"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12402"/> <rdf:li 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<rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRROLINECARBDEHYDROG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.12"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.88"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00707"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102301"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16417"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16418"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16419"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16420"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1083"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00503"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> <speciesReference 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</rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3dhgulnp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xu5p__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4196"/> <fbc:geneProductRef fbc:geneProduct="G_b3581"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SPMDAT2" fast="false" reversible="false" name="Spermidine acetyltransferase (N8)" metaid="R_SPMDAT2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SPMDAT2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SPMDAT2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-7165"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.29"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.57"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104492"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28272"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28273"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28270"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28271"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09265"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_spmd_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_n8aspmd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1584"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TDPADGAT" fast="false" reversible="false" name="DTDP-4-amino-4,6-dideoxy-D-glucose acetyltransferase" metaid="R_TDPADGAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TDPADGAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TDPADGAT"/> <rdf:li 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<speciesReference species="M_dtdp4addg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dtdp4aaddg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3790"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALS" fast="false" reversible="false" name="Malate synthase" metaid="R_MALS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.3.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00472"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101347"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18181"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18182"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18184"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18183"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00330"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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 id="R_X5PL3E" fast="false" reversible="false" name="L-xylulose 5-phosphate 3-epimerase" metaid="R_X5PL3E" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_X5PL3E"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/X5PL3E"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:LXULRU5P-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.-.-.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.22"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03244"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105224"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18498"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18500"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18499"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18497"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02321"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_xu5p__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ru5p__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4197"/> <fbc:geneProductRef fbc:geneProduct="G_b3582"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DOGULNR" fast="false" reversible="false" name="2,3 dioxo-L-gulonate reductase" metaid="R_DOGULNR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DOGULNR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DOGULNR"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-703"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.130"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02637"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97688"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21927"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21925"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21926"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21924"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01911"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23doguln_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3dhguln_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3575"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TRE6PP" fast="false" reversible="false" name="Trehalose-phosphatase" metaid="R_TRE6PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TRE6PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TRE6PP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TREHALOSEPHOSPHA-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.12"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02778"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06228"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104926"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MTU-868608"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23420"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23423"/> <rdf:li 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<bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_met__D_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101473"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34913"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34912"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34914"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34911"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08911"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_met__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_tartr__L_e" fast="false" reversible="false" name="L-tartrate exchange" metaid="R_EX_tartr__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation 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rdf:resource="http://identifiers.org/rhea/15308"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15307"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2478"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01867"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_betald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyb_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0312"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_BETALDHy" fast="false" reversible="false" name="Betaine-aldehyde dehydrogenase" metaid="R_BETALDHy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BETALDHy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BETALDHy"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.8"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02566"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96238"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30070"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30069"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30068"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30067"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2479"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01868"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_betald_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_glyb_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0312"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLTG3" fast="false" reversible="false" name="Maltodextrin glucosidase (maltopentaose)" metaid="R_MLTG3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLTG3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTG3"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14281"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.20"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.74"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101621"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08934"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_maltpt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_maltttr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0403"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_taur_e" fast="false" reversible="false" name="Taurine exchange" metaid="R_EX_taur_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_taur_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_taur_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104733"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09286"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13402"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_taur_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_maltpt_e" fast="false" reversible="false" name="Maltopentaose exchange" metaid="R_EX_maltpt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_maltpt_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_maltpt_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101356"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08873"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_maltpt_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_glyald_e" fast="false" reversible="false" name="D-Glyceraldehyde exchange" metaid="R_EX_glyald_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_glyald_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glyald_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100311"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08636"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08635"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10164"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyald_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_glcur_e" fast="false" reversible="false" name="D-Glucuronate exchange" metaid="R_EX_glcur_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_glcur_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glcur_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100235"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08623"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glcur_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ADPRDP" fast="false" reversible="false" name="ADPribose diphosphatase" metaid="R_ADPRDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADPRDP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADPRDP"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.13"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95480"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adprib_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3397"/> <fbc:geneProductRef fbc:geneProduct="G_b3034"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DKGLCNR1" fast="false" reversible="false" name="2,5-diketo-D-gluconate reductase" metaid="R_DKGLCNR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DKGLCNR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DKGLCNR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97489"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08345"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_25dkglcn_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_2dhguln_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3012"/> <fbc:geneProductRef fbc:geneProduct="G_b0207"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADTRHD" fast="false" reversible="false" name="NAD transhydrogenase" metaid="R_NADTRHD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADTRHD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADTRHD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRNUTRANSHYDROGEN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00112"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101898"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11692"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11695"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11694"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11693"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00083"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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:geneProductRef fbc:geneProduct="G_b3962"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AACPS2" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase (n-C14:1)" metaid="R_AACPS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AACPS2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AACPS2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.20"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95141"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdeACP_c" stoichiometry="1" 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constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2563"/> <fbc:geneProductRef fbc:geneProduct="G_b3475"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_nmn_e" fast="false" reversible="false" name="NMN exchange" metaid="R_EX_nmn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_nmn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_nmn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101972"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28485"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28483"/> <rdf:li 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name="Glycerol-3-phosphate dehydrogenase (NADP)" metaid="R_G3PD2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PD2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PD2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.94"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00844"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99877"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11096"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11099"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11098"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11097"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1184"/> 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</fbc:geneProductAssociation> </reaction> <reaction id="R_FCI" fast="false" reversible="true" name="L-fucose isomerase" metaid="R_FCI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FCI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FCI"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99468"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fuc__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fcl__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2802"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FCLK" fast="false" reversible="false" name="L-fuculokinase" metaid="R_FCLK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FCLK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FCLK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:FUCULOKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.51"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03241"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99469"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12376"/> <rdf:li 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fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FCLPA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FCLPA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:FUCPALDOL-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.17"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02262"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99470"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12934"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12936"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12935"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12933"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2229"/> <rdf:li 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xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GMPS2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GMP-SYN-GLUT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.5.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01231"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100384"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11680"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11682"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11681"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11683"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/215"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00917"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xmp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2507"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AMPN" fast="false" reversible="false" name="AMP nucleosidase" metaid="R_AMPN" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMPN"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMPN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95827"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/> <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1982"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GSNK" fast="false" reversible="false" name="Guanosine kinase" metaid="R_GSNK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GSNK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GSNK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GUANOSINEKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.73"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01228"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100432"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27711"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27710"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27712"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27713"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00914"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gsn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0477"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACCOAL" fast="false" reversible="false" name="Acetate-CoA ligase (ADP-forming)" metaid="R_ACCOAL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACCOAL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACCOAL"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.13"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95221"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppa_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_ppcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4069"/> <fbc:geneProductRef fbc:geneProduct="G_b0335"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALUi" fast="false" reversible="false" name="UTP-glucose-1-phosphate uridylyltransferase (irreversible)" metaid="R_GALUi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALUi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALUi"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUC1PURIDYLTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.9"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.64"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00289"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143121"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-70286"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-70286"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19889"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19892"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19890"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19891"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/8973"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/68"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00213"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1236"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AACPS3" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase (n-C16:0)" metaid="R_AACPS3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AACPS3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AACPS3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.20"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95142"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_U23GAAT" fast="false" reversible="false" name="UDP-3-O-(3-hydroxymyristoyl)glucosamine acyltransferase" metaid="R_U23GAAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_U23GAAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/U23GAAT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.191"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04550"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105007"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn06723"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hmrsACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_u3hga_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_u23ga_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0179"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_f6p_e" fast="false" reversible="false" name="D-fructose 6-phosphate exchange" metaid="R_EX_f6p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_f6p_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_f6p_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99076"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_f6p_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_UAAGDS" fast="false" reversible="false" name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase" metaid="R_UAAGDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UAAGDS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UAAGDS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.13"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105013"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_26dap__M_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uamag_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"/> <speciesReference species="M_ugmd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0085"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AACPS4" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase (n-C16:1)" metaid="R_AACPS4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AACPS4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AACPS4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95143"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_UAMAS" fast="false" reversible="false" name="UDP-N-acetylmuramoyl-L-alanine synthetase" metaid="R_UAMAS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UAMAS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UAMAS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDP-NACMUR-ALA-LIG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.8"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03193"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR141024"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23372"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23374"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23373"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23375"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11251"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02286"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uamr_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"/> <speciesReference species="M_uama_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0091"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UAMAGS" fast="false" reversible="false" name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase" metaid="R_UAMAGS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UAMAGS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UAMAGS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDP-NACMURALA-GLU-LIG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02783"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105038"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16430"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16429"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16431"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16432"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2659"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02008"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11252"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uama_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"/> <speciesReference species="M_uamag_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0088"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UGLYCH" fast="false" reversible="false" name="Ureidoglycolate hydrolase" metaid="R_UGLYCH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UGLYCH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UGLYCH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UREIDOGLYCOLATE-HYDROLASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.3.19"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.116"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00469"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105091"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19811"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19810"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19812"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19809"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00327"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_urdglyc_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glx_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0505"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTPP3" fast="false" reversible="false" name="Nucleoside triphosphate pyrophosphorylase (dctp)" metaid="R_NTPP3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTPP3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPP3"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DCTP-PYROPHOSPHATASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.9"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.12"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.65"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01668"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97203"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22637"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22636"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22639"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22638"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/483"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01222"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dcmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2251"/> <fbc:geneProductRef fbc:geneProduct="G_b2781"/> <fbc:geneProductRef fbc:geneProduct="G_b1759"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTPP6" fast="false" reversible="false" name="Nucleoside triphosphate pyrophosphorylase (atp)" metaid="R_NTPP6" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTPP6"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPP6"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ATP-PYROPHOSPHATASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00087"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102054"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14248"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14247"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14245"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14246"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/245"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05822"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00063"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2781"/> <fbc:geneProductRef fbc:geneProduct="G_b0905"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTPP7" fast="false" reversible="false" name="Nucleoside triphosphate pyrophosphorylase (dttp)" metaid="R_NTPP7" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTPP7"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPP7"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5107"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.19"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R11323"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97809"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28537"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28534"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28536"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28535"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/10421"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09014"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dttp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dtmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2781"/> <fbc:geneProductRef fbc:geneProduct="G_b2251"/> <fbc:geneProductRef fbc:geneProduct="G_b3248"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_OP4ENH" fast="false" reversible="false" name="2-oxopent-4-enoate hydratase" metaid="R_OP4ENH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OP4ENH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OP4ENH"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.80"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR126136"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22582"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22581"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22580"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22583"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_op4en_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4h2opntn_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0350"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_rmn_e" fast="false" reversible="false" name="L-Rhamnose exchange" metaid="R_EX_rmn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_rmn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_rmn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104042"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34995"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34998"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34997"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34996"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09229"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_rmn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_HOPNTAL" fast="false" reversible="false" name="4-hydroxy-2-oxopentanoate aldolase" metaid="R_HOPNTAL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HOPNTAL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HOPNTAL"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.3.39"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.n4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00750"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100679"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1109"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00540"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4h2opntn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0352"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTPP8" fast="false" reversible="false" name="Nucleoside triphosphate pyrophosphorylase (utp)" metaid="R_NTPP8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTPP8"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPP8"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14139"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00662"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102055"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29397"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29398"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29395"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29396"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/202"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00463"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2781"/> <fbc:geneProductRef fbc:geneProduct="G_b3248"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_P5CR" fast="false" reversible="false" name="Pyrroline-5-carboxylate reductase" metaid="R_P5CR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_P5CR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/P5CR"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01251"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102302"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-6783955"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-6783955"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-6783955"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-6783955"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-6783955"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-6783955"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-6783955"/> <rdf:li 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rdf:resource="http://identifiers.org/sabiork/1470"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00931"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0386"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYANST" fast="false" reversible="false" name="Cyanide sulfurtransferase" metaid="R_CYANST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation 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constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5apru_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0414"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HPPPNH" fast="false" reversible="false" name="3-(3-hydroxy-phenyl)propionate hydroxylase" metaid="R_3HPPPNH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HPPPNH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HPPPNH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MHPHYDROXY-RXN"/> <rdf:li 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stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GMAND" fast="false" reversible="false" name="GDP-D-mannose dehydratase" metaid="R_GMAND" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GMAND"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GMAND"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GDPMANDEHYDRA-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.47"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00888"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100377"/> <rdf:li 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fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPCSCT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPCSCT"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.8.3.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103103"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ppcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ppa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2920"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYTD" fast="false" reversible="false" name="Cytidine deaminase" metaid="R_CYTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYTD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYTD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CYTIDEAM2-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01878"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97039"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16069"/> <rdf:li 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sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYCDx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYCDx"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLYCDEH-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.6"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01034"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100326"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13770"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13772"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13769"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13771"/> <rdf:li 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</rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala_B_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0131"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UGMDDS" fast="false" reversible="false" name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine synthetase" metaid="R_UGMDDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UGMDDS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UGMDDS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.10"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105094"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/4284"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_alaala_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ugmd_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"/> <speciesReference species="M_ugmda_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0086"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DCYTD" fast="false" reversible="false" name="Deoxycytidine deaminase" metaid="R_DCYTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DCYTD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DCYTD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CYTIDEAM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02485"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97207"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-73608"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-73608"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13436"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13434"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13433"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13435"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/364"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01800"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcyt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_duri_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2143"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DBTS" fast="false" reversible="false" name="Dethiobiotin synthase" metaid="R_DBTS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DBTS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DBTS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DETHIOBIOTIN-SYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.3.3"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03182"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97180"/> <rdf:li 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</listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0778"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DCTPD" fast="false" reversible="false" name="DCTP deaminase" metaid="R_DCTPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DCTPD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DCTPD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DCTP-DEAM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.13"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02325"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97201"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22683"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22681"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22682"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22680"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01672"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dutp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2065"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UHGADA" fast="false" reversible="false" name="UDP-3-O-acetylglucosamine deacetylase" metaid="R_UHGADA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UHGADA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UHGADA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDPACYLGLCNACDEACETYL-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.108"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04587"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105110"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25212"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25209"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25211"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25210"/> <rdf:li 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rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-4085028"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-4085028"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-4085028"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25253"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25256"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25254"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25255"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2597"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01951"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acmana_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acmanap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3222"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UAGAAT" fast="false" reversible="true" name="UDP-N-acetylglucosamine acyltransferase" metaid="R_UAGAAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UAGAAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UAGAAT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDPNACETYLGLUCOSAMACYLTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.129"/> <rdf:li 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fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ATPPRT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ATPPRT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ATPPHOSPHORIBOSYLTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.17"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01071"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96132"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18476"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18475"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18473"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18474"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00789"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_prbatp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2019"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HISTD" fast="false" reversible="false" name="Histidinol dehydrogenase" metaid="R_HISTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HISTD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HISTD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-8001"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.23"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01158"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100587"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20641"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20642"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20643"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20644"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1398"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00859"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_histd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_his__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2020"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHDPS" fast="false" reversible="false" name="Dihydrodipicolinate synthase" metaid="R_DHDPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHDPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHDPS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR125801"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14846"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14848"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14847"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14845"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2256"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01644"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_aspsa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23dhdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2478"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G1PACT" fast="false" reversible="false" name="Glucosamine-1-phosphate N-acetyltransferase" metaid="R_G1PACT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G1PACT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G1PACT"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.157"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99841"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/4940"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03638"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gam1p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam1p_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_b3730"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GART" fast="false" reversible="false" name="GAR transformylase-T" metaid="R_GART" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GART"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GART"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GARTRANSFORMYL2-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.2.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06974"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100042"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24830"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24832"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24831"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24829"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04783"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gar_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fgam_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1849"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CSND" fast="false" reversible="false" name="Cytosine deaminase" metaid="R_CSND" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CSND"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CSND"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CYTDEAM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00974"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96927"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20605"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20606"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20607"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20608"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00717"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_csn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0337"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GF6PTA" fast="false" reversible="false" name="Glutamine-fructose-6-phosphate transaminase" metaid="R_GF6PTA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GF6PTA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GF6PTA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:L-GLN-FRUCT-6-P-AMINOTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.16"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100107"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gam6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3729"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_IGPDH" fast="false" reversible="false" name="Imidazoleglycerol-phosphate dehydratase" metaid="R_IGPDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_IGPDH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/IGPDH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:IMIDPHOSDEHYD-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.19"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03457"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100813"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11041"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11043"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11040"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11042"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02473"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_eig3p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_imacp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2022"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_glyclt_e" fast="false" reversible="false" name="Glycolate exchange" metaid="R_EX_glyclt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_glyclt_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glyclt_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5111"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100333"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29448"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29450"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29449"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29447"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12468"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08653"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12426"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyclt_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PRPPS" fast="false" reversible="true" name="Phosphoribosylpyrophosphate synthetase" metaid="R_PRPPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PRPPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PRPPS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.6.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103215"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1207"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_H2SO" fast="false" reversible="false" name="Hydrogen sulfide oxidation" metaid="R_H2SO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_H2SO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/H2SO"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100493"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08688"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_so4_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_GLUCYS" fast="false" reversible="false" name="Gamma-glutamylcysteine synthetase" metaid="R_GLUCYS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLUCYS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLUCYS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUTCYSLIG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.2"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b2026"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLUN" fast="false" reversible="false" name="Glutaminase" metaid="R_GLUN" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLUN"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLUN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUTAMIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.5.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.3.6"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.5.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.7.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.5.4"/> 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<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_b1524"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PRMICI" fast="false" reversible="true" name="1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase" metaid="R_PRMICI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PRMICI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PRMICI"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PRIBFAICARPISOM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04640"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103169"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15471"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15472"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15469"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15470"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03175"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_prfp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_prlp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2024"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLUPRT" fast="false" reversible="false" name="Glutamine phosphoribosyldiphosphate amidotransferase" metaid="R_GLUPRT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLUPRT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLUPRT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PRPPAMIDOTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.14"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01072"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100287"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-419152"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-73815"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-73815"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14905"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14908"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14906"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14907"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/114"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00790"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pram_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2312"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_g6p_e" fast="false" reversible="false" name="D-Glucose 6-phosphate exchange" metaid="R_EX_g6p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_g6p_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_g6p_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99915"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08570"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09644"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13641"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g6p_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GMPR" fast="false" reversible="false" name="GMP reductase" metaid="R_GMPR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GMPR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GMPR"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GMP-REDUCT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.7.1.7"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01134"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100382"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17186"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17188"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17187"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17185"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00837"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0104"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SERAT" fast="false" reversible="true" name="Serine O-acetyltransferase" metaid="R_SERAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SERAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SERAT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SERINE-O-ACETTRAN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.30"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00586"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104275"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MTU-936615"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24560"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24563"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24562"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24561"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/986"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00423"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acser_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3607"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYSS" fast="false" reversible="false" name="Cysteine synthase" metaid="R_CYSS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYSS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYSS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACSERLY-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.47"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.65"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00897"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97007"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14829"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14831"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14830"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14832"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1220"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00649"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acser_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2s_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2421"/> <fbc:geneProductRef fbc:geneProduct="G_b2414"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADS1" fast="false" reversible="false" name="NAD synthase (nh3)" metaid="R_NADS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADS1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADS1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:NAD-SYNTH-NH3-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.5.1"/> <rdf:li 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fbc:geneProduct="G_b3781"/> <fbc:geneProductRef fbc:geneProduct="G_b2762"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASPK" fast="false" reversible="true" name="Aspartate kinase" metaid="R_ASPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASPK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ASPARTATEKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.2.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00480"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96085"/> <rdf:li 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dehydrogenase" metaid="R_PPND" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPND"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPND"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PREPHENATEDEHYDROG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.12"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01728"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103121"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13872"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13870"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13869"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13871"/> <rdf:li 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fbc:geneProduct="G_b2942"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASCBPL" fast="false" reversible="false" name="L-ascorbate 6-phosphate lactonase" metaid="R_ASCBPL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASCBPL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASCBPL"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5214"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07677"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138067"/> <rdf:li 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stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2026"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADOCBLS" fast="false" reversible="false" name="Adenosylcobalamin 5'-phosphate synthase" metaid="R_ADOCBLS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADOCBLS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADOCBLS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:COBALAMINSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.26"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05223"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95469"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03538"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_agdpcbi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rdmbzi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adocbl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1992"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_galct__D_e" fast="false" reversible="false" name="D-Galactarate exchange" metaid="R_EX_galct__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_galct__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_galct__D_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-203"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99963"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28478"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28480"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28479"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28481"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12441"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08581"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galct__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ADOCBIK" fast="false" reversible="false" name="Adenosyl cobinamide kinase" metaid="R_ADOCBIK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADOCBIK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADOCBIK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:COBINAMIDEKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.156"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05221"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95465"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03536"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adocbi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adocbip_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1993"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TMPK" fast="false" reversible="false" name="Thiamine-phosphate kinase" metaid="R_TMPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TMPK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TMPK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THI-P-KIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00617"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104907"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15913"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15916"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15915"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15914"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1007"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00438"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thmmp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thmpp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0417"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HPPPNDO" fast="false" reversible="false" name="2,3-dihydroxypheylpropionate 1,2-dioxygenase" metaid="R_HPPPNDO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HPPPNDO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HPPPNDO"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:1.13.11.16-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.13.11.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04376"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100695"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23840"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23843"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23841"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23842"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/4072"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03038"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhpppn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hkndd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0348"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MCITL2" fast="false" reversible="true" name="Methylisocitrate lyase" metaid="R_MCITL2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MCITL2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MCITL2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:METHYLISOCITRATE-LYASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.3.30"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00409"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101415"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16812"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16811"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16810"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16809"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/866"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00289"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_micit_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0331"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DXYLK" fast="false" reversible="false" name="1-Deoxy-D-xylulose kinase" metaid="R_DXYLK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DXYLK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DXYLK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-382"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97832"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27991"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27990"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27993"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27992"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08380"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dxyl_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dxyl5p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3564"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MDH3" fast="false" reversible="false" name="Malate dehydrogenase (menaquinone 8 as acceptor)" metaid="R_MDH3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDH3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDH3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101441"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29090"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29089"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29088"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29087"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08901"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2210"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SOTA" fast="false" reversible="false" name="Succinylornithine transaminase" metaid="R_SOTA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SOTA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SOTA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUCCORNTRANSAM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.81"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04217"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104477"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16954"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16953"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16956"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16955"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02944"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sucorn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sucgsa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1748"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHCINDO" fast="false" reversible="false" name="2,3-dihydroxycinnamate 1,2-dioxygenase" metaid="R_DHCINDO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHCINDO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHCINDO"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.13.11.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06788"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97379"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04603"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhcinnm_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hkntd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0348"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SGSAD" fast="false" reversible="false" name="Succinylglutamic semialdehyde dehydrogenase" metaid="R_SGSAD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SGSAD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SGSAD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUCCGLUALDDEHYD-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.71"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05049"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104368"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10813"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10812"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10815"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10814"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03422"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sucgsa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sucglu_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1746"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HKNDDH" fast="false" reversible="false" name="2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase" metaid="R_HKNDDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HKNDDH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HKNDDH"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.7.1.14"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138518"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hkndd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_op4en_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0349"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_idon__L_e" fast="false" reversible="false" name="L-Idonate exchange" metaid="R_EX_idon__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_idon__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_idon__L_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100804"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08743"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_idon__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_HKNTDH" fast="false" reversible="false" name="2-hydroxy-6-ketononotrienedioate hydrolase" metaid="R_HKNTDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HKNTDH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HKNTDH"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.7.1.14"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138519"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hkntd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_op4en_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0349"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYCK2" fast="false" reversible="false" name="Glycerate kinase" metaid="R_GLYCK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYCK2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYCK2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GKI-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.31"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.165"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R08572"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100329"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27380"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27378"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27379"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27377"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11393"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08647"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc__R_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3124"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PTA2" fast="false" reversible="false" name="Phosphate acetyltransferase" metaid="R_PTA2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PTA2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PTA2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PTAALT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.222"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00921"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102416"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28046"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28049"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28048"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28047"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00670"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppap_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2297"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MDH2" fast="false" reversible="false" name="Malate dehydrogenase (ubiquinone 8 as acceptor)" metaid="R_MDH2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDH2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDH2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101440"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29084"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29086"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29083"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29085"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08900"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2210"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_indole_e" fast="false" reversible="false" name="Indole exchange" metaid="R_EX_indole_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_indole_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_indole_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-563"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100836"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08751"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_indole_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ACOTA" fast="false" reversible="true" name="Acetylornithine transaminase" metaid="R_ACOTA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" 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rdf:resource="http://identifiers.org/seed.reaction/rxn01637"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acorn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acg5sa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1748"/> <fbc:geneProductRef fbc:geneProduct="G_b3359"/> <fbc:geneProductRef fbc:geneProduct="G_b2662"/> <fbc:geneProductRef fbc:geneProduct="G_b1302"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GPDDA5" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoinositol)" metaid="R_GPDDA5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" 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rdf:resource="http://identifiers.org/sabiork/1430"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00889"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_inost_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3449"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PDX5PS" fast="false" reversible="false" name="Pyridoxine 5'-phosphate synthase" metaid="R_PDX5PS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation 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</sbml:annotation> <listOfReactants> <speciesReference species="M_5aop_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppbng_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0369"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ENTCS" fast="false" reversible="false" name="Enterochelin synthase" metaid="R_ENTCS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ENTCS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li 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constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0583"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SULR" fast="false" reversible="false" name="Sulfite reductase (NADPH2)" metaid="R_SULR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SULR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SULR"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SULFITE-REDUCT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00858"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104650"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13802"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13803"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13804"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13801"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00623"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="5" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="3" constant="true"/> <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="3" constant="true"/> <speciesReference species="M_h2s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="3" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2764"/> <fbc:geneProductRef fbc:geneProduct="G_b2763"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_MANPGH" fast="false" reversible="false" name="2-O-alpha-mannosyl-6-phosphate-D-glycerate hydrolase" metaid="R_MANPGH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MANPGH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MANPGH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5216"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.170"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09645"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101397"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08884"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_man6pglyc_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc__R_c" stoichiometry="1" constant="true"/> <speciesReference species="M_man6p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0732"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_URDGLYCD" fast="false" reversible="false" name="Ureidoglycolate dehydrogenase" metaid="R_URDGLYCD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_URDGLYCD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URDGLYCD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-7024"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.154"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.350"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02935"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105152"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15330"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15331"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15332"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15329"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02102"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_urdglyc_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_oxur_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0517"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CBMKr" fast="false" reversible="true" name="Carbamate kinase" metaid="R_CBMKr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CBMKr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CBMKr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CARBAMATE-KINASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.2.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00150"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96482"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10154"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10152"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10155"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10153"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/93"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00114"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_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_cbp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0521"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPNCL2" fast="false" reversible="false" name="Phosphopantothenate-cysteine ligase" metaid="R_PPNCL2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPNCL2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPNCL2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:P-PANTOCYSLIG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04231"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103119"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19399"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19400"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19397"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19398"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/3942"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09177"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4ppan_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4ppcys_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3639"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PRAGSr" fast="false" reversible="true" name="Phosphoribosylglycinamide synthase" metaid="R_PRAGSr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PRAGSr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PRAGSr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLYRIBONUCSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.4.13"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04144"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103139"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02895"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pram_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gar_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4005"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PRFGS" fast="false" reversible="false" name="Phosphoribosylformylglycinamidine synthase" metaid="R_PRFGS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PRFGS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PRFGS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.5.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138721"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-419144"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-73812"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-73812"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17132"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17129"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17131"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17130"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fgam_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fpram_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2557"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AMANAPEr" fast="false" reversible="true" name="N-acetylmannosamine 6-phosphate epimerase" metaid="R_AMANAPEr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMANAPEr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMANAPEr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:NANE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02087"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95804"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25259"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25257"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25258"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25260"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01506"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acmanap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam6p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3223"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_3hcinnm_e" fast="false" reversible="false" name="3-hydroxycinnamic acid exchange" metaid="R_EX_3hcinnm_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_3hcinnm_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_3hcinnm_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100571"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08702"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hcinnm_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ACM6PH" fast="false" reversible="false" name="N-acetylmuramate 6-phosphate hydrolase" metaid="R_ACM6PH" sboTerm="SBO:0000176" 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stoichiometry="1" constant="true"/> <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2mcit_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_b0333"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPAKr" fast="false" reversible="true" name="Propionate kinase" metaid="R_PPAKr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPAKr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPAKr"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.2.15"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95897"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3115"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HEX1" fast="false" reversible="false" name="Hexokinase (D-glucose:ATP)" metaid="R_HEX1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HEX1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HEX1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUCOKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00299"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100612"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17827"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17828"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17826"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17825"/> <rdf:li 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rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-71299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-71299"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10116"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10117"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10118"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10119"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/108"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01115"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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 id="R_TAUDO" fast="false" reversible="false" name="Taurine dioxygenase" metaid="R_TAUDO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TAUDO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TAUDO"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-299"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.11.17"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05320"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104730"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15909"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15910"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15912"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15911"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/4928"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03630"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_taur_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_aacald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0368"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DM_amob_c" fast="false" reversible="false" name="Sink needed to allow S-Adenosyl-4-methylthio-2-oxobutanoate to leave system" metaid="R_DM_amob_c" sboTerm="SBO:0000628" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DM_amob_c"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DM_amob_c"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142748"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amob_c" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_NTP3" fast="false" reversible="false" name="Nucleoside-triphosphatase (GTP)" metaid="R_NTP3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTP3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTP3"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5462"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.15"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.6"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00335"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102043"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19669"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19671"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19672"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19670"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/816"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00241"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> 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<rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01986"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dr1p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2dr5p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4383"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MOAT2" fast="false" reversible="false" name="3-deoxy-D-manno-octulosonic acid transferase" metaid="R_MOAT2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MOAT2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li 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fast="false" reversible="false" name="3-methyl-2-oxobutanoate hydroxymethyltransferase" metaid="R_MOHMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MOHMT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOHMT"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.2.11"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01226"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101702"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11824"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11827"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11825"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11826"/> </rdf:Bag> </bqbiol:is> 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rdf:resource="http://identifiers.org/rhea/39808"/> <rdf:li rdf:resource="http://identifiers.org/rhea/39809"/> <rdf:li rdf:resource="http://identifiers.org/rhea/39810"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09034"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09669"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ocdca_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_cbl1_e" fast="false" reversible="false" name="Cob(I)alamin exchange" metaid="R_EX_cbl1_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cbl1_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li 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fbc:geneProduct="G_b2538"/> <fbc:geneProductRef fbc:geneProduct="G_b2540"/> <fbc:geneProductRef fbc:geneProduct="G_b2539"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_26DAHtex" fast="false" reversible="true" name="Meso-2,6-Diaminoheptanedioate transport via diffusion (extracellular to periplasm)" metaid="R_26DAHtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_26DAHtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/26DAHtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94741"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07931"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> 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fbc:geneProduct="G_b0010"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SUCFUMtpp" fast="false" reversible="true" name="Succinate:fumarate antiporter (periplasm)" metaid="R_SUCFUMtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SUCFUMtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCFUMtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-106"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104633"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29326"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29324"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29323"/> <rdf:li 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name="Homoserine dehydrogenase (NADPH)" metaid="R_HSDy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HSDy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HSDy"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.3"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01775"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100734"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15761"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15764"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15763"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15762"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1868"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01302"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hom__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_aspsa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3940"/> <fbc:geneProductRef fbc:geneProduct="G_b0002"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYSTL" fast="false" reversible="false" name="Cystathionine b-lyase" metaid="R_CYSTL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYSTL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYSTL"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.4.1.8"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01286"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96469"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13967"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13965"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13968"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13966"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1501"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cyst__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3008"/> <fbc:geneProductRef fbc:geneProduct="G_b1622"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACMAMUT" fast="false" reversible="false" name="UDP-N-acetyl-D-mannosaminuronic acid transferase" metaid="R_ACMAMUT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACMAMUT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACMAMUT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDPMANACATRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.180"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04477"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95274"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28367"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28369"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28368"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28366"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08045"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_uacmamu_c" stoichiometry="1" constant="true"/> <speciesReference species="M_unaga_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_unagamu_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3794"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SHSL1" fast="false" reversible="false" name="O-succinylhomoserine lyase (L-cysteine)" metaid="R_SHSL1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SHSL1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SHSL1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:O-SUCCHOMOSERLYASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.48"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03260"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104380"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20398"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20399"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20400"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20397"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/3081"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_suchms_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cyst__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3939"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SSALy" fast="false" reversible="false" name="Succinate-semialdehyde dehydrogenase (NADP)" metaid="R_SSALy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SSALy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SSALy"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUCCSEMIALDDEHYDROG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.79"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00714"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104541"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13216"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13215"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13214"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13213"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1086"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00509"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sucsal_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1525"/> <fbc:geneProductRef fbc:geneProduct="G_b2661"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SUCptspp" fast="false" reversible="false" name="Sucrose transport via PEP:Pyr (periplasm)" metaid="R_SUCptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SUCptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104643"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05655"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09274"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sucr_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_suc6p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2417"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b2429"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_SULabcpp" fast="false" reversible="false" name="Sulfate transport via ABC system (periplasm)" metaid="R_SULabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SULabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SULabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.25-RXN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-70-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.25"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104655"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10192#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10193#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10194#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10195#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09276"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05153"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_so4_p" 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"/> <speciesReference species="M_so4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2423"/> <fbc:geneProductRef fbc:geneProduct="G_b2424"/> <fbc:geneProductRef fbc:geneProduct="G_b2422"/> <fbc:geneProductRef fbc:geneProduct="G_b2425"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0764"/> <fbc:geneProductRef fbc:geneProduct="G_b0765"/> <fbc:geneProductRef fbc:geneProduct="G_b0763"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2422"/> <fbc:geneProductRef fbc:geneProduct="G_b2423"/> <fbc:geneProductRef fbc:geneProduct="G_b2424"/> <fbc:geneProductRef fbc:geneProduct="G_b3917"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TSULabcpp" fast="false" reversible="false" name="Thiosulfate transport via ABC system (periplasm)" metaid="R_TSULabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TSULabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TSULabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-7-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.25"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104964"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29872#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29873#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29874#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29871#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05176"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09329"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tsul_p" 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"/> <speciesReference species="M_tsul_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2423"/> <fbc:geneProductRef fbc:geneProduct="G_b2422"/> <fbc:geneProductRef fbc:geneProduct="G_b2424"/> <fbc:geneProductRef fbc:geneProduct="G_b3917"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2422"/> <fbc:geneProductRef fbc:geneProduct="G_b2425"/> <fbc:geneProductRef fbc:geneProduct="G_b2424"/> <fbc:geneProductRef fbc:geneProduct="G_b2423"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TARTRt7pp" fast="false" reversible="true" name="Tartrate/succinate antiporter (periplasm)" metaid="R_TARTRt7pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TARTRt7pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TARTRt7pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-127"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104723"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29259"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29260"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29262"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29261"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10137"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09283"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tartr__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/> <speciesReference species="M_tartr__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3063"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_dad_2_e" fast="false" reversible="false" name="Deoxyadenosine exchange" metaid="R_EX_dad_2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dad_2_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dad_2_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97081"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08293"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10939"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dad_2_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_ser__D_e" fast="false" reversible="false" name="D-Serine exchange" metaid="R_EX_ser__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ser__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ser__D_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-495"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97799"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29457"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29456"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29455"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29458"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08373"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10965"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ser__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_DDGALK" fast="false" reversible="false" name="2-dehydro-3-deoxygalactonokinase" metaid="R_DDGALK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DDGALK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DDGALK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DEHYDDEOXGALACTKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.58"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.178"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03387"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97213"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16527"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16525"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16526"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16528"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02429"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dh3dgal_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2dh3dgal6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3693"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_gam6p_e" fast="false" reversible="false" name="D-Glucosamine 6-phosphate exchange" metaid="R_EX_gam6p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_gam6p_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gam6p_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100031"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13642"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08591"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05568"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gam6p_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_15dap_e" fast="false" reversible="false" name="1,5-Diaminopentane exchange" metaid="R_EX_15dap_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_15dap_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_15dap_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97147"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08305"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_15dap_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_AB6PGH" fast="false" reversible="false" name="Arbutin 6-phosphate glucohydrolase" metaid="R_AB6PGH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AB6PGH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AB6PGH"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95165"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08025"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbt6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hqn_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2901"/> <fbc:geneProductRef fbc:geneProduct="G_b3721"/> <fbc:geneProductRef fbc:geneProduct="G_b2716"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_ocdcea_e" fast="false" reversible="false" name="Octadecenoate (n-C18:1) exchange" metaid="R_EX_ocdcea_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ocdcea_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ocdcea_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99110"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33658"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33655"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33656"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33657"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/10346"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ocdcea_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_cynt_e" fast="false" reversible="false" name="Cyanate exchange" metaid="R_EX_cynt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cynt_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cynt_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-14"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96963"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08279"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cynt_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_galctn__D_e" fast="false" reversible="false" name="D-Galactonate exchange" metaid="R_EX_galctn__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_galctn__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_galctn__D_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99961"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08579"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galctn__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_AMALT1" fast="false" reversible="false" name="Amylomaltase (maltotriose)" metaid="R_AMALT1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMALT1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMALT1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:AMYLOMALT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.25"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95800"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08126"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malttr_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_maltttr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3416"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_glyb_e" fast="false" reversible="false" name="Glycine betaine exchange" metaid="R_EX_glyb_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_glyb_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glyb_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-490"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100317"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6797957"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28945"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28944"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28946"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28943"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11693"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08639"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12430"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyb_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_AHGDx" fast="false" reversible="true" name="(S)-alpha-hydroxyglutarate dehydrogenase" metaid="R_AHGDx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AHGDx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AHGDx"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-16701"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.M7"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.272"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.399"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95630"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/9820"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10432"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_S2hglut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_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_nadh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2913"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLTP2" fast="false" reversible="true" name="Maltodextrin phosphorylase (maltohexaose)" metaid="R_MLTP2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLTP2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTP2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14285"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101633"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29683"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29684"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29686"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29685"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/10080"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08942"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_maltpt_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3417"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TAURabcpp" fast="false" reversible="false" name="Taurine transport via ABC system (periplasm)" metaid="R_TAURabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TAURabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TAURabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-64-RXN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.36-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.36"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104732"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14614#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14615#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14613#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14616#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09285"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05172"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_taur_p" 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" 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rdf:resource="http://identifiers.org/ec-code/2.4.1.325"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95151"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08023"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dtdp4aaddg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_unagamu_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dtdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_unagamuf_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4481"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAL160t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (hexadecanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL160t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAL160t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL160t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99155"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51716"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51719"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51717"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51718"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pmtcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1701"/> <fbc:geneProductRef fbc:geneProduct="G_b1805"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAL180t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (octadecanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL180t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAL180t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL180t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99167"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51723"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51720"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51722"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51721"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_stcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1701"/> <fbc:geneProductRef fbc:geneProduct="G_b1805"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SPODMpp" fast="false" reversible="false" name="Superoxide dismutase" metaid="R_SPODMpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SPODMpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SPODMpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUPEROX-DISMUT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.15.1.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00275"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104498"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20696"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20699"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20698"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20697"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_o2s_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1646"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_lyx__L_e" fast="false" reversible="false" name="L-Lyxose exchange" metaid="R_EX_lyx__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_lyx__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_lyx__L_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101272"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08859"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lyx__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_acmum_e" fast="false" reversible="false" name="N-Acetylmuramate exchange" metaid="R_EX_acmum_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_acmum_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_acmum_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95279"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08049"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acmum_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_dca_e" fast="false" reversible="false" name="Decanoate (n-C10:0) exchange" metaid="R_EX_dca_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dca_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dca_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97181"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dca_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_all__D_e" fast="false" reversible="false" name="D-Allose exchange" metaid="R_EX_all__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_all__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_all__D_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95776"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08115"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_all__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_NO3R1bpp" fast="false" reversible="false" name="Nitrate reductase (Ubiquinol-8)" metaid="R_NO3R1bpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NO3R1bpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO3R1bpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101987"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29126"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29125"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29123"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29124"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09000"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_no3_p" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2205"/> <fbc:geneProductRef fbc:geneProduct="G_b2202"/> <fbc:geneProductRef fbc:geneProduct="G_b2204"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2206"/> <fbc:geneProductRef fbc:geneProduct="G_b2203"/> </fbc:and> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_O2tpp" fast="false" reversible="true" name="O2 transport via diffusion (periplasm)" metaid="R_O2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O2tpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O2tpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-474"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102090"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09641"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09032"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09734"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o2_p" 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 id="R_EX_octa_e" fast="false" reversible="false" name="Octanoate (n-C8:0) exchange" metaid="R_EX_octa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_octa_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_octa_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-272"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99126"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29761"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29762"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29759"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29760"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09036"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09840"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_octa_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PHYTSpp" fast="false" reversible="false" name="Phytase (periplasm)" metaid="R_PHYTSpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PHYTSpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PHYTSpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102659"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09119"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="6" constant="true"/> <speciesReference species="M_minohp_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_inost_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="6" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0980"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_gbbtn_e" fast="false" reversible="false" name="Gamma-butyrobetaine exchange" metaid="R_EX_gbbtn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_gbbtn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gbbtn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100053"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32838"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32837"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32835"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32836"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08595"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gbbtn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PPTHpp" fast="false" reversible="false" name="Phosphonate hydrogenase (periplasm)" metaid="R_PPTHpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPTHpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPTHpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103149"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29453"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29454"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29451"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29452"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09184"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ppt_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0383"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PYRt2rpp" fast="false" reversible="true" name="Pyruvate reversible transport via proton symport (periplasm)" metaid="R_PYRt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PYRt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYRt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103385"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-372347"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-372342"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-372359"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05469"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09832"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09717"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09217"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_p" 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 id="R_NO3R2pp" fast="false" reversible="false" name="Nitrate reductase (Menaquinol-8) (periplasm)" metaid="R_NO3R2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NO3R2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO3R2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101988"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29141#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29142#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29140#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29139#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09003"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10121"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no3_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1467"/> <fbc:geneProductRef fbc:geneProduct="G_b1468"/> <fbc:geneProductRef fbc:geneProduct="G_b1466"/> <fbc:geneProductRef fbc:geneProduct="G_b1465"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1224"/> <fbc:geneProductRef fbc:geneProduct="G_b1227"/> <fbc:geneProductRef fbc:geneProduct="G_b1226"/> <fbc:geneProductRef fbc:geneProduct="G_b1225"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_xylu__L_e" fast="false" reversible="false" name="L-Xylulose exchange" metaid="R_EX_xylu__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_xylu__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_xylu__L_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138931"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09387"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_xylu__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_gdp_e" fast="false" reversible="false" name="GDP exchange" metaid="R_EX_gdp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_gdp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gdp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100096"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-111812"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08600"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09815"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gdp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_gtp_e" fast="false" reversible="false" name="GTP exchange" metaid="R_EX_gtp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_gtp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gtp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100462"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08680"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12663"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_NTP3pp" fast="false" reversible="false" name="Nucleoside-triphosphatase (GTP) (periplasm)" metaid="R_NTP3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTP3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTP3pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5462"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.15"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.6"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00335"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102043"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19669"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19671"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19672"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19670"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/816"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00241"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gdp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0980"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NO3R2bpp" fast="false" reversible="false" name="Nitrate reductase (Menaquinol-8) (periplasm)" metaid="R_NO3R2bpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NO3R2bpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO3R2bpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.7.99.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101989"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09002"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no3_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2206"/> <fbc:geneProductRef fbc:geneProduct="G_b2203"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2202"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_THMabcpp" fast="false" reversible="false" name="Thiamine transport via ABC system (periplasm)" metaid="R_THMabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THMabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THMabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138862"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05177"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09297"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thm_p" 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"/> <speciesReference species="M_thm_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0066"/> <fbc:geneProductRef fbc:geneProduct="G_b0068"/> <fbc:geneProductRef fbc:geneProduct="G_b0067"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_THMDt2pp_copy2" fast="false" reversible="true" name="Thymidine transport in via proton symport (periplasm)" metaid="R_THMDt2pp_copy2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THMDt2pp_copy2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THMDt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108H"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104818"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29957"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29958"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29955"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29956"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09298"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05200"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_thymd_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thymd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2406"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_THRabcpp" fast="false" reversible="false" name="L-threonine transport via ABC system (periplasm)" metaid="R_THRabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THRabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104849"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09301"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05169"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thr__L_p" 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"/> <speciesReference species="M_thr__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3456"/> <fbc:geneProductRef fbc:geneProduct="G_b3455"/> <fbc:geneProductRef fbc:geneProduct="G_b3460"/> <fbc:geneProductRef fbc:geneProduct="G_b3457"/> <fbc:geneProductRef fbc:geneProduct="G_b3454"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_TREptspp" fast="false" reversible="false" name="Trehalose transport via PEP:Pyr PTS (periplasm)" metaid="R_TREptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TREptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TREptspp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.69"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104931"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09322"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02005"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tre_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tre6p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2417"/> <fbc:geneProductRef fbc:geneProduct="G_b4240"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_THD2pp" fast="false" reversible="false" name="NAD(P) transhydrogenase (periplasm)" metaid="R_THD2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THD2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THD2pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104805"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10125"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09295"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" 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 id="R_TMAOR1pp" fast="false" reversible="false" name="Trimethylamine N-oxide reductase (menaquinol 8) (periplasm)" metaid="R_TMAOR1pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TMAOR1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TMAOR1pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104879"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09314"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10127"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tmao_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tma_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0997"/> <fbc:geneProductRef fbc:geneProduct="G_b0996"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1872"/> <fbc:geneProductRef fbc:geneProduct="G_b1873"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TMAOR2pp" fast="false" reversible="false" name="Trimethylamine N-oxide reductase (demethylmenaquinol 8) (periplasm)" metaid="R_TMAOR2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TMAOR2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TMAOR2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104881"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09316"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10128"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_tmao_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2dmmq8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_tma_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0997"/> <fbc:geneProductRef fbc:geneProduct="G_b0996"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1872"/> <fbc:geneProductRef fbc:geneProduct="G_b1873"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_XANtpp" fast="false" reversible="true" name="Xanthine reversible transport (periplasm)" metaid="R_XANtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_XANtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XANtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-561"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105226"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09379"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09652"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09378"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_xan_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_xan_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_DAPtex" fast="false" reversible="true" name="1,5-Diaminopentane transport via diffusion (extracellular to periplasm)" metaid="R_DAPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97147"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08305"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_15dap_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_15dap_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TRPt2rpp" fast="false" reversible="true" name="L-tryptophan reversible transport via proton symport (periplasm)" metaid="R_TRPt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TRPt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TRPt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-76"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104950"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28882"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28881"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28880"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28879"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09709"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09326"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05663"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_trp__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trp__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3161"/> <fbc:geneProductRef fbc:geneProduct="G_b3709"/> <fbc:geneProductRef fbc:geneProduct="G_b0112"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TYRt2rpp" fast="false" reversible="true" name="L-tyrosine reversible transport via proton symport (periplasm)" metaid="R_TYRt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TYRt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TYRt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-77"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105003"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28876"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28875"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28877"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28878"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09831"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09338"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13412"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05301"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09708"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_tyr__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1907"/> <fbc:geneProductRef fbc:geneProduct="G_b0112"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_tma_e" fast="false" reversible="false" name="Trimethylamine exchange" metaid="R_EX_tma_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_tma_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tma_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104884"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09318"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tma_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_URIt2pp_copy1" fast="false" reversible="false" name="Uridine transport in via proton symport (periplasm)" metaid="R_URIt2pp_copy1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_URIt2pp_copy1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URIt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108I"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105166"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29953"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29954"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29952"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29951"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09371"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05199"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_uri_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2964"/> <fbc:geneProductRef fbc:geneProduct="G_b2393"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_URIt2pp_copy2" fast="false" reversible="true" name="Uridine transport in via proton symport (periplasm)" metaid="R_URIt2pp_copy2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_URIt2pp_copy2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URIt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108I"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105166"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29953"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29954"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29952"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29951"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09371"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05199"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_uri_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2406"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_VALabcpp" fast="false" reversible="false" name="L-valine transport via ABC system (periplasm)" metaid="R_VALabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_VALabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/VALabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-36-RXN"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105187"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29805#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29803#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29806#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29804#2"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05168"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09373"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_val__L_p" 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"/> <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3457"/> <fbc:geneProductRef fbc:geneProduct="G_b3456"/> <fbc:geneProductRef fbc:geneProduct="G_b3460"/> <fbc:geneProductRef fbc:geneProduct="G_b3455"/> <fbc:geneProductRef fbc:geneProduct="G_b3454"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_12PPDStex" fast="false" reversible="true" name="(S)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)" metaid="R_12PPDStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_12PPDStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/12PPDStex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94684"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12ppd__S_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12ppd__S_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DDGLCNtex" fast="false" reversible="true" name="2-dehydro-3-deoxy-D-gluconate transport via diffusion (extracellular to periplasm)" metaid="R_DDGLCNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DDGLCNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DDGLCNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138208"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08320"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2ddglcn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2ddglcn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_XTSNt2rpp" fast="false" reversible="true" name="Xanthosine transport via proton symport (periplasm)" metaid="R_XTSNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_XTSNt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XTSNt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-31"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105246"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28940"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28942"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28941"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28939"/> <rdf:li 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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_XYLabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYLabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105268"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29902#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29900#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29899#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29901#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05167"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09383"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xyl__D_p" 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"/> <speciesReference species="M_xyl__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3568"/> <fbc:geneProductRef fbc:geneProduct="G_b3566"/> <fbc:geneProductRef fbc:geneProduct="G_b3567"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_GMHEPK" fast="false" reversible="false" name="D-glycero-D-manno-heptose 7-phosphate kinase" metaid="R_GMHEPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GMHEPK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GMHEPK"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143147"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gmhep7p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gmhep17bp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3052"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_XYLUt2pp" fast="false" reversible="false" name="L-xylulose transport in via proton symport (periplasm)" metaid="R_XYLUt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_XYLUt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYLUt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138930"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09386"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_xylu__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xylu__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3577"/> <fbc:geneProductRef fbc:geneProduct="G_b3578"/> <fbc:geneProductRef fbc:geneProduct="G_b3579"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_THRt4pp" fast="false" reversible="false" name="L-threonine via sodium symport (periplasm)" metaid="R_THRt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THRt4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRt4pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104842"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10186"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09306"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> <speciesReference species="M_thr__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thr__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3089"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALURtex" fast="false" reversible="true" name="D-galacturonate transport via diffusion (extracellular to periplasm)" metaid="R_GALURtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALURtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALURtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100021"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08589"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galur_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_galur_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GTPCI" fast="false" reversible="false" name="GTP cyclohydrolase I" metaid="R_GTPCI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GTPCI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GTPCI"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GTP-CYCLOHYDRO-I-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00424"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100453"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-1474146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-1474146"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17476"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17473"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17474"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17475"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/9177"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00299"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11232"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ahdt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2153"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FDMO" fast="false" reversible="false" name="FMNH2-dependent monooxygenase" metaid="R_FDMO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FDMO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FDMO"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-13418"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.14.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99485"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29718"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29715"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29716"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29717"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08467"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_isetac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gcald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0935"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEOXAMabcpp" fast="false" reversible="false" name="Ferroxamine transport via ABC system (periplasm)" metaid="R_FEOXAMabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEOXAMabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEOXAMabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143100"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08509"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05558"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_feoxam_p" 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_feoxam_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_b0152"/> <fbc:geneProductRef fbc:geneProduct="G_b0153"/> <fbc:geneProductRef fbc:geneProduct="G_b0151"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_fruur_e" fast="false" reversible="false" name="D-Fructuronate exchange" metaid="R_EX_fruur_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_fruur_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fruur_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99659"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08539"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fruur_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GALtex" fast="false" reversible="true" name="D-galactose transport via diffusion (extracellular to periplasm)" metaid="R_GALtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100025"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34918"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34917"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34916"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34915"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7001"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10911"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08585"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gal_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gal_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CBL1abcpp" fast="false" reversible="false" name="Cob(1)alamin transport via ABC system (periplasm)" metaid="R_CBL1abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CBL1abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CBL1abcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-5-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.33"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96471"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cbl1_p" 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_cbl1_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_b1709"/> <fbc:geneProductRef fbc:geneProduct="G_b0158"/> <fbc:geneProductRef fbc:geneProduct="G_b1711"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_malttr_e" fast="false" reversible="false" name="Maltotriose exchange" metaid="R_EX_malttr_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_malttr_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_malttr_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101359"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11212"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08876"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_malttr_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ACACt2pp" fast="false" reversible="true" name="Acetoacetate transport via proton symport (periplasm)" metaid="R_ACACt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACACt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACACt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95207"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05484"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08029"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acac_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2223"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACGAptspp" fast="false" reversible="false" name="N-Acetyl-D-glucosamine transport via PEP:Pyr PTS (periplasm)" metaid="R_ACGAptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACGAptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95253"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08041"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05485"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgam_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam6p_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_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b2417"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b1101"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b0679"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACMANAptspp" fast="false" reversible="false" name="N-acetyl-D-mannosamine transport via PTS (periplasm)" metaid="R_ACMANAptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACMANAptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACMANAptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95275"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08046"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10183"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acmana_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acmanap_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_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b1817"/> <fbc:geneProductRef fbc:geneProduct="G_b1819"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACNAMt2pp" fast="false" reversible="false" name="N-acetylneuraminate proton symport (periplasm)" metaid="R_ACNAMt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACNAMt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACNAMt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-25"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-15314"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95291"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28990"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28989"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28987"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28988"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05487"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08050"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acnam_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acnam_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3224"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALCTtex" fast="false" reversible="true" name="D-galactarte transport via diffusion (extracellular to periplasm)" metaid="R_GALCTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALCTtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALCTtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-203"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99963"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28478"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28480"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28479"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28481"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12441"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08581"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galct__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_galct__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALCTNtex" fast="false" reversible="true" name="D-galactonate transport via diffusion (extracellular to periplasm)" metaid="R_GALCTNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALCTNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALCTNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99961"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08579"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galctn__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_galctn__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALTtex" fast="false" reversible="true" name="Galactitol transport via diffusion (extracellular to periplasm)" metaid="R_GALTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALTtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALTtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100019"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33146"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33144"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33143"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33145"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08587"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galt_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_galt_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_cbi_e" fast="false" reversible="false" name="Cobinamide exchange" metaid="R_EX_cbi_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cbi_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cbi_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-283"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR124011"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29695"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29697"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29696"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29698"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cbi_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_CHOLD" fast="false" reversible="false" name="Choline dehydrogenase" metaid="R_CHOLD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CHOLD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHOLD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-6021"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R08557"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96697"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33054"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33052"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33051"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33053"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10770"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_chol_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_betald_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_b0311"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TRE6PS" fast="false" reversible="false" name="Alpha,alpha-trehalose-phosphate synthase (UDP-forming)" metaid="R_TRE6PS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TRE6PS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TRE6PS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TREHALOSE6PSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.15"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00836"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06043"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143415"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18890"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18891"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18889"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18892"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00605"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tre6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1896"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DRPA" fast="false" reversible="false" name="Deoxyribose-phosphate aldolase" metaid="R_DRPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DRPA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DRPA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DEOXYRIBOSE-P-ALD-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01066"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97787"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-6787321"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-6787321"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12823"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12822"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12821"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12824"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/64"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00784"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dr5p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4381"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TKT2" fast="false" reversible="true" name="Transketolase" metaid="R_TKT2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TKT2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TKT2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2TRANSKETO-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.2.1.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01830"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104869"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27627"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27628"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27626"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27629"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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 id="R_EX_arbtn_fe3_e" fast="false" reversible="false" name="Aerobactin exchange" metaid="R_EX_arbtn_fe3_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_arbtn_fe3_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_arbtn_fe3_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142930"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbtn_fe3_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_UDCPDP" fast="false" reversible="false" name="Undecaprenyl-diphosphatase" metaid="R_UDCPDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDCPDP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDCPDP"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105042"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17069"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17070"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17072"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17071"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/5225"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0841"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> <fbc:geneProductRef fbc:geneProduct="G_b3057"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_cpgn_e" fast="false" reversible="false" name="Coprogen exchange" metaid="R_EX_cpgn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cpgn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cpgn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142942"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cpgn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_ch4_e" fast="false" reversible="false" name="EX ch4 LPAREN e RPAREN " metaid="R_EX_ch4_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ch4_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ch4_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-526"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96664"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13109"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10471"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ch4_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_FEENTERabcpp" fast="false" reversible="false" name="Fe-enterobactin transport via ABC system (periplasm)" metaid="R_FEENTERabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEENTERabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEENTERabcpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.34"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99546"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_feenter_p" 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_feenter_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_b0589"/> <fbc:geneProductRef fbc:geneProduct="G_b0592"/> <fbc:geneProductRef fbc:geneProduct="G_b0590"/> <fbc:geneProductRef fbc:geneProduct="G_b0588"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_adocbl_e" fast="false" reversible="false" name="Adenosylcobalamin exchange" metaid="R_EX_adocbl_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_adocbl_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_adocbl_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96480"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adocbl_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_FECRMabcpp" fast="false" reversible="false" name="Ferrichrome transport via ABC system (periplasm)" metaid="R_FECRMabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FECRMabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FECRMabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-298"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.34"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99535"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08493"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05188"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fecrm_p" 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_fecrm_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_b0153"/> <fbc:geneProductRef fbc:geneProduct="G_b0152"/> <fbc:geneProductRef fbc:geneProduct="G_b0151"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_TREH" fast="false" reversible="false" name="Alpha,alpha-trehalase" metaid="R_TREH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TREH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TREH"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.28"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00010"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06103"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95163"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20868"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20869"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20870"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20871"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/6476"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00007"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tre_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glc__D_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3519"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GAMtex" fast="false" reversible="true" name="D-glucosamine transport via diffusion (extracellular to periplasm)" metaid="R_GAMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GAMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GAMtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100035"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08593"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gam_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gam_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GBBTNtex" fast="false" reversible="true" name="Gamma-butyrobetaine transport via diffusion (extracellular to periplasm)" metaid="R_GBBTNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GBBTNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GBBTNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100053"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32838"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32837"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32835"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32836"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08595"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gbbtn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gbbtn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ATPS4rpp" fast="false" reversible="true" name="ATP synthase (four protons for one ATP) (periplasm)" metaid="R_ATPS4rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ATPS4rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ATPS4rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ATPSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.14"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96136"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08173"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10042"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference 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<fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3731"/> <fbc:geneProductRef fbc:geneProduct="G_b3733"/> <fbc:geneProductRef fbc:geneProduct="G_b3735"/> <fbc:geneProductRef fbc:geneProduct="G_b3734"/> <fbc:geneProductRef fbc:geneProduct="G_b3732"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3738"/> <fbc:geneProductRef fbc:geneProduct="G_b3736"/> <fbc:geneProductRef fbc:geneProduct="G_b3737"/> </fbc:and> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_INDOLEtex" fast="false" reversible="true" name="Indole transport via diffusion (extracellular to periplasm)" metaid="R_INDOLEtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_INDOLEtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> 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xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHAtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-559"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97367"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08325"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08326"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05532"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dha_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dha_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_DMSOR1pp" fast="false" reversible="false" name="Dimethyl sulfoxide reductase (Menaquinol 8) (periplasm)" metaid="R_DMSOR1pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DMSOR1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DMSOR1pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97530"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08355"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10129"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dmso_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dms_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1872"/> <fbc:geneProductRef fbc:geneProduct="G_b1873"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARGabcpp" fast="false" reversible="false" name="L-arginine transport via ABC system (periplasm)" metaid="R_ARGabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARGabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARGabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-4-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95952"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29880#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29882#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29881#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29879#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08151"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11236"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05154"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arg__L_p" stoichiometry="1" constant="true"/> <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_arg__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:and> <fbc:geneProductRef fbc:geneProduct="G_b2308"/> <fbc:geneProductRef fbc:geneProduct="G_b2306"/> <fbc:geneProductRef fbc:geneProduct="G_b2310"/> <fbc:geneProductRef fbc:geneProduct="G_b2307"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0864"/> <fbc:geneProductRef fbc:geneProduct="G_b0860"/> <fbc:geneProductRef fbc:geneProduct="G_b0863"/> <fbc:geneProductRef fbc:geneProduct="G_b0862"/> <fbc:geneProductRef fbc:geneProduct="G_b0861"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADNt2pp_copy1" fast="false" reversible="false" name="Adenosine transport in via proton symport (periplasm)" metaid="R_ADNt2pp_copy1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADNt2pp_copy1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADNt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-203"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108A"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95461"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29988"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29990"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29987"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29989"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05318"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08068"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2964"/> <fbc:geneProductRef fbc:geneProduct="G_b2393"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADNt2pp_copy2" fast="false" reversible="true" name="Adenosine transport in via proton symport (periplasm)" metaid="R_ADNt2pp_copy2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADNt2pp_copy2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADNt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-203"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108A"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95461"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29988"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29990"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29987"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29989"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05318"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08068"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2406"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALAabcpp" fast="false" reversible="false" name="L-alanine transport via ABC system (periplasm)" metaid="R_ALAabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALAabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALAabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95703"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10170"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08097"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala__L_p" stoichiometry="1" constant="true"/> <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_ala__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_b3454"/> <fbc:geneProductRef fbc:geneProduct="G_b3456"/> <fbc:geneProductRef fbc:geneProduct="G_b3455"/> <fbc:geneProductRef fbc:geneProduct="G_b3460"/> <fbc:geneProductRef fbc:geneProduct="G_b3457"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALLabcpp" fast="false" reversible="false" name="D-allose transport via ABC system (periplasm)" metaid="R_ALLabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALLabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALLabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-42-RXN"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95775"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05185"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08112"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_all__D_p" stoichiometry="1" constant="true"/> <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_all__D_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_b4087"/> <fbc:geneProductRef fbc:geneProduct="G_b4088"/> <fbc:geneProductRef fbc:geneProduct="G_b4086"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALLTNt2rpp" fast="false" reversible="true" name="Allantoin transport in via proton symport (periplasm)" metaid="R_ALLTNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALLTNt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALLTNt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95770"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08116"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05682"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_alltn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_alltn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0511"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARBabcpp" fast="false" reversible="false" name="L-arabinose transport via ABC system (periplasm)" metaid="R_ARBabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-2-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.17"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95935"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arab__L_p" stoichiometry="1" constant="true"/> <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_arab__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_b4460"/> <fbc:geneProductRef fbc:geneProduct="G_b1901"/> <fbc:geneProductRef fbc:geneProduct="G_b1900"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARGAGMt7pp" fast="false" reversible="true" name="Arginine/agmatine antiport (periplasm)" metaid="R_ARGAGMt7pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARGAGMt7pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARGAGMt7pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2162"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95938"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29654"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29653"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29652"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29651"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13809"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08152"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_agm_c" stoichiometry="1" constant="true"/> <speciesReference species="M_arg__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_agm_p" stoichiometry="1" constant="true"/> <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4115"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASCBptspp" fast="false" reversible="false" name="L-ascorbate transport via PEP:Pyr PTS (periplasm)" metaid="R_ASCBptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASCBptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASCBptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138069"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08158"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13758"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ascb__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ascb6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4195"/> <fbc:geneProductRef fbc:geneProduct="G_b4193"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b4194"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYTK2" fast="false" reversible="true" name="Cytidylate kinase (dCMP)" metaid="R_CYTK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYTK2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYTK2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-7913"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.13"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.14"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.25"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01665"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97053"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25096"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25094"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25097"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25095"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/84"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01219"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dcmp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dcdp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0910"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASNt2rpp" fast="false" reversible="true" name="L-asparagine reversible transport via proton symport (periplasm)" metaid="R_ASNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASNt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASNt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-262"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96066"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09782"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05508"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08161"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11321"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13230"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asn__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_asn__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1453"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASPabcpp" fast="false" reversible="false" name="L-aspartate transport via ABC system (periplasm)" metaid="R_ASPabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASPabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-222"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96103"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29039#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29040#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29041#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29042#1"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13284#2"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05152"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08165"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asp__L_p" stoichiometry="1" constant="true"/> <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_asp__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_b0654"/> <fbc:geneProductRef fbc:geneProduct="G_b0652"/> <fbc:geneProductRef fbc:geneProduct="G_b0655"/> <fbc:geneProductRef fbc:geneProduct="G_b0653"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASPt2pp" fast="false" reversible="false" name="L-aspartate transport in via proton symport (periplasm)" metaid="R_ASPt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASPt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96106"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09781"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05217"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09825"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13233"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asp__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_asp__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 id="R_ECOAH8" fast="false" reversible="true" name="3-hydroxyacyl-CoA dehydratase (3-hydroxyoctadecanoyl-CoA)" metaid="R_ECOAH8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ECOAH8"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ECOAH8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.134"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.17"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97893"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08413"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hodcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_od2coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2341"/> <fbc:geneProductRef fbc:geneProduct="G_b3846"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLCDpp" fast="false" reversible="false" name="Glucose dehydrogenase (ubiquinone-8 as acceptor) (periplasm)" metaid="R_GLCDpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCDpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCDpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100177"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08608"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10116"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glc__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glcn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0124"/> <fbc:geneProductRef fbc:geneProduct="G_b0837"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GUAtpp" fast="false" reversible="true" name="Guanine transport via diffusion (periplasm)" metaid="R_GUAtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GUAtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GUAtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-578"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100465"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12299"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10142"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08683"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08682"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09746"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gua_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gua_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4464"/> <fbc:geneProductRef fbc:geneProduct="G_b4064"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASPt2_2pp" fast="false" reversible="false" name="Aspartate transport via proton symport (2 H) (periplasm)" metaid="R_ASPt2_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASPt2_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPt2_2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-122A"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96104"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29288"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29289"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29287"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29290"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08169"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10151"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asp__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_asp__L_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 id="R_HYD2pp" fast="false" reversible="false" name="Hydrogenase (menaquinone8: 2 protons) (periplasm)" metaid="R_HYD2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HYD2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HYD2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100754"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29052#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29051#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29054#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29053#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08735"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10119"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0973"/> <fbc:geneProductRef fbc:geneProduct="G_b0974"/> <fbc:geneProductRef fbc:geneProduct="G_b0972"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2994"/> <fbc:geneProductRef fbc:geneProduct="G_b2997"/> <fbc:geneProductRef fbc:geneProduct="G_b2996"/> <fbc:geneProductRef fbc:geneProduct="G_b2995"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GK1" fast="false" reversible="true" name="Guanylate kinase (GMP:ATP)" metaid="R_GK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GK1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GK1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GUANYL-KIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.8"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00332"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100144"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20783"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20782"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20780"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20781"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/77"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00239"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3648"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HYXNtpp" fast="false" reversible="true" name="Hypoxanthine transport (periplasm)" metaid="R_HYXNtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HYXNtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HYXNtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-579"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-562"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100749"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10143"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08737"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08738"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hxan_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hxan_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4064"/> <fbc:geneProductRef fbc:geneProduct="G_b4464"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NACtpp" fast="false" reversible="false" name="Nicotinic acid uptake (periplasm)" metaid="R_NACtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NACtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NACtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101808"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-8869603"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08970"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05310"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08969"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nac_p" stoichiometry="1" 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</reaction> <reaction id="R_O2tex" fast="false" reversible="true" name="Oxygen transport via diffusion (extracellular to periplasm)" metaid="R_O2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O2tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O2tex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-474"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102090"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09641"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRULYStex" fast="false" reversible="true" name="Fructoselysine transporter via diffusion (extracellular)" metaid="R_FRULYStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRULYStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRULYStex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-417"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99657"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28457"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28455"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28456"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28454"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08534"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_frulys_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_frulys_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALTtexi" fast="false" reversible="false" name="MaltoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" metaid="R_MALTtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALTtexi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTtexi"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14351"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-575"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1741"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101364"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33173"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33172"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33171"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33174"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11211"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08874"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_malt_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_malt_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4036"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ECOAH5" fast="false" reversible="true" name="3-hydroxyacyl-CoA dehydratase (3-hydroxydodecanoyl-CoA)" metaid="R_ECOAH5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ECOAH5"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li 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rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-77256"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77256"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-77256"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-77256"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-77256"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-77256"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31078"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31075"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31077"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31076"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/3890"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02911"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hddcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dd2coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2341"/> <fbc:geneProductRef fbc:geneProduct="G_b3846"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHFS" fast="false" reversible="false" name="Dihydrofolate synthase" metaid="R_DHFS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHFS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHFS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DIHYDROFOLATESYNTH-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.12"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.17"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02237"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR140043"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23585"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23587"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23584"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23586"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01603"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dhpt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dhf_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2315"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CITt7pp" fast="false" reversible="false" name="Citrate transport via succinate antiport (periplasm)" metaid="R_CITt7pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CITt7pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CITt7pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-201"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96752"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28837"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28836"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28838"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28835"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08216"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10150"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cit_p" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0612"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CRNt7pp" fast="false" reversible="false" name="Carnitine/butyrobetaine antiporter (periplasm)" metaid="R_CRNt7pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNt7pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNt7pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-100"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96908"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29427"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29430"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29429"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29428"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08263"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10149"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_crn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_gbbtn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gbbtn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0040"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_ni2_e" fast="false" reversible="true" name="Ni2+ exchange" metaid="R_EX_ni2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ni2_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ni2_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-141B"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101958"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29833"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29831"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29834"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29832"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ni2_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GLCtex_copy1" fast="false" reversible="false" name="Glucose transport via diffusion (extracellular to periplasm)" metaid="R_GLCtex_copy1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCtex_copy1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-574"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100188"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7002"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/601"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09875"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09679"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08617"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glc__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4036"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_no_e" fast="false" reversible="false" name="Nitric oxide exchange" metaid="R_EX_no_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_no_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_no_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101998"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_no_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_CHLabcpp" fast="false" reversible="false" name="Choline transport via ABC system (periplasm)" metaid="R_CHLabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CHLabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHLabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96691"/> <rdf:li rdf:resource="http://identifiers.org/rhea/38715#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/38718#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/38717#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/38716#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05159"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08212"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_chol_p" 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_chol_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_b2129"/> <fbc:geneProductRef fbc:geneProduct="G_b2128"/> <fbc:geneProductRef fbc:geneProduct="G_b2131"/> <fbc:geneProductRef fbc:geneProduct="G_b2130"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DGSNt2pp" fast="false" reversible="false" name="Deoxyguanosine transport in via proton symport (periplasm)" metaid="R_DGSNt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DGSNt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DGSNt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97325"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09688"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08323"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dgsn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dgsn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2964"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE3DCITtonex" fast="false" reversible="false" name="Ferric-dicitrate transport via ton system (extracellular)" metaid="R_FE3DCITtonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3DCITtonex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3DCITtonex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99509"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08479"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3dcit_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe3dcit_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1252"/> <fbc:geneProductRef fbc:geneProduct="G_b3005"/> <fbc:geneProductRef fbc:geneProduct="G_b3006"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4291"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DINSt2pp" fast="false" reversible="false" name="Deoxyinosine transport in via proton symport (periplasm)" metaid="R_DINSt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DINSt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DINSt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108E"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97465"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29971"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29972"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29974"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29973"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08343"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09687"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_din_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_din_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2964"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DURIt2pp" fast="false" reversible="false" name="Deoxyuridine transport in via proton symport (periplasm)" metaid="R_DURIt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DURIt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DURIt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108F"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97820"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29970"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29969"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29968"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29967"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09685"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08376"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_duri_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_duri_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2393"/> <fbc:geneProductRef fbc:geneProduct="G_b2964"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE2abcpp" fast="false" reversible="false" name="Iron (II) transport via ABC system (periplasm)" metaid="R_FE2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE2abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE2abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99504"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05555"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08472"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_p" 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_fe2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3409"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRUptspp" fast="false" reversible="false" name="D-fructose transport via PEP:Pyr PTS (periplasm)" metaid="R_FRUptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRUptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRUptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99661"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05560"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08536"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fru_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_f1p_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_b2167"/> <fbc:geneProductRef fbc:geneProduct="G_b2169"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FUCtpp" fast="false" reversible="true" name="L-fucose transport via proton symport (periplasm)" metaid="R_FUCtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FUCtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FUCtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-20"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99703"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fuc__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fuc__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2801"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_fad_e" fast="false" reversible="false" name="Exchange of Flavin adenine dinucleotide oxidized" metaid="R_EX_fad_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_fad_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fad_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-272"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99217"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fad_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GALCTt2rpp" fast="false" reversible="true" name="D-galactarte transport via proton symport, reversible (periplasm)" metaid="R_GALCTt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALCTt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALCTt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99962"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05565"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08580"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galct__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_galct__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2789"/> <fbc:geneProductRef fbc:geneProduct="G_b3127"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALt2pp" fast="false" reversible="false" name="D-galactose transport in via proton symport (periplasm)" metaid="R_GALt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100026"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29019"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29022"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29021"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29020"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05566"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08584"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gal_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gal_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2943"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASPtex" fast="false" reversible="true" name="L-aspartate transport via diffusion (extracellular to periplasm)" metaid="R_ASPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-554"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96107"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10906"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08170"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13232"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asp__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_asp__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ABUTt2pp" fast="false" reversible="false" name="4-aminobutyrate transport in via proton symport (periplasm)" metaid="R_ABUTt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ABUTt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ABUTt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-57"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94994"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28916"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28917"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28918"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28915"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08027"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05564"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4abut_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4abut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2663"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FUMt2_2pp" fast="false" reversible="false" name="Fumarate transport via proton symport (2 H) (periplasm)" metaid="R_FUMt2_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FUMt2_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FUMt2_2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-121B"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99711"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29332"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29334"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29333"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29331"/> <rdf:li 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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FUMt2_3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FUMt2_3pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-299"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99712"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08543"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10158"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fum_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="3" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4138"/> <fbc:geneProductRef fbc:geneProduct="G_b4123"/> <fbc:geneProductRef fbc:geneProduct="G_b0621"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PHEtex" fast="false" reversible="true" name="L-phenylalanine transport via diffusion (extracellular to periplasm)" metaid="R_PHEtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PHEtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PHEtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-445"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102637"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27952"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27951"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27950"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27953"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13470"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/14018"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11018"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09118"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_phe__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_phe__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEENTERtonex" fast="false" reversible="false" name="Fe-enterobactin transport via ton system (extracellular)" metaid="R_FEENTERtonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEENTERtonex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEENTERtonex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99549"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_feenter_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_feenter_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0584"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1252"/> <fbc:geneProductRef fbc:geneProduct="G_b3005"/> <fbc:geneProductRef fbc:geneProduct="G_b3006"/> </fbc:and> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CSNt2pp" fast="false" reversible="false" name="Cytosine transport in via proton symport (periplasm)" metaid="R_CSNt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CSNt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CSNt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-116"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-199"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96929"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29937"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29935"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29936"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29938"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05527"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08266"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_csn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_csn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0336"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYNTt2pp" fast="false" reversible="false" name="Cyanate transport via proton symport (periplasm)" metaid="R_CYNTt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYNTt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYNTt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96962"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29233"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29232"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29231"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29234"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08278"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10132"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cynt_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cynt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0341"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYSabcpp" fast="false" reversible="false" name="L-cysteine uptake via ABC system (periplasm)" metaid="R_CYSabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYSabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYSabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-265"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97025"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32798#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32796#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29785#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29786#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29783#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32795#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29784#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32797#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05237"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08281"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cys__L_p" 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_cys__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_b1918"/> <fbc:geneProductRef fbc:geneProduct="G_b1920"/> <fbc:geneProductRef fbc:geneProduct="G_b1917"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_SBTptspp" fast="false" reversible="false" name="D-sorbitol transport via PEP:Pyr PTS (periplasm)" metaid="R_SBTptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SBTptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SBTptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104290"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09242"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10184"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sbt__D_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sbt6p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b2704"/> <fbc:geneProductRef fbc:geneProduct="G_b2703"/> <fbc:geneProductRef fbc:geneProduct="G_b2702"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PItex" fast="false" reversible="true" name="Phosphate transport via diffusion (extracellular to periplasm)" metaid="R_PItex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PItex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PItex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-470"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102871"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32824"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32826"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32825"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32823"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/10985"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10838"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09722"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09121"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13178"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pi_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TREHpp" fast="false" reversible="false" name="Alpha,alpha-trehalase (periplasm)" metaid="R_TREHpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TREHpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TREHpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.28"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00010"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06103"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95163"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20868"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20869"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20870"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20871"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/6476"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00007"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_tre_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glc__D_p" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1197"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYTBDpp" fast="false" reversible="false" name="Cytochrome oxidase bd (ubiquinol-8: 2 protons) (periplasm)" metaid="R_CYTBDpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYTBDpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYTBDpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97031"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12494"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10112"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08288"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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_p" 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_b0734"/> <fbc:geneProductRef fbc:geneProduct="G_b0733"/> <fbc:geneProductRef fbc:geneProduct="G_b4515"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYTDt2pp_copy1" fast="false" reversible="false" name="Cytidine transport in via proton symport (periplasm)" metaid="R_CYTDt2pp_copy1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYTDt2pp_copy1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYTDt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108B"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97044"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29986"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29984"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29985"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29983"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08289"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05198"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cytd_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cytd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2393"/> <fbc:geneProductRef fbc:geneProduct="G_b2964"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYTDt2pp_copy2" fast="false" reversible="true" name="Cytidine transport in via proton symport (periplasm)" metaid="R_CYTDt2pp_copy2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYTDt2pp_copy2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYTDt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108B"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97044"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29986"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29984"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29985"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29983"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08289"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05198"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cytd_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cytd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2406"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DADNt2pp" fast="false" reversible="false" name="Deoxyadenosine transport in via proton symport (periplasm)" metaid="R_DADNt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DADNt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DADNt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108C"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97080"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29982"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29979"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29981"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29980"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05317"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08292"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dad_2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> 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<rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97209"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29975"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29976"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29978"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29977"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05205"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08316"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcyt_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dcyt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2393"/> <fbc:geneProductRef fbc:geneProduct="G_b2964"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYTBD2pp" fast="false" reversible="false" name="Cytochrome oxidase bd (menaquinol-8: 2 protons) (periplasm)" metaid="R_CYTBD2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYTBD2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYTBD2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97032"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08287"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10806"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="0.5" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0978"/> <fbc:geneProductRef fbc:geneProduct="G_b0979"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACGAMK" fast="false" reversible="false" name="N-acetylglucosamine kinase" metaid="R_ACGAMK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACGAMK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAMK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:N-ACETYLGLUCOSAMINE-KINASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.59"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01201"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95249"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17420"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17418"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17419"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17417"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1435"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00892"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgam_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1119"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACALDtpp" fast="false" reversible="true" name="Acetaldehyde reversible transport (periplasm)" metaid="R_ACALDtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACALDtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACALDtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95212"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-449872"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09700"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08033"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13212"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08032"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acald_p" 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 id="R_ACt2rpp" fast="false" reversible="true" name="Acetate reversible transport via proton symport (periplasm)" metaid="R_ACt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-571"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95429"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08061"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05488"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ac_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" 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rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-113"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138207"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29945"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29943"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29946"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29944"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05681"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08319"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2ddglcn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2ddglcn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3909"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RMNtex" fast="false" reversible="true" name="L-rhamnose transport via diffusion (extracellular to periplasm)" metaid="R_RMNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RMNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RMNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104042"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34995"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34998"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34997"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34996"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09229"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_rmn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_rmn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_meoh_e" fast="false" reversible="false" name="Methanol exchange" metaid="R_EX_meoh_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description 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fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_fe3dcit_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fe3dcit_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142958"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3dcit_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_fe3hox_e" fast="false" reversible="false" name="Fe(III)hydroxamate exchange" metaid="R_EX_fe3hox_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_fe3hox_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fe3hox_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142961"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3hox_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_fecrm_e" fast="false" reversible="false" name="Ferrichrome exchange" metaid="R_EX_fecrm_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_fecrm_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fecrm_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1701"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2241"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR123118"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fecrm_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_feenter_e" fast="false" reversible="false" name="Fe-enterobactin exchange" metaid="R_EX_feenter_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_feenter_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li 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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALTPTtexi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTPTtexi"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101356"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08873"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_maltpt_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_maltpt_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4036"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_METS" fast="false" reversible="false" name="Methionine synthase" metaid="R_METS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" 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stoichiometry="1" constant="true"/> <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4019"/> <fbc:geneProductRef fbc:geneProduct="G_b3829"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASPO3" fast="false" reversible="false" name="L-aspartate oxidase" metaid="R_ASPO3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASPO3"> <bqbiol:is 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constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2574"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASPO5" fast="false" reversible="false" name="L-aspartate oxidase" metaid="R_ASPO5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASPO5"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPO5"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9772"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.99"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96093"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30043"/> <rdf:li 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fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASPO4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPO4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96092"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29192"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29193"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29191"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29194"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08167"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" 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</sbml:annotation> <listOfReactants> <speciesReference species="M_3ump_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ASPO6" fast="false" reversible="false" name="L-aspartate oxidase" metaid="R_ASPO6" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASPO6"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPO6"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:L-ASPARTATE-OXID-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.3.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00481"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96094"/> <rdf:li 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rdf:resource="http://identifiers.org/seed.reaction/rxn08780"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lcts_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_lcts_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LEUtex" fast="false" reversible="true" name="L-leucine transport via diffusion (extracellular to periplasm)" metaid="R_LEUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LEUtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LEUtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-447"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101057"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13056"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08786"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11003"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_leu__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_leu__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LYStex" fast="false" reversible="true" name="L-lysine transport via diffusion (extracellular to periplasm)" metaid="R_LYStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LYStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYStex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-569"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101269"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7984"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10834"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08856"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lys__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_lys__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_glyc__R_e" fast="false" reversible="false" name="(R)-Glycerate exchange" metaid="R_EX_glyc__R_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_glyc__R_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glyc__R_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-523"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100323"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08645"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc__R_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_eca4colipa_e" fast="false" reversible="false" name="(enterobacterial common antigen)x4 core oligosaccharide lipid A exchange" metaid="R_EX_eca4colipa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_eca4colipa_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_eca4colipa_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97872"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08406"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_eca4colipa_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GLYOX3" fast="false" reversible="false" name="Glyoxalase III" metaid="R_GLYOX3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYOX3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYOX3"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLYOXIII-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.130"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09796"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100354"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27757"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27755"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27756"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27754"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08659"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mthgxl_c" 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:geneProductRef fbc:geneProduct="G_b1967"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FDMO3" fast="false" reversible="false" name="FMNH2-dependent monooxygenase (ethanesulfonate)" metaid="R_FDMO3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FDMO3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FDMO3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99489"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29730"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29727"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29729"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29728"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08469"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ethso3_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0935"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LYXtex" fast="false" reversible="true" name="L-Lyxose transport via diffusion (extracellular to periplasm)" metaid="R_LYXtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LYXtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYXtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101272"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08859"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lyx__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_lyx__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MANtex" fast="false" reversible="true" name="D-mannose transport via diffusion (extracellular to periplasm)" metaid="R_MANtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MANtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MANtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101402"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11452"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12997"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08886"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_man_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_man_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MAN6Ptex" fast="false" reversible="true" name="Mannose 6-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_MAN6Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MAN6Ptex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MAN6Ptex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101385"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13644"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08880"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_man6p_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_man6p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FDMO4" fast="false" reversible="false" name="FMNH2-dependent monooxygenase (butanesulfonate)" metaid="R_FDMO4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FDMO4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FDMO4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.14.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99491"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08470"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_butso3_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0935"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYSabc2pp" fast="false" reversible="false" name="L-cysteine export via ABC system (cytoplasm to periplasm)" metaid="R_CYSabc2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYSabc2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYSabc2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97026"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32796#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32797#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29783#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29786#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32798#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29784#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29785#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32795#2"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08280"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cys__L_p" 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_b0887"/> <fbc:geneProductRef fbc:geneProduct="G_b0886"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_BUTSO3abcpp" fast="false" reversible="false" name="Butanesulfonate transport via ABC system (periplasm)" metaid="R_BUTSO3abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BUTSO3abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BUTSO3abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96350"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05512"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08181"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_butso3_p" 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_butso3_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:and> <fbc:geneProductRef fbc:geneProduct="G_b0934"/> <fbc:geneProductRef fbc:geneProduct="G_b0933"/> <fbc:geneProductRef fbc:geneProduct="G_b0936"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0366"/> <fbc:geneProductRef fbc:geneProduct="G_b0365"/> <fbc:geneProductRef fbc:geneProduct="G_b0367"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ETHSO3abcpp" fast="false" reversible="false" name="Ethanesulfonate transport via ABC system (periplasm)" metaid="R_ETHSO3abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ETHSO3abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ETHSO3abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97977"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05552"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08425"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ethso3_p" 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_ethso3_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_b0934"/> <fbc:geneProductRef fbc:geneProduct="G_b0933"/> <fbc:geneProductRef fbc:geneProduct="G_b0936"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_MELIBtex" fast="false" reversible="true" name="Melibiose transport via diffusion (extracellular to periplasm)" metaid="R_MELIBtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MELIBtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MELIBtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138589"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_melib_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_melib_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DMSOtex" fast="false" reversible="true" name="Dimethyl sulfoxide transport via diffusion (extracellular to periplasm)" metaid="R_DMSOtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DMSOtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DMSOtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-273"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97533"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29700"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29701"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29702"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29699"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08358"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dmso_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dmso_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DURItex" fast="false" reversible="true" name="Deoxyuridine transport via diffusion (extracellular to periplasm)" metaid="R_DURItex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DURItex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DURItex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97819"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10984"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08377"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_duri_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_duri_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0411"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_mal__D_e" fast="false" reversible="false" name="D-Malate exchange" metaid="R_EX_mal__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_mal__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mal__D_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101341"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08864"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mal__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_FRUtex" fast="false" reversible="true" name="D-fructose transport via diffusion (extracellular to periplasm)" metaid="R_FRUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRUtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRUtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99663"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-189222"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-189222"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13415"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12996"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08537"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fru_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fru_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FUCtex" fast="false" reversible="true" name="L-fucose transport via diffusion (extracellular to periplasm)" metaid="R_FUCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FUCtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FUCtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99704"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fuc__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fuc__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_sel_e" fast="false" reversible="true" name="Selenate exchange" metaid="R_EX_sel_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_sel_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_sel_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104327"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34889"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34887"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34888"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34890"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sel_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_hg2_e" fast="false" reversible="false" name="Hg2+ exchange" metaid="R_EX_hg2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_hg2_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_hg2_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100625"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32815"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32817"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32816"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32818"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05586"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08717"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hg2_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_O16GLCT1" fast="false" reversible="false" name="Glucosyltransferase I (LPS O16 antigen biosynthesis)" metaid="R_O16GLCT1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O16GLCT1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16GLCT1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143258"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09028"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_aragund_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_garagund_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2032"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_O16AP2pp" fast="false" reversible="false" name="O16 antigen polymerase (periplasm)" metaid="R_O16AP2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O16AP2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16AP2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138661"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o16a2und_p" stoichiometry="1" constant="true"/> <speciesReference species="M_o16aund_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_o16a3und_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2027"/> <fbc:geneProductRef fbc:geneProduct="G_b2035"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_O16AP3pp" fast="false" reversible="false" name="O16 antigen polymerase (periplasm)" metaid="R_O16AP3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O16AP3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16AP3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138662"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o16a3und_p" stoichiometry="1" constant="true"/> <speciesReference species="M_o16aund_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_o16a4und_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2027"/> <fbc:geneProductRef fbc:geneProduct="G_b2035"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FUMtex" fast="false" reversible="true" name="Fumarate transport via diffusion (extracellular to periplasm)" metaid="R_FUMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FUMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FUMtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-553"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99715"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08544"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11013"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fum_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fum_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACACT5r" fast="false" reversible="true" name="Acetyl-CoA C-acyltransferase (decanoyl-CoA) (r)" metaid="R_ACACT5r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACACT5r"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACACT5r"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.9"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95199"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dcacoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3oddcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3845"/> <fbc:geneProductRef fbc:geneProduct="G_b2342"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_O16A4Lpp" fast="false" reversible="false" name="O16 anitgen (x4) ligase (periplasm)" metaid="R_O16A4Lpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O16A4Lpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16A4Lpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143257"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_colipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_o16a4und_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_o16a4colipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3622"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PRASCSi" fast="false" reversible="false" name="Phosphoribosylaminoimidazolesuccinocarboxamide synthase" metaid="R_PRASCSi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PRASCSi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PRASCSi"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SAICARSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.6"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04591"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR108987"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-419223"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-73805"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-73805"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22631"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22628"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22629"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22630"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5aizc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_25aics_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2476"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALTATr" fast="false" reversible="true" name="Maltose O-acetyltransferase" metaid="R_MALTATr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALTATr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTATr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALTACETYLTRAN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.79"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01556"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06251"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101351"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01133"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acmalt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0459"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHBSH" fast="false" reversible="false" name="2,3-dihydroxybenzoylserine hydrolase" metaid="R_DHBSH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHBSH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHBSH"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97370"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08328"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23dhbzs_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23dhb_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_MALDDH" fast="false" reversible="false" name="Malate decarboxylating oxidoreductase (decarboxylating)" metaid="R_MALDDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALDDH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALDDH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:1.1.1.83-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.83"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00215"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101339"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18366"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18365"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18368"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18367"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/744"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00160"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mal__D_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_b1800"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE2tex" fast="false" reversible="true" name="Iron (II) transport via diffusion (extracellular to periplasm)" metaid="R_FE2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE2tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE2tex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99505"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28488"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28487"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28489"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28486"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08476"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08475"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13286"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10963"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe2_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NMNtex" fast="false" reversible="true" name="NMN transport via diffusion (extracellular to periplasm)" metaid="R_NMNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NMNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NMNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101972"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28485"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28483"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28482"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28484"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08997"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08995"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10181"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nmn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nmn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ENTERES" fast="false" reversible="false" name="Enterochelin Esterase" metaid="R_ENTERES" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ENTERES"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ENTERES"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1661"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97934"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28021"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28019"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28020"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28018"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08421"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_enter_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="3" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23dhbzs_c" stoichiometry="3" constant="true"/> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0585"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NO2tex" fast="false" reversible="true" name="Nitrite transport via diffusion (extracellular to periplasm)" metaid="R_NO2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NO2tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO2tex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-137"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101912"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28983"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28986"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28984"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28985"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10823"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08999"/> </rdf:Bag> </bqbiol:is> </rdf:Description> 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<rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TRSARr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5289"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.60"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01745"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100682"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18846"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18845"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18847"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18848"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01280"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2h3oppan_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference 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constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3177"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEOXAMUtex" fast="false" reversible="false" name="Ferroxamine (minus Fe3) secretion (to extracellular)" metaid="R_FEOXAMUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEOXAMUtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEOXAMUtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99554"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08515"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference 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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MTHFD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MTHFD"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01220"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101749"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22814"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22813"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22815"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22812"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0529"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LYXI" fast="false" reversible="false" name="Lyxose isomerase" metaid="R_LYXI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LYXI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYXI"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01906"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138561"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01394"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lyx__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_xylu__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3903"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_BUTt2rpp" fast="false" reversible="true" name="Butyrate transport via proton symport, reversible (periplasm)" metaid="R_BUTt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BUTt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BUTt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96353"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_but_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_but_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2223"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CADVtpp" fast="false" reversible="false" name="Lysine/Cadaverine antiporter (periplasm)" metaid="R_CADVtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CADVtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CADVtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96445"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08187"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10148"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_15dap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lys__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_15dap_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4132"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_QULNS" fast="false" reversible="false" name="Quinolinate synthase" metaid="R_QULNS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_QULNS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/QULNS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:QUINOLINATE-SYNTHA-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.72"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04292"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103400"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25889"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25891"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25890"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25888"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02988"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_iasp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_quln_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0750"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_23CAMPtex" fast="false" reversible="true" name="23cAMP transport via diffusion (extracellular to periplasm)" metaid="R_23CAMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_23CAMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/23CAMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94718"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07925"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23camp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23camp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_23CCMPtex" fast="false" reversible="true" name="23cCMP transport via diffusion (extracellular to periplasm)" metaid="R_23CCMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_23CCMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/23CCMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94720"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07926"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23ccmp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23ccmp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_23CUMPtex" fast="false" reversible="true" name="23cUMP transport via diffusion (extracellular to periplasm)" metaid="R_23CUMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_23CUMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/23CUMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94726"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07928"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23cump_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23cump_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_23CGMPtex" fast="false" reversible="true" name="23cGMP transport via diffusion (extracellular to periplasm)" metaid="R_23CGMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_23CGMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/23CGMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94721"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07927"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23cgmp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23cgmp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3AMPtex" fast="false" reversible="true" name="3AMP transport via diffusion (extracellular to periplasm)" metaid="R_3AMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3AMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3AMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94857"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07973"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3amp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3amp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3CMPtex" fast="false" reversible="true" name="3CMP transport via diffusion (extracellular to periplasm)" metaid="R_3CMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3CMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3CMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94861"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07974"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3cmp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3cmp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LADGMDH" fast="false" reversible="false" name="L-alanyl-gamma-D-glutamyl-meso-diaminopimelate hydrolase" metaid="R_LADGMDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LADGMDH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LADGMDH"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101002"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08773"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDgluMdap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_26dap__M_c" stoichiometry="1" constant="true"/> <speciesReference species="M_LalaDglu_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1326"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALKP" fast="false" reversible="false" name="Alkaline phosphatase" metaid="R_ALKP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALKP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALKP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-7249"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01010"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95764"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51731"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51728"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51730"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51729"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00743"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dha_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2690"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GDPtex" fast="false" reversible="true" name="GDP transport via diffusion (extracellular to periplasm)" metaid="R_GDPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GDPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GDPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100096"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-111812"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08600"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09815"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gdp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gdp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_cobalt2_e" fast="false" reversible="true" name="Co2+ exchange" metaid="R_EX_cobalt2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cobalt2_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cobalt2_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-141A"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96821"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28579"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28580"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28581"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28578"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12148"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08241"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08242"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10474"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cobalt2_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ALAGLUE" fast="false" reversible="true" name="L-alanyl-gamma-glutamate epimerase" metaid="R_ALAGLUE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALAGLUE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALAGLUE"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5228"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.1.20"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10938"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95690"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28394"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28395"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28396"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28397"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7810"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08100"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDglu_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaLglu_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1325"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEENTERtpp" fast="false" reversible="false" name="Enterochelin transport (secretion)" metaid="R_FEENTERtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEENTERtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEENTERtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99550"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29435"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29438"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29437"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29436"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08508"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_enter_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_enter_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0591"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TMAtex" fast="false" reversible="true" name="Trimethylamine transport via diffusion (extracellular to periplasm)" metaid="R_TMAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TMAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TMAtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104884"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09318"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tma_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tma_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_pheme_e" fast="false" reversible="false" name="Protoheme exchange" metaid="R_EX_pheme_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_pheme_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pheme_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102625"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-917892"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pheme_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_TMAOtex" fast="false" reversible="true" name="Trimethylamine N-oxide transport via diffusion (extracellular to periplasm)" metaid="R_TMAOtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TMAOtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TMAOtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104882"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09317"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tmao_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tmao_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TREtex" fast="false" reversible="true" name="Trehalose transport via diffusion (extracellular to periplasm)" metaid="R_TREtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TREtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TREtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104933"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17631"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17632"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17630"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17629"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09323"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tre_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tre_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_L_LACD3" fast="false" reversible="false" name="L-Lactate dehydrogenase (menaquinone)" metaid="R_L_LACD3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_L_LACD3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/L_LACD3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.2.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101275"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08793"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lac__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mql8_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_b0306"/> <fbc:geneProductRef fbc:geneProduct="G_b0308"/> <fbc:geneProductRef fbc:geneProduct="G_b0307"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3605"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEENTERtex" fast="false" reversible="false" name="Enterochelin transport (secretion periplasm)" metaid="R_FEENTERtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEENTERtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEENTERtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99548"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08506"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_enter_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_enter_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE3HOXUtpp" fast="false" reversible="false" name="Fe(III)hydroxamate unloaded secretion (extracellular)" metaid="R_FE3HOXUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3HOXUtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3HOXUtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99518"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08490"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3hox_un_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe3hox_un_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_FEOXAMUtpp" fast="false" reversible="false" name="Ferroxamine (minus Fe3) secretion (to periplasm)" metaid="R_FEOXAMUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEOXAMUtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEOXAMUtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99555"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08516"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_feoxam_un_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_feoxam_un_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_FECRMUtpp" fast="false" reversible="false" name="Ferrichrome (minus Fe) secretion (to periplasm)" metaid="R_FECRMUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FECRMUtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FECRMUtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99534"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08500"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fecrm_un_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fecrm_un_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_FE3HOXR2" fast="false" reversible="false" name="Fe(III)hydroxamate reductase" metaid="R_FE3HOXR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3HOXR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3HOXR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99515"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08486"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3hox_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe3hox_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_L_LACD2" fast="false" reversible="false" name="L-Lactate dehydrogenase (ubiquinone)" metaid="R_L_LACD2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_L_LACD2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/L_LACD2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.2.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101273"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08792"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lac__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0308"/> <fbc:geneProductRef fbc:geneProduct="G_b0306"/> <fbc:geneProductRef fbc:geneProduct="G_b0307"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3605"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACACT6r" fast="false" reversible="true" name="Acetyl-CoA C-acyltransferase (dodecanoyl-CoA) (r)" metaid="R_ACACT6r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACACT6r"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACACT6r"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14268"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.9"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03858"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95201"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-77271"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-77271"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-77271"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-77271"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-77271"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-77271"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-77271"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-77271"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77271"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-77271"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-77271"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31093"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31094"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31092"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31091"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn06510"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ddcacoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3otdcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2342"/> <fbc:geneProductRef fbc:geneProduct="G_b3845"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TRPtex" fast="false" reversible="true" name="L-tryptophan transport via diffusion (extracellular to periplasm)" metaid="R_TRPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TRPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TRPtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-449"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104949"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/14017"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13425"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09327"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05222"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_trp__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_trp__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PTRCt2pp" fast="false" reversible="false" name="Putrescine transport in via proton symport" metaid="R_PTRCt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PTRCt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PTRCt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-69"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103340"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28891"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28892"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28894"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28893"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05687"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09215"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ptrc_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0692"/> <fbc:geneProductRef fbc:geneProduct="G_b1296"/> <fbc:geneProductRef fbc:geneProduct="G_b2014"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GGGABAH" fast="false" reversible="false" name="Gamma-glutamyl-gamma-aminobutyric acid hydrolase" metaid="R_GGGABAH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GGGABAH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GGGABAH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-3942"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.94"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07419"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100114"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19740"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19739"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19738"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19737"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05128"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gg4abut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4abut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1298"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PNTOtex" fast="false" reversible="true" name="Pantothenate transport via diffusion (extracellular to periplasm)" metaid="R_PNTOtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PNTOtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PNTOtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103051"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34978"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34975"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34976"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34977"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09166"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pnto__R_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pnto__R_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRULYSK" fast="false" reversible="false" name="Fructoselysine Kinase" metaid="R_FRULYSK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRULYSK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRULYSK"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99655"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08532"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_frulys_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_frulysp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3374"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FDMO6" fast="false" reversible="false" name="FMNH2-dependent monooxygenase (sulfoacetate)" metaid="R_FDMO6" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FDMO6"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FDMO6"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99495"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29312"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29311"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29314"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29313"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08471"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fmnh2_c" stoichiometry="1" 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<fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TYRtex" fast="false" reversible="true" name="L-tyrosine transport via diffusion (extracellular to periplasm)" metaid="R_TYRtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TYRtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TYRtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-446"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105002"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13471"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09339"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10974"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tyr__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tyr__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_URAtex" fast="false" reversible="true" name="Uracil transport via diffusion (extracellular to periplasm)" metaid="R_URAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_URAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URAtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-560"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105147"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27320"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28622"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27319"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27318"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12300"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10993"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09366"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ura_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ura_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_UREAtex" fast="false" reversible="true" name="Urea transport via diffusion (extracellular to periplasm)" metaid="R_UREAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF 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<bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URItex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105165"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10987"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09372"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_uri_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_uri_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0411"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SULFACabcpp" fast="false" reversible="false" name="Sulfoacetate transport via ABC system (periplasm)" metaid="R_SULFACabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SULFACabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SULFACabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104645"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05656"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09277"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sulfac_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" 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<rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ETHSO3tex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97978"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08426"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ethso3_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ethso3_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_BUTSO3tex" fast="false" reversible="true" name="Butanesulfonate transport via diffusion (extracellular to periplasm)" metaid="R_BUTSO3tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BUTSO3tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BUTSO3tex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96351"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08182"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_butso3_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_butso3_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPOtex" fast="false" reversible="true" name="Lipoate transport via diffusion (extracellular to periplasm)" metaid="R_LIPOtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPOtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPOtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-278"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101092"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29755"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29758"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29756"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29757"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lipoate_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_lipoate_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYANSTpp" fast="false" reversible="false" name="Cyanide sulfurtransferase (periplasmic)" metaid="R_CYANSTpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF 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<fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALBDtex" fast="false" reversible="true" name="Beta D-galactose transport via diffusion (extracellular to periplasm)" metaid="R_GALBDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALBDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALBDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99953"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08574"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gal_bD_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gal_bD_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPAHT2ex" fast="false" reversible="false" name="Core oligosaccharide lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" metaid="R_LIPAHT2ex" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPAHT2ex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPAHT2ex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101078"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_colipa_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_e" stoichiometry="1" constant="true"/> <speciesReference species="M_hacolipa_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0622"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DATPHs" fast="false" reversible="false" name="DATP amine hydrolysis (spontaneous)" metaid="R_DATPHs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DATPHs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DATPHs"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97174"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08313"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_datp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ditp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLCTR1" fast="false" reversible="false" name="Glucosyltransferase I (LPS core synthesis)" metaid="R_GLCTR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCTR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCTR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143137"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_icolipa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gicolipa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3631"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPAabcpp" fast="false" reversible="false" name="Lipid A transport via ABC system (periplasm)" metaid="R_LIPAabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPAabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPAabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101082"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35251#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35254#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35253#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35252#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08787"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lipa_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_lipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPAHTex" fast="false" reversible="false" name="Lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" metaid="R_LIPAHTex" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPAHTex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPAHTex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101079"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08790"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_e" stoichiometry="1" constant="true"/> <speciesReference species="M_lipa_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_e" stoichiometry="1" constant="true"/> <speciesReference species="M_halipa_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0622"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPACabcpp" fast="false" reversible="false" name="Lipid (cold) A transport via ABC system (periplasm)" metaid="R_LIPACabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPACabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPACabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101077"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08788"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lipa_cold_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_lipa_cold_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ECAP1pp" fast="false" reversible="false" name="Enterobacterial common antigen polymerase (periplasm)" metaid="R_ECAP1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ECAP1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ECAP1pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97874"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_unagamuf_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_eca2und_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3785"/> <fbc:geneProductRef fbc:geneProduct="G_b3793"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PTRCtex" fast="false" reversible="true" name="Putrescine transport via diffusion (extracellular to periplasm)" metaid="R_PTRCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PTRCtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PTRCtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103339"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09216"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13393"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ptrc_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ptrc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_UDCPDPpp" fast="false" reversible="false" name="Undecaprenyl-diphosphatase (periplasm)" metaid="R_UDCPDPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDCPDPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDCPDPpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105042"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17069"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17070"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17072"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17071"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/5225"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> <fbc:geneProductRef fbc:geneProduct="G_b3057"/> <fbc:geneProductRef fbc:geneProduct="G_b0841"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GGGABADr" fast="false" reversible="true" name="Gamma-glutamyl-gamma aminobutyric acid dehydrogenase" metaid="R_GGGABADr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GGGABADr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GGGABADr"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07418"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100113"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28410"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28412"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28411"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28413"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05127"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ggbutal_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_gg4abut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1300"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_mso3_e" fast="false" reversible="false" name="Methanesulfonate exchange" metaid="R_EX_mso3_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_mso3_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mso3_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101742"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08960"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mso3_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_23camp_e" fast="false" reversible="false" name="2',3'-Cyclic AMP exchange" metaid="R_EX_23camp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_23camp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_23camp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94718"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07925"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23camp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_23cgmp_e" fast="false" reversible="false" name="2',3'-Cyclic GMP exchange" metaid="R_EX_23cgmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_23cgmp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_23cgmp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94721"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07927"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23cgmp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_23cump_e" fast="false" reversible="false" name="2',3'-Cyclic UMP exchange" metaid="R_EX_23cump_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_23cump_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_23cump_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94726"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07928"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23cump_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ECAP2pp" fast="false" reversible="false" name="Enterobacterial common antigen polymerase (periplasm)" metaid="R_ECAP2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ECAP2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ECAP2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142826"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_eca2und_p" stoichiometry="1" constant="true"/> <speciesReference species="M_unagamuf_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_eca3und_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3785"/> <fbc:geneProductRef fbc:geneProduct="G_b3793"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ECA4OALpp" fast="false" reversible="false" name="Enterobacterial common antigen (x4) O-antigen ligase (periplasm)" metaid="R_ECA4OALpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ECA4OALpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ECA4OALpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142825"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_colipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_eca4und_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_eca4colipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3622"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE3Ri" fast="false" reversible="false" name="Fe(III) reduction" metaid="R_FE3Ri" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3Ri"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3Ri"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99524"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30155"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30157"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30158"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30156"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08491"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe3_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3844"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE3HOXR3" fast="false" reversible="false" name="Fe(III)hydroxamate reductase" metaid="R_FE3HOXR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3HOXR3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3HOXR3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99516"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08487"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3hox_c" stoichiometry="2" constant="true"/> <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe3hox_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_FEENTERR1" fast="false" reversible="false" name="Fe-enterobactin reduction (Fe(III)-unloading)" metaid="R_FEENTERR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEENTERR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEENTERR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99543"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_feenter_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_enter_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_NODOy" fast="false" reversible="false" name="Nitric oxide dioxygenase" metaid="R_NODOy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NODOy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NODOy"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.12.17"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05725"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101997"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19465"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19467"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19466"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19468"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no_c" stoichiometry="2" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no3_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2552"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PYRtex" fast="false" reversible="true" name="Pyruvate transport via diffusion (extracellular to periplasm)" metaid="R_PYRtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PYRtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYRtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-506"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-570"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103384"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12168"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10929"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09218"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pyr_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pyr_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALM2pp" fast="false" reversible="false" name="Aldose-1-epimerase" metaid="R_GALM2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALM2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALM2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ALDOSE1EPIM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99987"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28677"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28675"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28676"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28678"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7775"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08582"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gal_bD_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gal_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0756"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CU1abcpp" fast="false" reversible="false" name="Copper (Cu +1) ABC transporter (periplasm)" metaid="R_CU1abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CU1abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CU1abcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-207"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14455"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.54"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96949"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25795#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25794#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25793#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25792#1"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12237#1"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cu_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_cu_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0484"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HG2abcpp" fast="false" reversible="false" name="Mercury (Hg+2) ABC transporter (periplasm)" metaid="R_HG2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HG2abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HG2abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100623"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10343"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08715"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hg2_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_hg2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3469"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEENTERR3" fast="false" reversible="false" name="Fe-enterobactin reduction (Fe(III)-unloading)" metaid="R_FEENTERR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEENTERR3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEENTERR3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99545"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_feenter_c" stoichiometry="2" constant="true"/> <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_enter_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_SULFACtex" fast="false" reversible="true" name="Sulfoaceate transport via diffusion (extracellular to periplasm)" metaid="R_SULFACtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SULFACtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SULFACtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104646"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09278"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sulfac_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_sulfac_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_sulfac_e" fast="false" reversible="false" name="Sulfoacetate exchange" metaid="R_EX_sulfac_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_sulfac_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_sulfac_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104646"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09278"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sulfac_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_butso3_e" fast="false" reversible="false" name="Butanesulfonate exchange" metaid="R_EX_butso3_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_butso3_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_butso3_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96351"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08182"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_butso3_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GLCTR3" fast="false" reversible="false" name="Glucosyltransferase III (LPS core synthesis)" metaid="R_GLCTR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCTR3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCTR3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143139"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08620"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ggagicolipa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gggagicolipa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3626"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HEPT4" fast="false" reversible="false" name="Heptosyltransferase IV (LPS core synthesis)" metaid="R_HEPT4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HEPT4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HEPT4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.56"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100607"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08713"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adphep_LD_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gggagicolipa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_colipa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3623"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_ethso3_e" fast="false" reversible="false" name="Ethanesulfonate exchange" metaid="R_EX_ethso3_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ethso3_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ethso3_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97978"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08426"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ethso3_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_DSERtex" fast="false" reversible="true" name="D-serine transport via diffusion (extracellular to periplasm)" metaid="R_DSERtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DSERtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DSERtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-495"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97799"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29457"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29456"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29455"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29458"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08373"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10965"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ser__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ser__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LA4NTpp" fast="false" reversible="false" name="4-amino-4-deoxy-L-arabinotransferase (LPS lipid A modification, periplasmic face of membrane))" metaid="R_LA4NTpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LA4NTpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LA4NTpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100954"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08772"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_colipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_uLa4n_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acolipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2257"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NODOx" fast="false" reversible="false" name="Nitric oxide dioxygenase" metaid="R_NODOx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NODOx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NODOx"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.12.17"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05724"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101996"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19472"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19469"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19470"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19471"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no_c" stoichiometry="2" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no3_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2552"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SERtex" fast="false" reversible="true" name="L-serine transport via diffusion (extracellular to periplasm)" metaid="R_SERtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SERtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SERtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-8932980"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-8932980"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35033"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35034"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35032"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35031"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13463"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13973"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09248"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10999"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13110"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ser__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ser__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NOtex" fast="false" reversible="true" name="Nitric oxide transport via diffusion (extracellular to periplasm)" metaid="R_NOtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NOtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NOtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101998"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_no_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_no_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NOtpp" fast="false" reversible="true" name="NO transport (diffusion)" metaid="R_NOtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NOtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NOtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101998"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_no_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_no_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NHFRBO" fast="false" reversible="false" name="NADH:flavorubredoxin oxidoreductase" metaid="R_NHFRBO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NHFRBO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NHFRBO"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14138"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.7.1.14"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02492"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101954"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29610"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29609"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29607"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29608"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_n2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2711"/> <fbc:geneProductRef fbc:geneProduct="G_b2710"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_N2Otpp" fast="false" reversible="true" name="Nitrious oxide transport (diffusion)" metaid="R_N2Otpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_N2Otpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/N2Otpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101797"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08966"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08967"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_n2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_n2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_N2Otex" fast="false" reversible="true" name="Nitrious oxide transport via diffusion (extracellular to periplasm)" metaid="R_N2Otex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_N2Otex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/N2Otex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101797"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08966"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08967"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_n2o_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_n2o_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CRNt8pp" fast="false" reversible="false" name="L-carnitine/D-carnitine antiporter (periplasm)" metaid="R_CRNt8pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNt8pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNt8pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96909"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08264"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_crn__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_crn_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_crn__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0040"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CRNt2rpp" fast="false" reversible="true" name="L-carnitine outward transport (H+ antiport)" metaid="R_CRNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96907"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08262"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12605"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_crn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4111"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CRNDt2rpp" fast="false" reversible="true" name="D-carnitine outward transport (H+ antiport)" metaid="R_CRNDt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNDt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNDt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96903"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08261"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_crn__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_crn__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4111"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CTBTt2rpp" fast="false" reversible="true" name="Cronobetaine outward transport (H+ antiport)" metaid="R_CTBTt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CTBTt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CTBTt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96939"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ctbt_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ctbt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4111"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_42A12BOOXpp" fast="false" reversible="false" name="4-(2-Aminoethyl)-1,2-benzenediol:oxygen oxidoreductase(deaminating)(flavin-containing)" metaid="R_42A12BOOXpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_42A12BOOXpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/42A12BOOXpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN6666-4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.3.4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.9.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.3.21"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.99.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04300"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94989"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27949"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27947"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27946"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27948"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/4000"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02993"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dopa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_34dhpac_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1386"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TYROXDApp" fast="false" reversible="false" name="Tyramine:oxygen oxidoreductase(deaminating)(flavin-containing) (periplasm)" metaid="R_TYROXDApp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TYROXDApp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TYROXDApp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-5821"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.3.4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.3.22"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.9.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.3.21"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.99.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02382"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104996"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-141202"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-141202"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-141202"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-141202"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-141202"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-141202"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-141202"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-141202"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-141202"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-5696146"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-141202"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30593"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30594"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30592"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30591"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2326"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01715"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_tym_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4hoxpacd_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1386"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PACALDt2rpp" fast="false" reversible="true" name="Phenylacetaldehyde reversible transport via proton symport (periplasm)" metaid="R_PACALDt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PACALDt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PACALDt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102313"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09060"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11408"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pacald_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pacald_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_PEAMNtex" fast="false" reversible="true" name="Phenethylamine transport via diffusion (extracellular to periplasm)" metaid="R_PEAMNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PEAMNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PEAMNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102462"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29745"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29744"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29746"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29743"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11405"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09080"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_peamn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_peamn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PACALDtex" fast="false" reversible="true" name="Phenethylacetaldehyde transport via diffusion (extracellular to periplasm)" metaid="R_PACALDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PACALDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PACALDtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-284"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102312"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09061"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13374"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13373"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pacald_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pacald_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPOt2pp" fast="false" reversible="false" name="Lipoate transport via proton symport (periplasm)" metaid="R_LIPOt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPOt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPOt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101091"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lipoate_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lipoate_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_AGM4PA" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase" metaid="R_AGM4PA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGM4PA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM4PA"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95546"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08076"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDgluMdapDala_c" stoichiometry="1" constant="true"/> <speciesReference species="M_anhgm_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0110"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RNDR3b" fast="false" reversible="false" name="Ribonucleoside-diphosphate reductase (CDP) (glutaredoxin)" metaid="R_RNDR3b" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RNDR3b"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNDR3b"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104065"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09233"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_grxrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dcdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_grxox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0849"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3610"/> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1064"/> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1654"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_RNDR4b" fast="false" reversible="false" name="Ribonucleoside-diphosphate reductase (UDP) (glutaredoxin)" metaid="R_RNDR4b" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RNDR4b"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNDR4b"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104067"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09234"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_grxrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dudp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_grxox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0849"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3610"/> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1654"/> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1064"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACGAL1Ptex" fast="false" reversible="true" name="N-acetyl-D-galactosamine 1-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_ACGAL1Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACGAL1Ptex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAL1Ptex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95234"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08036"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgal1p_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgal1p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACGALtex" fast="false" reversible="true" name="N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)" metaid="R_ACGALtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACGALtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGALtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95244"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08037"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgal_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgal_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLCUR1Ptex" fast="false" reversible="true" name="D-glucuronate 1-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_GLCUR1Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCUR1Ptex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCUR1Ptex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100231"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08621"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glcur1p_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glcur1p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_UDPGLCURtex" fast="false" reversible="true" name="UDP-D-glucuronate transport via diffusion (extracellular to periplasm)" metaid="R_UDPGLCURtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDPGLCURtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGLCURtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105066"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09352"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udpglcur_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_udpglcur_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_UDPGALPpp" fast="false" reversible="false" name="UDPgalactose pyrophosphohydrolase" metaid="R_UDPGALPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDPGALPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGALPpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.45"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105060"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09348"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udpgal_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gal1p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UACGAMPpp" fast="false" reversible="false" name="UDP-N-acetyl-D-glucosamine pyrophosphohydrolase (periplasm)" metaid="R_UACGAMPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UACGAMPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UACGAMPpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.45"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105020"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09341"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_uacgam_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam1p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UACGALPpp" fast="false" reversible="false" name="UDP-N-acetyl-D-galactosamine pyrophosphohydrolase (periplasm)" metaid="R_UACGALPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UACGALPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UACGALPpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.45"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105017"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09340"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udpacgal_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgal1p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UGLCURPpp" fast="false" reversible="false" name="UDP-D-glucuronate pyrophosphohydrolase (periplasm)" metaid="R_UGLCURPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UGLCURPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UGLCURPpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105055"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29562"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29559"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29561"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29560"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09355"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udpglcur_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glcur1p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEROpp" fast="false" reversible="false" name="Ferroxidase" metaid="R_FEROpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEROpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEROpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1483"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.16.3.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00078"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99561"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11437"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11149"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11438"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11151"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11439"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11436"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11150"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11148"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/665"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00056"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe2_p" stoichiometry="4" constant="true"/> <speciesReference species="M_h_p" stoichiometry="4" constant="true"/> <speciesReference species="M_o2_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe3_p" stoichiometry="4" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0123"/> <fbc:geneProductRef fbc:geneProduct="G_b3336"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ISETACabcpp" fast="false" reversible="false" name="Isethionate transport via ABC system (periplasm)" metaid="R_ISETACabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ISETACabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ISETACabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100880"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08758"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05594"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_isetac_p" 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_isetac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0365"/> <fbc:geneProductRef fbc:geneProduct="G_b0366"/> <fbc:geneProductRef fbc:geneProduct="G_b0367"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0933"/> <fbc:geneProductRef fbc:geneProduct="G_b0934"/> <fbc:geneProductRef fbc:geneProduct="G_b0936"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ISETACtex" fast="false" reversible="true" name="Isethionate transport via diffusion (extracellular to periplasm)" metaid="R_ISETACtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ISETACtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ISETACtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100881"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08759"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_isetac_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_isetac_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GUR1PPpp" fast="false" reversible="false" name="Glucuronate 1-phosphate phosphatase (periplasm)" metaid="R_GUR1PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GUR1PPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GUR1PPpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100480"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08684"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glcur1p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glcur_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_UDPGtex" fast="false" reversible="true" name="UDPglucose transport via diffusion (extracellular to periplasm)" metaid="R_UDPGtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDPGtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143086"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11025"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09353"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udpg_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_udpg_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACGAL1PPpp" fast="false" reversible="false" name="N-acetyl-D-galactosamine 1-phosphatase (periplasm)" metaid="R_ACGAL1PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACGAL1PPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAL1PPpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.10"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95233"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08035"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgal1p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgal_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_UDPGALtex" fast="false" reversible="true" name="UDPgalactose transport via diffusion (extracellular to periplasm)" metaid="R_UDPGALtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDPGALtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGALtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105061"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09349"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13413"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udpgal_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_udpgal_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACGAM1Ptex" fast="false" reversible="true" name="N-acetyl-D-glucosamine 1-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_ACGAM1Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACGAM1Ptex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAM1Ptex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95246"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08039"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgam1p_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam1p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_UACGAMtex" fast="false" reversible="true" name="UDP-N-acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)" metaid="R_UACGAMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UACGAMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UACGAMtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105021"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-742354"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09342"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_uacgam_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_uacgam_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_UDPACGALtex" fast="false" reversible="true" name="UDP-N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)" metaid="R_UDPACGALtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDPACGALtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPACGALtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105046"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09347"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udpacgal_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_udpacgal_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_AM4PCP" fast="false" reversible="false" name="Anhydrous-N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" metaid="R_AM4PCP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AM4PCP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AM4PCP"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95794"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08125"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhm4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_anhm3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1192"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AM3PA" fast="false" reversible="false" name="Anhydrous-N-Acetylmuramyl-tripeptide amidase" metaid="R_AM3PA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AM3PA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AM3PA"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95792"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08123"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhm3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDgluMdap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_anhm_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0110"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UM4PCP" fast="false" reversible="false" name="UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine L,D-carboxypeptidase" metaid="R_UM4PCP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UM4PCP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UM4PCP"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105116"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_um4p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ugmd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1192"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CBLAT" fast="false" reversible="true" name="Cob(I)alamin adenosyltransferase" metaid="R_CBLAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CBLAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CBLAT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:COBALADENOSYLTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.17"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01492"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96476"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cbl1_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adocbl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1270"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTRIR4pp" fast="false" reversible="false" name="Nitrite Reductase (Menaquinole-8, periplasm)" metaid="R_NTRIR4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTRIR4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTRIR4pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102065"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29164"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29166"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29165"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29163"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09019"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="3" constant="true"/> <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_p" stoichiometry="2" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="3" constant="true"/> <speciesReference species="M_nh4_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4070"/> <fbc:geneProductRef fbc:geneProduct="G_b4071"/> <fbc:geneProductRef fbc:geneProduct="G_b4072"/> <fbc:geneProductRef fbc:geneProduct="G_b4073"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTRIR3pp" fast="false" reversible="false" name="Nitrite Reductase (Ubiquinole-8, periplasm)" metaid="R_NTRIR3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTRIR3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTRIR3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102064"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29157"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29155"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29156"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29158"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09018"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="3" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_p" stoichiometry="2" constant="true"/> <speciesReference species="M_nh4_p" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="3" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4070"/> <fbc:geneProductRef fbc:geneProduct="G_b4071"/> <fbc:geneProductRef fbc:geneProduct="G_b4072"/> <fbc:geneProductRef fbc:geneProduct="G_b4073"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_INOSTt4pp" fast="false" reversible="false" name="Na+/myo-inositol symporter (periplasm)" metaid="R_INOSTt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_INOSTt4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INOSTt4pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100840"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08752"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_inost_p" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_inost_c" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3679"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PHEMEtiex" fast="false" reversible="false" name="Protoheme transport irreversible out via diffusion (periplasm to extracellular)" metaid="R_PHEMEtiex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PHEMEtiex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PHEMEtiex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102625"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-917892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-917892"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pheme_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pheme_e" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_AGM3PA" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase" metaid="R_AGM3PA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGM3PA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM3PA"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95543"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08073"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDgluMdap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_anhgm_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0110"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYANtex" fast="false" reversible="true" name="Cyanide transport via diffusion (extracellular to periplasm)" metaid="R_CYANtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYANtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYANtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96957"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08276"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cyan_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cyan_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SO3tex" fast="false" reversible="true" name="Sulfite transport via diffusion (extracellular to periplasm)" metaid="R_SO3tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SO3tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SO3tex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104460"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12453"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09260"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_so3_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_so3_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TCYNTtex" fast="false" reversible="true" name="Thiocyanate transport via diffusion (extracellular to periplasm)" metaid="R_TCYNTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TCYNTtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TCYNTtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104749"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09287"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tcynt_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tcynt_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACANTHAT" fast="false" reversible="false" name="Acetyl-CoA:anthranilate acetyltransferase" metaid="R_ACANTHAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACANTHAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACANTHAT"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95213"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28551"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28550"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28553"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28552"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08034"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_anth_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acanth_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1463"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_METSOX2abcpp" fast="false" reversible="false" name="L-methionine R-oxide transport via ABC system (periplasm)" metaid="R_METSOX2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METSOX2abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METSOX2abcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-7185"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138592"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08916"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_metsox_R__L_p" 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_metsox_R__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_METSOX1tex" fast="false" reversible="true" name="L-methionine S-oxide diffusion (extracellular)" metaid="R_METSOX1tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METSOX1tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METSOX1tex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101483"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08915"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_metsox_S__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_metsox_S__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_METSOX2tex" fast="false" reversible="true" name="L-methionine R-oxide diffusion (extracellular)" metaid="R_METSOX2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METSOX2tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METSOX2tex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138593"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08917"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_metsox_R__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_metsox_R__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3UMPtex" fast="false" reversible="true" name="3UMP transport via diffusion (extracellular to periplasm)" metaid="R_3UMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3UMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3UMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94983"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08005"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ump_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3ump_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MSO3abcpp" fast="false" reversible="false" name="Methanesulfonate transport via ABC system (periplasm)" metaid="R_MSO3abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MSO3abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MSO3abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101741"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05621"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08959"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mso3_p" 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_mso3_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0933"/> <fbc:geneProductRef fbc:geneProduct="G_b0936"/> <fbc:geneProductRef fbc:geneProduct="G_b0934"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_MSO3tex" fast="false" reversible="true" name="Methanesulfonate transport via diffusion (extracellular to periplasm)" metaid="R_MSO3tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MSO3tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MSO3tex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101742"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08960"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mso3_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mso3_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FECRMR1" fast="false" reversible="false" name="Ferrichrome reductase" metaid="R_FECRMR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FECRMR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FECRMR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99530"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08495"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fecrm_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fecrm_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_FECRMR2" fast="false" reversible="false" name="Ferrichrome reductase" metaid="R_FECRMR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FECRMR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FECRMR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99531"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08496"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fecrm_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fecrm_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_TDP" fast="false" reversible="false" name="Thiamin pyrophosphatase" metaid="R_TDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TDP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TDP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-3542"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.15"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00615"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104756"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27998"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28000"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28001"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27999"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00436"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thmpp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thmmp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1134"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3PEPTabcpp" fast="false" reversible="false" name="Tripeptide (LalaDgluMdap) transport via ABC system (periplasm)" metaid="R_3PEPTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3PEPTabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3PEPTabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94970"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08003"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDgluMdap_p" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDgluMdap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1245"/> <fbc:geneProductRef fbc:geneProduct="G_b1247"/> <fbc:geneProductRef fbc:geneProduct="G_b1244"/> <fbc:geneProductRef fbc:geneProduct="G_b1329"/> <fbc:geneProductRef fbc:geneProduct="G_b1246"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2177"/> <fbc:geneProductRef fbc:geneProduct="G_b2180"/> <fbc:geneProductRef fbc:geneProduct="G_b2178"/> <fbc:geneProductRef fbc:geneProduct="G_b2179"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1245"/> <fbc:geneProductRef fbc:geneProduct="G_b1247"/> <fbc:geneProductRef fbc:geneProduct="G_b1246"/> <fbc:geneProductRef fbc:geneProduct="G_b1244"/> <fbc:geneProductRef fbc:geneProduct="G_b1243"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_4PEPTabcpp" fast="false" reversible="false" name="Tetrapeptide (LalaDgluMdapDala) transport via ABC system (periplasm)" metaid="R_4PEPTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_4PEPTabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4PEPTabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95050"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08008"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDgluMdapDala_p" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDgluMdapDala_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1243"/> <fbc:geneProductRef fbc:geneProduct="G_b1247"/> <fbc:geneProductRef fbc:geneProduct="G_b1244"/> <fbc:geneProductRef fbc:geneProduct="G_b1245"/> <fbc:geneProductRef fbc:geneProduct="G_b1246"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2177"/> <fbc:geneProductRef fbc:geneProduct="G_b2180"/> <fbc:geneProductRef fbc:geneProduct="G_b2178"/> <fbc:geneProductRef fbc:geneProduct="G_b2179"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3GMPtex" fast="false" reversible="true" name="3GMP transport via diffusion (extracellular to periplasm)" metaid="R_3GMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3GMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3GMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94868"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07975"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3gmp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3gmp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FALDtpp" fast="false" reversible="true" name="Formaldehyde transport via diffusion (periplasm)" metaid="R_FALDtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FALDtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FALDtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99238"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08461"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08462"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fald_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fald_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_tym_e" fast="false" reversible="false" name="Tyramine exchange" metaid="R_EX_tym_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_tym_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tym_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104985"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09335"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tym_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_AGM3Pt2pp" fast="false" reversible="false" name="GlcNAc-anhMurNAc tripeptide transport in via proton symport (periplasm)" metaid="R_AGM3Pt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGM3Pt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM3Pt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95545"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08075"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_anhgm3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0433"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SO4tex" fast="false" reversible="true" name="Sulfate transport via diffusion (extracellular to periplasm)" metaid="R_SO4tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SO4tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SO4tex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104469"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-8875871"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-8875871"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34983"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34984"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34986"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34985"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09261"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05238"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_so4_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_so4_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGM4Pt2pp" fast="false" reversible="false" name="GlcNAc-anhMurNAc tetrapeptide transport in via proton symport (periplasm)" metaid="R_AGM4Pt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGM4Pt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM4Pt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95549"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08079"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm4p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_anhgm4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0433"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGMt2pp" fast="false" reversible="false" name="GlcNAc-anhMurNAc transport in via proton symport (periplasm)" metaid="R_AGMt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGMt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGMt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95555"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08081"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_anhgm_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0433"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FECRMexs" fast="false" reversible="false" name="Ferrichrome Fe(III)-loading reaction (spontaneous)" metaid="R_FECRMexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FECRMexs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FECRMexs"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99536"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08494"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/> <speciesReference species="M_fecrm_un_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fecrm_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARBTNR1" fast="false" reversible="false" name="Aerobactin reductase" metaid="R_ARBTNR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBTNR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95924"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08145"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbtn_fe3_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arbtn_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_ARBTNR2" fast="false" reversible="false" name="Aerobactin reductase" metaid="R_ARBTNR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBTNR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95925"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08146"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbtn_fe3_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arbtn_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_METSOXR1" fast="false" reversible="false" name="L-methionine-S-oxide reductase" metaid="R_METSOXR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METSOXR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METSOXR1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.4.14"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.4.13"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02025"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101484"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn06077"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08918"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_metsox_S__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2582"/> <fbc:geneProductRef fbc:geneProduct="G_b4219"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3781"/> <fbc:geneProductRef fbc:geneProduct="G_b4219"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3551"/> <fbc:geneProductRef fbc:geneProduct="G_b2582"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3551"/> <fbc:geneProductRef fbc:geneProduct="G_b3781"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_METSOXR2" fast="false" reversible="false" name="L-methionine-R-sulfoxide reductase" metaid="R_METSOXR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METSOXR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METSOXR2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:1.8.4.14-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.4.14"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07608"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138594"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08919"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07439"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_metsox_R__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2582"/> <fbc:geneProductRef fbc:geneProduct="G_b1778"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3781"/> <fbc:geneProductRef fbc:geneProduct="G_b1778"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1832"/> <fbc:geneProductRef fbc:geneProduct="G_b3781"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1832"/> <fbc:geneProductRef fbc:geneProduct="G_b2582"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DAPAL" fast="false" reversible="false" name="2,3-diaminopropionate amonnia lyase" metaid="R_DAPAL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAPAL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAPAL"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:4.3.1.15-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.15"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00195"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97138"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22085"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22087"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22084"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22086"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/741"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/9888"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00144"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23dappa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nh4_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2871"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AMPTASECG" fast="false" reversible="false" name="Alanyl aminopeptidase (cys-gly)" metaid="R_AMPTASECG" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMPTASECG"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMPTASECG"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-6622"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.11.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.13.18"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.11.23"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.11.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.13.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00899"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-1247910"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-1247910"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28786"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28785"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28784"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28783"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1221"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00650"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cgly_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0932"/> <fbc:geneProductRef fbc:geneProduct="G_b4260"/> <fbc:geneProductRef fbc:geneProduct="G_b2523"/> <fbc:geneProductRef fbc:geneProduct="G_b0237"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_imp_e" fast="false" reversible="false" name="IMP exchange" metaid="R_EX_imp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_imp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_imp_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-566"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100831"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08749"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_imp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_DOPAtex" fast="false" reversible="true" name="Dopamine transport via diffusion (extracellular to periplasm)" metaid="R_DOPAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DOPAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DOPAtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97758"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-351596"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7032"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08363"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dopa_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dopa_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_4HOXPACDtex" fast="false" reversible="true" name="4-hydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)" metaid="R_4HOXPACDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_4HOXPACDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4HOXPACDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95017"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08006"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4hoxpacd_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4hoxpacd_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARBTNR3" fast="false" reversible="false" name="Aerobactin reductase" metaid="R_ARBTNR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBTNR3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNR3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95926"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08147"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbtn_fe3_c" stoichiometry="2" constant="true"/> <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arbtn_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_ARBTNexs" fast="false" reversible="false" name="Aerobactin Fe-loading reaction (spontaneous)" metaid="R_ARBTNexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBTNexs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNexs"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95928"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08144"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbtn_e" stoichiometry="1" constant="true"/> <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arbtn_fe3_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEOXAMexs" fast="false" reversible="false" name="Ferroxamine Fe3-loading reaction (spontaneous)" metaid="R_FEOXAMexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEOXAMexs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEOXAMexs"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143101"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08510"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/> <speciesReference species="M_feoxam_un_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_feoxam_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LACZpp" fast="false" reversible="false" name="B-galactosidase" metaid="R_LACZpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LACZpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LACZpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.23"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.108"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06114"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01100"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101000"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10077"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10078"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10076"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10079"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/9724"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00816"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11244"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lcts_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gal_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glc__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2132"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SPMDtex" fast="false" reversible="true" name="Spermidine transport via diffusion (extracellular to periplasm)" metaid="R_SPMDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SPMDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SPMDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104495"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35040"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35039"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35042"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35041"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13767"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13397"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09266"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_spmd_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_spmd_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GPDDA1pp" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphocholine)" metaid="R_GPDDA1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GPDDA1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GPDDA1pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.1.4.2-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.46"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01030"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100410"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-6814137"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1483116"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6814132"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-1483112"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16061"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16063"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16062"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16064"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1318"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00758"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pc_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_chol_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2239"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GPDDA5pp" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoinositol)" metaid="R_GPDDA5pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GPDDA5pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GPDDA5pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.1.4.44-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.44"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01193"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100414"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-6813740"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-6813740"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16502"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16501"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16503"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16504"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1430"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00889"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_inost_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2239"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ETHAtex" fast="false" reversible="true" name="Ethanolamine transport via diffusion (extracellular)" metaid="R_ETHAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ETHAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ETHAtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-476"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97974"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32750"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32749"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32747"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32748"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08424"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10841"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_etha_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_etha_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PStex" fast="false" reversible="true" name="Glycerophosphserine transport via diffusion (extracellular to periplasm)" metaid="R_G3PStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PStex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99893"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08566"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3ps_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3ps_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEOXAMR1" fast="false" reversible="false" name="Ferroxamine reductase" metaid="R_FEOXAMR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEOXAMR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEOXAMR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143097"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08511"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_feoxam_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_feoxam_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4367"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEOXAMR2" fast="false" reversible="false" name="Ferroxamine reductase" metaid="R_FEOXAMR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEOXAMR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEOXAMR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143098"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08512"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_feoxam_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_feoxam_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4367"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEOXAMR3" fast="false" reversible="false" name="Ferroxamine reductase" metaid="R_FEOXAMR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEOXAMR3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEOXAMR3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143099"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08513"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_feoxam_c" stoichiometry="2" constant="true"/> <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_feoxam_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4367"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PTHRpp" fast="false" reversible="false" name="Phospho-L-threonine phosphatase (periplasmic)" metaid="R_PTHRpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation 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<rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEENTERR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99544"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_feenter_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_enter_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_FLVR" fast="false" reversible="false" name="Flavin reductase" metaid="R_FLVR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation 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rdf:resource="http://identifiers.org/seed.reaction/rxn03976"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3844"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2764"/> <fbc:geneProductRef fbc:geneProduct="G_b2763"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SUCCtex" fast="false" reversible="true" name="Succinate transport via diffusion (extracellular to periplasm)" metaid="R_SUCCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SUCCtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCCtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-552"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104619"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10952"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09271"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_succ_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE3HOXR1" fast="false" reversible="false" name="Fe(III)hydroxamate reductase" metaid="R_FE3HOXR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3HOXR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3HOXR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99514"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08485"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe3hox_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe3hox_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_FEENTERexs" fast="false" reversible="false" name="Enterobactin Fe(III) binding (spontaneous)" metaid="R_FEENTERexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEENTERexs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEENTERexs"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99547"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_enter_e" stoichiometry="1" constant="true"/> <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_feenter_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SUCRtex" fast="false" reversible="true" name="Sucrose transport transport via diffusion (extracellular to periplasm)" metaid="R_SUCRtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation 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<fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE3HOXexs" fast="false" reversible="false" name="Fe(III) hydroxamate Fe-loading reaction (spontaneaous)" metaid="R_FE3HOXexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3HOXexs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3HOXexs"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99520"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08484"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/> <speciesReference species="M_fe3hox_un_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe3hox_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FECRMR3" fast="false" reversible="false" name="Ferrichrome reductase" metaid="R_FECRMR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FECRMR3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FECRMR3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99532"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08497"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fecrm_c" stoichiometry="2" constant="true"/> <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fecrm_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_FDMO2" fast="false" reversible="false" name="FMNH2-dependent monooxygenase (methanesulfonate)" metaid="R_FDMO2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FDMO2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FDMO2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-18086"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.14.ah"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.14.34"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.14.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10206"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99487"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29307"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29309"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29310"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29308"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08468"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mso3_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0935"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LALGP" fast="false" reversible="false" name="L-alanyl-gamma-L-glutamate peptidase" metaid="R_LALGP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" 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name="L-fucose isomerase" metaid="R_ARABDI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARABDI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARABDI"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DARABISOM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.3"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01577"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95909"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13849"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13852"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13851"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13850"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01152"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arab__D_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_rbl__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2802"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGt3" fast="false" reversible="false" name="Silver transport out via proton antiport" metaid="R_AGt3" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGt3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGt3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95620"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08091"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ag_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ag_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0572"/> <fbc:geneProductRef fbc:geneProduct="G_b0574"/> <fbc:geneProductRef fbc:geneProduct="G_b0573"/> <fbc:geneProductRef fbc:geneProduct="G_b0575"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CD2t3pp" fast="false" reversible="false" name="Cadmium (Cd+2) transport out via proton antiport (periplasm)" metaid="R_CD2t3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CD2t3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CD2t3pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-244"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96497"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28740"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28741"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28742"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28739"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13814"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08196"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cd2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cd2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3915"/> <fbc:geneProductRef fbc:geneProduct="G_b0752"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ZNabcpp" fast="false" reversible="false" name="Zinc (Zn+2) transport via ABC system (periplasm)" metaid="R_ZNabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ZNabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ZNabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-63-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105281"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29796"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29798"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29797"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29795"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13430#2"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05150"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09392"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_zn2_p" 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"/> <speciesReference species="M_zn2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1859"/> <fbc:geneProductRef fbc:geneProduct="G_b1858"/> <fbc:geneProductRef fbc:geneProduct="G_b1857"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_SKMt2pp" fast="false" reversible="false" name="Shikimate transport in via proton symport (periplasm)" metaid="R_SKMt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SKMt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SKMt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104393"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28973"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28972"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28971"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28974"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10827"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09256"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_skm_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_skm_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1981"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE2t2pp" fast="false" reversible="false" name="Iron (II) transport in via proton symport (periplasm)" metaid="R_FE2t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE2t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE2t2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2421"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99501"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29579"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29582"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29581"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29580"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08473"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2392"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYC2Ptex" fast="false" reversible="true" name="Glycerol-2-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_GLYC2Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYC2Ptex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYC2Ptex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100319"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08640"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc2p_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc2p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSERtex" fast="false" reversible="true" name="Phospho-L-serine transport via diffusion (extracellular to periplasm)" metaid="R_PSERtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSERtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSERtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103246"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09204"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pser__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pser__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TARTRtex" fast="false" reversible="true" name="Tartrate transport via diffusion (extracellular to periplasm)" metaid="R_TARTRtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TARTRtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TARTRtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104724"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09284"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tartr__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tartr__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_R5Ptex" fast="false" reversible="true" name="Ribose 5-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_R5Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_R5Ptex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/R5Ptex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103411"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_r5p_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_r5p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_THRPtex" fast="false" reversible="true" name="Phospho-L-threonine transport via diffusion (extracellular to periplasm)" metaid="R_THRPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THRPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104845"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09303"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_thrp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_thrp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TYRPtex" fast="false" reversible="true" name="Phopho-L-tyrosine transport via diffusion (extracellular to periplasm)" metaid="R_TYRPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TYRPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TYRPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104999"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09337"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tyrp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tyrp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_R5PPpp" fast="false" reversible="false" name="Ribose 5-phosphate phosphatase" metaid="R_R5PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_R5PPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/R5PPpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103410"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_r5p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_rib__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> <fbc:geneProductRef fbc:geneProduct="G_b0383"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSP_Lpp" fast="false" reversible="false" name="Phospho-L-serine phosphatase (periplasmic)" metaid="R_PSP_Lpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSP_Lpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSP_Lpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5114"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.3"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00582"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103260"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-977324"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-977324"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21208"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21211"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21210"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21209"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/10330"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/983"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00420"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pser__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> <fbc:geneProductRef fbc:geneProduct="G_b0383"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TYRPpp" fast="false" reversible="false" name="Phospho-L-tyrosine phosphatase (periplasmic)" metaid="R_TYRPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TYRPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TYRPpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14534"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104998"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30866"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30863"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30865"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30864"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/9571"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09336"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_tyrp_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_tyr__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_R1PK" fast="false" reversible="false" name="Ribose 1-phosphokinase" metaid="R_R1PK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_R1PK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/R1PK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1402"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103408"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29776"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29775"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29777"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29778"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09221"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_r1p_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_r15bp_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_PAPSR2" fast="false" reversible="false" name="Phosphoadenylyl-sulfate reductase (glutaredoxin)" metaid="R_PAPSR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPSR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPSR2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.4.8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102377"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09069"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_grxrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_paps_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_grxox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3610"/> <fbc:geneProductRef fbc:geneProduct="G_b2762"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0849"/> <fbc:geneProductRef fbc:geneProduct="G_b2762"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1064"/> <fbc:geneProductRef fbc:geneProduct="G_b2762"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1654"/> <fbc:geneProductRef fbc:geneProduct="G_b2762"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GRXR" fast="false" reversible="false" name="Glutaredoxin reductase" metaid="R_GRXR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GRXR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GRXR"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.4.2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100431"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08670"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_grxox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_grxrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1064"/> <fbc:geneProductRef fbc:geneProduct="G_b3610"/> <fbc:geneProductRef fbc:geneProduct="G_b1654"/> <fbc:geneProductRef fbc:geneProduct="G_b0849"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_RNDR1b" fast="false" reversible="false" name="Ribonucleoside-diphosphate reductase (ADP) (glutaredoxin)" metaid="R_RNDR1b" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RNDR1b"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNDR1b"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104061"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09231"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_grxrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_grxox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1064"/> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3610"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0849"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1654"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_R15BPK" fast="false" reversible="false" name="Ribose-1,5-bisphosphokinase" metaid="R_R15BPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_R15BPK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/R15BPK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1401"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.23"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06836"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103407"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20110"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20111"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20109"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20112"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04651"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_r15bp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4094"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_Kabcpp" fast="false" reversible="false" name="Potassium ABC transporter (periplasm)" metaid="R_Kabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_Kabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/Kabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.12-RXN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.10-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.10"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.12"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100657"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16777#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16778#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16779#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16780#1"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/9646#2"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08762"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10168"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10558"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_k_p" 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_k_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0698"/> <fbc:geneProductRef fbc:geneProduct="G_b0697"/> <fbc:geneProductRef fbc:geneProduct="G_b0696"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0698"/> <fbc:geneProductRef fbc:geneProduct="G_b0696"/> <fbc:geneProductRef fbc:geneProduct="G_b0697"/> <fbc:geneProductRef fbc:geneProduct="G_b4513"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_RNDR2b" fast="false" reversible="false" name="Ribonucleoside-diphosphate reductase (GDP) (glutaredoxin)" metaid="R_RNDR2b" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RNDR2b"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNDR2b"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104063"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09232"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_grxrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dgdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_grxox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0849"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1064"/> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1654"/> </fbc:and> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2675"/> <fbc:geneProductRef fbc:geneProduct="G_b2676"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3610"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TAURtex" fast="false" reversible="true" name="Taurine transport via diffusion (extracellular to periplasm)" metaid="R_TAURtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TAURtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TAURtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104733"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09286"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13402"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_taur_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_taur_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAE181" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (octadecenoate)" metaid="R_FACOAE181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAE181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAE181"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99134"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_odecoa_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_ocdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0452"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAE160" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (hexadecanoate)" metaid="R_FACOAE160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAE160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAE160"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PALMITOYL-COA-HYDROLASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.22"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01274"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99131"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16648"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16645"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16646"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16647"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1490"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00943"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pmtcoa_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_hdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0452"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAE140" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (tetradecanoate)" metaid="R_FACOAE140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAE140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAE140"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99129"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdcoa_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_ttdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0452"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LEUabcpp" fast="false" reversible="false" name="L-leucine transport via ABC system (periplasm)" metaid="R_LEUabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LEUabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LEUabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-35-RXN"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101054"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29810#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29808#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29809#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29807#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05161"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08784"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_leu__L_p" 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_leu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3455"/> <fbc:geneProductRef fbc:geneProduct="G_b3460"/> <fbc:geneProductRef fbc:geneProduct="G_b3457"/> <fbc:geneProductRef fbc:geneProduct="G_b3454"/> <fbc:geneProductRef fbc:geneProduct="G_b3456"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3458"/> <fbc:geneProductRef fbc:geneProduct="G_b3456"/> <fbc:geneProductRef fbc:geneProduct="G_b3455"/> <fbc:geneProductRef fbc:geneProduct="G_b3457"/> <fbc:geneProductRef fbc:geneProduct="G_b3454"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_L_LACt2rpp" fast="false" reversible="true" name="L-lactate reversible transport via proton symport (periplasm)" metaid="R_L_LACt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_L_LACt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/L_LACt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-104"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101277"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373889"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-373875"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-373875"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373887"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-373875"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-373875"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-373875"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-373867"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-373875"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-373875"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-373875"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373875"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-373875"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-373875"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29418"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29415"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29416"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29417"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05602"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08794"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13334"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lac__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lac__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3603"/> <fbc:geneProductRef fbc:geneProduct="G_b2975"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALt2_2pp" fast="false" reversible="false" name="Malate transport via proton symport (2 H) (periplasm)" metaid="R_MALt2_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALt2_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALt2_2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-121A"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101370"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29341"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29340"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29342"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29339"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08865"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10153"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_mal__L_p" 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 id="R_CPGNR1" fast="false" reversible="false" name="Coprogen(Fe(III)) reductase" metaid="R_CPGNR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPGNR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96868"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08247"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cpgn_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cpgn_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_CPGNR2" fast="false" reversible="false" name="Coprogen(Fe(III)) reductase" metaid="R_CPGNR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPGNR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96869"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08248"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cpgn_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cpgn_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_THRtex" fast="false" reversible="true" name="L-threonine transport via diffusion (extracellular to periplasm)" metaid="R_THRtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THRtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104852"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35022"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35020"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35019"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35021"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13464"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09307"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13117"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10898"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_thr__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_thr__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CPGNR3" fast="false" reversible="false" name="Coprogen(Fe(III)) reductase" metaid="R_CPGNR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPGNR3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNR3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96870"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08249"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cpgn_c" stoichiometry="2" constant="true"/> <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cpgn_un_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_CPGNUtpp" fast="false" reversible="false" name="Coprogen unloaded secretion" metaid="R_CPGNUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPGNUtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNUtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96872"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08252"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cpgn_un_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cpgn_un_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_CPGNUtex" fast="false" reversible="false" name="Coprogen unloaded secretion (extracellular)" metaid="R_CPGNUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPGNUtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNUtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96871"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08251"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cpgn_un_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cpgn_un_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_MALt2_3pp" fast="false" reversible="false" name="Malate transport via proton symport (3 H) (periplasm)" metaid="R_MALt2_3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALt2_3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALt2_3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101371"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10156"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08866"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="3" constant="true"/> <speciesReference species="M_mal__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4123"/> <fbc:geneProductRef fbc:geneProduct="G_b4138"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALTabcpp" fast="false" reversible="false" name="Maltose transport via ABC system (periplasm)" metaid="R_MALTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALTabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.19-RXN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-16-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.19"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101362"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22134#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22135#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22132#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22133#1"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12365#2"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08867"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05170"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malt_p" 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_malt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4033"/> <fbc:geneProductRef fbc:geneProduct="G_b4035"/> <fbc:geneProductRef fbc:geneProduct="G_b4032"/> <fbc:geneProductRef fbc:geneProduct="G_b4034"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALTHXabcpp" fast="false" reversible="false" name="Maltohexaose transport via ABC system (periplasm)" metaid="R_MALTHXabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALTHXabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTHXabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101353"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08869"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10174"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malthx_p" 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_malthx_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4034"/> <fbc:geneProductRef fbc:geneProduct="G_b4032"/> <fbc:geneProductRef fbc:geneProduct="G_b4033"/> <fbc:geneProductRef fbc:geneProduct="G_b4035"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALTPTabcpp" fast="false" reversible="false" name="Maltopentaose transport via ABC system (periplasm)" metaid="R_MALTPTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALTPTabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTPTabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101355"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08871"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10172"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_maltpt_p" 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_maltpt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4035"/> <fbc:geneProductRef fbc:geneProduct="G_b4032"/> <fbc:geneProductRef fbc:geneProduct="G_b4033"/> <fbc:geneProductRef fbc:geneProduct="G_b4034"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_AAMYL" fast="false" reversible="false" name="Alpha-amylase" metaid="R_AAMYL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AAMYL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AAMYL"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95153"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_14glucan_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1927"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AAMYLpp" fast="false" reversible="false" name="Alpha-amylase (periplasm)" metaid="R_AAMYLpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AAMYLpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AAMYLpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95153"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_14glucan_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_malthx_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3571"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALTTRabcpp" fast="false" reversible="false" name="Maltotriose transport via ABC system (periplasm)" metaid="R_MALTTRabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALTTRabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTTRabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-503"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101358"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05608"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08875"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malttr_p" 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_malttr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4034"/> <fbc:geneProductRef fbc:geneProduct="G_b4035"/> <fbc:geneProductRef fbc:geneProduct="G_b4033"/> <fbc:geneProductRef fbc:geneProduct="G_b4032"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_THMDtex" fast="false" reversible="true" name="Thymidine transport via diffusion (extracellular to periplasm)" metaid="R_THMDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THMDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THMDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104821"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10916"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09299"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_thymd_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_thymd_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALTTTRabcpp" fast="false" reversible="false" name="Maltotetraose transport via ABC system (periplasm)" metaid="R_MALTTTRabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALTTTRabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTTTRabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-504"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101360"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08877"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10173"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_maltttr_p" 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_maltttr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4033"/> <fbc:geneProductRef fbc:geneProduct="G_b4032"/> <fbc:geneProductRef fbc:geneProduct="G_b4034"/> <fbc:geneProductRef fbc:geneProduct="G_b4035"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_MAN6Pt6_2pp" fast="false" reversible="false" name="Mannose-6-phosphate transport via phosphate antiport (periplasm)" metaid="R_MAN6Pt6_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MAN6Pt6_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MAN6Pt6_2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101384"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10187"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08879"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_man6p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_man6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3666"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAL80t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (octanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL80t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAL80t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL80t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99206"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51824"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51825"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51827"/> <rdf:li rdf:resource="http://identifiers.org/rhea/51826"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_octa_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_occoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1805"/> <fbc:geneProductRef fbc:geneProduct="G_b1701"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPGPPDP" fast="false" reversible="false" name="Guanosine-3',5'-bis(diphosphate) 3'-diphosphatase" metaid="R_PPGPPDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPGPPDP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPGPPDP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PPGPPSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.7.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00336"/> <rdf:li 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name="Coprogen transport via ABC system (periplasm)" metaid="R_CPGNabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPGNabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96873"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08245"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cpgn_p" 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_cpgn_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_b0151"/> <fbc:geneProductRef fbc:geneProduct="G_b0153"/> <fbc:geneProductRef fbc:geneProduct="G_b0152"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CPGNexs" fast="false" reversible="false" name="Coprogen Fe-loading reaction (spontaneaous)" metaid="R_CPGNexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPGNexs"> <bqbiol:is 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fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MANGLYCptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MANGLYCptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101394"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08882"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_manglyc_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_man6pglyc_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_b0731"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_MELIBt2pp" fast="false" reversible="false" name="Melibiose transport in via symport (periplasm)" metaid="R_MELIBt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MELIBt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MELIBt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-94"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138587"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_melib_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_melib_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4120"/> <fbc:geneProductRef fbc:geneProduct="G_b0343"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CBIuabcpp" fast="false" reversible="false" name="Cobinamide transport via ABC system (uptake, periplasm)" metaid="R_CBIuabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CBIuabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CBIuabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-296"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.33"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96467"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cbi_p" 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_cbi_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_b1711"/> <fbc:geneProductRef fbc:geneProduct="G_b0158"/> <fbc:geneProductRef fbc:geneProduct="G_b1709"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_METabcpp" fast="false" reversible="false" name="L-methionine transport via ABC system (periplasm)" metaid="R_METabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-4522"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101489"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACGAtex" fast="false" reversible="true" name="N-Acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)" metaid="R_ACGAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACGAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95252"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08042"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgam_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DDCAtexi" fast="false" reversible="false" name="Fatty acid (dodecanoate) transport via facilitated irreversible diffusion (extracellular to periplasm)" metaid="R_DDCAtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DDCAtexi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DDCAtexi"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97211"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ddca_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2344"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TTDCAtexi" fast="false" reversible="false" name="Tetradecanoate transport via facilitated irreversible diffusion (extracellular to periplasm)" metaid="R_TTDCAtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF 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metaid="R_EX_fe3hox_un_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_fe3hox_un_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fe3hox_un_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142962"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3hox_un_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GGPTRCS" fast="false" reversible="false" name="Gamma glutamyl putrescine synthase" metaid="R_GGPTRCS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GGPTRCS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GGPTRCS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.1.11"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100132"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08604"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ggptrc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1297"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_23dappa_e" fast="false" reversible="false" name="2,3-diaminopropionate exchange" metaid="R_EX_23dappa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_23dappa_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_23dappa_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94728"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07930"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23dappa_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_RMNtpp" fast="false" reversible="false" name="L-rhamnose transport via proton symport (periplasm)" metaid="R_RMNtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RMNtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RMNtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-112"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104041"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29949"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29950"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29948"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29947"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05646"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09230"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_rmn_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rmn_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3907"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_23PDE2pp" fast="false" reversible="false" name="2',3'-cyclic-nucleotide phosphodiesterase (UMP) (periplasm)" metaid="R_23PDE2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_23PDE2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/23PDE2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14091"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03538"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94723"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27879"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27881"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27878"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27880"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/516"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02522"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23cump_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3ump_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4213"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_23PDE4pp" fast="false" reversible="false" name="2',3'-cyclic-nucleotide phosphodiesterase (CMP) (periplasm)" metaid="R_23PDE4pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_23PDE4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/23PDE4pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14112"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03929"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94724"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27882"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27884"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27883"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27885"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/518"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02762"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23ccmp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3cmp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4213"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_23PDE9pp" fast="false" reversible="false" name="2',3'-cyclic-nucleotide phosphodiesterase (GMP) (periplasm)" metaid="R_23PDE9pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_23PDE9pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/23PDE9pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14064"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05135"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94725"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27858"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27860"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27861"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27859"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/4755"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03483"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23cgmp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3gmp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4213"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SERt4pp" fast="false" reversible="false" name="L-serine via sodium symport (periplasm)" metaid="R_SERt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SERt4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SERt4pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-4083"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104346"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29576"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29577"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29578"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29575"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10185"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09247"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3089"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_METDtex" fast="false" reversible="true" name="D-methionine transport via diffusion (extracellular to periplasm)" metaid="R_METDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101473"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34913"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34912"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34914"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34911"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08911"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_met__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_met__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SUCCt2_3pp" fast="false" reversible="false" name="Succintate transport via proton symport (3 H) (periplasm)" metaid="R_SUCCt2_3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SUCCt2_3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCCt2_3pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-300"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104621"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10157"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="3" constant="true"/> <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4123"/> <fbc:geneProductRef fbc:geneProduct="G_b4138"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MNLptspp" fast="false" reversible="false" name="Mannitol transport via PEP:Pyr PTS (periplasm)" metaid="R_MNLptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MNLptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MNLptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101677"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08949"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13944"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13934"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05617"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mnl_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mnl1p_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_b3599"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b2934"/> <fbc:geneProductRef fbc:geneProduct="G_b2933"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b2704"/> <fbc:geneProductRef fbc:geneProduct="G_b2702"/> <fbc:geneProductRef fbc:geneProduct="G_b2703"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NAt3_1p5pp" fast="false" reversible="false" name="Sodium proton antiporter (H:NA is 1.5) (periplasm)" metaid="R_NAt3_1p5pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NAt3_1p5pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NAt3_1p5pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-130"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101914"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29249"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29250"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29247"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29248"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10179"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08982"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="3" constant="true"/> <speciesReference species="M_na1_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_na1_p" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1186"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ATPHs" fast="false" reversible="false" name="ATP amine hydrolysis (spontaneous)" metaid="R_ATPHs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ATPHs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ATPHs"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ATP-DEAMINASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.17"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.18"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00088"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96130"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13038"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13040"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13039"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13037"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00064"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_itp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SARCOX" fast="false" reversible="false" name="Sarcosine oxidase" metaid="R_SARCOX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SARCOX"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SARCOX"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SARCOX-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.3.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00610"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104272"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13315"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13314"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13313"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13316"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1001"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00433"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sarcs_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1059"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GTPHs" fast="false" reversible="false" name="GTP amine hydrolysis (spontaneous)" metaid="R_GTPHs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GTPHs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GTPHs"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100459"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08679"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xtp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MN6PP" fast="false" reversible="false" name="Mannose 6-phosphate phosphatase" metaid="R_MN6PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MN6PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MN6PP"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101671"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28556"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28557"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28555"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28554"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/9955"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7278"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08948"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_man6p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_man_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0822"/> <fbc:geneProductRef fbc:geneProduct="G_b1727"/> <fbc:geneProductRef fbc:geneProduct="G_b3697"/> <fbc:geneProductRef fbc:geneProduct="G_b3826"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NAt3_2pp" fast="false" reversible="false" name="Sodium proton antiporter (H:NA is 2) (periplasm)" metaid="R_NAt3_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NAt3_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NAt3_2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-129"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101915"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29252"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29251"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29254"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29253"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10178"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08983"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0019"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NH4tpp" fast="false" reversible="true" name="Ammonia reversible transport (periplasm)" metaid="R_NH4tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NH4tpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NH4tpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-206"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9615"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-544"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101950"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-444416"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-444416"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28749"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28748"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28750"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28747"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11683"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13364"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09835"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05466"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08987"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08986"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09736"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nh4_p" 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 id="R_3KGK" fast="false" reversible="false" name="3-keto-L-gulonate kinase" metaid="R_3KGK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3KGK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3KGK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-704"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.53"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07127"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94909"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28222"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28223"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28225"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28224"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04930"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3dhguln_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3dhgulnp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3580"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_METtex" fast="false" reversible="true" name="L-methionine transport via diffusion (extracellular to periplasm)" metaid="R_METtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101493"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13469"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13461"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08920"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10976"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_met__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_met__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_cd2_e" fast="false" reversible="false" name="Cadmium exchange" metaid="R_EX_cd2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cd2_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cd2_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-10"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96499"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28709"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28708"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28707"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28710"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13041"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08198"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08197"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cd2_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_F6PP" fast="false" reversible="false" name="D-fructose 6-phosphate phosphatase" metaid="R_F6PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_F6PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/F6PP"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99077"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fru_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0822"/> <fbc:geneProductRef fbc:geneProduct="G_b3697"/> <fbc:geneProductRef fbc:geneProduct="G_b2690"/> <fbc:geneProductRef fbc:geneProduct="G_b2293"/> <fbc:geneProductRef fbc:geneProduct="G_b3826"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NMNPtpp" fast="false" reversible="false" name="NMN permease (periplasm)" metaid="R_NMNPtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NMNPtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NMNPtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101972"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28485"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28483"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28482"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28484"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08997"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08995"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10181"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nmn_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nmn_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0751"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NO2t2rpp" fast="false" reversible="true" name="Nitrite transport in via proton symport, reversible (periplasm)" metaid="R_NO2t2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NO2t2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO2t2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101984"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05625"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08998"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1223"/> <fbc:geneProductRef fbc:geneProduct="G_b3367"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NO3t7pp" fast="false" reversible="false" name="Nitrate transport in via nitrite antiport (periplasm)" metaid="R_NO3t7pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NO3t7pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO3t7pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-239"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101995"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28746"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28743"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28744"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28745"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09004"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10177"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_no2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_no3_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_no3_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1223"/> <fbc:geneProductRef fbc:geneProduct="G_b1469"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ORNabcpp" fast="false" reversible="false" name="Ornithine transport via ABC system (periplasm)" metaid="R_ORNabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ORNabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ORNabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-37-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102222"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29883#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29885#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29886#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29884#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09046"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05156"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_orn_p" 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_orn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2307"/> <fbc:geneProductRef fbc:geneProduct="G_b2308"/> <fbc:geneProductRef fbc:geneProduct="G_b2306"/> <fbc:geneProductRef fbc:geneProduct="G_b2310"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PIuabcpp" fast="false" reversible="false" name="Phosphate transport via ABC system (uptake, periplasm)" metaid="R_PIuabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PIuabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PIuabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-27-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102870"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24441#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24442#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24443#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24440#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05145"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09122"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" 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="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3725"/> <fbc:geneProductRef fbc:geneProduct="G_b3727"/> <fbc:geneProductRef fbc:geneProduct="G_b3728"/> <fbc:geneProductRef fbc:geneProduct="G_b3726"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PNTOt4pp" fast="false" reversible="false" name="Pantothenate sodium symporter (periplasm)" metaid="R_PNTOt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PNTOt4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PNTOt4pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-117"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103054"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29927"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29930"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29929"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29928"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09165"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10180"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pnto__R_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pnto__R_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3258"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRULYSDG" fast="false" reversible="true" name="Fructoselysine phosphate deglycase" metaid="R_FRULYSDG" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRULYSDG"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRULYSDG"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99653"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08530"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_frulysp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3371"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_METDabcpp" fast="false" reversible="false" name="D-methionine transport via ABC system (periplasm)" metaid="R_METDabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METDabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METDabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-202"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101472"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29770#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29767#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29769#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29768#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08910"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05183"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_met__D_p" 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_met__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0198"/> <fbc:geneProductRef fbc:geneProduct="G_b0199"/> <fbc:geneProductRef fbc:geneProduct="G_b0197"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_GDPMNH" fast="false" reversible="false" name="GDP-mannose mannosyl hydrolase" metaid="R_GDPMNH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GDPMNH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GDPMNH"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100091"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28102"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28104"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28103"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28105"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08599"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gdpmann_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_man_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2051"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAL60t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (hexanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL60t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAL60t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL60t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99204"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hxa_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hxcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1805"/> <fbc:geneProductRef fbc:geneProduct="G_b1701"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_IDONt2rpp" fast="false" reversible="true" name="L-idonate transport via proton symport, reversible (periplasm)" metaid="R_IDONt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_IDONt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/IDONt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-181A"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100803"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29572"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29573"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29571"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29574"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08742"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10167"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_idon__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_idon__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4265"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ILEabcpp" fast="false" reversible="false" name="L-isoleucine transport via ABC system (periplasm)" metaid="R_ILEabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ILEabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ILEabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-15-RXN"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100821"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29820#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29819#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29821#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29822#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08745"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05179"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ile__L_p" 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_ile__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3456"/> <fbc:geneProductRef fbc:geneProduct="G_b3455"/> <fbc:geneProductRef fbc:geneProduct="G_b3460"/> <fbc:geneProductRef fbc:geneProduct="G_b3457"/> <fbc:geneProductRef fbc:geneProduct="G_b3454"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_INDOLEt2pp" fast="false" reversible="false" name="Indole transport via proton symport, irreversible (periplasm)" metaid="R_INDOLEt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_INDOLEt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INDOLEt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-142"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100835"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29228"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29227"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29230"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29229"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08750"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10176"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_indole_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_indole_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3266"/> <fbc:geneProductRef fbc:geneProduct="G_b3265"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_INSt2pp" fast="false" reversible="false" name="Inosine transport in via proton symport (periplasm)" metaid="R_INSt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_INSt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INSt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108G"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100850"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29965"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29964"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29966"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29963"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05316"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08753"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ins_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ins_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2964"/> <fbc:geneProductRef fbc:geneProduct="G_b2406"/> <fbc:geneProductRef fbc:geneProduct="G_b2393"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PROabcpp" fast="false" reversible="false" name="L-proline transport via ABC system (periplasm)" metaid="R_PROabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PROabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PROabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-26-RXN"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103210"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29816#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29817#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29815#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29818#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09187"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05165"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pro__L_p" 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"/> <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2677"/> <fbc:geneProductRef fbc:geneProduct="G_b2678"/> <fbc:geneProductRef fbc:geneProduct="G_b2679"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PROt2rpp" fast="false" reversible="true" name="L-proline reversible transport via proton symport (periplasm)" metaid="R_PROt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PROt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PROt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-29"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103211"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28963"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28964"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28965"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28966"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11167"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09191"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05638"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pro__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4111"/> <fbc:geneProductRef fbc:geneProduct="G_b0402"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MNLtex" fast="false" reversible="true" name="Mannitol transport via diffusion (extracellular to periplasm)" metaid="R_MNLtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MNLtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MNLtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101678"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08950"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mnl_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mnl_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PROt4pp" fast="false" reversible="false" name="Na+/Proline-L symporter (periplasm)" metaid="R_PROt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PROt4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PROt4pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-118"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103197"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-352052"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-352052"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-352052"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-352052"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-352052"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-352052"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-352052"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-352052"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-352052"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28968"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28969"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28970"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28967"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05221"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09192"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pro__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1015"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PTRCabcpp" fast="false" reversible="false" name="Putrescine transport via ABC system (periplasm)" metaid="R_PTRCabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PTRCabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PTRCabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-25-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.31"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103338"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29998#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29996#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29995#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29997#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11263"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05163"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09213"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ptrc_p" 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"/> <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0854"/> <fbc:geneProductRef fbc:geneProduct="G_b0855"/> <fbc:geneProductRef fbc:geneProduct="G_b0857"/> <fbc:geneProductRef fbc:geneProduct="G_b0856"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1440"/> <fbc:geneProductRef fbc:geneProduct="G_b1442"/> <fbc:geneProductRef fbc:geneProduct="G_b1441"/> <fbc:geneProductRef fbc:geneProduct="G_b1443"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1125"/> <fbc:geneProductRef fbc:geneProduct="G_b1126"/> <fbc:geneProductRef fbc:geneProduct="G_b1124"/> <fbc:geneProductRef fbc:geneProduct="G_b1123"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LYXt2pp" fast="false" reversible="false" name="L-Lyxose transport via proton symport (periplasm)" metaid="R_LYXt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LYXt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYXt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-236"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101271"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08858"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05692"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lyx__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lyx__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3907"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GDPDPK" fast="false" reversible="false" name="GDP diphosphokinase" metaid="R_GDPDPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GDPDPK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GDPDPK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GDPPYPHOSKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.6.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100088"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28098"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28101"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28099"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28100"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08598"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppgpp_c" stoichiometry="1" 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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MOBDabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOBDabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.29-RXN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-19-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.29"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101689"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22020#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22023#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22021#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22022#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05619"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08955"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mobd_p" 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_mobd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0764"/> <fbc:geneProductRef fbc:geneProduct="G_b0765"/> <fbc:geneProductRef fbc:geneProduct="G_b0763"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2422"/> <fbc:geneProductRef fbc:geneProduct="G_b2423"/> <fbc:geneProductRef fbc:geneProduct="G_b2424"/> <fbc:geneProductRef fbc:geneProduct="G_b3917"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2425"/> <fbc:geneProductRef fbc:geneProduct="G_b2422"/> <fbc:geneProductRef fbc:geneProduct="G_b2423"/> <fbc:geneProductRef fbc:geneProduct="G_b2424"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MOBDtex" fast="false" reversible="true" name="Molybdate transport via diffusion (extracellular to periplasm)" metaid="R_MOBDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MOBDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOBDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101690"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34909"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34907"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34910"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34908"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08956"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mobd_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mobd_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NI2uabcpp" fast="false" reversible="false" name="Nickel transport via ABC system (uptake, periplasm)" metaid="R_NI2uabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NI2uabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NI2uabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-20-RXN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.24-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.24"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101959"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15557#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15558#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15560#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15559#1"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ni2_p" 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_ni2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3480"/> <fbc:geneProductRef fbc:geneProduct="G_b3476"/> <fbc:geneProductRef fbc:geneProduct="G_b3479"/> <fbc:geneProductRef fbc:geneProduct="G_b3477"/> <fbc:geneProductRef fbc:geneProduct="G_b3478"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4242"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FECRMtonex" fast="false" reversible="false" name="Ferrichrome transport via ton system (extracellular)" metaid="R_FECRMtonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FECRMtonex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FECRMtonex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99537"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08498"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fecrm_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fecrm_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1252"/> <fbc:geneProductRef fbc:geneProduct="G_b3005"/> <fbc:geneProductRef fbc:geneProduct="G_b3006"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0150"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARBTNtonex" fast="false" reversible="false" name="Aerobactin transport via ton system (extracellular)" metaid="R_ARBTNtonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBTNtonex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNtonex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95930"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08149"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbtn_fe3_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arbtn_fe3_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_ADOCBLabcpp" fast="false" reversible="false" name="Adenosylcobalamin transport via ABC system (periplasm)" metaid="R_ADOCBLabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADOCBLabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADOCBLabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95471"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08070"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adocbl_p" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adocbl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1709"/> <fbc:geneProductRef fbc:geneProduct="G_b0158"/> <fbc:geneProductRef fbc:geneProduct="G_b1711"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_enter_e" fast="false" reversible="false" name="Enterochelin exchange" metaid="R_EX_enter_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_enter_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_enter_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-8"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-496"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR123417"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_enter_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_fecrm_un_e" fast="false" reversible="false" name="Ferrichrome minus Fe(III) exchange" metaid="R_EX_fecrm_un_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_fecrm_un_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fecrm_un_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142964"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fecrm_un_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_cgly_e" fast="false" reversible="false" name="Cys-Gly exchange" metaid="R_EX_cgly_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cgly_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cgly_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96658"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08211"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cgly_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_NI2tex" fast="false" reversible="true" name="Nickel transport via diffusion (extracellular to periplasm)" metaid="R_NI2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NI2tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NI2tex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-141B"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101958"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29833"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29831"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29834"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29832"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ni2_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ni2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTD10pp" fast="false" reversible="false" name="5'-nucleotidase (XMP)" metaid="R_NTD10pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD10pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD10pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:XMPXAN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02719"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102029"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28532"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28530"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28531"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28533"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/129"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01961"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_xmp_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_xtsn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTD1pp" fast="false" reversible="false" name="5'-nucleotidase (dUMP)" metaid="R_NTD1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD1pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14143"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.89"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02102"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102028"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29358"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29355"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29357"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29356"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/501"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01521"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dump_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_duri_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_chtbs_e" fast="false" reversible="false" name="Chitobiose exchange" metaid="R_EX_chtbs_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_chtbs_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_chtbs_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138171"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_chtbs_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_gmp_e" fast="false" reversible="false" name="GMP exchange" metaid="R_EX_gmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_gmp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gmp_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-565"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100386"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08664"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gmp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_NTD2pp" fast="false" reversible="false" name="5'-nucleotidase (UMP)" metaid="R_NTD2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14025"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00963"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102032"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29362"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29360"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29361"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29359"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/210"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00708"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_uri_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> <fbc:geneProductRef fbc:geneProduct="G_b0383"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NACtex" fast="false" reversible="true" name="Nicotinic acid transport via diffusion (extracellular to periplasm)" metaid="R_NACtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NACtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NACtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101808"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-8869603"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-8869603"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08970"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05310"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08969"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nac_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nac_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTD3pp" fast="false" reversible="false" name="5'-nucleotidase (dCMP)" metaid="R_NTD3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD3pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5292"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.89"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01664"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102033"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29364"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29365"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29366"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29363"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/480"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01218"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcmp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dcyt_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTD4pp" fast="false" reversible="false" name="5'-nucleotidase (CMP)" metaid="R_NTD4pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD4pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14026"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.91"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00511"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102034"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29370"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29368"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29369"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29367"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/211"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00363"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cmp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cytd_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> <fbc:geneProductRef fbc:geneProduct="G_b0383"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTD5pp" fast="false" reversible="false" name="5'-nucleotidase (dTMP)" metaid="R_NTD5pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD5pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD5pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THYMIDYLATE-5-PHOSPHATASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.35"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.89"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01569"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102035"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11081"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11083"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11082"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11080"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/479"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01145"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dtmp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_thymd_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_h2o2_e" fast="false" reversible="false" name="Hydrogen peroxide exchange" metaid="R_EX_h2o2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_h2o2_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_h2o2_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-284"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-572"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR98640"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-3779389"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-3779381"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13308"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08685"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o2_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_ump_e" fast="false" reversible="false" name="UMP exchange" metaid="R_EX_ump_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ump_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ump_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105127"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27927"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27929"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27926"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27928"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09808"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09361"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ump_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_pydam_e" fast="false" reversible="false" name="Pyridoxamine exchange" metaid="R_EX_pydam_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_pydam_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pydam_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-213"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103358"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28468"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28467"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28469"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28466"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pydam_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_CRNabcpp" fast="false" reversible="false" name="L-carnitine transport via ABC system (periplasm)" metaid="R_CRNabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96905"/> <rdf:li rdf:resource="http://identifiers.org/rhea/38719#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/38722#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/38720#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/38721#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05180"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08253"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_crn_p" 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_crn_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_b2679"/> <fbc:geneProductRef fbc:geneProduct="G_b2677"/> <fbc:geneProductRef fbc:geneProduct="G_b2678"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CRNDabcpp" fast="false" reversible="false" name="D-carnitine transport via ABC system (periplasm)" metaid="R_CRNDabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNDabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNDabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96902"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08259"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_crn__D_p" 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_crn__D_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_b2679"/> <fbc:geneProductRef fbc:geneProduct="G_b2677"/> <fbc:geneProductRef fbc:geneProduct="G_b2678"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DNTPPA" fast="false" reversible="false" name="Dihydroneopterin triphosphate pyrophosphatase" metaid="R_DNTPPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DNTPPA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DNTPPA"/> <rdf:li 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</fbc:geneProductAssociation> </reaction> <reaction id="R_CTBTabcpp" fast="false" reversible="false" name="Crotonobetaine transport via ABC system (periplasm)" metaid="R_CTBTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CTBTabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CTBTabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96938"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ctbt_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> 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<fbc:geneProductRef fbc:geneProduct="G_b4084"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALLULPE" fast="false" reversible="true" name="Allulose 6-phosphate epimerase" metaid="R_ALLULPE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALLULPE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALLULPE"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-304"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09031"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95774"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_allul6p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4085"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADEtex" fast="false" reversible="true" name="Adenine transport via diffusion (extracellular to periplasm)" metaid="R_ADEtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADEtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADEtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-577"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95445"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10918"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08065"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09786"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ade_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ade_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADNtex" fast="false" reversible="true" name="Adenosine transport via diffusion (extracellular to periplasm)" metaid="R_ADNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95460"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08069"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11000"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0411"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADPHQR2" fast="false" reversible="false" name="NADPH Quinone Reductase (Ubiquinone-8)" metaid="R_NADPHQR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADPHQR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADPHQR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101891"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29114"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29112"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29113"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29111"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08977"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3028"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADPHQR3" fast="false" reversible="false" name="NADPH Quinone Reductase (Menaquinone-8)" metaid="R_NADPHQR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADPHQR3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADPHQR3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101892"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29116"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29115"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29117"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29118"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08978"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3028"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADPHQR4" fast="false" reversible="false" name="NADPH Quinone Reductase (2-Demethylmenaquinone-8)" metaid="R_NADPHQR4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADPHQR4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADPHQR4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101893"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30511"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30513"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30514"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30512"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08979"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dmmq8_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_2dmmql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3028"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLBRAN2" fast="false" reversible="false" name="1,4-alpha-glucan branching enzyme (glycogen -> bglycogen)" metaid="R_GLBRAN2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLBRAN2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLBRAN2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.18"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100155"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08605"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glycogen_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_bglycogen_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3432"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASR" fast="false" reversible="false" name="Arsenate reductase" metaid="R_ASR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASR"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.20.4.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96113"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08171"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_aso4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_aso3_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1064"/> <fbc:geneProductRef fbc:geneProduct="G_b3503"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASO3tex" fast="false" reversible="true" name="Arsenite transport via diffusion (extracellular to periplasm)" metaid="R_ASO3tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASO3tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASO3tex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-551"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96073"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05507"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08164"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_aso3_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_aso3_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGMtex" fast="false" reversible="true" name="Agmatine transport via diffusion (extracellular to periplasm)" metaid="R_AGMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGMtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95556"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08082"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_agm_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_agm_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALAtex" fast="false" reversible="true" name="L-alanine transport via diffusion (extracellular to periplasm)" metaid="R_ALAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALAtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95706"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/10375"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08104"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10921"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13221"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_BALAtex" fast="false" reversible="true" name="Beta-alanine transport via diffusion (extracellular to periplasm)" metaid="R_BALAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BALAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BALAtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95682"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-909763"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-909765"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08175"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala_B_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala_B_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DALAtex" fast="false" reversible="true" name="D-Alanine transport via diffusion (extracellular to periplasm)" metaid="R_DALAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DALAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DALAtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95702"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08302"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10991"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MANGLYCtex" fast="false" reversible="true" name="2-O-alpha-mannosyl-D-glycerate transport via diffusion (extracellular to periplasm)" metaid="R_MANGLYCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MANGLYCtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MANGLYCtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101395"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08883"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_manglyc_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_manglyc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_frulys_e" fast="false" reversible="false" name="Fructoselysine exchange" metaid="R_EX_frulys_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_frulys_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_frulys_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-417"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99657"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28457"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28455"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28456"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28454"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08534"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_frulys_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_AMPtex" fast="false" reversible="true" name="AMP transport via diffusion (extracellular to periplasm)" metaid="R_AMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95830"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08134"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13227"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_METOX1s" fast="false" reversible="false" name="Methionine oxidation (spontaneous)" metaid="R_METOX1s" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METOX1s"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METOX1s"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101479"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08912"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09942"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_metsox_S__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_XTSNH" fast="false" reversible="false" name="Xanthosine hydrolase" metaid="R_XTSNH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_XTSNH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XTSNH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-363"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02143"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105245"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27994"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27995"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27997"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27996"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01545"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xtsn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xan_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0030"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_METOX2s" fast="false" reversible="false" name="Methionine oxidation 2 (spontaneous)" metaid="R_METOX2s" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METOX2s"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METOX2s"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-7188"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138590"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08913"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_metsox_R__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRUURt2rpp" fast="false" reversible="true" name="D-fructuronate transport via proton symport, reversible (periplasm)" metaid="R_FRUURt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRUURt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRUURt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-81"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99658"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28871"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28873"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28872"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28874"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08538"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fruur_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fruur_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4321"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRUURtex" fast="false" reversible="true" name="D-fructuronate transport via diffusion (extracellular)" metaid="R_FRUURtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRUURtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRUURtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99659"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08539"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fruur_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fruur_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARBtex" fast="false" reversible="true" name="L-arabinose transport via diffusion (extracellular to periplasm)" metaid="R_ARBtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95913"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arab__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arab__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARGtex" fast="false" reversible="true" name="L-arginine transport via diffusion (extracellular to periplasm)" metaid="R_ARGtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARGtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARGtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-448"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95951"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32145"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32143"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32144"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32146"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7983"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10840"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08155"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arg__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arg__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_INSH" fast="false" reversible="false" name="Inosine hydrolase" metaid="R_INSH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_INSH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INSH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:INOSINE-NUCLEOSIDASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01770"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100844"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16658"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16657"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16659"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16660"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01299"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ins_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hxan_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0030"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASCBtex" fast="false" reversible="true" name="L-ascorbate transport via diffusion (extracellular to periplasm)" metaid="R_ASCBtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASCBtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASCBtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138070"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08159"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ascb__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ascb__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAL100t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (decanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL100t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAL100t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL100t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99142"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dca_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dcacoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1805"/> <fbc:geneProductRef fbc:geneProduct="G_b1701"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_RIBabcpp" fast="false" reversible="false" name="D-ribose transport via ABC system (periplasm)" metaid="R_RIBabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RIBabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RIBabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-28-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.17"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104034"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29904#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29905#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29903#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29906#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05160"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09227"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rib__D_p" 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"/> <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4230"/> <fbc:geneProductRef fbc:geneProduct="G_b4227"/> <fbc:geneProductRef fbc:geneProduct="G_b4485"/> <fbc:geneProductRef fbc:geneProduct="G_b4231"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3750"/> <fbc:geneProductRef fbc:geneProduct="G_b3751"/> <fbc:geneProductRef fbc:geneProduct="G_b3749"/> <fbc:geneProductRef fbc:geneProduct="G_b3748"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4088"/> <fbc:geneProductRef fbc:geneProduct="G_b4086"/> <fbc:geneProductRef fbc:geneProduct="G_b4087"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ECAtpp" fast="false" reversible="false" name="Enterobacterial common antigen transferase (flippase, cytoplasm to periplasm)" metaid="R_ECAtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ECAtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ECAtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-279"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97878"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08411"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_unagamuf_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_unagamuf_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3792"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_O16AT" fast="false" reversible="false" name="Rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate O-acetyltransferase (LPS O16 antigen biosynthesis)" metaid="R_O16AT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O16AT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16AT"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102081"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09025"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ragund_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_aragund_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2033"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_O16GALFT" fast="false" reversible="false" name="Galactofuranosyltransferase (LPS O16 antigen biosynthesis)" metaid="R_O16GALFT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O16GALFT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16GALFT"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102085"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09027"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_garagund_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpgalfur_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gfgaragund_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2034"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_O16GLCT2" fast="false" reversible="false" name="Glucosyltransferase II (LPS O16 antigen biosynthesis)" metaid="R_O16GLCT2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O16GLCT2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16GLCT2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143259"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09029"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gfgaragund_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o16aund_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_O16AUNDtpp" fast="false" reversible="false" name="O16 antigen (flippase, cytoplasm to periplasm)" metaid="R_O16AUNDtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O16AUNDtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16AUNDtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102082"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09026"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o16aund_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_o16aund_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2037"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_O16AP1pp" fast="false" reversible="false" name="O16 antigen polymerase (periplasm)" metaid="R_O16AP1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O16AP1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16AP1pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102078"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o16aund_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_o16a2und_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2027"/> <fbc:geneProductRef fbc:geneProduct="G_b2035"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_GPDDA3pp" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoserine)" metaid="R_GPDDA3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GPDDA3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GPDDA3pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14136"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.46"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100412"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29877"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29875"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29878"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29876"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08668"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3ps_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2239"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GPDDA4pp" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoglycerol)" metaid="R_GPDDA4pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GPDDA4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GPDDA4pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14073"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.46"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100413"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13035"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08669"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2239"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GPDDA2pp" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoethanolamine)" metaid="R_GPDDA2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GPDDA2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GPDDA2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.46"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01470"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100411"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29320"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29322"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29321"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29319"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/397"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01073"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_etha_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2239"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAL120t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (dodecanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL120t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAL120t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL120t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99144"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ddcacoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1701"/> <fbc:geneProductRef fbc:geneProduct="G_b1805"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYCAt2rpp" fast="false" reversible="true" name="D-glycerate transport via proton symport, reversible (periplasm)" metaid="R_GLYCAt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYCAt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYCAt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100322"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08644"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13711"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc__R_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc__R_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3127"/> <fbc:geneProductRef fbc:geneProduct="G_b2789"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYCAtex" fast="false" reversible="true" name="D-glycerate transport via diffusion (extracellular to periplasm)" metaid="R_GLYCAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYCAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYCAtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-523"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100323"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08645"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc__R_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc__R_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAL140t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (tetradecanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL140t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAL140t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL140t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99147"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1701"/> <fbc:geneProductRef fbc:geneProduct="G_b1805"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_enlipa_e" fast="false" reversible="false" name="Phosphoethanolamine KDO(2)-lipid (A) exchange" metaid="R_EX_enlipa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_enlipa_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_enlipa_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97923"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08419"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_enlipa_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_BUTtex" fast="false" reversible="true" name="Butyrate transport via diffusion (extracellular to periplasm)" metaid="R_BUTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BUTtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BUTtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96352"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_but_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_but_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_hacolipa_e" fast="false" reversible="false" name="Hepta-acylated core oligosaccharide lipid A (E. coli) exchange" metaid="R_EX_hacolipa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_hacolipa_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_hacolipa_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143008"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hacolipa_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_AGM4PCP" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" metaid="R_AGM4PCP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGM4PCP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM4PCP"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95547"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08077"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_anhgm3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1192"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_4PCP" fast="false" reversible="false" name="Tetrapeptide L,D-carboxypeptidase" metaid="R_4PCP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_4PCP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4PCP"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95049"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08007"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDgluMdapDala_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDgluMdap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ala__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1192"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE3HOXtonex" fast="false" reversible="false" name="Fe(III)hydroxamine transport via ton system (extracellular)" metaid="R_FE3HOXtonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3HOXtonex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3HOXtonex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99521"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08488"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3hox_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe3hox_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1252"/> <fbc:geneProductRef fbc:geneProduct="G_b3005"/> <fbc:geneProductRef fbc:geneProduct="G_b3006"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0150"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CU2abcpp" fast="false" reversible="false" name="Copper (Cu+2) ABC transporter (periplasm)" metaid="R_CU2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CU2abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CU2abcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-178"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.4-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96950"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-936802"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-936895"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-936895"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10376#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10377#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10379#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10378#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08271"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05528"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cu2_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_cu2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3469"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_COBALT2abcpp" fast="false" reversible="false" name="Cobalt (Co+2) ABC transporter (periplasm)" metaid="R_COBALT2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_COBALT2abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/COBALT2abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96819"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32782#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32779#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32780#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32781#2"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08239"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cobalt2_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_cobalt2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3469"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NI2abcpp" fast="false" reversible="false" name="Nickle (Ni+2) ABC transporter (periplasm)" metaid="R_NI2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NI2abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NI2abcpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.24"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101955"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15560#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15559#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15557#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15558#2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ni2_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_ni2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3469"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MG2uabcpp" fast="false" reversible="false" name="Magnesium (Mg+2) ABC transporter (ubtake, periplasm)" metaid="R_MG2uabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MG2uabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MG2uabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-250"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.2-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101505"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10261#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10262#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10260#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10263#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08924"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10571"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mg2_p" stoichiometry="1" constant="true"/> </listOfReactants> 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rdf:resource="http://identifiers.org/seed.reaction/rxn09744"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05299"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11327"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08719"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_his__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_his__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0112"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CBIAT" fast="false" reversible="true" name="Cobinamide adenyltransferase" metaid="R_CBIAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CBIAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CBIAT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:BTUR2-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.17"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96465"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cbi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adocbi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1270"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLUt4pp" fast="false" reversible="false" name="Na+/glutamate symport (periplasm)" metaid="R_GLUt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLUt4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLUt4pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100285"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29034"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29033"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29032"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29031"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05298"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08632"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glu__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3653"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYALDtpp" fast="false" reversible="true" name="Glyceraldehyde facilitated diffusion (periplasm)" metaid="R_GLYALDtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYALDtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYALDtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100311"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08636"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08635"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10164"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyald_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyald_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3927"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CRNtex" fast="false" reversible="true" name="L-carnitine transport via diffusion (extracellular to periplasm)" metaid="R_CRNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96906"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34962"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34960"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34959"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34961"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09773"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09858"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09691"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08265"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_crn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_crn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_etha_e" fast="false" reversible="false" name="Ethanolamine exchange" metaid="R_EX_etha_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_etha_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_etha_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-476"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97974"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32750"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32749"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32747"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32748"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08424"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10841"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_etha_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ACGK" fast="false" reversible="false" name="Acetylglutamate kinase" metaid="R_ACGK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACGK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACETYLGLUTKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.2.8"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02649"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95256"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14632"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14631"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14630"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14629"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2545"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01917"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acglu_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acg5p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3959"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LYSabcpp" fast="false" reversible="false" name="L-lysine transport via ABC system (periplasm)" metaid="R_LYSabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LYSabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYSabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-3-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101265"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29887#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29888#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29890#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29889#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05151"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08853"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lys__L_p" 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_lys__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2308"/> <fbc:geneProductRef fbc:geneProduct="G_b2306"/> <fbc:geneProductRef fbc:geneProduct="G_b2310"/> <fbc:geneProductRef fbc:geneProduct="G_b2307"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_COBALT2tex" fast="false" reversible="true" name="Cobalt (Co+2) transport via diffusion (extracellular to periplasm)" metaid="R_COBALT2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_COBALT2tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/COBALT2tex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-141A"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96821"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28579"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28580"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28581"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28578"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12148"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08241"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08242"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10474"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cobalt2_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cobalt2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LCTSt3ipp" fast="false" reversible="false" name="Lactose transport via proton aniport (periplasm)" metaid="R_LCTSt3ipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LCTSt3ipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LCTSt3ipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101026"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28864"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28866"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28865"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28863"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08779"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lcts_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lcts_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1528"/> <fbc:geneProductRef fbc:geneProduct="G_b2170"/> <fbc:geneProductRef fbc:geneProduct="G_b0070"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPK2" fast="false" reversible="false" name="Polyphosphate kinase" metaid="R_PPK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPK2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPK2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2501"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARBt3ipp" fast="false" reversible="false" name="L-arabinose transport via proton antiport (periplasm)" metaid="R_ARBt3ipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBt3ipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBt3ipp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-40"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95937"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arab__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arab__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1528"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_14GLUCANabcpp" fast="false" reversible="false" name="1,4-alpha-D-glucan transport via ABC system (periplasm)" metaid="R_14GLUCANabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_14GLUCANabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/14GLUCANabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94693"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_14glucan_p" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_14glucan_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4032"/> <fbc:geneProductRef fbc:geneProduct="G_b4034"/> <fbc:geneProductRef fbc:geneProduct="G_b4035"/> <fbc:geneProductRef fbc:geneProduct="G_b4033"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_14GLUCANtexi" fast="false" reversible="false" name="1,4-alpha-D-glucan transport via diffusion (extracellular to periplasm) irreversible" metaid="R_14GLUCANtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_14GLUCANtexi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/14GLUCANtexi"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94694"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_14glucan_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_14glucan_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4036"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DINStex" fast="false" reversible="true" name="Deoxyinosine transport via diffusion (extracellular to periplasm)" metaid="R_DINStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DINStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DINStex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97466"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08344"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_din_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_din_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHPTPE" fast="false" reversible="true" name="Dihydroneopterin triphosphate 2'-epimerase" metaid="R_DHPTPE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHPTPE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHPTPE"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.99.d"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142300"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08341"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ahdt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhmptp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2303"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPDOy" fast="false" reversible="false" name="Propane-1,2-diol:NADP+ 1-oxidoreductase" metaid="R_PPDOy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPDOy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPDOy"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-15743"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103108"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lald__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12ppd__R_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0325"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FALGTHLs" fast="false" reversible="true" name="Formaldehyde glutathione ligase (spontaneous)" metaid="R_FALGTHLs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FALGTHLs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FALGTHLs"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-2961"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.4.1.22"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06982"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99239"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22488"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22490"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22491"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22489"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7488"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08463"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04791"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hmgth_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTD12pp" fast="false" reversible="false" name="5'-nucleotidase (dIMP) (periplasm)" metaid="R_NTD12pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD12pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD12pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102031"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29386"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29384"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29383"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29385"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11288"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09010"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dimp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_din_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPA2" fast="false" reversible="false" name="Inorganic triphosphatase" metaid="R_PPA2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPA2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPA2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRIPHOSPHATASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.25"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00138"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103069"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14158"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14160"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14157"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14159"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/707"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00106"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2502"/> <fbc:geneProductRef fbc:geneProduct="G_b2744"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DIMPtex" fast="false" reversible="true" name="DIMP transport via diffusion (extracellular to periplasm)" metaid="R_DIMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DIMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DIMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97463"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08342"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dimp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dimp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_hdca_e" fast="false" reversible="false" name="Hexadecanoate (n-C16:0) exchange" metaid="R_EX_hdca_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_hdca_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_hdca_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99101"/> <rdf:li rdf:resource="http://identifiers.org/rhea/45257"/> <rdf:li rdf:resource="http://identifiers.org/rhea/45256"/> <rdf:li rdf:resource="http://identifiers.org/rhea/45258"/> <rdf:li rdf:resource="http://identifiers.org/rhea/45259"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08704"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09848"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09676"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hdca_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_glcr_e" fast="false" reversible="false" name="D-Glucarate exchange" metaid="R_EX_glcr_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_glcr_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glcr_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-204"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100222"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28477"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28476"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28474"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28475"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12442"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08614"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glcr_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GNK" fast="false" reversible="false" name="Gluconokinase" metaid="R_GNK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GNK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GNK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUCONOKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.12"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01737"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100390"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19434"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19436"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19433"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19435"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1845"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01275"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glcn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3437"/> <fbc:geneProductRef fbc:geneProduct="G_b4268"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_HMBS" fast="false" reversible="false" name="Hydroxymethylbilane synthase" metaid="R_HMBS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation 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transport via diffusion (extracellular to periplasm)" metaid="R_DMStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DMStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DMStex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97534"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08359"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10500"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dms_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dms_p" stoichiometry="1" constant="true"/> 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<rdf:li rdf:resource="http://identifiers.org/rhea/27891"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27890"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27892"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27893"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/487"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01367"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ump_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_uri_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4213"/> <fbc:geneProductRef fbc:geneProduct="G_b0383"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3NTD9pp" fast="false" reversible="false" name="3'-nucleotidase (GMP) (periplasm)" metaid="R_3NTD9pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3NTD9pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3NTD9pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14124"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.6"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02148"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94936"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27864"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27865"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27862"/> <rdf:li 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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:or> <fbc:geneProductRef fbc:geneProduct="G_b1761"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3213"/> <fbc:geneProductRef fbc:geneProduct="G_b3212"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_23PDE7pp" fast="false" reversible="false" name="2',3'-cyclic-nucleotide phosphodiesterase (AMP) (periplasm)" metaid="R_23PDE7pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" 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rdf:resource="http://identifiers.org/seed.reaction/rxn02521"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23camp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3amp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4213"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALTptspp" fast="false" reversible="false" name="Galactitol transport via PEP:Pyr PTS (periplasm)" metaid="R_GALTptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALTptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALTptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100018"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08586"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05567"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galt_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_galt1p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2092"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b2094"/> <fbc:geneProductRef fbc:geneProduct="G_b2093"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALURt2rpp" fast="false" reversible="true" name="D-galacturonate transport via proton symport, reversible (periplasm)" metaid="R_GALURt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALURt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALURt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100020"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08588"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05673"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galur_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_galur_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ZN2abcpp" fast="false" reversible="false" name="Zinc (Zn+2) ABC transporter, efflux (periplasm)" metaid="R_ZN2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ZN2abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ZN2abcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5205"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105277"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20622"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20624"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20623"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20621"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13430#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13918"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09388"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_zn2_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"/> <speciesReference species="M_zn2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3469"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CSNtex" fast="false" reversible="true" name="Cytosine transport via diffusion (extracellular to periplasm)" metaid="R_CSNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CSNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CSNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96928"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08267"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_csn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_csn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYCLTDy" fast="false" reversible="false" name="Glycolate dehydrogenase (NADP)" metaid="R_GLYCLTDy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYCLTDy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYCLTDy"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLYOXYLATE-REDUCTASE-NADP+-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.79"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00465"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100332"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-389826"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-389826"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10995"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10994"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10993"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10992"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/159"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00324"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glx_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_glyclt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1033"/> <fbc:geneProductRef fbc:geneProduct="G_b3553"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LYSDC" fast="false" reversible="false" name="Lysine decarboxylase" metaid="R_LYSDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LYSDC"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYSDC"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:LYSDECARBOX-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.18"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00462"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101256"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22353"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22354"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22352"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22355"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/899"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00322"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_15dap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0186"/> <fbc:geneProductRef fbc:geneProduct="G_b4131"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DAAD" fast="false" reversible="false" name="D-Amino acid dehydrogenase" metaid="R_DAAD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAAD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAAD"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.99.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97073"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08291"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1189"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLCNt2rpp" fast="false" reversible="true" name="D-gluconate transport via proton symport, reversible (periplasm)" metaid="R_GLCNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCNt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCNt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-209"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100209"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28834"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28831"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28833"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28832"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08609"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05571"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glcn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glcn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4321"/> <fbc:geneProductRef fbc:geneProduct="G_b4476"/> <fbc:geneProductRef fbc:geneProduct="G_b3415"/> <fbc:geneProductRef fbc:geneProduct="G_b4265"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLCptspp" fast="false" reversible="false" name="D-glucose transport via PEP:Pyr PTS (periplasm)" metaid="R_GLCptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCptspp"/> <rdf:li 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fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b2417"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1819"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b1818"/> <fbc:geneProductRef fbc:geneProduct="G_b1817"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLCRt2rpp" fast="false" reversible="true" name="D-glucarate transport via proton symport, reversible (periplasm)" metaid="R_GLCRt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCRt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li 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symport (periplasm)" metaid="R_GLCt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-7077"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100238"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08616"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05573"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glc__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> 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<fbc:geneProductRef fbc:geneProduct="G_b3927"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_XANt2pp" fast="false" reversible="false" name="Xanthine transport in via proton symport (periplasm)" metaid="R_XANt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_XANt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XANt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-206"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-5076"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105227"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29663"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29665"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b3453"/> <fbc:geneProductRef fbc:geneProduct="G_b3450"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPPNt2rpp" fast="false" reversible="true" name="3-phenylpropionate transport via proton symport, reversible (periplasm)" metaid="R_PPPNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPPNt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPPNt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103135"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09182"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10133"/> </rdf:Bag> </bqbiol:is> 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xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PTRCORNt7pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-211"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103336"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28828"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28830"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28829"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28827"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10182"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09214"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ptrc_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_orn_p" stoichiometry="1" 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<reaction id="R_THDPS" fast="false" reversible="false" name="Tetrahydrodipicolinate succinylase" metaid="R_THDPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THDPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THDPS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TETHYDPICSUCC-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.117"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04365"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104806"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17325"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17327"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17326"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17328"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03031"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thdp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sl2a6o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0166"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACONMT" fast="false" reversible="false" name="Trans-aconitate methyltransferase" metaid="R_ACONMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACONMT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACONMT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2441"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.144"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05763"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95383"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14971"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14970"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14969"/> <rdf:li rdf:resource="http://identifiers.org/rhea/14972"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04016"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acon_T_c" stoichiometry="1" constant="true"/> <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_aconm_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1519"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_XTSNtex" fast="false" reversible="true" name="Xanthosine transport via diffusion (extracellular to periplasm)" metaid="R_XTSNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_XTSNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XTSNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105247"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09382"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_xtsn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_xtsn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ATPM" fast="false" reversible="false" name="ATP maintenance requirement" metaid="R_ATPM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="R_ATPM_lower_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ATPM"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ATPM"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ATPASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.34"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.20"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.53"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.32"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.4.12"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.48"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.40"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.9"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.23"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.22"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.54"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.29"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.17"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.50"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.39"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.19"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.35"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.16"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.4.4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.37"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.4.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.31"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.6"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.4.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.52"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.14"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.51"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.25"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.38"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.33"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.43"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.4.10"/> <rdf:li 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rdf:resource="http://identifiers.org/ec-code/3.6.3.49"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00086"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96131"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13066"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13065"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13068"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13067"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/75"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11300"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09694"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00062"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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 id="R_CYStex" fast="false" reversible="true" name="L-cysteine transport via diffusion (extracellular to periplasm)" metaid="R_CYStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYStex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1924"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97029"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29655"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29656"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29658"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29657"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13465"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08284"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10998"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08286"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cys__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cys__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADPPPS" fast="false" reversible="false" name="NADP phosphatase" metaid="R_NADPPPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADPPPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADPPPS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-5822"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00118"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101798"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28050"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28052"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28053"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28051"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/697"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00088"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_EX_mnl_e" fast="false" reversible="false" name="D-Mannitol exchange" metaid="R_EX_mnl_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_mnl_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mnl_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101678"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08950"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mnl_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_THRD_L" fast="false" reversible="false" name="L-threonine deaminase" metaid="R_THRD_L" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THRD_L"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRD_L"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THREDEHYD-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.19"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00996"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104714"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22108"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22111"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22109"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22110"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1290"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00737"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_thr__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2obut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3772"/> <fbc:geneProductRef fbc:geneProduct="G_b3117"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_malt_e" fast="false" reversible="false" name="Maltose exchange" metaid="R_EX_malt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_malt_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_malt_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14351"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-575"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1741"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101364"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33173"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33172"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33171"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33174"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11211"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08874"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_malt_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_NTD3" fast="false" reversible="false" name="5'-nucleotidase (dCMP)" metaid="R_NTD3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD3"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5292"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.89"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01664"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102033"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29364"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29365"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29366"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29363"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/480"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01218"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dcyt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2744"/> <fbc:geneProductRef fbc:geneProduct="G_b2291"/> <fbc:geneProductRef fbc:geneProduct="G_b2361"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYTDtex" fast="false" reversible="true" name="Cytidine transport via diffusion (extracellular to periplasm)" metaid="R_CYTDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYTDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYTDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97043"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13338"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08290"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10997"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cytd_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cytd_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYOX" fast="false" reversible="false" name="Hydroxyacylglutathione hydrolase" metaid="R_GLYOX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYOX"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYOX"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLYOXII-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.6"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01736"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100353"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25246"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25247"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25245"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25248"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/9752"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/283"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01274"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lgt__S_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lac__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0212"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DADNtex" fast="false" reversible="true" name="Deoxyadenosine transport via diffusion (extracellular to periplasm)" metaid="R_DADNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DADNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DADNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97081"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08293"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10939"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dad_2_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dad_2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0411"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_4PEPTtex" fast="false" reversible="true" name="LalaDgluMdapDala (pentapeptide) transport via diffusion (extracellular to periplasm)" metaid="R_4PEPTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_4PEPTtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4PEPTtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95051"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08009"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDgluMdapDala_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDgluMdapDala_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NAMNPP" fast="false" reversible="false" name="Nicotinic acid mononucleotide pyrophosphorylase" metaid="R_NAMNPP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NAMNPP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NAMNPP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:NICOTINATEPRIBOSYLTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.4.21"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01724"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101909"/> <rdf:li rdf:resource="http://identifiers.org/rhea/36164"/> <rdf:li rdf:resource="http://identifiers.org/rhea/36163"/> <rdf:li rdf:resource="http://identifiers.org/rhea/36166"/> <rdf:li rdf:resource="http://identifiers.org/rhea/36165"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08981"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nicrnt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0931"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_pnto__R_e" fast="false" reversible="false" name="(R)-Pantothenate exchange" metaid="R_EX_pnto__R_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_pnto__R_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pnto__R_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103051"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34978"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34975"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34976"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34977"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09166"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pnto__R_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_SELNPS" fast="false" reversible="false" name="Selenophosphate synthase" metaid="R_SELNPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SELNPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SELNPS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2.7.9.3-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.9.3"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03595"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104322"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18740"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18739"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18737"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18738"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02569"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_seln_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_selnp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1764"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHAtex" fast="false" reversible="true" name="Dihydroxyacetone transport via diffusion (extracellular to periplasm)" metaid="R_DHAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHAtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-559"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97367"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08325"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08326"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05532"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dha_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dha_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ETOHtex" fast="false" reversible="true" name="Ethanol transport via diffusion (extracellular to periplasm)" metaid="R_ETOHtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ETOHtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ETOHtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-546"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97980"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35269"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35267"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35270"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35268"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09683"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08428"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09764"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_etoh_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_etoh_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MTRPOX" fast="false" reversible="false" name="N-methyltryptophan oxidase" metaid="R_MTRPOX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MTRPOX"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MTRPOX"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-301"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.3.2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101761"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28009"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28008"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28006"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28007"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7294"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08965"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_Nmtrp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trp__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1059"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGM4PCPpp" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase (periplasmic)" metaid="R_AGM4PCPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGM4PCPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM4PCPpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95547"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08077"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm4p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_anhgm3p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2175"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GTPDPDP" fast="false" reversible="false" name="Guanosine-5'-triphosphate,3'-diphosphate diphosphatase" metaid="R_GTPDPDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GTPDPDP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GTPDPDP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PPPGPPHYDRO-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.40"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.11"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03409"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100099"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13074"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13073"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13075"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13076"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02449"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gdptp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppgpp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3779"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CRNCAR" fast="false" reversible="true" name="Carnitine-CoA racemase" metaid="R_CRNCAR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNCAR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNCAR"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CARNCOARACE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96896"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30541"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30542"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30539"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30540"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_crncoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_crnDcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0036"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALabcpp" fast="false" reversible="false" name="D-galactose transport via ABC system (periplasm)" metaid="R_GALabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-18-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.17"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100023"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08573"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05162"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gal_p" 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_gal_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:and> <fbc:geneProductRef fbc:geneProduct="G_b2148"/> <fbc:geneProductRef fbc:geneProduct="G_b2149"/> <fbc:geneProductRef fbc:geneProduct="G_b2150"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4227"/> <fbc:geneProductRef fbc:geneProduct="G_b4230"/> <fbc:geneProductRef fbc:geneProduct="G_b4485"/> <fbc:geneProductRef fbc:geneProduct="G_b4231"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYCLTt2rpp" fast="false" reversible="true" name="Glycolate transport via proton symport, reversible (periplasm)" metaid="R_GLYCLTt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYCLTt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYCLTt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-105"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100334"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29414"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29413"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29411"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29412"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05470"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08651"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyclt_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyclt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3603"/> <fbc:geneProductRef fbc:geneProduct="G_b2975"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GUAt2pp" fast="false" reversible="false" name="Guanine transport in via proton symport (periplasm)" metaid="R_GUAt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GUAt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GUAt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100466"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08681"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05203"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gua_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gua_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3654"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HPPPNt2rpp" fast="false" reversible="true" name="3-(3-hydroxyphenyl)propionate transport via proton symport, reversible (periplasm)" metaid="R_HPPPNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HPPPNt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HPPPNt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-61"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100696"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28910"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28907"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28909"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28908"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08725"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10134"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hpppn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3hpppn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0353"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RNDR2" fast="false" reversible="false" name="Ribonucleoside-diphosphate reductase (GDP)" metaid="R_RNDR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RNDR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNDR2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GDPREDUCT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.17.4.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02019"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104062"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05233"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dgdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3781"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2234"/> <fbc:geneProductRef fbc:geneProduct="G_b2235"/> </fbc:and> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2582"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2234"/> <fbc:geneProductRef fbc:geneProduct="G_b2235"/> </fbc:and> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_asn__L_e" fast="false" reversible="false" name="L-Asparagine exchange" metaid="R_EX_asn__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_asn__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_asn__L_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96069"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13466"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05220"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08162"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asn__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ANHMK" fast="false" reversible="false" name="1,6-anhydrous-N-Acetylmuramate kinase" metaid="R_ANHMK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ANHMK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ANHMK"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95840"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08136"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhm_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acmum6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1640"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DCAtex" fast="false" reversible="true" name="Decanoate transport via diffusion (extracellular to periplasm)" metaid="R_DCAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DCAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DCAtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97181"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dca_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef 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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_skm5p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3390"/> <fbc:geneProductRef fbc:geneProduct="G_b0388"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DCYTtex" fast="false" reversible="true" name="Deoxycytidine transport via diffusion (extracellular to periplasm)" metaid="R_DCYTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DCYTtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DCYTtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97208"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08317"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11014"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcyt_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dcyt_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0411"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_gam_e" fast="false" reversible="false" name="D-Glucosamine exchange" metaid="R_EX_gam_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_gam_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gam_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100035"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08593"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gam_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ACACtex" fast="false" reversible="true" name="Acetoacetate transport via diffusion (extracellular to periplasm)" metaid="R_ACACtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACACtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACACtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-281"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95208"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29753"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29752"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29754"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29751"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12476"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08030"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10960"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13115"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acac_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acac_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACNAMtex" fast="false" reversible="true" name="N-acetylneuraminate transport via diffusion (extracellular to periplasm)" metaid="R_ACNAMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACNAMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACNAMtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-15315"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-0"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95292"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28994"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28993"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28992"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28991"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08051"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acnam_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acnam_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4311"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARBTNabcpp" fast="false" reversible="false" name="Aerobactin transport via ABC system (periplasm)" metaid="R_ARBTNabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBTNabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95927"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13800"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08143"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbtn_fe3_p" stoichiometry="1" constant="true"/> <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_arbtn_fe3_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_b0151"/> <fbc:geneProductRef fbc:geneProduct="G_b0153"/> <fbc:geneProductRef fbc:geneProduct="G_b0152"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_inost_e" fast="false" reversible="false" name="Myo-Inositol exchange" metaid="R_EX_inost_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_inost_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_inost_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100848"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32867"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32869"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32870"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32868"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08755"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_inost_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_mobd_e" fast="false" reversible="true" name="Molybdate exchange" metaid="R_EX_mobd_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_mobd_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mobd_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101690"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34909"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34907"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34910"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34908"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08956"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mobd_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_NNDMBRT" fast="false" reversible="false" name="Nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase" metaid="R_NNDMBRT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NNDMBRT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NNDMBRT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DMBPPRIBOSYLTRANS-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.21"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04148"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101979"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11196"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11197"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11199"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11198"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02897"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dmbzid_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nicrnt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5prdmbz_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nac_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1991"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DGSNtex" fast="false" reversible="true" name="Deoxyguanosine transport via diffusion (extracellular to periplasm)" metaid="R_DGSNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DGSNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DGSNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97324"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08324"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dgsn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dgsn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_THRA2" fast="false" reversible="false" name="L-allo-Threonine Aldolase" metaid="R_THRA2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THRA2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRA2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_athr__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2551"/> <fbc:geneProductRef fbc:geneProduct="G_b0870"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASO3t8pp" fast="false" reversible="false" name="Arsenite efflux via ATP hydrolysis (periplasm)" metaid="R_ASO3t8pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASO3t8pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASO3t8pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.16-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.16"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96072"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11351#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11348#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11350#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11349#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08163"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_aso3_c" stoichiometry="1" constant="true"/> <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_aso3_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3502"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_H2Stex" fast="false" reversible="true" name="H2s transport via diffusion (extracellular to periplasm)" metaid="R_H2Stex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_H2Stex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/H2Stex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-310"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100494"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08690"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08689"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10541"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2s_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2s_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPK" fast="false" reversible="false" name="Polyphosphate kinase" metaid="R_PPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPK"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2501"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_so4_e" fast="false" reversible="true" name="Sulfate exchange" metaid="R_EX_so4_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> 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<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04189"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104239"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19534"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19535"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19533"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19536"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02927"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_sucarg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="2" constant="true"/> <speciesReference species="M_sucorn_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1745"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLUSy" fast="false" reversible="false" name="Glutamate synthase (NADPH)" metaid="R_GLUSy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLUSy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLUSy"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUTAMATESYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.1.13"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00114"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100291"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b3213"/> <fbc:geneProductRef fbc:geneProduct="G_b3212"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_GUAPRT" fast="false" reversible="false" name="Guanine phosphoribosyltransferase" metaid="R_GUAPRT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GUAPRT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GUAPRT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GUANPRIBOSYLTRAN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.7"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.22"/> <rdf:li 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fbc:geneProduct="G_b0125"/> <fbc:geneProductRef fbc:geneProduct="G_b0238"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_phe__L_e" fast="false" reversible="false" name="L-Phenylalanine exchange" metaid="R_EX_phe__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_phe__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_phe__L_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-445"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102637"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27952"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27951"/> <rdf:li 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xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_thr__L_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104852"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35022"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35020"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35019"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35021"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13464"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09307"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13117"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10898"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_thr__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_uri_e" fast="false" reversible="false" name="Uridine exchange" metaid="R_EX_uri_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_uri_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_uri_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105165"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10987"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09372"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_uri_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_OMCDC" fast="false" reversible="false" name="2-Oxo-4-methyl-3-carboxypentanoate decarboxylation" metaid="R_OMCDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OMCDC"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OMCDC"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-7800"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.85"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01652"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102180"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25078"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25080"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25081"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25079"/> <rdf:li 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rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100755"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08736"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10117"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dmmq8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0973"/> <fbc:geneProductRef fbc:geneProduct="G_b0974"/> <fbc:geneProductRef fbc:geneProduct="G_b0972"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2994"/> <fbc:geneProductRef fbc:geneProduct="G_b2997"/> <fbc:geneProductRef fbc:geneProduct="G_b2996"/> <fbc:geneProductRef fbc:geneProduct="G_b2995"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NO3R1pp" fast="false" reversible="false" name="Nitrate reductase (Ubiquinol-8) (periplasm)" metaid="R_NO3R1pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NO3R1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO3R1pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101986"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29149#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29148#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29150#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29147#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09001"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10120"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_no3_c" stoichiometry="1" 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_p" stoichiometry="2" constant="true"/> <speciesReference species="M_no2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1467"/> <fbc:geneProductRef fbc:geneProduct="G_b1468"/> <fbc:geneProductRef fbc:geneProduct="G_b1466"/> <fbc:geneProductRef fbc:geneProduct="G_b1465"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1224"/> <fbc:geneProductRef fbc:geneProduct="G_b1227"/> <fbc:geneProductRef fbc:geneProduct="G_b1226"/> <fbc:geneProductRef fbc:geneProduct="G_b1225"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTP5" fast="false" reversible="false" name="Nucleoside-triphosphatase (CTP)" metaid="R_NTP5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTP5"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTP5"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12195"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.15"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00569"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102045"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29389"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29387"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29388"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29390"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00408"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4161"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CELBpts" fast="false" reversible="false" name="Cellobiose transport via PEPPyr PTS" metaid="R_CELBpts" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CELBpts"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CELBpts"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96586"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cellb_e" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_6pgg_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_b2715"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1738"/> <fbc:geneProductRef fbc:geneProduct="G_b1737"/> <fbc:geneProductRef fbc:geneProduct="G_b1736"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FORt2pp" fast="false" reversible="false" name="Formate transport via proton symport (uptake only, periplasm)" metaid="R_FORt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FORt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FORt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99621"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08524"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05559"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_for_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" 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 id="R_EX_r5p_e" fast="false" reversible="false" name="Alpha-D-Ribose 5-phosphate exchange" metaid="R_EX_r5p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_r5p_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_r5p_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103411"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_r5p_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_glyc2p_e" fast="false" reversible="false" name="Glycerol 2-phosphate exchange" metaid="R_EX_glyc2p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_glyc2p_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glyc2p_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100319"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08640"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc2p_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_MTAN" fast="false" reversible="false" name="Methylthioadenosine nucleosidase" metaid="R_MTAN" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MTAN"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MTAN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:METHYLTHIOADENOSINE-NUCLEOSIDASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.9"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01401"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101744"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13620"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13619"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13617"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13618"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1593"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01021"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5mta_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5mtr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0159"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DPR" fast="false" reversible="false" name="2-dehydropantoate 2-reductase" metaid="R_DPR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DPR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DPR"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2-DEHYDROPANTOATE-REDUCT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.169"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02472"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97779"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16233"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16234"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16235"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16236"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2405"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01790"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dhp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pant__R_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0425"/> <fbc:geneProductRef fbc:geneProduct="G_b3774"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_halipa_e" fast="false" reversible="false" name="Hepta-acylated KDO(2)-lipid (A) exchange" metaid="R_EX_halipa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_halipa_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_halipa_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143009"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_halipa_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_AACPS5" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase (n-C18:1)" metaid="R_AACPS5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AACPS5"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AACPS5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95144"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_MANptspp" fast="false" reversible="false" name="D-mannose transport via PEP:Pyr PTS (periplasm)" metaid="R_MANptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MANptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MANptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101401"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05610"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08885"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_man_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_man6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1819"/> <fbc:geneProductRef fbc:geneProduct="G_b1818"/> <fbc:geneProductRef fbc:geneProduct="G_b1817"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_cmp_e" fast="false" reversible="false" name="CMP exchange" metaid="R_EX_cmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cmp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cmp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96806"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08236"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09776"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cmp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_NTD8" fast="false" reversible="false" name="5'-nucleotidase (dGMP)" metaid="R_NTD8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD8"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD8"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14142"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.89"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01968"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102038"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29382"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29380"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29381"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29379"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/304"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01445"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dgmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dgsn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2744"/> <fbc:geneProductRef fbc:geneProduct="G_b2291"/> <fbc:geneProductRef fbc:geneProduct="G_b3399"/> <fbc:geneProductRef fbc:geneProduct="G_b2361"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALCTD" fast="false" reversible="false" name="Galactarate dehydratase" metaid="R_GALCTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALCTD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALCTD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GALACTARDEHYDRA-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.42"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05608"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99955"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16008"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16006"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16005"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16007"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03887"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galct__D_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5dh4dglc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3128"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_malthx_e" fast="false" reversible="false" name="Maltohexaose exchange" metaid="R_EX_malthx_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_malthx_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_malthx_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101354"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08870"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_malthx_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_MLTG4" fast="false" reversible="false" name="Maltodextrin glucosidase (maltohexaose)" metaid="R_MLTG4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLTG4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTG4"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14282"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.20"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101622"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08935"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_maltpt_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0403"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UDPGDC" fast="false" reversible="false" name="UDP-glucuronate C-4'' decarboxylase" metaid="R_UDPGDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDPGDC"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGDC"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1861"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.305"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07658"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105064"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24703"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24705"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24704"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24702"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12883"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07473"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09351"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpglcur_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_udpLa4o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2255"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PUNP4" fast="false" reversible="true" name="Purine-nucleoside phosphorylase (Deoxyguanosine)" metaid="R_PUNP4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PUNP4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PUNP4"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DEOXYGUANPHOSPHOR-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01969"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103346"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27741"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27738"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27740"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27739"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/360"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01446"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dgsn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2dr1p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gua_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2407"/> <fbc:geneProductRef fbc:geneProduct="G_b4384"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_AMAOTr" fast="false" reversible="true" name="Adenosylmethionine-8-amino-7-oxononanoate transaminase" metaid="R_AMAOTr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMAOTr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMAOTr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DAPASYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.62"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03231"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95806"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16863"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16861"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16862"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16864"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/3057"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02312"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_8aonn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amob_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dann_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0774"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_csn_e" fast="false" reversible="false" name="Cytosine exchange" metaid="R_EX_csn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_csn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_csn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96928"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08267"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_csn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_etoh_e" fast="false" reversible="false" name="Ethanol exchange" metaid="R_EX_etoh_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_etoh_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_etoh_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-546"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97980"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35269"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35267"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35270"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35268"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09683"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08428"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09764"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_etoh_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_G6PP" fast="false" reversible="false" name="Glucose-6-phosphate phosphatase" metaid="R_G6PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G6PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G6PP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-526"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.9"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.58"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00303"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99912"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16691"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16689"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16692"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16690"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7713"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/796"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00220"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/> 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<rdf:Description rdf:about="#R_UPLA4FNT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UPLA4FNT"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105133"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udcpp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpLa4fn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_uLa4fn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2254"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UPLA4FNF" fast="false" reversible="false" name="Undecaprenyl phosphate-L-Ara4FN formylase" metaid="R_UPLA4FNF" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UPLA4FNF"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UPLA4FNF"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105132"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09363"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uLa4fn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uLa4n_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2256"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ULA4Ntppi" fast="false" reversible="false" name="Transport (cytoplasm to periplasm)" metaid="R_ULA4Ntppi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ULA4Ntppi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ULA4Ntppi"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105114"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09357"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_uLa4n_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_uLa4n_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2258"/> <fbc:geneProductRef fbc:geneProduct="G_b4544"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_HEPT1" fast="false" reversible="false" name="Heptosyltransferase I (LPS core synthesis)" metaid="R_HEPT1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HEPT1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HEPT1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100602"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28404"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28405"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28402"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28403"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08710"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adphep_LD_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lipa_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_hlipa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3621"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FALDtex" fast="false" reversible="true" name="Formaldehyde transport via diffusion (extracellular to periplasm)" metaid="R_FALDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FALDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FALDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99238"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08461"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08462"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fald_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fald_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MCITD" fast="false" reversible="false" name="2-methylcitrate dehydratase" metaid="R_MCITD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MCITD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MCITD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2-METHYLCITRATE-DEHYDRATASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.79"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04424"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101413"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17725"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17728"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17726"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17727"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/4111"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03060"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2mcit_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2mcacn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0334"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CU2tex" fast="false" reversible="true" name="Copper (Cu+2) transport via diffusion (extracellular to periplasm)" metaid="R_CU2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CU2tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CU2tex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-14"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96951"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-437300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-437300"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28705"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28706"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28704"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28703"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08274"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05212"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08273"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cu2_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cu2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_glcur1p_e" fast="false" reversible="false" name="D-Glucuronate 1-phosphate exchange" metaid="R_EX_glcur1p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_glcur1p_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glcur1p_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100231"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08621"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glcur1p_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GLCATr" fast="false" reversible="true" name="D-glucose O-acetyltransferase" metaid="R_GLCATr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCATr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCATr"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.79"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143129"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08607"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acglc__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0459"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALR2" fast="false" reversible="false" name="Aldose reductase (methylglyoxal)" metaid="R_ALR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALR2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-4281"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02528"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95788"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27986"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27988"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27987"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27989"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2450"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01832"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mthgxl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acetol_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3012"/> <fbc:geneProductRef fbc:geneProduct="G_b0207"/> <fbc:geneProductRef fbc:geneProduct="G_b1781"/> <fbc:geneProductRef fbc:geneProduct="G_b3001"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_AMALT2" fast="false" reversible="false" name="Amylomaltase (maltotetraose)" metaid="R_AMALT2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMALT2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMALT2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14260"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.25"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95801"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08127"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_maltttr_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_maltpt_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3416"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLTP1" fast="false" reversible="true" name="Maltodextrin phosphorylase (maltopentaose)" metaid="R_MLTP1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLTP1"> <bqbiol:is 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stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_HXAND" fast="false" reversible="false" name="Hypoxanthine dehydrogenase" metaid="R_HXAND" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HXAND"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HXAND"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-7682"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.17.1.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01768"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100747"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-421161"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24671"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24672"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24670"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24673"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/323"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01297"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hxan_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_xan_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2866"/> <fbc:geneProductRef fbc:geneProduct="G_b2867"/> <fbc:geneProductRef fbc:geneProduct="G_b2868"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_fald_e" fast="false" reversible="false" name="Formaldehyde exchange" metaid="R_EX_fald_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_fald_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fald_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99238"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08461"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08462"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fald_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_pydxn_e" fast="false" reversible="false" name="Pyridoxine exchange" metaid="R_EX_pydxn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_pydxn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pydxn_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-205"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103364"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28472"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28470"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28473"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28471"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13097"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pydxn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_acgal_e" fast="false" reversible="false" name="N-Acetyl-D-galactosamine exchange" metaid="R_EX_acgal_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_acgal_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_acgal_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95244"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08037"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgal_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_so2_e" fast="false" reversible="false" name="Sulfur dioxide exchange" metaid="R_EX_so2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_so2_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_so2_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104456"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09258"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09259"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_so2_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_dms_e" fast="false" reversible="false" name="Dimethyl sulfide exchange" metaid="R_EX_dms_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dms_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dms_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97534"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08359"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10500"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dms_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GMPtex" fast="false" reversible="true" name="GMP transport via diffusion (extracellular to periplasm)" metaid="R_GMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GMPtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-565"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100386"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08664"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gmp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gmp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_IMPtex" fast="false" reversible="true" name="IMP transport via diffusion (extracellular to periplasm)" metaid="R_IMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_IMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/IMPtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-566"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100831"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08749"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_imp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_imp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PItex" fast="false" reversible="true" name="Glycero-3-phospho-1-inositol transport via diffusion (extracellular to periplasm)" metaid="R_G3PItex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PItex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PItex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99888"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32918"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32917"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32916"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32915"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13292"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08564"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pi_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CD2abcpp" fast="false" reversible="false" name="Cadmium (Cd+2) ABC transporter (periplasm)" metaid="R_CD2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CD2abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CD2abcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.3-RXN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.46-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.46"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96495"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12134#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12135#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12133#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12132#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05516"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08195"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cd2_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_cd2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3469"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PGtex" fast="false" reversible="true" name="Glycerophoglycerol transport via diffusion (extracellular to periplasm)" metaid="R_G3PGtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PGtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PGtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99886"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08562"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pg_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PEtex" fast="false" reversible="true" name="Glycero-3-phosphoethanolamine transport via diffusion (extracellular to periplasm)" metaid="R_G3PEtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PEtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PEtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99884"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08560"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pe_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PCtex" fast="false" reversible="true" name="Glycero-3-phosphocholine transport via diffusion (extracellular to periplasm)" metaid="R_G3PCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PCtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PCtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99874"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32912"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32911"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32913"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32914"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08554"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13291"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pc_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MOAT3C" fast="false" reversible="false" name="3-deoxy-D-manno-octulosonic acid transferase III (LPS core biosynthesis)" metaid="R_MOAT3C" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MOAT3C"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOAT3C"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101686"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08954"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ckdo_c" stoichiometry="1" constant="true"/> <speciesReference species="M_phphhlipa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_kphphhlipa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3624"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UMPtex" fast="false" reversible="true" name="UMP transport via diffusion (extracellular to periplasm)" metaid="R_UMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105127"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27927"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27929"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27926"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27928"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09808"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09361"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ump_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_G1Ptex" fast="false" reversible="true" name="D-glucose 1-phosphate transport via diffusion" metaid="R_G1Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G1Ptex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G1Ptex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99849"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08545"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g1p_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g1p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADNK1" fast="false" reversible="false" name="Adenosine kinase" metaid="R_ADNK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADNK1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADNK1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ADENOSINE-KINASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.74"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.20"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00185"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95456"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20827"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20824"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20826"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20825"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/252"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00134"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0474"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CUt3" fast="false" reversible="false" name="Copper transport out via proton antiport" metaid="R_CUt3" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CUt3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CUt3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96953"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cu_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cu_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0572"/> <fbc:geneProductRef fbc:geneProduct="G_b0574"/> <fbc:geneProductRef fbc:geneProduct="G_b0573"/> <fbc:geneProductRef fbc:geneProduct="G_b0575"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ZN2t3pp" fast="false" reversible="false" name="Zinc (Zn+2) transport out via proton antiport (periplasm)" metaid="R_ZN2t3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ZN2t3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ZN2t3pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-200"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105278"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28842"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28840"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28841"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28839"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13919"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09389"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_zn2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_zn2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3915"/> <fbc:geneProductRef fbc:geneProduct="G_b0752"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SKMtex" fast="false" reversible="true" name="Shikimate transport via diffusion (extracellular to periplasm)" metaid="R_SKMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SKMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SKMtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104394"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09257"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_skm_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_skm_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MNt2pp" fast="false" reversible="false" name="Manganese (Mn+2) transport in via proton symport (periplasm)" metaid="R_MNt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MNt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MNt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-241"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101681"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29007"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29010"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29008"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29009"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05618"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08951"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mn2_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mn2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2392"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RHAT1" fast="false" reversible="false" name="Rhamnosyltransferase I (LPS core biosynthesis)" metaid="R_RHAT1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RHAT1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RHAT1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104025"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dtdprmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_kphphhlipa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dtdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_icolipa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3629"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLCabcpp" fast="false" reversible="false" name="D-glucose transport via ABC system (periplasm)" metaid="R_GLCabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-320"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.17"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100236"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08606"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05147"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glc__D_p" 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_glc__D_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_b2149"/> <fbc:geneProductRef fbc:geneProduct="G_b2148"/> <fbc:geneProductRef fbc:geneProduct="G_b2150"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALT1" fast="false" reversible="false" name="Galactosyltransferase I (LPS core synthesis)" metaid="R_GALT1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALT1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALT1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143120"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08583"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gicolipa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gagicolipa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3628"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MNtex" fast="false" reversible="true" name="Manganese (Mn+2) transport via diffusion (extracellular to periplasm)" metaid="R_MNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MNtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-16"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-487"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101670"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28702"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28699"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28700"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28701"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08952"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08947"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mn2_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mn2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GAL1Ptex" fast="false" reversible="true" name="D-galactose 1-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_GAL1Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GAL1Ptex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GAL1Ptex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99923"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08572"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gal1p_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gal1p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLCTR2" fast="false" reversible="false" name="Glucosyltransferase II (LPS core synthesis)" metaid="R_GLCTR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCTR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCTR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143138"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08619"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gagicolipa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ggagicolipa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3627"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G2PPpp" fast="false" reversible="false" name="Glycerol 2-phosphate phosphatase (periplasmic)" metaid="R_G2PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G2PPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G2PPpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLYCEROL-2-PHOSPHATASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.19"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01043"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99852"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13106"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13108"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13107"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13105"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1325"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00766"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc2p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4055"/> <fbc:geneProductRef fbc:geneProduct="G_b0383"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_UDPGPpp" fast="false" reversible="false" name="UDPglucose pyrophosphohydrolase" metaid="R_UDPGPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDPGPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGPpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.45"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.9"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00287"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143430"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-6810464"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-6810464"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-6810464"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-6810464"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-6810464"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6810464"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-6810464"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-6810464"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-6810464"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-6810464"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-6810464"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29558"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29557"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29555"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29556"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/446"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00212"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udpg_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g1p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0480"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_acgal1p_e" fast="false" reversible="false" name="N-Acetyl-D-galactosamine 1-phosphate exchange" metaid="R_EX_acgal1p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_acgal1p_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_acgal1p_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95234"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08036"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgal1p_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_cyan_e" fast="false" reversible="false" name="Hydrogen cyanide exchange" metaid="R_EX_cyan_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cyan_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cyan_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96957"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08276"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cyan_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_tyrp_e" fast="false" reversible="false" name="Phosphotyrosine exchange" metaid="R_EX_tyrp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_tyrp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tyrp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104999"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09337"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tyrp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_O2Stex" fast="false" reversible="true" name="Superoxide anion transport via diffusion (extracellular to periplasm)" metaid="R_O2Stex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O2Stex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O2Stex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102089"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1222342"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o2s_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_o2s_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_HEPK1" fast="false" reversible="false" name="LPS heptose kinase I (LPS core synthesis)" metaid="R_HEPK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HEPK1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HEPK1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138511"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08708"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hhlipa_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_phhlipa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3630"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HEPT3" fast="false" reversible="false" name="Heptosyltransferase III (LPS core synthesis)" metaid="R_HEPT3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HEPT3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HEPT3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100606"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08712"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adphep_LD_c" stoichiometry="1" constant="true"/> <speciesReference species="M_phhlipa_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_hphhlipa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3632"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HEPK2" fast="false" reversible="false" name="LPS heptose kinase II (LPS core synthesis)" metaid="R_HEPK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HEPK2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HEPK2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138512"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08709"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hphhlipa_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_phphhlipa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3625"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALDD3y" fast="false" reversible="false" name="Aldehyde dehydrogenase (propanal, NADP)" metaid="R_ALDD3y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALDD3y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALDD3y"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95754"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppal_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3588"/> <fbc:geneProductRef fbc:geneProduct="G_b4269"/> <fbc:geneProductRef fbc:geneProduct="G_b3011"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_uacgam_e" fast="false" reversible="false" name="UDP-N-acetyl-D-glucosamine exchange" metaid="R_EX_uacgam_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_uacgam_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_uacgam_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105021"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-742354"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-742354"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09342"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_uacgam_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_Kt3pp" fast="false" reversible="false" name="Potassium transport out via proton antiport (periplasm)" metaid="R_Kt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_Kt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/Kt3pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-42"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100939"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29470"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29467"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29468"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29469"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05596"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08770"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_k_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_k_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3350"/> <fbc:geneProductRef fbc:geneProduct="G_b0047"/> <fbc:geneProductRef fbc:geneProduct="G_b1216"/> <fbc:geneProductRef fbc:geneProduct="G_b0842"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_udpacgal_e" fast="false" reversible="false" name="UDP-N-acetyl-D-galactosamine exchange" metaid="R_EX_udpacgal_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_udpacgal_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_udpacgal_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105046"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09347"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udpacgal_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_udpg_e" fast="false" reversible="false" name="UDPglucose exchange" metaid="R_EX_udpg_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_udpg_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_udpg_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143086"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11025"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09353"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udpg_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_udpgal_e" fast="false" reversible="false" name="UDPgalactose exchange" metaid="R_EX_udpgal_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_udpgal_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_udpgal_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105061"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09349"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13413"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udpgal_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_udpglcur_e" fast="false" reversible="false" name="UDP-D-glucuronate exchange" metaid="R_EX_udpglcur_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_udpglcur_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_udpglcur_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105066"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09352"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udpglcur_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_14glucan_e" fast="false" reversible="false" name="1,4-alpha-D-glucan exchange" metaid="R_EX_14glucan_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_14glucan_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_14glucan_e"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94694"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_14glucan_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_pser__L_e" fast="false" reversible="false" name="O-Phospho-L-serine exchange" metaid="R_EX_pser__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_pser__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pser__L_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103246"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09204"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pser__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_R5PP" fast="false" reversible="false" name="Ribose 5-phosphate phosphatase" metaid="R_R5PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_R5PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/R5PP"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103410"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0822"/> <fbc:geneProductRef fbc:geneProduct="G_b2690"/> <fbc:geneProductRef fbc:geneProduct="G_b0675"/> <fbc:geneProductRef fbc:geneProduct="G_b2293"/> <fbc:geneProductRef fbc:geneProduct="G_b3697"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_xmp_e" fast="false" reversible="false" name="Xanthosine 5'-phosphate exchange" metaid="R_EX_xmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_xmp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_xmp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105231"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09380"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_xmp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_damp_e" fast="false" reversible="false" name="DAMP exchange" metaid="R_EX_damp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_damp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_damp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97136"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08303"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_damp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_CYSSADS" fast="false" reversible="false" name="L-cysteine sulfinic acid desulfurase" metaid="R_CYSSADS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYSSADS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYSSADS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.12"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.4.1.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00863"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97008"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1198"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00624"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3sala_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_so2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2810"/> <fbc:geneProductRef fbc:geneProduct="G_b1680"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_dimp_e" fast="false" reversible="false" name="DIMP exchange" metaid="R_EX_dimp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dimp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dimp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97463"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08342"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dimp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_CPPPGO2" fast="false" reversible="false" name="Oxygen Independent coproporphyrinogen-III oxidase" metaid="R_CPPPGO2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPPPGO2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPPPGO2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:HEMN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.98.3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.22"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06895"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96881"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15425"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15427"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15428"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15426"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04704"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/> <speciesReference species="M_cpppg3_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_dad_5_c" stoichiometry="2" constant="true"/> <speciesReference species="M_met__L_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pppg9_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3867"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_isetac_e" fast="false" reversible="false" name="Isethionic acid exchange" metaid="R_EX_isetac_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_isetac_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_isetac_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100881"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08759"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_isetac_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_AGM3PH" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide beta -1,4-N-acetylglucosaminidase" metaid="R_AGM3PH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGM3PH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM3PH"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95544"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08074"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam_c" stoichiometry="1" constant="true"/> <speciesReference species="M_anhm3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1107"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HOMt2pp" fast="false" reversible="false" name="L-homoserineserine efflux via proton symport" metaid="R_HOMt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HOMt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HOMt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-242"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100676"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29004"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29003"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29005"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29006"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08722"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hom__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hom__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0813"/> <fbc:geneProductRef fbc:geneProduct="G_b3824"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_aso3_e" fast="false" reversible="false" name="Arsenite exchange" metaid="R_EX_aso3_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_aso3_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_aso3_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-551"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96073"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05507"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08164"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_aso3_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_tcynt_e" fast="false" reversible="false" name="Thiocyanate exchange" metaid="R_EX_tcynt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_tcynt_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tcynt_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104749"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09287"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tcynt_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_fe3dhbzs_e" fast="false" reversible="false" name="Ferric 2,3-dihydroxybenzoylserine exchange" metaid="R_EX_fe3dhbzs_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_fe3dhbzs_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fe3dhbzs_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142960"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3dhbzs_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_AGM3PApp" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase (periplasm)" metaid="R_AGM3PApp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGM3PApp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM3PApp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95543"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08073"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDgluMdap_p" stoichiometry="1" constant="true"/> <speciesReference species="M_anhgm_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4169"/> <fbc:geneProductRef fbc:geneProduct="G_b2435"/> <fbc:geneProductRef fbc:geneProduct="G_b2817"/> <fbc:geneProductRef fbc:geneProduct="G_b0867"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPPGO" fast="false" reversible="false" name="Protoporphyrinogen oxidase (aerobic)" metaid="R_PPPGO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPPGO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPPGO"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.3.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103128"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-421452"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/3048"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09179"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02304"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o2_c" stoichiometry="1.5" constant="true"/> <speciesReference species="M_pppg9_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="3" constant="true"/> <speciesReference species="M_ppp9_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3850"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_feoxam_un_e" fast="false" reversible="false" name="Ferroxamine minus Fe(3) exchange" metaid="R_EX_feoxam_un_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_feoxam_un_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_feoxam_un_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142966"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_feoxam_un_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_HOMtex" fast="false" reversible="true" name="L-homoserine transport via diffusion (extracellular to periplasm)" metaid="R_HOMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HOMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HOMtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100678"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08723"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hom__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hom__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SO2tex" fast="false" reversible="true" name="SO2 transport via diffusion (extracellular to periplasm)" metaid="R_SO2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SO2tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SO2tex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104456"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09258"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09259"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_so2_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_so2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SO2tpp" fast="false" reversible="true" name="SO2 transport via diffusion (periplasm)" metaid="R_SO2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SO2tpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SO2tpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104456"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09258"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09259"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_so2_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_so2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LDH_D2" fast="false" reversible="false" name="D-lactate dehydrogenase" metaid="R_LDH_D2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LDH_D2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LDH_D2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101039"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29081"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29080"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29082"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29079"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08783"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lac__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2133"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_g3pc_e" fast="false" reversible="false" name="Sn-Glycero-3-phosphocholine exchange" metaid="R_EX_g3pc_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_g3pc_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_g3pc_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99874"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32912"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32911"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32913"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32914"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08554"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13291"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pc_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_g3pg_e" fast="false" reversible="false" name="Glycerophosphoglycerol exchange" metaid="R_EX_g3pg_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_g3pg_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_g3pg_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99886"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08562"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pg_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_g3pi_e" fast="false" reversible="false" name="Sn-Glycero-3-phospho-1-inositol exchange" metaid="R_EX_g3pi_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_g3pi_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_g3pi_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99888"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32918"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32917"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32916"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32915"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13292"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08564"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pi_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_SHCHF" fast="false" reversible="false" name="Sirohydrochlorin ferrochelatase" metaid="R_SHCHF" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SHCHF"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SHCHF"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SIROHEME-FERROCHELAT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.99.1.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02864"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104375"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24360"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24361"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24362"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24363"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02056"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_scl_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_sheme_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3368"/> </fbc:geneProductAssociation> </reaction> 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rdf:resource="http://identifiers.org/biocyc/META:O-SUCCINYLBENZOATE-COA-LIG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.26"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04030"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104612"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17012"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17011"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17009"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17010"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02831"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sucbz_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sbzcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2260"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYSDDS" fast="false" reversible="false" name="D-cysteine desulfhydrase" metaid="R_CYSDDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYSDDS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYSDDS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DCYSDESULF-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.4.1.15"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01874"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96992"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11269"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11270"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11271"/> <rdf:li rdf:resource="http://identifiers.org/rhea/11268"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01365"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cys__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1919"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYStpp" fast="false" reversible="false" name="L-cysteine export via facilitated transport" metaid="R_CYStpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYStpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYStpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1924"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97029"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29655"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29656"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29658"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29657"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13465"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08284"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10998"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08286"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cys__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2578"/> <fbc:geneProductRef fbc:geneProduct="G_b1533"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_g3ps_e" fast="false" reversible="false" name="Glycerophosphoserine exchange" metaid="R_EX_g3ps_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_g3ps_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_g3ps_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99893"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08566"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3ps_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_peamn_e" fast="false" reversible="false" name="Phenethylamine exchange" metaid="R_EX_peamn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_peamn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_peamn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102462"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29745"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29744"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29746"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29743"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11405"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09080"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_peamn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_34dhpac_e" fast="false" reversible="false" name="3,4-Dihydroxyphenylacetaldehyde exchange" metaid="R_EX_34dhpac_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_34dhpac_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_34dhpac_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94848"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07972"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_34dhpac_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_NTP1" fast="false" reversible="false" name="Nucleoside-triphosphatase (ATP)" metaid="R_NTP1" sboTerm="SBO:0000176" 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</fbc:geneProductAssociation> </reaction> <reaction id="R_DGMPtex" fast="false" reversible="true" name="DGMP transport via diffusion (extracellular to periplasm)" metaid="R_DGMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DGMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DGMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97322"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08322"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dgmp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dgmp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DTMPtex" fast="false" reversible="true" name="DTMP transport via diffusion (extracellular to periplasm)" metaid="R_DTMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DTMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DTMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97806"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08374"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dtmp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dtmp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACSERtpp" fast="false" reversible="false" name="O-Acetyl-L-serine export via facilitated transport" metaid="R_ACSERtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACSERtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACSERtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1923"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95416"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29659"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29660"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29662"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29661"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08060"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08059"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acser_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acser_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2578"/> <fbc:geneProductRef fbc:geneProduct="G_b1533"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACSERtex" fast="false" reversible="true" name="O-Acetyl-L-serine transport via diffusion (extracellular to periplasm)" metaid="R_ACSERtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACSERtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACSERtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1923"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95416"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29659"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29660"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29662"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29661"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08060"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08059"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acser_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acser_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LALDO3" fast="false" reversible="false" name="L-Lactaldehyde:NADP+ 1-oxidoreductase" metaid="R_LALDO3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LALDO3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LALDO3"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:1.1.1.283-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.283"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.49"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02260"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101010"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21750"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21749"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21751"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21748"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/550"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/9214"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04937"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01618"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mthgxl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_lald__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_NTP10" fast="false" reversible="false" name="Nucleoside-triphosphatase (ITP)" metaid="R_NTP10" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTP10"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTP10"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5073"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00719"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100892"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28331"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28332"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28333"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28330"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1090"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00513"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_itp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_idp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4161"/> <fbc:geneProductRef fbc:geneProduct="G_b4394"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PRAIS" fast="false" reversible="false" name="Phosphoribosylaminoimidazole synthase" metaid="R_PRAIS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PRAIS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PRAIS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.3.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138720"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23033"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23032"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23034"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23035"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fpram_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_air_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2499"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GDMANE" fast="false" reversible="false" name="GDP-4-dehydro-6-deoxy-D-mannose epimerase" metaid="R_GDMANE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GDMANE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GDMANE"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100087"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08597"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gdpddman_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gdpofuc_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2052"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GPDDA4" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoglycerol)" metaid="R_GPDDA4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GPDDA4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GPDDA4"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14073"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.46"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100413"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13035"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08669"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3449"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATG120" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C12:0)" metaid="R_LPLIPAL2ATG120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATG120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATG120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101176"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg120_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1E140pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylethanolamine, n-C14:0) (periplasm)" metaid="R_PLIPA1E140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1E140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1E140pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102975"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe140_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2E140" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C14:0)" metaid="R_LPLIPAL2E140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2E140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2E140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101184"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1E160pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylethanolamine, n-C16:0) (periplasm)" metaid="R_PLIPA1E160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1E160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1E160pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.32"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102977"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09133"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALKr" fast="false" reversible="true" name="Galactokinase" metaid="R_GALKr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALKr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALKr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GALACTOKIN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.6"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01092"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99985"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13556"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13554"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13555"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13553"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1354"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00808"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gal_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gal1p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0757"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1E161pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylethanolamine, n-C16:1) (periplasm)" metaid="R_PLIPA1E161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1E161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1E161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102978"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AACPS8" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase (n-C10:0)" metaid="R_AACPS8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AACPS8"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AACPS8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.20"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95147"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_AACPS9" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase (n-C8:0)" metaid="R_AACPS9" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AACPS9"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AACPS9"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.l"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95148"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2E180" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C18:0)" metaid="R_LPLIPAL2E180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2E180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2E180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101188"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08843"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2G161" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C16:1)" metaid="R_LPLIPAL2G161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2G161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2G161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101194"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2G181" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C18:1)" metaid="R_LPLIPAL2G181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2G181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2G181"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101196"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPE120tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPE120tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPE120tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPE120tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94750"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe120_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HXCT" fast="false" reversible="false" name="Acetyl-CoA:hexanoate-CoA transferase" metaid="R_HXCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HXCT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HXCT"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.8.3.8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100751"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hxa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hxcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2222"/> <fbc:geneProductRef fbc:geneProduct="G_b2221"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_AACPS6" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase (n-C18:0)" metaid="R_AACPS6" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AACPS6"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AACPS6"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.20"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95145"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPEAT160" fast="false" reversible="false" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C16:0)" metaid="R_2AGPEAT160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPEAT160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPEAT160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.40"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94760"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07949"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AACPS7" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase (n-C12:0)" metaid="R_AACPS7" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AACPS7"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AACPS7"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.l"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95146"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PANTS" fast="false" reversible="false" name="Pantothenate synthase" metaid="R_PANTS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PANTS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PANTS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PANTOATE-BETA-ALANINE-LIG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02473"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102345"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10914"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10913"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10915"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10912"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2406"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01791"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala_B_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pant__R_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pnto__R_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0133"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PGabcpp" fast="false" reversible="false" name="Sn-glycerol-3-phosphoglycerol transport via ABC system (periplasm)" metaid="R_G3PGabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PGabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PGabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99885"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08561"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pg_p" 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_g3pg_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_b3450"/> <fbc:geneProductRef fbc:geneProduct="G_b3451"/> <fbc:geneProductRef fbc:geneProduct="G_b3453"/> <fbc:geneProductRef fbc:geneProduct="G_b3452"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PIabcpp" fast="false" reversible="false" name="Sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)" metaid="R_G3PIabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PIabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PIabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99887"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08563"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pi_p" 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_g3pi_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_b3450"/> <fbc:geneProductRef fbc:geneProduct="G_b3451"/> <fbc:geneProductRef fbc:geneProduct="G_b3453"/> <fbc:geneProductRef fbc:geneProduct="G_b3452"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DURADx" fast="false" reversible="true" name="Dihydrouracil dehydrogenase (NAD)" metaid="R_DURADx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DURADx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DURADx"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DIHYDROURACIL-DEHYDROGENASE-NAD+-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00977"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97816"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20189"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20192"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20191"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20190"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/470"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00719"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_56dura_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_ura_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2147"/> <fbc:geneProductRef fbc:geneProduct="G_b2146"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ECOAH7" fast="false" reversible="true" name="3-hydroxyacyl-CoA dehydratase (3-hydroxyhexadecanoyl-CoA)" metaid="R_ECOAH7" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ECOAH7"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ECOAH7"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14272"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.17"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.74"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04738"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97892"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-77301"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-77301"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-77301"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77301"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-77301"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-77301"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-77301"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-77301"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-77301"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-77301"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-77301"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31163"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31166"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31164"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31165"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/4394"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03240"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hhdcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdd2coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2341"/> <fbc:geneProductRef fbc:geneProduct="G_b3846"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_G1PPpp" fast="false" reversible="false" name="Glucose-1-phosphatase" metaid="R_G1PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G1PPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G1PPpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUCOSE-1-PHOSPHAT-RXN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-17330"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.10"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00304"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99844"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19933"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19936"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19935"/> <rdf:li 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<rdf:li rdf:resource="http://identifiers.org/sabiork/2882"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02173"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galctn__D_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2dh3dgal_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4478"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GCALDD" fast="false" reversible="false" name="Glycolaldehyde dehydrogenase" metaid="R_GCALDD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description 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<speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyclt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1415"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HISTP" fast="false" reversible="false" name="Histidinol-phosphatase" metaid="R_HISTP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HISTP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li 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<speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2022"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PSabcpp" fast="false" reversible="false" name="Sn-glycerol-3-phosphoserine transport via ABC system (periplasm)" metaid="R_G3PSabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PSabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PSabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99892"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08565"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3ps_p" 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_g3ps_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_b3450"/> <fbc:geneProductRef fbc:geneProduct="G_b3451"/> <fbc:geneProductRef fbc:geneProduct="G_b3453"/> <fbc:geneProductRef fbc:geneProduct="G_b3452"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_QMO2" fast="false" reversible="false" name="Quinol monooxygenase (Ubiquinol-8)" metaid="R_QMO2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_QMO2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/QMO2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103392"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29176"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29178"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29177"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29175"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_o2s_c" stoichiometry="2" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3029"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_QMO3" fast="false" reversible="false" name="Quinol monooxygenase (menaquinol 8)" metaid="R_QMO3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_QMO3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/QMO3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103393"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29186"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29184"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29185"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29183"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2s_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3029"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2E141" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C14:1)" metaid="R_LPLIPAL2E141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2E141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2E141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101185"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2E161" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C16:1)" metaid="R_LPLIPAL2E161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2E161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2E161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101187"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LDH_D" fast="false" reversible="true" name="D-lactate dehydrogenase" metaid="R_LDH_D" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LDH_D"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LDH_D"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DLACTDEHYDROGNAD-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.28"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00704"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101037"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16370"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16371"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16372"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16369"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/155"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00500"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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:geneProductRef fbc:geneProduct="G_b1380"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AMALT4" fast="false" reversible="false" name="Amylomaltase (maltohexaose)" metaid="R_AMALT4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMALT4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMALT4"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALTODEG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.25"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95803"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08129"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malthp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3416"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTD11" fast="false" reversible="false" name="5'-nucleotidase (IMP)" metaid="R_NTD11" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTD11"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD11"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-7607"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.99"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01126"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102030"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-421179"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27721"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27718"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27720"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27719"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/124"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00831"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ins_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2744"/> <fbc:geneProductRef fbc:geneProduct="G_b3399"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2E181" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C18:1)" metaid="R_LPLIPAL2E181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2E181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2E181"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101189"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_YUMPS" fast="false" reversible="true" name="YUMP synthetase" metaid="R_YUMPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_YUMPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/YUMPS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103310"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_psd5p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2165"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2G180" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C18:0)" metaid="R_LPLIPAL2G180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2G180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2G180"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101195"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2G141" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C14:1)" metaid="R_LPLIPAL2G141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2G141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2G141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101192"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPA120tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphatidate (n-C12:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPA120tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPA120tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPA120tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94743"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07932"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2ddecg3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2ddecg3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPG180tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPG180tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPG180tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPG180tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94769"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg180_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg180_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_IPDDI" fast="false" reversible="true" name="Isopentenyl-diphosphate D-isomerase" metaid="R_IPDDI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_IPDDI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/IPDDI"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:IPPISOM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.3.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01123"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100796"/> 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<rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-13403"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.107"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03194"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105137"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32462"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32461"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32459"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32460"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02287"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/> <speciesReference species="M_uppg3_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ahcys_c" stoichiometry="2" constant="true"/> <speciesReference species="M_dscl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3368"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_KAS15" fast="false" reversible="false" name="Beta-ketoacyl-ACP synthase (2)" metaid="R_KAS15" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_KAS15"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/KAS15"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2.3.1.180-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.180"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10707"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100913"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08766"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_actACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1091"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALAALAtex" fast="false" reversible="true" name="D-alanyl-D-alanine (DalaDala) transport via diffusion (extracellular to periplasm)" metaid="R_ALAALAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALAALAtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALAALAtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95679"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08099"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_alaala_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_alaala_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAL181t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (octadecenoate transport via vectoral Co-A coupling)" metaid="R_FACOAL181t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAL181t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL181t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99173"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_odecoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1805"/> <fbc:geneProductRef fbc:geneProduct="G_b1701"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_T2DECAI" fast="false" reversible="true" name="Trans-2-decenoyl-ACP isomerase" metaid="R_T2DECAI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_T2DECAI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/T2DECAI"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104659"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tdec2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdec3eACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPGAT180" fast="false" reversible="false" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C18:0)" metaid="R_2AGPGAT180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPGAT180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPGAT180"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94776"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg180_c" 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<speciesReference species="M_2agpg181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAS161" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:1)" metaid="R_3OAS161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS161"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94960"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3ocpalm9eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHQS" fast="false" reversible="false" name="3-dehydroquinate synthase" metaid="R_DHQS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHQS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHQS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3-DEHYDROQUINATE-SYNTHASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.3.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03083"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97447"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21968"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21970"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21971"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21969"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2923"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02212"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dda7p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3dhq_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3389"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR141y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:1)" metaid="R_EAR141y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR141y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR141y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.10"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97854"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_t3c7mrseACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR161x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:1)" metaid="R_EAR161x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR161x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR161x"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.9"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97857"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_t3c9palmeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPG141tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPG141tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPG141tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPG141tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94766"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg141_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg141_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPG161tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPG161tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPG161tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPG161tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94768"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg161_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPG181tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPG181tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPG181tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPG181tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94770"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg181_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg181_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPEAT140" fast="false" reversible="false" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C14:0)" metaid="R_2AGPEAT140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPEAT140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPEAT140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94758"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPEAT120" fast="false" reversible="false" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C12:0)" metaid="R_2AGPEAT120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPEAT120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPEAT120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94757"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DASYN160" fast="false" reversible="false" name="CDP-diacylglycerol synthetase (n-C16:0)" metaid="R_DASYN160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DASYN160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DASYN160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97157"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08309"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa160_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdpdhdecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0175"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DASYN161" fast="false" reversible="false" name="CDP-diacylglycerol synthetase (n-C16:1)" metaid="R_DASYN161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DASYN161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DASYN161"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97159"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08310"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa161_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdpdhdec9eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0175"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DASYN181" fast="false" reversible="false" name="CDP-diacylglycerol synthetase (n-C18:1)" metaid="R_DASYN181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DASYN181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DASYN181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97161"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08312"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa181_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdpdodec11eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0175"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CDAPPA161" fast="false" reversible="false" name="CDP-Diacylglycerol pyrophostatase (n-C16:1)" metaid="R_CDAPPA161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CDAPPA161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDAPPA161"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.26"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96505"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08203"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdhdec9eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pa161_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3918"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPEAT161" fast="false" reversible="false" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C16:1)" metaid="R_2AGPEAT161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPEAT161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPEAT161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94761"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPEAT141" fast="false" reversible="false" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C14:1)" metaid="R_2AGPEAT141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPEAT141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPEAT141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94759"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPGAT160" fast="false" reversible="false" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C16:0)" metaid="R_2AGPGAT160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPGAT160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPGAT160"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94774"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGSA180" fast="false" reversible="false" name="Phosphatidylglycerol synthase (n-C18:0)" metaid="R_PGSA180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGSA180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGSA180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102595"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09113"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdodecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp180_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1912"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGCD" fast="false" reversible="false" name="Phosphoglycerate dehydrogenase" metaid="R_PGCD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGCD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGCD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PGLYCDEHYDROG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.95"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01513"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102527"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-977348"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-977348"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12644"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12643"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12642"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12641"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/8970"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01101"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3php_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2913"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSSA140" fast="false" reversible="false" name="Phosphatidylserine syntase (n-C14:0)" metaid="R_PSSA140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSSA140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSSA140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103267"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdtdecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps140_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2585"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPGAT141" fast="false" reversible="false" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C14:1)" metaid="R_2AGPGAT141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPGAT141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPGAT141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94773"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAE180" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (octadecanoate)" metaid="R_FACOAE180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAE180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAE180"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9624"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R08174"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99133"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30142"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30140"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30141"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30139"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/6573"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08444"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_stcoa_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_ocdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0452"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATG140" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C14:0)" metaid="R_LPLIPAL2ATG140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATG140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATG140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101177"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg140_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATG141" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C14:1)" metaid="R_LPLIPAL2ATG141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATG141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATG141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101178"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg141_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATG160" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C16:0)" metaid="R_LPLIPAL2ATG160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATG160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATG160"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101179"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg160_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATG180" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C18:0)" metaid="R_LPLIPAL2ATG180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATG180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATG180"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101181"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg180_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATG161" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C16:1)" metaid="R_LPLIPAL2ATG161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATG161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATG161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101180"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg161_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATG181" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C18:1)" metaid="R_LPLIPAL2ATG181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATG181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATG181"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101182"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg181_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAE100" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (decanoate)" metaid="R_FACOAE100" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAE100"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAE100"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99127"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcacoa_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_dca_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0452"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAE80" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (octanoate)" metaid="R_FACOAE80" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAE80"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAE80"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99140"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30143"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30144"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30145"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30146"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/6581"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08447"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_occoa_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_octa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0452"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAE60" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (hexanoate)" metaid="R_FACOAE60" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAE60"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAE60"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99139"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hxcoa_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_hxa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0452"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNS180pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C18:0)" metaid="R_CLPNS180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNS180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNS180pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96787"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pg180_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_clpn180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1249"/> <fbc:geneProductRef fbc:geneProduct="G_b0789"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1E120pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylethanolamine, n-C12:0) (periplasm)" metaid="R_PLIPA1E120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1E120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1E120pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102974"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNS181pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C18:1)" metaid="R_CLPNS181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNS181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNS181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96788"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pg181_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_clpn181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1249"/> <fbc:geneProductRef fbc:geneProduct="G_b0789"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_cys__L_e" fast="false" reversible="false" name="L-Cysteine exchange" metaid="R_EX_cys__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cys__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cys__L_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1924"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97029"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29655"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29656"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29658"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29657"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13465"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08284"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10998"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08286"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cys__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PG161abcpp" fast="false" reversible="false" name="Phosphatidylglycerol transport via ABC system (n-C16:1, periplasm)" metaid="R_PG161abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PG161abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PG161abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102520"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09089"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg161_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_pg161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGP120abcpp" fast="false" reversible="false" name="Phosphatidylglycerophosphate transport via ABC system (n-C12:0, periplasm)" metaid="R_PGP120abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGP120abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGP120abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102550"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp120_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_pgp120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALtex" fast="false" reversible="true" name="Malate transport via diffusion (extracellular to periplasm)" metaid="R_MALtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-225"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-224"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101367"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13793"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10967"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08868"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mal__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mal__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NO3tex" fast="false" reversible="true" name="Nitrate transport via diffusion (extracellular to periplasm)" metaid="R_NO3tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NO3tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO3tex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101992"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34924"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34926"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34923"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34925"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09005"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10935"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_no3_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_no3_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAS141" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:1)" metaid="R_3OAS141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS141"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94958"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cddec5eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3ocmrs7eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR121" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:1)" metaid="R_3OAR121" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR121"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR121"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94943"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07987"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ocddec5eACP_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_3hcddec5eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CFAS160G" fast="false" reversible="false" name="Cyclopropane fatty acid synthase (Phosphatidylglycerol, n-C16:0)" metaid="R_CFAS160G" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CFAS160G"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CFAS160G"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.79"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96653"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08207"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pg161_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ahcys_c" stoichiometry="2" constant="true"/> <speciesReference species="M_cpg160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1661"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGP161abcpp" fast="false" reversible="false" name="Phosphatidylglycerophosphate transport via ABC system (n-C16:1, periplasm)" metaid="R_PGP161abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGP161abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGP161abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102554"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09098"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp161_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_pgp161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGP181abcpp" fast="false" reversible="false" name="Phosphatidylglycerophosphate transport via ABC system (n-C18:1, periplasm)" metaid="R_PGP181abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGP181abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGP181abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102558"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp181_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_pgp181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PA120abcpp" fast="false" reversible="false" name="Phosphatidate transport via ABC system (n-C12:0, periplasm)" metaid="R_PA120abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PA120abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PA120abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102304"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09053"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa120_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_pa120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1G120pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylglycerol, n-C12:0) (periplasm)" metaid="R_PLIPA1G120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1G120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1G120pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102981"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_URAt2pp" fast="false" reversible="false" name="Uracil transport in via proton symport (periplasm)" metaid="R_URAt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_URAt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URAt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-132"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105148"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29242"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29239"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29241"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29240"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09365"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05197"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ura_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2497"/> <fbc:geneProductRef fbc:geneProduct="G_b1006"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAE141" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (tetradecenoate)" metaid="R_FACOAE141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAE141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAE141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99130"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdecoa_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_ttdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0452"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNS120pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C12:0)" metaid="R_CLPNS120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNS120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNS120pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96781"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pg120_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_clpn120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0789"/> <fbc:geneProductRef fbc:geneProduct="G_b1249"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALPATE160pp" fast="false" reversible="false" name="Apolipoprotein N-acyltransferase (phosphatidylethanolamine, periplasm)" metaid="R_ALPATE160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALPATE160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALPATE160pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95782"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08119"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_alpp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lpp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1677"/> <fbc:geneProductRef fbc:geneProduct="G_b0657"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAE161" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (hexadecenoate)" metaid="R_FACOAE161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAE161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAE161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99132"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcoa_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_hdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0452"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_gsn_e" fast="false" reversible="false" name="Guanosine exchange" metaid="R_EX_gsn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_gsn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gsn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100433"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08672"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10897"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gsn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_TTDCEAtexi" fast="false" reversible="false" name="Tetradecenoate transport via facilitated irreversible diffusion (extracellular to periplasm)" metaid="R_TTDCEAtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TTDCEAtexi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TTDCEAtexi"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99096"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ttdcea_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2344"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HDCEAtexi" fast="false" reversible="false" name="Hexadecenoate transport via facilitated irreversible diffusion (extracellular to periplasm)" metaid="R_HDCEAtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HDCEAtexi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HDCEAtexi"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99102"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hdcea_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2344"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALPATG160pp" fast="false" reversible="false" name="Apolipoprotein N-acyltransferase (phosphatidylglycerol, periplasm)" metaid="R_ALPATG160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALPATG160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALPATG160pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95784"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_alpp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lpp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1677"/> <fbc:geneProductRef fbc:geneProduct="G_b0657"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPGAT120" fast="false" reversible="false" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C12:0)" metaid="R_2AGPGAT120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPGAT120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPGAT120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94771"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATE120" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C12:0)" metaid="R_LPLIPAL2ATE120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATE120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATE120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101169"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg120_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALAALAD" fast="false" reversible="false" name="D-alanine-D-alanine dipeptidase" metaid="R_ALAALAD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALAALAD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALAALAD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.4.13.22-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.13.22"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07651"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95675"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20662"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20664"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20663"/> <rdf:li rdf:resource="http://identifiers.org/rhea/20661"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7268"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07466"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_alaala_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1488"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPEAT180" fast="false" reversible="false" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C18:0)" metaid="R_2AGPEAT180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPEAT180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPEAT180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.40"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94762"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07951"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATE140" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C14:0)" metaid="R_LPLIPAL2ATE140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATE140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATE140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101170"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg140_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_orot_e" fast="false" reversible="false" name="Orotate exchange" metaid="R_EX_orot_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_orot_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_orot_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102230"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10908"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09050"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_orot_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_LPLIPAL2ATE160" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C16:0)" metaid="R_LPLIPAL2ATE160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATE160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATE160"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101172"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg160_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATE180" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C18:0)" metaid="R_LPLIPAL2ATE180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATE180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATE180"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101174"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg180_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATE141" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C14:1)" metaid="R_LPLIPAL2ATE141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATE141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATE141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101171"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg141_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPEAT181" fast="false" reversible="false" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C18:1)" metaid="R_2AGPEAT181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPEAT181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPEAT181"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94763"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPGAT140" fast="false" reversible="false" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C14:0)" metaid="R_2AGPGAT140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPGAT140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPGAT140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94772"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1E181pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylethanolamine, n-C18:1) (periplasm)" metaid="R_PLIPA1E181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1E181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1E181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102980"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe181_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1G180pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylglycerol, n-C18:0) (periplasm)" metaid="R_PLIPA1G180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1G180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1G180pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102986"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg180_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATE161" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C16:1)" metaid="R_LPLIPAL2ATE161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATE161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATE161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101173"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg161_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2ATE181" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C18:1)" metaid="R_LPLIPAL2ATE181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2ATE181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2ATE181"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101175"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg181_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_apg181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAL141t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (tetradecenoate transport via vectoral Co-A coupling)" metaid="R_FACOAL141t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAL141t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL141t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99149"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdecoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1701"/> <fbc:geneProductRef fbc:geneProduct="G_b1805"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAL161t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (hexadecenoate transport via vectoral Co-A coupling)" metaid="R_FACOAL161t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAL161t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL161t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99158"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1805"/> <fbc:geneProductRef fbc:geneProduct="G_b1701"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PA160abcpp" fast="false" reversible="false" name="Phosphatidate transport via ABC system (n-C16:0, periplasm)" metaid="R_PA160abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PA160abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PA160abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102307"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09056"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa160_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_pa160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1G181pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylglycerol, n-C18:1) (periplasm)" metaid="R_PLIPA1G181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1G181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1G181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102987"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg181_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALAALAabcpp" fast="false" reversible="false" name="D-alanyl-D-alanine (DalaDala) transport via ABC system (periplasm)" metaid="R_ALAALAabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALAALAabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALAALAabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95677"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08098"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_alaala_p" stoichiometry="1" constant="true"/> <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_alaala_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:and> <fbc:geneProductRef fbc:geneProduct="G_b3544"/> <fbc:geneProductRef fbc:geneProduct="G_b3542"/> <fbc:geneProductRef fbc:geneProduct="G_b3543"/> <fbc:geneProductRef fbc:geneProduct="G_b3540"/> <fbc:geneProductRef fbc:geneProduct="G_b3541"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1487"/> <fbc:geneProductRef fbc:geneProduct="G_b1486"/> <fbc:geneProductRef fbc:geneProduct="G_b1483"/> <fbc:geneProductRef fbc:geneProduct="G_b1485"/> <fbc:geneProductRef fbc:geneProduct="G_b1484"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_HEXt2rpp" fast="false" reversible="true" name="Hexanoate transport via proton symport, reversible (periplasm)" metaid="R_HEXt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HEXt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HEXt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100622"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12596"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08714"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hxa_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hxa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2223"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PEabcpp" fast="false" reversible="false" name="Sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)" metaid="R_G3PEabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PEabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PEabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99883"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08559"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pe_p" 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_g3pe_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_b3450"/> <fbc:geneProductRef fbc:geneProduct="G_b3451"/> <fbc:geneProductRef fbc:geneProduct="G_b3453"/> <fbc:geneProductRef fbc:geneProduct="G_b3452"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PCabcpp" fast="false" reversible="false" name="Sn-glycerol-3-phosphocholine transport via ABC system (periplasm)" metaid="R_G3PCabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PCabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PCabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99873"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08553"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pc_p" 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_g3pc_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_b3450"/> <fbc:geneProductRef fbc:geneProduct="G_b3451"/> <fbc:geneProductRef fbc:geneProduct="G_b3453"/> <fbc:geneProductRef fbc:geneProduct="G_b3452"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPGAT161" fast="false" reversible="false" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C16:1)" metaid="R_2AGPGAT161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPGAT161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPGAT161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94775"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2836"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PA181abcpp" fast="false" reversible="false" name="Phosphatidate transport via ABC system (n-C18:1, periplasm)" metaid="R_PA181abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PA181abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PA181abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102310"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09059"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa181_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_pa181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_12DGR141tipp" fast="false" reversible="false" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:1)" metaid="R_12DGR141tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_12DGR141tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/12DGR141tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94677"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr141_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr141_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_AMPTASEPG" fast="false" reversible="false" name="Aminopeptidase (pro-gly)" metaid="R_AMPTASEPG" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMPTASEPG"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMPTASEPG"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95829"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28802"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28799"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28801"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28800"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08133"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_progly_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2523"/> <fbc:geneProductRef fbc:geneProduct="G_b0932"/> <fbc:geneProductRef fbc:geneProduct="G_b4260"/> <fbc:geneProductRef fbc:geneProduct="G_b0237"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADSL1r" fast="false" reversible="true" name="Adenylsuccinate lyase" metaid="R_ADSL1r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADSL1r"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADSL1r"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:AMPSYN-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.2.2"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01083"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95493"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-421197"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-73828"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-73828"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16854"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16853"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16856"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16855"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/306"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00800"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcamp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1131"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PROGLYabcpp" fast="false" reversible="false" name="L-Prolinylglycine (Pro-Gly) transport via ABC system (periplasm)" metaid="R_PROGLYabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PROGLYabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PROGLYabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103190"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09189"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_progly_p" 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"/> <speciesReference species="M_progly_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3544"/> <fbc:geneProductRef fbc:geneProduct="G_b3542"/> <fbc:geneProductRef fbc:geneProduct="G_b3540"/> <fbc:geneProductRef fbc:geneProduct="G_b3541"/> <fbc:geneProductRef fbc:geneProduct="G_b3543"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_GTHRDabcpp" fast="false" reversible="false" name="Reduced glutathione via ABC system (periplasm)" metaid="R_GTHRDabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GTHRDabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GTHRDabcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-11"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100448"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29788#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29787#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29792#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29790#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29793#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29789#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29794#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29791#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08676"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13306"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gthrd_p" 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_gthrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0831"/> <fbc:geneProductRef fbc:geneProduct="G_b0830"/> <fbc:geneProductRef fbc:geneProduct="G_b0829"/> <fbc:geneProductRef fbc:geneProduct="G_b0832"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP140pp" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (periplasm, n-C14:0)" metaid="R_PGPP140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP140pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102561"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp140_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP141pp" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (periplasm, n-C14:1)" metaid="R_PGPP141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP141pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP141pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102562"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp141_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP160pp" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (periplasm, n-C16:0)" metaid="R_PGPP160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP160pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102563"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09104"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPG140tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPG140tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPG140tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPG140tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94765"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg140_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg140_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP180pp" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (periplasm, n-C18:0)" metaid="R_PGPP180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP180pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102566"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09106"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp180_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPG160tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPG160tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPG160tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPG160tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94767"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg160_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SERD_D" fast="false" reversible="false" name="D-serine deaminase" metaid="R_SERD_D" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SERD_D"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SERD_D"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DSERDEAM-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.18"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00221"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104338"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13980"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13979"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13977"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13978"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/746"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00166"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ser__D_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2366"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNH141pp" fast="false" reversible="false" name="Cardiolipin hydrolase (periplasm, n-C14:1)" metaid="R_CLPNH141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNH141pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNH141pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96776"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_clpn141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg141_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_CLPNH160pp" fast="false" reversible="false" name="Cardiolipin hydrolase (periplasm, n-C16:0)" metaid="R_CLPNH160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNH160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNH160pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96777"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08222"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_clpn160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg160_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_CLPNH161pp" fast="false" reversible="false" name="Cardiolipin hydrolase (periplasm, n-C16:1)" metaid="R_CLPNH161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNH161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNH161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96778"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_clpn161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg161_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_AICART" fast="false" reversible="true" name="Phosphoribosylaminoimidazolecarboxamide formyltransferase" metaid="R_AICART" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AICART"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AICART"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.2.3"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04560"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95639"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-419254"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-73798"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-73798"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22192"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22193"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22195"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22194"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/122"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> <speciesReference species="M_aicar_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fprica_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4006"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNH181pp" fast="false" reversible="false" name="Cardiolipin hydrolase (periplasm, n-C18:1)" metaid="R_CLPNH181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNH181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNH181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96780"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_clpn181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg181_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_D_LACt2pp" fast="false" reversible="true" name="D-lactate transport via proton symport (periplasm)" metaid="R_D_LACt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_D_LACt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/D_LACt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-515"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97838"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10171"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09772"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08350"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lac__D_p" 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_b3603"/> <fbc:geneProductRef fbc:geneProduct="G_b2975"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1E180pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylethanolamine, n-C18:0) (periplasm)" metaid="R_PLIPA1E180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1E180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1E180pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.32"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102979"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09135"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe180_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RIBtex" fast="false" reversible="true" name="Ribose transport via diffusion (extracellular to periplasm)" metaid="R_RIBtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RIBtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RIBtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104036"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09228"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_rib__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_rib__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FLVRx" fast="false" reversible="false" name="Flavin reductase (NAD)" metaid="R_FLVRx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FLVRx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FLVRx"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.41"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.36"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09750"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99602"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31458"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31457"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31455"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31456"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7291"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08521"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3844"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_THMtex" fast="false" reversible="true" name="Thiamine transport via diffusion (extracellular to periplasm)" metaid="R_THMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THMtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR131128"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12167"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11006"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09300"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_thm_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_thm_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_XYLUtex" fast="false" reversible="true" name="L-xylulose transport via diffusion (extracellular to periplasm)" metaid="R_XYLUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_XYLUtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYLUtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138931"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09387"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_xylu__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_xylu__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1G140pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylglycerol, n-C14:0) (periplasm)" metaid="R_PLIPA1G140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1G140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1G140pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102982"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg140_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1G161pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylglycerol, n-C16:1) (periplasm)" metaid="R_PLIPA1G161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1G161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1G161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102985"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNS160pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C16:0)" metaid="R_CLPNS160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNS160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNS160pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96784"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08229"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pg160_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_clpn160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0789"/> <fbc:geneProductRef fbc:geneProduct="G_b1249"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNS161pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C16:1)" metaid="R_CLPNS161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNS161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNS161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96786"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pg161_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_clpn161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1249"/> <fbc:geneProductRef fbc:geneProduct="G_b0789"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_manglyc_e" fast="false" reversible="false" name="2(alpha-D-Mannosyl)-D-glycerate exchange" metaid="R_EX_manglyc_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_manglyc_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_manglyc_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101395"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08883"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_manglyc_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ALLtex" fast="false" reversible="true" name="Allose transport via diffusion (extracellular to periplasm)" metaid="R_ALLtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALLtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALLtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95776"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08115"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_all__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_all__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PG160abcpp" fast="false" reversible="false" name="Phosphatidylglycerol transport via ABC system (n-C16:0, periplasm)" metaid="R_PG160abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PG160abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PG160abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102519"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09088"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg160_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_pg160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRUpts2pp" fast="false" reversible="false" name="Fructose transport via PEP:Pyr PTS (f6p generating) (periplasm)" metaid="R_FRUpts2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRUpts2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRUpts2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99662"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fru_p" 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_b1818"/> <fbc:geneProductRef fbc:geneProduct="G_b1817"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b1819"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGP140abcpp" fast="false" reversible="false" name="Phosphatidylglycerophosphate transport via ABC system (n-C14:0, periplasm)" metaid="R_PGP140abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGP140abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGP140abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102551"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp140_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_pgp140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAPA120pp" fast="false" reversible="false" name="Phosphatidate phosphatase (periplasmic, n-C12:0)" metaid="R_PAPA120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA120pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102347"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAPA140pp" fast="false" reversible="false" name="Phosphatidate phosphatase (periplasmic, n-C14:0)" metaid="R_PAPA140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA140pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102348"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa140_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GGPTRCO" fast="false" reversible="false" name="Gamma glutamyl putrescine oxidase" metaid="R_GGPTRCO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GGPTRCO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GGPTRCO"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100131"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08603"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ggptrc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ggbutal_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1301"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_metsox_R__L_e" fast="false" reversible="false" name="L-methionine-R-sulfoxide exchange" metaid="R_EX_metsox_R__L_e" sboTerm="SBO:0000627" 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</reaction> <reaction id="R_34dhpactex" fast="false" reversible="true" name="Dihydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)" metaid="R_34dhpactex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_34dhpactex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/34dhpactex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94848"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07972"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_34dhpac_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference 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rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102350"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G6Pt6_2pp" fast="false" reversible="false" name="Glucose-6-phosphate transport via phosphate antiport (periplasm)" metaid="R_G6Pt6_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G6Pt6_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G6Pt6_2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99913"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08569"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05563"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g6p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3666"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAPA161pp" fast="false" reversible="false" name="Phosphatidate phosphatase (periplasmic, n-C16:1)" metaid="R_PAPA161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102353"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr161_p" 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rdf:resource="http://identifiers.org/rhea/15117"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15120"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15118"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09320"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dpcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2tpr3dpcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0613"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACGAM1PPpp" fast="false" reversible="false" name="N-acetyl-D-glucosamine 1-phosphatase (periplasm)" metaid="R_ACGAM1PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACGAM1PPpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAM1PPpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.10"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95245"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08038"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acgam1p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_EX_dgmp_e" fast="false" reversible="false" name="DGMP exchange" metaid="R_EX_dgmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dgmp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dgmp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97322"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08322"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dgmp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GAMptspp" fast="false" reversible="false" name="D-glucosamine transport via PEP:Pyr PTS (periplasm)" metaid="R_GAMptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GAMptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GAMptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100034"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08592"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05569"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gam_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gam6p_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_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b1819"/> <fbc:geneProductRef fbc:geneProduct="G_b1817"/> <fbc:geneProductRef fbc:geneProduct="G_b1818"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_GSNt2pp" fast="false" reversible="false" name="Guanosine transport in via proton symport (periplasm)" metaid="R_GSNt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GSNt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GSNt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100434"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08671"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05204"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09747"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gsn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gsn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2964"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_4hoxpacd_e" fast="false" reversible="false" name="4-Hydroxyphenylacetaldehyde exchange" metaid="R_EX_4hoxpacd_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_4hoxpacd_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_4hoxpacd_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95017"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08006"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4hoxpacd_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_FMNRx" fast="false" reversible="false" name="FMN reductase" metaid="R_FMNRx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FMNRx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FMNRx"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9510"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.41"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.42"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.36"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.39"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05705"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99607"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21620"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21622"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21623"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21621"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/5301"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03974"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0937"/> <fbc:geneProductRef fbc:geneProduct="G_b3844"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_3hpppn_e" fast="false" reversible="false" name="3-(3-hydroxy-phenyl)propionate exchange" metaid="R_EX_3hpppn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_3hpppn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_3hpppn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100697"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08726"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hpppn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_man6p_e" fast="false" reversible="false" name="D-Mannose 6-phosphate exchange" metaid="R_EX_man6p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_man6p_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_man6p_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101385"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13644"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08880"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_man6p_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GSNtex" fast="false" reversible="true" name="Guanosine transport via diffusion (extracellular to periplasm)" metaid="R_GSNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GSNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GSNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100433"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08672"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10897"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gsn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gsn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SBTtex" fast="false" reversible="true" name="D-sorbitol transport via diffusion (extracellular to periplasm)" metaid="R_SBTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SBTtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SBTtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104288"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09243"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09662"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sbt__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_sbt__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FORtex" fast="false" reversible="true" name="Formate transport via diffusion (extracellular to periplasm)" metaid="R_FORtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FORtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FORtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99620"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6803255"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29681"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29680"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29682"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29679"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12483"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09754"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08525"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09682"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08526"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_for_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_for_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_tsul_e" fast="false" reversible="false" name="Thiosulfate exchange" metaid="R_EX_tsul_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_tsul_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tsul_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104966"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32808"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32810"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32807"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32809"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09330"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tsul_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PHEt2rpp" fast="false" reversible="true" name="L-phenylalanine reversible transport via proton symport (periplasm)" metaid="R_PHEt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PHEt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PHEt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-56"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102635"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28926"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28923"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28924"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28925"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09117"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09724"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11337"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05306"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_phe__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_phe__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0576"/> <fbc:geneProductRef fbc:geneProduct="G_b0112"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHBS" fast="false" reversible="false" name="2,3-dihydroxybenzoate adenylate synthase" metaid="R_DHBS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF 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<speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23dhba_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0594"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_THIORDXi" fast="false" reversible="false" name="Hydrogen peroxide reductase (thioredoxin)" metaid="R_THIORDXi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THIORDXi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li 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fbc:geneProduct="G_b3781"/> <fbc:geneProductRef fbc:geneProduct="G_b2480"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1710"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2582"/> <fbc:geneProductRef fbc:geneProduct="G_b2480"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_n2o_e" fast="false" reversible="false" name="Nitrous oxide exchange" metaid="R_EX_n2o_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_n2o_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_n2o_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101797"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08966"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08967"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_n2o_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PPPGO3" fast="false" reversible="false" name="Protoporphyrinogen oxidase (anaerobic)" metaid="R_PPPGO3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPPGO3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPPGO3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.3.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103130"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09180"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fum_c" stoichiometry="3" constant="true"/> <speciesReference species="M_pppg9_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ppp9_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="3" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3850"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PFK" fast="false" reversible="false" name="Phosphofructokinase" metaid="R_PFK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PFK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PFK"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.11"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102507"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16111"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16109"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16110"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16112"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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 id="R_PDX5POi" fast="false" reversible="false" name="Pyridoxine 5'-phosphate oxidase" metaid="R_PDX5POi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PDX5POi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PDX5POi"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PNPOXI-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.3.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00278"/> <rdf:li 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rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-965019"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-965019"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-965019"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15151"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15149"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15152"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15150"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/778"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00209"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pdx5p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pydx5p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1638"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PDX5PO2" fast="false" reversible="false" name="Pyridoxine 5'-phosphate oxidase (anaerboic" metaid="R_PDX5PO2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PDX5PO2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PDX5PO2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102437"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09071"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pdx5p_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_pydx5p_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_MDDCP1pp" fast="false" reversible="false" name="Murein D,D-carboxypeptidase (murein5px4p) (periplasm)" metaid="R_MDDCP1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDDCP1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDDCP1pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.16.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143206"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08890"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5px4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein4px4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0632"/> <fbc:geneProductRef fbc:geneProduct="G_b3182"/> <fbc:geneProductRef fbc:geneProduct="G_b0839"/> <fbc:geneProductRef fbc:geneProduct="G_b2010"/> <fbc:geneProductRef fbc:geneProduct="G_b0376"/> <fbc:geneProductRef fbc:geneProduct="G_b2430"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GUI2" fast="false" reversible="true" name="Glucuronate isomerase (D-galacturonate)" metaid="R_GUI2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GUI2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GUI2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.12"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01983"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100469"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01457"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galur_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tagur_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3092"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_OMBZLM" fast="false" reversible="false" name="2-Octaprenyl-6-methoxy-benzoquinol methylase" metaid="R_OMBZLM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OMBZLM"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OMBZLM"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.201"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR115030"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27774"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27777"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27776"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27775"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09039"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2ombzl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2ommbl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3833"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1A181pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidate, n-C18:1) (periplasm)" metaid="R_PLIPA1A181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1A181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1A181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102973"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa181_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference 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rdf:resource="http://identifiers.org/rhea/18586"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18585"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/4"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00747"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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> <reaction id="R_EAR181y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:1)" metaid="R_EAR181y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF 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</fbc:geneProductAssociation> </reaction> <reaction id="R_G3PAT141" fast="false" reversible="false" name="Glycerol-3-phosphate acyltransferase (C14:1)" metaid="R_G3PAT141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PAT141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PAT141"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.15"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99856"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1tdec7eg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b4041"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_2DOXG6PP" fast="false" reversible="false" name="2 deoxyglucose 6 phosphatase" metaid="R_2DOXG6PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2DOXG6PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2DOXG6PP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.1.3.68-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.68"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02587"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94794"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22239"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22237"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22236"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22238"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2493"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01883"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2doxg6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2dglc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3826"/> <fbc:geneProductRef fbc:geneProduct="G_b1727"/> <fbc:geneProductRef fbc:geneProduct="G_b2293"/> <fbc:geneProductRef fbc:geneProduct="G_b0446"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_OXAMTC" fast="false" reversible="false" name="Oxamate transcarbamoylase" metaid="R_OXAMTC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OXAMTC"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OXAMTC"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:OXAMATE-CARBAMOYLTRANSFERASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.3.5"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02937"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102236"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22986"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22985"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22984"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22987"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02104"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_oxur_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cbp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oxam_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_UDCPPtppi" fast="false" reversible="false" name="Undecaprenyl phosphate transport (cytoplasm to periplasm)" metaid="R_UDCPPtppi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UDCPPtppi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDCPPtppi"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105045"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09346"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_udcpp_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_udcpp_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_AGMH" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl beta -1,4-N-acetylglucosaminidase" metaid="R_AGMH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGMH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGMH"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95550"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08080"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam_c" stoichiometry="1" constant="true"/> <speciesReference species="M_anhm_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1107"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PAT181" fast="false" reversible="false" name="Glycerol-3-phosphate acyltransferase (C18:1)" metaid="R_G3PAT181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PAT181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PAT181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.15"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99862"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1odec11eg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b4041"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DASYN140" fast="false" reversible="false" name="CDP-diacylglycerol synthetase (n-C14:0)" metaid="R_DASYN140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DASYN140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DASYN140"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97155"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08307"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa140_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdpdtdecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0175"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MPTG" fast="false" reversible="false" name="Murein polymerizing transglycosylase" metaid="R_MPTG" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MPTG"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MPTG"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143249"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_uaagmda_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_murein5p5p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1069"/> <fbc:geneProductRef fbc:geneProduct="G_b0089"/> <fbc:geneProductRef fbc:geneProduct="G_b3208"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3396"/> <fbc:geneProductRef fbc:geneProduct="G_b1069"/> <fbc:geneProductRef fbc:geneProduct="G_b0089"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2519"/> <fbc:geneProductRef fbc:geneProduct="G_b1069"/> <fbc:geneProductRef fbc:geneProduct="G_b0089"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0149"/> <fbc:geneProductRef fbc:geneProduct="G_b1069"/> <fbc:geneProductRef fbc:geneProduct="G_b0089"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DASYN180" fast="false" reversible="false" name="CDP-diacylglycerol synthetase (n-C18:0)" metaid="R_DASYN180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DASYN180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DASYN180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97160"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08311"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa180_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdpdodecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0175"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MPTG2" fast="false" reversible="false" name="Murein polymerizing transglycosylase 2 (three linked units)" metaid="R_MPTG2" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MPTG2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MPTG2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143250"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_murein5p5p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_uaagmda_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5p5p5p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0149"/> <fbc:geneProductRef fbc:geneProduct="G_b1069"/> <fbc:geneProductRef fbc:geneProduct="G_b0089"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1069"/> <fbc:geneProductRef fbc:geneProduct="G_b0089"/> <fbc:geneProductRef fbc:geneProduct="G_b3208"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3396"/> <fbc:geneProductRef fbc:geneProduct="G_b1069"/> <fbc:geneProductRef fbc:geneProduct="G_b0089"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2519"/> <fbc:geneProductRef fbc:geneProduct="G_b1069"/> <fbc:geneProductRef fbc:geneProduct="G_b0089"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DASYN141" fast="false" reversible="false" name="CDP-diacylglycerol synthetase (n-C14:1)" metaid="R_DASYN141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DASYN141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DASYN141"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97156"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08308"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa141_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdpdtdec7eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0175"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RPI" fast="false" reversible="true" name="Ribose-5-phosphate isomerase" metaid="R_RPI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RPI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RPI"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.6"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104084"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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 id="R_MCTP1App" fast="false" reversible="false" name="Murein crosslinking transpeptidase 1A:(A2pm->D-ala) (periplasm)" metaid="R_MCTP1App" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MCTP1App"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MCTP1App"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101426"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08887"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_murein5p5p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5px4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0635"/> <fbc:geneProductRef fbc:geneProduct="G_b0084"/> <fbc:geneProductRef fbc:geneProduct="G_b3396"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0635"/> <fbc:geneProductRef fbc:geneProduct="G_b0084"/> <fbc:geneProductRef fbc:geneProduct="G_b0149"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MCTP2App" fast="false" reversible="false" name="Murein crosslinking transpeptidase 1A:(A2pm->D-ala) (periplasm)" metaid="R_MCTP2App" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MCTP2App"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MCTP2App"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143205"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08889"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_murein5p5p5p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="2" constant="true"/> <speciesReference species="M_murein5px4px4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0635"/> <fbc:geneProductRef fbc:geneProduct="G_b0084"/> <fbc:geneProductRef fbc:geneProduct="G_b3396"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0635"/> <fbc:geneProductRef fbc:geneProduct="G_b0084"/> <fbc:geneProductRef fbc:geneProduct="G_b0149"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CDAPPA160" fast="false" reversible="false" name="CDP-Diacylglycerol pyrophostatase (n-C16:0)" metaid="R_CDAPPA160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CDAPPA160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDAPPA160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.26"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96503"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08202"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdhdecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pa160_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3918"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CDAPPA141" fast="false" reversible="false" name="CDP-Diacylglycerol pyrophostatase (n-C14:1)" metaid="R_CDAPPA141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CDAPPA141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDAPPA141"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.26"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96502"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08201"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdtdec7eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pa141_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3918"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MCTP1Bpp" fast="false" reversible="false" name="Murein crosslinking transpeptidase 1B:(A2pm->A2pm) (periplasm)" metaid="R_MCTP1Bpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MCTP1Bpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MCTP1Bpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143204"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08888"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_murein5p5p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_alaala_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5px3p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1678"/> <fbc:geneProductRef fbc:geneProduct="G_b0925"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PERD" fast="false" reversible="true" name="Erythronate 4-phosphate (4per) dehydrogenase" metaid="R_PERD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PERD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PERD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ERYTHRON4PDEHYDROG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.290"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04210"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102495"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18831"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18830"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18832"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18829"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02939"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4per_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_ohpb_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2320"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MELIBt3ipp" fast="false" reversible="false" name="Melibiose transport in via antiport (periplasm)" metaid="R_MELIBt3ipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MELIBt3ipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MELIBt3ipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138588"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_melib_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_melib_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1528"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGSA141" fast="false" reversible="false" name="Phosphatidylglycerol synthase (n-C14:1)" metaid="R_PGSA141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGSA141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGSA141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102591"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdtdec7eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp141_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1912"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_alaala_e" fast="false" reversible="false" name="D-Alanyl-D-alanine exchange" metaid="R_EX_alaala_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_alaala_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_alaala_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95679"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08099"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_alaala_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_dtmp_e" fast="false" reversible="false" name="DTMP exchange" metaid="R_EX_dtmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dtmp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dtmp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97806"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08374"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dtmp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_5DOAN" fast="false" reversible="false" name="5'-deoxyadenosine nuclosidase" metaid="R_5DOAN" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_5DOAN"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/5DOAN"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6550"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95069"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29862"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29860"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29859"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29861"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13649"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08013"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dad_5_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5drib_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0159"/> </fbc:geneProductAssociation> 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rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-964958"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-964958"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25104"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25106"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25107"/> <rdf:li rdf:resource="http://identifiers.org/rhea/25105"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2423"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01807"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pydam_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_pyam5p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2418"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHORDfum" fast="false" reversible="false" name="Fumarate dependent DHORD" metaid="R_DHORDfum" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHORDfum"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHORDfum"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9929"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.98.1"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01867"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97425"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30059"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30060"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30062"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30061"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/7103"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13251"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhor__S_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_orot_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_K2L4Aabcpp" fast="false" reversible="false" name="KDO(2)-lipid IV A transport via ABC system (periplasm)" metaid="R_K2L4Aabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_K2L4Aabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/K2L4Aabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100899"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35248#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35249#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35247#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35250#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08760"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_kdo2lipid4_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_kdo2lipid4_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FACOAE120" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (dodecanoate)" metaid="R_FACOAE120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FACOAE120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAE120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99128"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ddcacoa_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_ddca_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0452"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR120" fast="false" reversible="true" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:0)" metaid="R_3OAR120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04964"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94942"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05340"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3oddecACP_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_3hddecACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD80" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C8:0)" metaid="R_3HAD80" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD80"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD80"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:4.2.1.59-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.58"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.61"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.59"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04537"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94888"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05334"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hoctACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_toct2eACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD120" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:0)" metaid="R_3HAD120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.58"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.60"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.61"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.59"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04965"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94877"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05331"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hddecACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tddec2eACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DSBCGT" fast="false" reversible="false" name="DsbC:glutathione thiotransferase" metaid="R_DSBCGT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DSBCGT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DSBCGT"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97793"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08368"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dsbcox_p" stoichiometry="1" constant="true"/> <speciesReference species="M_gthrd_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dsbcrd_p" stoichiometry="1" constant="true"/> <speciesReference species="M_gthox_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2893"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DSBGGT" fast="false" reversible="false" name="DsbG:glutathione thiotransferase" metaid="R_DSBGGT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DSBGGT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DSBGGT"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97795"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08370"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dsbgox_p" stoichiometry="1" constant="true"/> <speciesReference species="M_gthrd_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dsbgrd_p" stoichiometry="1" constant="true"/> <speciesReference species="M_gthox_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0604"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR180x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:0)" metaid="R_EAR180x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR180x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR180x"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.9"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97859"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_toctd2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcaACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AKGtex" fast="false" reversible="true" name="Alpha-ketoglutarate transport via diffusion (extracellular to periplasm)" metaid="R_AKGtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AKGtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AKGtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95663"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13794"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10923"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08096"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13220"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_akg_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_akg_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SO4t2pp" fast="false" reversible="false" name="Sulfate transport in via proton symport (periplasm to cytoplasm)" metaid="R_SO4t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SO4t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SO4t2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104466"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28575"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28574"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28576"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28577"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13116"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05651"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_so4_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_so4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2413"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR180y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:0)" metaid="R_EAR180y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR180y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR180y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.10"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97860"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_toctd2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcaACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGPAT120" fast="false" reversible="false" name="1-tetradecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C12:0)" metaid="R_AGPAT120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGPAT120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGPAT120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.51"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95558"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1ddecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa120_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3018"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHNAOT4" fast="false" reversible="false" name="1,4-dihydroxy-2-naphthoate octaprenyltransferase" metaid="R_DHNAOT4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHNAOT4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHNAOT4"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DMK-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.74"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97408"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30101"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30100"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30099"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30102"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08333"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhna_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octdp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3930"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AMPMS2" fast="false" reversible="false" name="4-amino-2-methyl-5-phosphomethylpyrimidine synthetase" metaid="R_AMPMS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMPMS2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMPMS2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142626"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_air_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4ampm_c" stoichiometry="1" constant="true"/> <speciesReference species="M_for_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3994"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DM_oxam_c" fast="false" reversible="false" name="Sink needed to allow oxamate to leave system" metaid="R_DM_oxam_c" sboTerm="SBO:0000628" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DM_oxam_c"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DM_oxam_c"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR131355"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12467"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_oxam_c" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ALR4x" fast="false" reversible="false" name="Aldose reductase (acetol)" metaid="R_ALR4x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALR4x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALR4x"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95790"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08122"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acetol_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12ppd__R_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3945"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP120" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (n-C14:0)" metaid="R_PGPP120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102560"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp120_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DAGK120" fast="false" reversible="false" name="Diacylglycerol kinase (n-C12:0)" metaid="R_DAGK120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAGK120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAGK120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97091"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa120_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4042"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALLTNtex" fast="false" reversible="true" name="Allantoin transport via diffusion (extracellular to periplasm)" metaid="R_ALLTNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALLTNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALLTNtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-557"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95771"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08117"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09698"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_alltn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_alltn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSSA180" fast="false" reversible="false" name="Phosphatidylserine syntase (n-C18:0)" metaid="R_PSSA180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSSA180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSSA180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103271"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09210"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdodecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps180_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2585"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASNtex" fast="false" reversible="true" name="L-asparagine transport via diffusion (extracellular to periplasm)" metaid="R_ASNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96069"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13466"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05220"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08162"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asn__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_asn__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSSA161" fast="false" reversible="false" name="Phosphatidylserine syntase (n-C16:1)" metaid="R_PSSA161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSSA161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSSA161"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103270"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdhdec9eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps161_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2585"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSSA141" fast="false" reversible="false" name="Phosphatidylserine syntase (n-C14:1)" metaid="R_PSSA141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSSA141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSSA141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103268"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdtdec7eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps141_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2585"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSD160" fast="false" reversible="false" name="Phosphatidylserine decarboxylase (n-C16:0)" metaid="R_PSD160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSD160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSD160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.65"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103232"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09200"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps160_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe160_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4160"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSD161" fast="false" reversible="false" name="Phosphatidylserine decarboxylase (n-C16:1)" metaid="R_PSD161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSD161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSD161"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.65"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103233"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps161_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe161_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4160"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSD180" fast="false" reversible="false" name="Phosphatidylserine decarboxylase (n-C18:0)" metaid="R_PSD180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSD180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSD180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.65"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103234"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09202"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps180_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe180_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4160"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_COLIPAabcpp" fast="false" reversible="false" name="Core oligosaccharide lipid A transport via ABC system (periplasm)" metaid="R_COLIPAabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_COLIPAabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/COLIPAabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96844"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08243"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_colipa_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_colipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1G141pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C14:1) (periplasm)" metaid="R_LPLIPAL1G141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1G141pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G141pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101157"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpg141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1G180pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C18:0) (periplasm)" metaid="R_LPLIPAL1G180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1G180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G180pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101160"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpg180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1G181pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C18:1) (periplasm)" metaid="R_LPLIPAL1G181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1G181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101161"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpg181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACONIs" fast="false" reversible="true" name="Aconitate isomerase (spontaneous)" metaid="R_ACONIs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACONIs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACONIs"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACONITATE-DELTA-ISOMERASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.3.7"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02244"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95382"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17266"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17268"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17267"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17265"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2214"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01606"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acon_T_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acon_C_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACONTb" fast="false" reversible="true" name="Aconitase (half-reaction B, Isocitrate hydro-lyase)" metaid="R_ACONTb" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACONTb"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACONTb"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.3"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01900"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95387"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22145"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22144"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22146"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22147"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01388"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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 id="R_GLCP2" fast="false" reversible="false" name="Glycogen phosphorylase" metaid="R_GLCP2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLCP2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCP2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100215"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08611"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_bglycogen_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3417"/> <fbc:geneProductRef fbc:geneProduct="G_b3428"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_F6Pt6_2pp" fast="false" reversible="false" name="Fructose-6-phosphate transport via phosphate antiport (periplasm)" metaid="R_F6Pt6_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_F6Pt6_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/F6Pt6_2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99079"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_f6p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3666"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPALtpp" fast="false" reversible="true" name="Propanal transport via channel (periplasm)" metaid="R_PPALtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPALtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPALtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103071"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09169"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09170"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ppal_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ppal_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_PLIPA2A140pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidate, n-C14:0) (periplasm)" metaid="R_PLIPA2A140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2A140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2A140pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102990"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa140_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1tdecg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2A141pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidate, n-C14:1) (periplasm)" metaid="R_PLIPA2A141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2A141pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2A141pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102991"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa141_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1tdec7eg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_p" stoichiometry="1" 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<speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1E180pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C18:0) (periplasm)" metaid="R_LPLIPAL1E180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1E180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1E180pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143196"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpe180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ASNS1" fast="false" reversible="false" name="Asparagine synthase (glutamine-hydrolysing)" metaid="R_ASNS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASNS1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASNS1"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ASNSYNB-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.5.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00578"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96059"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-70599"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-70599"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12231"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12229"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12230"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12228"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00416"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11214"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_asn__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0674"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR80y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C8:0)" metaid="R_EAR80y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR80y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR80y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97868"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_toct2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR120y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:0)" metaid="R_EAR120y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR120y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR120y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97848"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tddec2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR181" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:1)" metaid="R_3OAR181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94949"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07993"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ocvac11eACP_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_3hcvac11eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD121" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:1)" metaid="R_3HAD121" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD121"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD121"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.61"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94878"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07976"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hcddec5eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_t3c5ddeceACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR121y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:1)" metaid="R_EAR121y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR121y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR121y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.10"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97850"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_t3c5ddeceACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cddec5eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1E181pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C18:1) (periplasm)" metaid="R_LPLIPAL1E181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1E181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1E181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101154"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpe181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1G160pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C16:0) (periplasm)" metaid="R_LPLIPAL1G160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1G160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G160pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101158"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpg160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1G161pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C16:1) (periplasm)" metaid="R_LPLIPAL1G161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1G161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101159"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpg161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GTHRDHpp" fast="false" reversible="false" name="Glutathione hydralase (periplasmic)" metaid="R_GTHRDHpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GTHRDHpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GTHRDHpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12618"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-15856"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.19"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.19.13"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00494"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100136"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-8943279"/> <rdf:li 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stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3447"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_o2_e" fast="false" reversible="true" name="O2 exchange" metaid="R_EX_o2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_o2_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_o2_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-474"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102090"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09641"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09032"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09734"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PROGLYtex" fast="false" reversible="true" name="L-Prolinylglycine transport via diffusion (extracellular to periplasm)" metaid="R_PROGLYtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PROGLYtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PROGLYtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103191"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09190"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_progly_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_progly_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_progly_e" fast="false" reversible="false" name="L-Prolinylglycine exchange" metaid="R_EX_progly_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_progly_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_progly_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103191"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09190"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_progly_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_MDDCP2pp" fast="false" reversible="false" name="Murein D,D-carboxypeptidase (murein5px4px4p) (periplasm)" metaid="R_MDDCP2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDDCP2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDDCP2pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.16.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143207"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08891"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5px4px4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein4px4px4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0632"/> <fbc:geneProductRef fbc:geneProduct="G_b3182"/> <fbc:geneProductRef fbc:geneProduct="G_b0839"/> <fbc:geneProductRef fbc:geneProduct="G_b2010"/> <fbc:geneProductRef fbc:geneProduct="G_b2430"/> <fbc:geneProductRef fbc:geneProduct="G_b0376"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1G120pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C12:0) (periplasm)" metaid="R_LPLIPAL1G120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1G120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G120pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101155"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpg120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2E140pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylethanolamine, n-C14:0) (periplasm)" metaid="R_PLIPA2E140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2E140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2E140pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102997"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe140_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1agpe140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2E160pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylethanolamine, n-C16:0) (periplasm)" metaid="R_PLIPA2E160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2E160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2E160pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102999"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1agpe160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2A161pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidate, n-C16:1) (periplasm)" metaid="R_PLIPA2A161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2A161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2A161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102993"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1hdec9eg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2A181pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidate, n-C18:1) (periplasm)" metaid="R_PLIPA2A181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2A181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2A181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102995"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa181_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1odec11eg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_F6Ptex" fast="false" reversible="true" name="Fructose 6-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_F6Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_F6Ptex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/F6Ptex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99076"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_f6p_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_f6p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MDDCP3pp" fast="false" reversible="false" name="Murein D,D-carboxypeptidase (murein5p5p) (periplasm)" metaid="R_MDDCP3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDDCP3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDDCP3pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.16.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101431"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08892"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5p5p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5p4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0632"/> <fbc:geneProductRef fbc:geneProduct="G_b3182"/> <fbc:geneProductRef fbc:geneProduct="G_b0839"/> <fbc:geneProductRef fbc:geneProduct="G_b2010"/> <fbc:geneProductRef fbc:geneProduct="G_b2430"/> <fbc:geneProductRef fbc:geneProduct="G_b0376"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR140x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C14:0)" metaid="R_EAR140x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR140x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR140x"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97851"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tmrs2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR40y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C4:0)" metaid="R_EAR40y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR40y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR40y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97864"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_but2eACP_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_butACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GAMAN6Ptex" fast="false" reversible="true" name="D-glucosamine 6-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_GAMAN6Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GAMAN6Ptex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GAMAN6Ptex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100031"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13642"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08591"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05568"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gam6p_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gam6p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_gal_bD_e" fast="false" reversible="false" name="Beta D-Galactose exchange" metaid="R_EX_gal_bD_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_gal_bD_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gal_bD_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99953"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08574"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gal_bD_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_3OAS181" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:1)" metaid="R_3OAS181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.179"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94962"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3ocvac11eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1095"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR161y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:1)" metaid="R_EAR161y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR161y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR161y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.10"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97858"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_t3c9palmeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PAT140" fast="false" reversible="false" name="Glycerol-3-phosphate acyltransferase (C14:0)" metaid="R_G3PAT140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PAT140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PAT140"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.15"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99855"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1tdecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b4041"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PAT160" fast="false" reversible="false" name="Glycerol-3-phosphate acyltransferase (C16:0)" metaid="R_G3PAT160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PAT160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PAT160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.15"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99857"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1hdecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b4041"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PAT161" fast="false" reversible="false" name="Glycerol-3-phosphate acyltransferase (C16:1)" metaid="R_G3PAT161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PAT161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PAT161"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.15"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99859"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1hdec9eg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b4041"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGPAT160" fast="false" reversible="false" name="1-hexadecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C16:0)" metaid="R_AGPAT160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGPAT160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGPAT160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.51"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95561"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1hdecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa160_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3018"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGPAT140" fast="false" reversible="false" name="1-tetradecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C14:0)" metaid="R_AGPAT140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGPAT140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGPAT140"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.51"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95559"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1tdecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa140_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3018"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGSA160" fast="false" reversible="false" name="Phosphatidylglycerol synthase (n-C16:0)" metaid="R_PGSA160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGSA160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGSA160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102592"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09111"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdhdecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp160_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1912"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLDCP2Bpp" fast="false" reversible="false" name="Murein L,D-carboxypeptidase (murein4p3p) (periplasm)" metaid="R_MLDCP2Bpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLDCP2Bpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLDCP2Bpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.17.13"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143240"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08929"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein4p3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein3p3p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1113"/> <fbc:geneProductRef fbc:geneProduct="G_b0819"/> <fbc:geneProductRef fbc:geneProduct="G_b1990"/> <fbc:geneProductRef fbc:geneProduct="G_b1678"/> <fbc:geneProductRef fbc:geneProduct="G_b0925"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAS140" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:0)" metaid="R_3OAS140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS140"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94957"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3omrsACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> <fbc:geneProductRef fbc:geneProduct="G_b1095"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR140" fast="false" reversible="true" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:0)" metaid="R_3OAR140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR140"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9536"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04566"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94944"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05342"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3omrsACP_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_3hmrsACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CDAPPA140" fast="false" reversible="false" name="CDP-Diacylglycerol pyrophostatase (n-C14:0)" metaid="R_CDAPPA140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CDAPPA140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDAPPA140"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.26"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96501"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08200"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdtdecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pa140_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3918"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLDCP1App" fast="false" reversible="false" name="Murein L,D-carboxypeptidase (murein5px4p) (periplasm)" metaid="R_MLDCP1App" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLDCP1App"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLDCP1App"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.17.13"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143237"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08926"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5px4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_alaala_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein3px4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0925"/> <fbc:geneProductRef fbc:geneProduct="G_b1990"/> <fbc:geneProductRef fbc:geneProduct="G_b1113"/> <fbc:geneProductRef fbc:geneProduct="G_b1678"/> <fbc:geneProductRef fbc:geneProduct="G_b0819"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR160y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:0)" metaid="R_EAR160y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR160y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR160y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.10"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97856"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tpalm2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR160" fast="false" reversible="true" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:0)" metaid="R_3OAR160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04543"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94946"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05336"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3opalmACP_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_3hpalmACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PDE4" fast="false" reversible="false" name="3',5'-cyclic-nucleotide phosphodiesterase" metaid="R_PDE4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PDE4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PDE4"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:35-CYCLIC-GMP-PHOSPHODIESTERASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.35"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.17"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01234"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100078"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16957"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16958"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16959"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16960"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00920"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_35cgmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1489"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGSA161" fast="false" reversible="false" name="Phosphatidylglycerol synthase (n-C16:1)" metaid="R_PGSA161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGSA161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGSA161"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102594"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09112"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdhdec9eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp161_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1912"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD181" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:1)" metaid="R_3HAD181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.61"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94884"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07980"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hcvac11eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_t3c11vaceACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP160" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (n-C16:0)" metaid="R_PGPP160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102563"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09104"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp160_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR100y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C10:0)" metaid="R_EAR100y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR100y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR100y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97846"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdec2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR141" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:1)" metaid="R_3OAR141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR141"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94945"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07989"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ocmrs7eACP_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_3hcmrs7eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR161" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:1)" metaid="R_3OAR161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR161"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94947"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07991"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ocpalm9eACP_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_3hcpalm9eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD141" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:1)" metaid="R_3HAD141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD141"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.61"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94880"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07977"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hcmrs7eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_t3c7mrseACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR121x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:1)" metaid="R_EAR121x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR121x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR121x"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.9"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97849"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_t3c5ddeceACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cddec5eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP180" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (n-C18:0)" metaid="R_PGPP180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102566"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09106"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp180_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP161" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (n-C16:1)" metaid="R_PGPP161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP161"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102565"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09105"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp161_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP181" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (n-C18:1)" metaid="R_PGPP181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102567"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp181_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSD140" fast="false" reversible="false" name="Phosphatidylserine decarboxylase (n-C14:0)" metaid="R_PSD140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSD140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSD140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103230"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps140_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe140_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4160"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MICITDr" fast="false" reversible="true" name="2-methylisocitrate dehydratase" metaid="R_MICITDr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MICITDr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MICITDr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:4.2.1.99-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.99"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04425"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101580"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17943"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17944"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17942"/> <rdf:li rdf:resource="http://identifiers.org/rhea/17941"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/4112"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03061"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2mcacn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_micit_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0118"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CDAPPA180" fast="false" reversible="false" name="CDP-Diacylglycerol pyrophostatase (n-C18:0)" metaid="R_CDAPPA180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CDAPPA180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDAPPA180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.26"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96506"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08204"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdodecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pa180_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3918"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGM4PH" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide beta -1,4-N-acetylglucosaminidase" metaid="R_AGM4PH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGM4PH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM4PH"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95548"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08078"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam_c" stoichiometry="1" constant="true"/> <speciesReference species="M_anhm4p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1107"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NTP12" fast="false" reversible="false" name="Nucleoside-triphosphatase (XTP)" metaid="R_NTP12" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTP12"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTP12"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5074"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102041"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28406"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28409"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28407"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28408"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09012"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xtp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xdp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4394"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PE141abcpp" fast="false" reversible="false" name="Phosphatidylethanolamine transport via ABC system (n-C14:1, periplasm)" metaid="R_PE141abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PE141abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PE141abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102443"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe141_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_pe141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CDAPPA181" fast="false" reversible="false" name="CDP-Diacylglycerol pyrophostatase (n-C18:1)" metaid="R_CDAPPA181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CDAPPA181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDAPPA181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.26"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96507"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08205"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdodec11eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pa181_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3918"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGSA140" fast="false" reversible="false" name="Phosphatidylglycerol synthase (n-C14:0)" metaid="R_PGSA140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGSA140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGSA140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102590"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdtdecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp140_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1912"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1A141pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C14:1) (periplasm)" metaid="R_LPLIPAL1A141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1A141pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1A141pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101143"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1tdec7eg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1A180pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C18:0) (periplasm)" metaid="R_LPLIPAL1A180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1A180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1A180pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101146"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08801"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1odecg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1E140pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C14:0) (periplasm)" metaid="R_LPLIPAL1E140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1E140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1E140pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101149"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpe140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1E161pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C16:1) (periplasm)" metaid="R_LPLIPAL1E161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1E161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1E161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101152"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpe161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1G140pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C14:0) (periplasm)" metaid="R_LPLIPAL1G140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1G140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1G140pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101156"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpg140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PE160abcpp" fast="false" reversible="false" name="Phosphatidylethanolamine transport via ABC system (n-C16:0, periplasm)" metaid="R_PE160abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PE160abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PE160abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102444"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09076"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe160_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_pe160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PE161abcpp" fast="false" reversible="false" name="Phosphatidylethanolamine transport via ABC system (n-C16:1, periplasm)" metaid="R_PE161abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PE161abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PE161abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102445"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe161_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_pe161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSD141" fast="false" reversible="false" name="Phosphatidylserine decarboxylase (n-C14:1)" metaid="R_PSD141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSD141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSD141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103231"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps141_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe141_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4160"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PG140abcpp" fast="false" reversible="false" name="Phosphatidylglycerol transport via ABC system (n-C14:0, periplasm)" metaid="R_PG140abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PG140abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PG140abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102517"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg140_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_pg140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PG141abcpp" fast="false" reversible="false" name="Phosphatidylglycerol transport via ABC system (n-C14:1, periplasm)" metaid="R_PG141abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PG141abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PG141abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102518"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg141_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_pg141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACONTa" fast="false" reversible="true" name="Aconitase (half-reaction A, Citrate hydro-lyase)" metaid="R_ACONTa" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACONTa"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACONTa"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACONITATEDEHYDR-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.3"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01325"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95386"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10230"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10229"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10231"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10228"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/268"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00974"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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 id="R_MLDCP2App" fast="false" reversible="false" name="Murein L,D-carboxypeptidase (murein5p5p) (periplasm)" metaid="R_MLDCP2App" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLDCP2App"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLDCP2App"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.17.13"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143239"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08928"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5p5p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_alaala_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5p3p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1113"/> <fbc:geneProductRef fbc:geneProduct="G_b1678"/> <fbc:geneProductRef fbc:geneProduct="G_b0819"/> <fbc:geneProductRef fbc:geneProduct="G_b0925"/> <fbc:geneProductRef fbc:geneProduct="G_b1990"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_12DGR140tipp" fast="false" reversible="false" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:0)" metaid="R_12DGR140tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_12DGR140tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/12DGR140tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94676"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr140_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr140_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_PG180abcpp" fast="false" reversible="false" name="Phosphatidylglycerol transport via ABC system (n-C18:0, periplasm)" metaid="R_PG180abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PG180abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PG180abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102521"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09090"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg180_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_pg180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_12DGR160tipp" fast="false" reversible="false" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:0)" metaid="R_12DGR160tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_12DGR160tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/12DGR160tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94678"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr160_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_PG181abcpp" fast="false" reversible="false" name="Phosphatidylglycerol transport via ABC system (n-C18:1, periplasm)" metaid="R_PG181abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PG181abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PG181abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102524"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg181_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_pg181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AM4PA" fast="false" reversible="false" name="Anhydrous-N-Acetylmuramyl-tetrapeptide amidase" metaid="R_AM4PA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AM4PA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AM4PA"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95793"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08124"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhm4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDgluMdapDala_c" stoichiometry="1" constant="true"/> <speciesReference species="M_anhm_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0110"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGP141abcpp" fast="false" reversible="false" name="Phosphatidylglycerophosphate transport via ABC system (n-C14:1, periplasm)" metaid="R_PGP141abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGP141abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGP141abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102552"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp141_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_pgp141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGP160abcpp" fast="false" reversible="false" name="Phosphatidylglycerophosphate transport via ABC system (n-C16:0, periplasm)" metaid="R_PGP160abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGP160abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGP160abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102553"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09097"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp160_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_pgp160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_12DGR180tipp" fast="false" reversible="false" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:0)" metaid="R_12DGR180tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_12DGR180tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/12DGR180tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94680"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr180_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr180_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_PGPP120pp" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (periplasm, n-C14:0)" metaid="R_PGPP120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP120pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102560"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP181pp" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (periplasm, n-C18:1)" metaid="R_PGPP181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP181pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102567"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp181_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNH120pp" fast="false" reversible="false" name="Cardiolipin hydrolase (periplasm, n-C12:0)" metaid="R_CLPNH120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNH120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNH120pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96774"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_clpn120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg120_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_PGP180abcpp" fast="false" reversible="false" name="Phosphatidylglycerophosphate transport via ABC system (n-C18:0, periplasm)" metaid="R_PGP180abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGP180abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGP180abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102555"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09099"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp180_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_pgp180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_dump_e" fast="false" reversible="false" name="DUMP exchange" metaid="R_EX_dump_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dump_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dump_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97813"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09816"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08375"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dump_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PAPA181pp" fast="false" reversible="false" name="Phosphatidate phosphatase (periplasmic, n-C18:1)" metaid="R_PAPA181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102356"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa181_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PA140abcpp" fast="false" reversible="false" name="Phosphatidate transport via ABC system (n-C14:0, periplasm)" metaid="R_PA140abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PA140abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PA140abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102305"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09054"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa140_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_pa140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNH140pp" fast="false" reversible="false" name="Cardiolipin hydrolase (periplasm, n-C14:0)" metaid="R_CLPNH140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNH140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNH140pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96775"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_clpn140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg140_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_EX_12ppd__R_e" fast="false" reversible="false" name="(R)-Propane-1,2-diol exchange" metaid="R_EX_12ppd__R_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_12ppd__R_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_12ppd__R_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-467"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94683"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07920"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07919"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12ppd__R_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PGSA181" fast="false" reversible="false" name="Phosphatidylglycerol synthase (n-C18:1)" metaid="R_PGSA181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGSA181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGSA181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102596"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdodec11eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp181_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1912"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP140" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (n-C14:0)" metaid="R_PGPP140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102561"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp140_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP141" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (n-C14:1)" metaid="R_PGPP141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102562"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp141_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MDDCP5pp" fast="false" reversible="false" name="Murein D,D-carboxypeptidase (murein5p3p) (periplasm)" metaid="R_MDDCP5pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDDCP5pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDDCP5pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.16.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143209"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08894"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5p3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein4p3p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0632"/> <fbc:geneProductRef fbc:geneProduct="G_b3182"/> <fbc:geneProductRef fbc:geneProduct="G_b0839"/> <fbc:geneProductRef fbc:geneProduct="G_b2010"/> <fbc:geneProductRef fbc:geneProduct="G_b2430"/> <fbc:geneProductRef fbc:geneProduct="G_b0376"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLTGY3pp" fast="false" reversible="false" name="Murein lytic transglycosylase (murein3p3p) (periplasm)" metaid="R_MLTGY3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLTGY3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTGY3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143247"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08939"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_murein3p3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_anhgm3p_p" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4392"/> <fbc:geneProductRef fbc:geneProduct="G_b2813"/> <fbc:geneProductRef fbc:geneProduct="G_b2701"/> <fbc:geneProductRef fbc:geneProduct="G_b1193"/> <fbc:geneProductRef fbc:geneProduct="G_b2963"/> <fbc:geneProductRef fbc:geneProduct="G_b2558"/> <fbc:geneProductRef fbc:geneProduct="G_b0211"/> <fbc:geneProductRef fbc:geneProduct="G_b1097"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_12DGR120tipp" fast="false" reversible="false" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C12:0)" metaid="R_12DGR120tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_12DGR120tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/12DGR120tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94675"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr120_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_MDDCP4pp" fast="false" reversible="false" name="Murein D,D-carboxypeptidase (murein5p4p) (periplasm)" metaid="R_MDDCP4pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDDCP4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDDCP4pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.16.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143208"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08893"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5p4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein4p4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0632"/> <fbc:geneProductRef fbc:geneProduct="G_b3182"/> <fbc:geneProductRef fbc:geneProduct="G_b0839"/> <fbc:geneProductRef fbc:geneProduct="G_b2010"/> <fbc:geneProductRef fbc:geneProduct="G_b2430"/> <fbc:geneProductRef fbc:geneProduct="G_b0376"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNS140pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C14:0)" metaid="R_CLPNS140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNS140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNS140pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96782"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pg140_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_clpn140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1249"/> <fbc:geneProductRef fbc:geneProduct="G_b0789"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNS141pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C14:1)" metaid="R_CLPNS141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNS141pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNS141pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96783"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pg141_p" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_clpn141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1249"/> <fbc:geneProductRef fbc:geneProduct="G_b0789"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PAT180" fast="false" reversible="false" name="Glycerol-3-phosphate acyltransferase (C18:0)" metaid="R_G3PAT180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PAT180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PAT180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.15"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99860"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcaACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1odecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b4041"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_o2s_e" fast="false" reversible="false" name="Superoxide anion exchange" metaid="R_EX_o2s_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_o2s_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_o2s_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102089"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1222342"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_o2s_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PLIPA1G160pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylglycerol, n-C16:0) (periplasm)" metaid="R_PLIPA1G160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1G160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1G160pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102984"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg160_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PG120abcpp" fast="false" reversible="false" name="Phosphatidylglycerol transport via ABC system (n-C12:0, periplasm)" metaid="R_PG120abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PG120abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PG120abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102516"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pg120_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_pg120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_gal1p_e" fast="false" reversible="false" name="Alpha-D-Galactose 1-phosphate exchange" metaid="R_EX_gal1p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_gal1p_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gal1p_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99923"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08572"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gal1p_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PE140abcpp" fast="false" reversible="false" name="Phosphatidylethanolamine transport via ABC system (n-C14:0, periplasm)" metaid="R_PE140abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PE140abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PE140abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102442"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe140_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_pe140_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CFAS160E" fast="false" reversible="false" name="Cyclopropane fatty acid synthase (Phosphatidylethanolamine, n-C16:0)" metaid="R_CFAS160E" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CFAS160E"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CFAS160E"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.79"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96652"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pe161_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ahcys_c" stoichiometry="2" constant="true"/> <speciesReference species="M_cpe160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1661"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1G141pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylglycerol, n-C14:1) (periplasm)" metaid="R_PLIPA1G141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1G141pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1G141pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102983"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg141_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2E160" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C16:0)" metaid="R_LPLIPAL2E160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2E160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2E160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101186"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08841"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2G140" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C14:0)" metaid="R_LPLIPAL2G140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2G140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2G140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101191"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2G160" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C16:0)" metaid="R_LPLIPAL2G160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2G160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2G160"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101193"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CFAS180E" fast="false" reversible="false" name="Cyclopropane fatty acid synthase (Phosphatidylethanolamine, n-C18:0)" metaid="R_CFAS180E" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CFAS180E"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CFAS180E"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.79"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96654"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pe181_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ahcys_c" stoichiometry="2" constant="true"/> <speciesReference species="M_cpe180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1661"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_dcmp_e" fast="false" reversible="false" name="DCMP exchange" metaid="R_EX_dcmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dcmp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dcmp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97186"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08315"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcmp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_CFAS180G" fast="false" reversible="false" name="Cyclopropane fatty acid synthase (Phosphatidylglycerol, n-C18:0)" metaid="R_CFAS180G" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CFAS180G"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CFAS180G"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.79"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96655"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pg181_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ahcys_c" stoichiometry="2" constant="true"/> <speciesReference species="M_cpg180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1661"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAPA160" fast="false" reversible="false" name="Phosphatidate phosphatase (n-C16:0)" metaid="R_PAPA160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102350"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa160_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPE140tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPE140tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPE140tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPE140tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94751"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe140_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe140_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPE160tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPE160tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPE160tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPE160tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94753"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07942"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe160_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPE180tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPE180tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPE180tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPE180tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94755"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07944"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe180_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe180_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAPA180" fast="false" reversible="false" name="Phosphatidate phosphatase (n-C18:0)" metaid="R_PAPA180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA180"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102354"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa180_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAPA181" fast="false" reversible="false" name="Phosphatidate phosphatase (n-C18:1)" metaid="R_PAPA181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA181"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102356"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa181_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPE141tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPE141tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPE141tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPE141tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94752"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe141_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe141_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPE161tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPE161tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPE161tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPE161tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94754"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe161_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_23ccmp_e" fast="false" reversible="false" name="2',3'-Cyclic CMP exchange" metaid="R_EX_23ccmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_23ccmp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_23ccmp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94720"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07926"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23ccmp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_2AGPA161tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphatidate (n-C16:1) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPA161tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPA161tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPA161tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94747"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07936"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2hdec9eg3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2hdec9eg3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPA181tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphatidate (n-C18:1) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPA181tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPA181tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPA181tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94749"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07938"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2odec11eg3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2odec11eg3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPG120tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPG120tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPG120tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPG120tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94764"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpg120_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2G120" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C12:0)" metaid="R_LPLIPAL2G120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2G120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2G120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101190"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpg120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ddca_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PA141abcpp" fast="false" reversible="false" name="Phosphatidate transport via ABC system (n-C14:1, periplasm)" metaid="R_PA141abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PA141abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PA141abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102306"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09055"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa141_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_pa141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PETNT161pp" fast="false" reversible="false" name="Phosphoethanolamine transferase (c-C16:1)" metaid="R_PETNT161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PETNT161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PETNT161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102499"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_enlipa_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3546"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSSA160" fast="false" reversible="false" name="Phosphatidylserine syntase (n-C16:0)" metaid="R_PSSA160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSSA160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSSA160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103269"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09208"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdhdecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps160_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2585"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSSA181" fast="false" reversible="false" name="Phosphatidylserine syntase (n-C18:1)" metaid="R_PSSA181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSSA181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSSA181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103272"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdodec11eg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps181_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2585"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DAGK140" fast="false" reversible="false" name="Diacylglycerol kinase (n-C14:0)" metaid="R_DAGK140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAGK140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAGK140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97092"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa140_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4042"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DAGK160" fast="false" reversible="false" name="Diacylglycerol kinase (n-C16:0)" metaid="R_DAGK160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAGK160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAGK160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.107"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97094"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr160_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa160_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4042"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DAGK141" fast="false" reversible="false" name="Diacylglycerol kinase (n-C14:1)" metaid="R_DAGK141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAGK141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAGK141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97093"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa141_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4042"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DAGK161" fast="false" reversible="false" name="Diacylglycerol kinase (n-C16:1)" metaid="R_DAGK161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAGK161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAGK161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97097"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa161_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4042"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGPAT181" fast="false" reversible="false" name="1-octadec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C18:1)" metaid="R_AGPAT181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGPAT181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGPAT181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.51"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95567"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1odec11eg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa181_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3018"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PA161abcpp" fast="false" reversible="false" name="Phosphatidate transport via ABC system (n-C16:1, periplasm)" metaid="R_PA161abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PA161abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PA161abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102308"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09057"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa161_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_pa161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PA180abcpp" fast="false" reversible="false" name="Phosphatidate transport via ABC system (n-C18:0, periplasm)" metaid="R_PA180abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PA180abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PA180abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102309"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09058"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa180_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_pa180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGPP161pp" fast="false" reversible="false" name="Phosphatidylglycerol phosphate phosphatase (periplasm, n-C16:1)" metaid="R_PGPP161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGPP161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGPP161pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.27"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102565"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09105"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pg161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0418"/> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PE120abcpp" fast="false" reversible="false" name="Phosphatidylethanolamine transport via ABC system (n-C12:0, periplasm)" metaid="R_PE120abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PE120abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PE120abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102441"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe120_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_pe120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MDDEP3pp" fast="false" reversible="false" name="Murein D,D-endopeptidase (murein5px4p) (periplasm)" metaid="R_MDDEP3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDDEP3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDDEP3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101436"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08897"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5px4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_murein5p4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3182"/> <fbc:geneProductRef fbc:geneProduct="G_b2328"/> <fbc:geneProductRef fbc:geneProduct="G_b2134"/> <fbc:geneProductRef fbc:geneProduct="G_b2175"/> <fbc:geneProductRef fbc:geneProduct="G_b0376"/> <fbc:geneProductRef fbc:geneProduct="G_b1655"/> <fbc:geneProductRef fbc:geneProduct="G_b1856"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MDDEP4pp" fast="false" reversible="false" name="Murein D,D-endopeptidase (murein4px4px4p) (periplasm)" metaid="R_MDDEP4pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDDEP4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDDEP4pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143211"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08898"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein4px4px4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_murein4px4p4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3182"/> <fbc:geneProductRef fbc:geneProduct="G_b2328"/> <fbc:geneProductRef fbc:geneProduct="G_b2134"/> <fbc:geneProductRef fbc:geneProduct="G_b0376"/> <fbc:geneProductRef fbc:geneProduct="G_b2175"/> <fbc:geneProductRef fbc:geneProduct="G_b1655"/> <fbc:geneProductRef fbc:geneProduct="G_b1856"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PE180abcpp" fast="false" reversible="false" name="Phosphatidylethanolamine transport via ABC system (n-C18:0, periplasm)" metaid="R_PE180abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PE180abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PE180abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102450"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09078"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe180_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_pe180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAPA140" fast="false" reversible="false" name="Phosphatidate phosphatase (n-C14:0)" metaid="R_PAPA140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102348"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa140_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr140_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLTGY1pp" fast="false" reversible="false" name="Murein lytic transglycosylase (murein4p4p) (periplasm)" metaid="R_MLTGY1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLTGY1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTGY1pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143245"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08937"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_murein4p4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_anhgm4p_p" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2963"/> <fbc:geneProductRef fbc:geneProduct="G_b4392"/> <fbc:geneProductRef fbc:geneProduct="G_b2813"/> <fbc:geneProductRef fbc:geneProduct="G_b2701"/> <fbc:geneProductRef fbc:geneProduct="G_b1193"/> <fbc:geneProductRef fbc:geneProduct="G_b2558"/> <fbc:geneProductRef fbc:geneProduct="G_b0211"/> <fbc:geneProductRef fbc:geneProduct="G_b1097"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_3cmp_e" fast="false" reversible="false" name="3'-cmp exchange" metaid="R_EX_3cmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_3cmp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_3cmp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94861"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07974"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3cmp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_CGLYtex" fast="false" reversible="true" name="L-Cysteinylglycine transport via diffusion (extracellular to periplasm)" metaid="R_CGLYtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CGLYtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CGLYtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96658"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08211"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cgly_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cgly_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD40" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C4:0)" metaid="R_3HAD40" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD40"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD40"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.58"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94885"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07981"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3haACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_but2eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1E141pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylethanolamine, n-C14:1) (periplasm)" metaid="R_PLIPA1E141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1E141pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1E141pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102976"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe141_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAS60" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C6:0)" metaid="R_3OAS60" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS60"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS60"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94963"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_butACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3ohexACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1095"/> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAS160" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:0)" metaid="R_3OAS160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94959"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3opalmACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> <fbc:geneProductRef fbc:geneProduct="G_b1095"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAPA141" fast="false" reversible="false" name="Phosphatidate phosphatase (n-C14:1)" metaid="R_PAPA141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102349"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa141_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr141_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAPA161" fast="false" reversible="false" name="Phosphatidate phosphatase (n-C16:1)" metaid="R_PAPA161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102353"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa161_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr161_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GTHOXtex" fast="false" reversible="true" name="Glutathione (ox) transport via diffusion (extracellular to periplasm)" metaid="R_GTHOXtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GTHOXtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GTHOXtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100443"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09677"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08674"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gthox_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gthox_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DSBAO1" fast="false" reversible="false" name="DsbA protein reoxidation reaction (aerobic)" metaid="R_DSBAO1" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DSBAO1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DSBAO1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97791"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08366"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dsbard_p" stoichiometry="1" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dsbaox_p" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1185"/> <fbc:geneProductRef fbc:geneProduct="G_b3860"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DSBAO2" fast="false" reversible="false" name="DsbA protein reoxidation reaction (anaerobic)" metaid="R_DSBAO2" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DSBAO2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DSBAO2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97792"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08367"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dsbard_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dsbaox_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1185"/> <fbc:geneProductRef fbc:geneProduct="G_b3860"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DSBDR" fast="false" reversible="false" name="DsbD reductase" metaid="R_DSBDR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DSBDR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DSBDR"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97794"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08369"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dsbdox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dsbdrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2582"/> <fbc:geneProductRef fbc:geneProduct="G_b4136"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3781"/> <fbc:geneProductRef fbc:geneProduct="G_b4136"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TDSR1" fast="false" reversible="false" name="Thiol:disulfide reductase (DsbC)" metaid="R_TDSR1" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TDSR1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TDSR1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104764"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09292"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dsbcox_p" stoichiometry="1" constant="true"/> <speciesReference species="M_dsbdrd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dsbcrd_p" stoichiometry="1" constant="true"/> <speciesReference species="M_dsbdox_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2893"/> <fbc:geneProductRef fbc:geneProduct="G_b4136"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CGLYabcpp" fast="false" reversible="false" name="L-Cysteinylglycine (Cys-Gly) transport via ABC system (periplasm)" metaid="R_CGLYabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CGLYabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CGLYabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96656"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05539"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08210"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cgly_p" 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_cgly_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_b3544"/> <fbc:geneProductRef fbc:geneProduct="G_b3542"/> <fbc:geneProductRef fbc:geneProduct="G_b3543"/> <fbc:geneProductRef fbc:geneProduct="G_b3540"/> <fbc:geneProductRef fbc:geneProduct="G_b3541"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2A120pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidate, n-C12:0) (periplasm)" metaid="R_PLIPA2A120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2A120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2A120pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102989"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1ddecg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2A160pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidate, n-C16:0) (periplasm)" metaid="R_PLIPA2A160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2A160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2A160pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.4"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102992"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09147"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa160_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1hdecg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLPNH180pp" fast="false" reversible="false" name="Cardiolipin hydrolase (periplasm, n-C18:0)" metaid="R_CLPNH180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLPNH180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLPNH180pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96779"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_clpn180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg180_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_3OAR60" fast="false" reversible="true" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C6:0)" metaid="R_3OAR60" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR60"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR60"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04953"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94952"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05337"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ohexACP_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_3hhexACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR80" fast="false" reversible="true" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C8:0)" metaid="R_3OAR80" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR80"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR80"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9524"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04536"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94953"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05341"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ooctACP_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_3hoctACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLDCP3App" fast="false" reversible="false" name="Murein L,D-carboxypeptidase (murein5px3p) (periplasm)" metaid="R_MLDCP3App" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLDCP3App"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLDCP3App"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.17.13"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143241"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08930"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5px3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_alaala_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein3px3p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0925"/> <fbc:geneProductRef fbc:geneProduct="G_b1990"/> <fbc:geneProductRef fbc:geneProduct="G_b1113"/> <fbc:geneProductRef fbc:geneProduct="G_b1678"/> <fbc:geneProductRef fbc:geneProduct="G_b0819"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLDCP1Bpp" fast="false" reversible="false" name="Murein L,D-carboxypeptidase (murein4p4p) (periplasm)" metaid="R_MLDCP1Bpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLDCP1Bpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLDCP1Bpp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.17.13"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143238"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08927"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein4p4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein4p3p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0925"/> <fbc:geneProductRef fbc:geneProduct="G_b1990"/> <fbc:geneProductRef fbc:geneProduct="G_b1113"/> <fbc:geneProductRef fbc:geneProduct="G_b1678"/> <fbc:geneProductRef fbc:geneProduct="G_b0819"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPE181tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPE181tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPE181tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPE181tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94756"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe181_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2agpe181_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPA140tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphatidate (n-C14:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPA140tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPA140tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPA140tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94744"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07933"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2tdecg3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2tdecg3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2E120" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C12:0)" metaid="R_LPLIPAL2E120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2E120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2E120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101183"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2agpe120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ddca_c" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR100x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C10:0)" metaid="R_EAR100x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR100x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR100x"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97845"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdec2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR120x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:0)" metaid="R_EAR120x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR120x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR120x"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97847"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tddec2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR160x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:0)" metaid="R_EAR160x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR160x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR160x"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.9"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97855"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tpalm2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPA160tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphatidate (n-C16:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPA160tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPA160tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPA160tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94746"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07935"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2hdecg3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2hdecg3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ATHRDHr" fast="false" reversible="true" name="L-allo-threonine dehydrogenase" metaid="R_ATHRDHr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ATHRDHr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ATHRDHr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-16000"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.381"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10851"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96121"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30057"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30058"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30056"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30055"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08172"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_athr__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2aobut_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_b1539"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPA180tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphatidate (n-C18:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPA180tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPA180tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPA180tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94748"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07937"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2odecg3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2odecg3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2AGPA141tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphatidate (n-C14:1) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPA141tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2AGPA141tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2AGPA141tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94745"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07934"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2tdec7eg3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2tdec7eg3p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2835"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR140y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:0)" metaid="R_EAR140y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR140y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR140y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97852"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tmrs2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAS121" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:1)" metaid="R_3OAS121" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS121"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS121"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94956"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdec3eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3ocddec5eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAS80" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C8:0)" metaid="R_3OAS80" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS80"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS80"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94964"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hexACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3ooctACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> <fbc:geneProductRef fbc:geneProduct="G_b1095"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAS100" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C10:0)" metaid="R_3OAS100" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS100"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS100"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94954"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3odecACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> <fbc:geneProductRef fbc:geneProduct="G_b1095"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAS120" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:0)" metaid="R_3OAS120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94955"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3oddecACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1095"/> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LSERDHr" fast="false" reversible="true" name="L-serine dehydrogenase" metaid="R_LSERDHr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LSERDHr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LSERDHr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2201"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.276"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06126"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101242"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21596"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21599"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21598"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21597"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04137"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2amsa_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_b1539"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR40" fast="false" reversible="true" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C4:0)" metaid="R_3OAR40" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR40"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR40"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94950"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07994"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_actACP_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_3haACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR100" fast="false" reversible="true" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C10:0)" metaid="R_3OAR100" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR100"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR100"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9528"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04534"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94941"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05338"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3odecACP_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_3hdecACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DSERDHr" fast="false" reversible="true" name="D-serine dehydrogenase" metaid="R_DSERDHr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DSERDHr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DSERDHr"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97797"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30107"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30109"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30110"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30108"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08371"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__D_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2amsa_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_b1539"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD60" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C6:0)" metaid="R_3HAD60" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD60"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD60"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.58"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.59"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04954"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94887"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05330"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hhexACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thex2eACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD100" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C10:0)" metaid="R_3HAD100" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD100"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD100"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.58"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.60"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.61"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.59"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04535"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94876"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05333"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hdecACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdec2eACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD140" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:0)" metaid="R_3HAD140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD140"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9537"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.61"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.59"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04568"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94879"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05335"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hmrsACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tmrs2eACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD160" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:0)" metaid="R_3HAD160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.61"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.59"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04544"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94881"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05332"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hpalmACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tpalm2eACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_urate_e" fast="false" reversible="false" name="Urate exchange" metaid="R_EX_urate_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_urate_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_urate_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105145"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-2872497"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-2872497"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-2872497"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-2872497"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-2872497"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-2872497"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-2872497"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_urate_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PSD120" fast="false" reversible="false" name="Phosphatidylserine decarboxylase (n-C12:0)" metaid="R_PSD120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSD120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSD120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.65"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103229"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps120_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe120_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4160"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGPAT180" fast="false" reversible="false" name="1-octadecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C18:0)" metaid="R_AGPAT180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGPAT180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGPAT180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.51"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95565"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1odecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcaACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa180_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3018"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGPAT141" fast="false" reversible="false" name="1-tetradec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C14:1)" metaid="R_AGPAT141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGPAT141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGPAT141"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.51"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95560"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1tdec7eg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa141_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3018"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAPA120" fast="false" reversible="false" name="Phosphatidate phosphatase (n-C12:0)" metaid="R_PAPA120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAPA120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPA120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102347"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa120_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr120_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1278"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_skm_e" fast="false" reversible="false" name="Shikimate exchange" metaid="R_EX_skm_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_skm_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_skm_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104394"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09257"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_skm_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_cpgn_un_e" fast="false" reversible="false" name="Coprogen unloaded (no Fe(III)) exchange" metaid="R_EX_cpgn_un_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cpgn_un_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cpgn_un_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142943"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cpgn_un_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_MDDEP1pp" fast="false" reversible="false" name="Murein D,D-endopeptidase (murein4px4p) (periplasm)" metaid="R_MDDEP1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDDEP1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDDEP1pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143210"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08895"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein4px4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_murein4p4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3182"/> <fbc:geneProductRef fbc:geneProduct="G_b2328"/> <fbc:geneProductRef fbc:geneProduct="G_b2134"/> <fbc:geneProductRef fbc:geneProduct="G_b1655"/> <fbc:geneProductRef fbc:geneProduct="G_b1856"/> <fbc:geneProductRef fbc:geneProduct="G_b2175"/> <fbc:geneProductRef fbc:geneProduct="G_b0376"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MDDEP2pp" fast="false" reversible="false" name="Murein D,D-endopeptidase (murein3px4p) (periplasm)" metaid="R_MDDEP2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MDDEP2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDDEP2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101435"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08896"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein3px4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_murein4p3p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3182"/> <fbc:geneProductRef fbc:geneProduct="G_b2328"/> <fbc:geneProductRef fbc:geneProduct="G_b2134"/> <fbc:geneProductRef fbc:geneProduct="G_b1655"/> <fbc:geneProductRef fbc:geneProduct="G_b1856"/> <fbc:geneProductRef fbc:geneProduct="G_b2175"/> <fbc:geneProductRef fbc:geneProduct="G_b0376"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_AGPAT161" fast="false" reversible="false" name="1-hexadec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C16:1)" metaid="R_AGPAT161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AGPAT161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGPAT161"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.51"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95564"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1hdec9eg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa161_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3018"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DASYN120" fast="false" reversible="false" name="CDP-diacylglycerol synthetase (n-C12:0)" metaid="R_DASYN120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DASYN120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DASYN120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97154"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08306"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa120_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdpdddecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0175"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR40x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C4:0)" metaid="R_EAR40x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR40x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR40x"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97863"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_but2eACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_butACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR60y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C6:0)" metaid="R_EAR60y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR60y"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR60y"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97866"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thex2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hexACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLDEP1pp" fast="false" reversible="false" name="Murein L,D-endopeptidase (murein3px3p) (periplasm)" metaid="R_MLDEP1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLDEP1pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLDEP1pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143242"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08931"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein3px3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_murein3p3p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2328"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSD181" fast="false" reversible="false" name="Phosphatidylserine decarboxylase (n-C18:1)" metaid="R_PSD181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSD181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSD181"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.65"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103235"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ps181_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe181_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4160"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DAGK180" fast="false" reversible="false" name="Diacylglycerol kinase (n-C18:0)" metaid="R_DAGK180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAGK180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAGK180"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97098"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr180_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa180_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4042"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DAGK181" fast="false" reversible="false" name="Diacylglycerol kinase (n-C18:1)" metaid="R_DAGK181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DAGK181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAGK181"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97100"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr181_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pa181_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4042"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLDEP2pp" fast="false" reversible="false" name="Murein L,D-endopeptidase (murein5px3p) (periplasm)" metaid="R_MLDEP2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLDEP2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLDEP2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143243"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08932"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein5px3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_murein5p3p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2328"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_ag_e" fast="false" reversible="false" name="Silver exchange" metaid="R_EX_ag_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ag_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ag_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142917"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ag_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_MLTGY2pp" fast="false" reversible="false" name="Murein lytic transglycosylase (murein4p3p) (periplasm)" metaid="R_MLTGY2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLTGY2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTGY2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143246"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08938"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_murein4p3p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_anhgm3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_anhgm4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2963"/> <fbc:geneProductRef fbc:geneProduct="G_b4392"/> <fbc:geneProductRef fbc:geneProduct="G_b2813"/> <fbc:geneProductRef fbc:geneProduct="G_b2701"/> <fbc:geneProductRef fbc:geneProduct="G_b1193"/> <fbc:geneProductRef fbc:geneProduct="G_b2558"/> <fbc:geneProductRef fbc:geneProduct="G_b0211"/> <fbc:geneProductRef fbc:geneProduct="G_b1097"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2E120pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylethanolamine, n-C12:0) (periplasm)" metaid="R_PLIPA2E120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2E120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2E120pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102996"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1agpe120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2G141pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylglycerol, n-C14:1) (periplasm)" metaid="R_PLIPA2G141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2G141pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2G141pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103005"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg141_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1agpg141_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MLTGY4pp" fast="false" reversible="false" name="Murein lytic transglycosylase (murein4px4p4p) (periplasm)" metaid="R_MLTGY4pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MLTGY4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTGY4pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143248"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08940"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_murein4px4p4p_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_anhgm4p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_murein4px4p_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4392"/> <fbc:geneProductRef fbc:geneProduct="G_b2813"/> <fbc:geneProductRef fbc:geneProduct="G_b2701"/> <fbc:geneProductRef fbc:geneProduct="G_b1193"/> <fbc:geneProductRef fbc:geneProduct="G_b2963"/> <fbc:geneProductRef fbc:geneProduct="G_b2558"/> <fbc:geneProductRef fbc:geneProduct="G_b0211"/> <fbc:geneProductRef fbc:geneProduct="G_b1097"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR60x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C6:0)" metaid="R_EAR60x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR60x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR60x"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97865"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thex2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hexACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2G161pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylglycerol, n-C16:1) (periplasm)" metaid="R_PLIPA2G161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2G161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2G161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103007"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1agpg161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_cys__D_e" fast="false" reversible="false" name="D-Cysteine exchange" metaid="R_EX_cys__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cys__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cys__D_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96997"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08283"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cys__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_LPLIPAL1A120pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C12:0) (periplasm)" metaid="R_LPLIPAL1A120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1A120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1A120pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101141"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1ddecg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1A140pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C14:0) (periplasm)" metaid="R_LPLIPAL1A140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1A140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1A140pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101142"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1tdecg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EAR80x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C8:0)" metaid="R_EAR80x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EAR80x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EAR80x"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97867"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_toct2eACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PE181abcpp" fast="false" reversible="false" name="Phosphatidylethanolamine transport via ABC system (n-C18:1, periplasm)" metaid="R_PE181abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PE181abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PE181abcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102459"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pe181_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_pe181_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0914"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_12DGR161tipp" fast="false" reversible="false" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:1)" metaid="R_12DGR161tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_12DGR161tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/12DGR161tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94679"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr161_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_12DGR181tipp" fast="false" reversible="false" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:1)" metaid="R_12DGR181tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_12DGR181tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/12DGR181tipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94681"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_12dgr181_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr181_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_NTP11" fast="false" reversible="false" name="Nucleoside-triphosphatase (dITP)" metaid="R_NTP11" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NTP11"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTP11"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102040"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30862"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30860"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30859"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30861"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09011"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ditp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_didp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4394"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1A181pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C18:1) (periplasm)" metaid="R_LPLIPAL1A181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1A181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1A181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101147"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1odec11eg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1E120pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C12:0) (periplasm)" metaid="R_LPLIPAL1E120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1E120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1E120pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101148"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1agpe120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAR180" fast="false" reversible="true" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:0)" metaid="R_3OAR180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAR180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAR180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.100"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94948"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07992"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ooctdACP_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_3hoctaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G3PAT120" fast="false" reversible="false" name="Glycerol-3-phosphate acyltransferase (C12:0)" metaid="R_G3PAT120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G3PAT120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PAT120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.15"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99854"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1ddecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b4041"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PGSA120" fast="false" reversible="false" name="Phosphatidylglycerol synthase (n-C12:0)" metaid="R_PGSA120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PGSA120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGSA120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102589"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdddecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pgp120_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1912"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3OAS180" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:0)" metaid="R_3OAS180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OAS180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OAS180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.41"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94961"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3ooctdACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1095"/> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HAD180" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:0)" metaid="R_3HAD180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HAD180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HAD180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.61"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07764"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94883"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07979"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hoctaACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_toctd2eACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0954"/> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CDAPPA120" fast="false" reversible="false" name="CDP-Diacylglycerol pyrophostatase (n-C12:0)" metaid="R_CDAPPA120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CDAPPA120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDAPPA120"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.26"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96500"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08199"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdpdddecg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pa120_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3918"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TDSR2" fast="false" reversible="false" name="Thiol:disulfide reductase (DsbG)" metaid="R_TDSR2" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TDSR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TDSR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104765"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09293"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dsbdrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dsbgox_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dsbdox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dsbgrd_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0604"/> <fbc:geneProductRef fbc:geneProduct="G_b4136"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_acser_e" fast="false" reversible="false" name="O-Acetyl-L-serine exchange" metaid="R_EX_acser_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_acser_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_acser_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1923"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95416"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29659"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29660"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29662"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29661"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08060"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08059"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acser_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GTHRDtex" fast="false" reversible="true" name="Glutathione transport via diffusion (extracellular to periplasm)" metaid="R_GTHRDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GTHRDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GTHRDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100449"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1247915"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1500817"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08677"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10829"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gthrd_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gthrd_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GTHRDabc2pp" fast="false" reversible="false" name="Glutathione export via ABC system (cytoplasm to periplasm)" metaid="R_GTHRDabc2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GTHRDabc2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GTHRDabc2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100447"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29788#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29791#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29790#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29789#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29787#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29792#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29794#2"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29793#2"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13712"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08675"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gthrd_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_gthrd_p" 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_b0886"/> <fbc:geneProductRef fbc:geneProduct="G_b0887"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_OMMBLHX3" fast="false" reversible="false" name="2-Octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase (anaerobic)" metaid="R_OMMBLHX3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OMMBLHX3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OMMBLHX3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138670"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09041"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2ommbl_c" stoichiometry="1" 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stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0606"/> <fbc:geneProductRef fbc:geneProduct="G_b0605"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACOAD7f" fast="false" reversible="true" name="Acyl-CoA dehydrogenase (hexadecanoyl-CoA)" metaid="R_ACOAD7f" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOAD7f"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACOAD7f"/> <rdf:li 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<rdf:li rdf:resource="http://identifiers.org/sabiork/1495"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00946"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pmtcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdd2coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0221"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACOAD8f" fast="false" reversible="true" name="Acyl-CoA dehydrogenase (octadecanoyl-CoA)" metaid="R_ACOAD8f" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOAD8f"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACOAD8f"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95317"/> <rdf:li rdf:resource="http://identifiers.org/rhea/40846"/> <rdf:li rdf:resource="http://identifiers.org/rhea/47240"/> <rdf:li rdf:resource="http://identifiers.org/rhea/40844"/> <rdf:li rdf:resource="http://identifiers.org/rhea/47243"/> <rdf:li rdf:resource="http://identifiers.org/rhea/40843"/> <rdf:li rdf:resource="http://identifiers.org/rhea/47242"/> <rdf:li rdf:resource="http://identifiers.org/rhea/40845"/> <rdf:li rdf:resource="http://identifiers.org/rhea/47241"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/11499"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08053"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_stcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_od2coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0221"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1A120pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidate, n-C12:0) (periplasm)" metaid="R_PLIPA1A120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1A120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1A120pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.32"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102967"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2ddecg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACOAD5f" fast="false" reversible="true" name="Acyl-CoA dehydrogenase (dodecanoyl-CoA)" metaid="R_ACOAD5f" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOAD5f"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACOAD5f"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.3.6"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.8.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.8.7"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03857"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95299"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-77263"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-77263"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-77263"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-77263"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-77263"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-77263"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-77263"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77263"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-77263"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-77263"/> <rdf:li rdf:resource="http://identifiers.org/rhea/47298"/> <rdf:li rdf:resource="http://identifiers.org/rhea/47296"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31040"/> <rdf:li rdf:resource="http://identifiers.org/rhea/47297"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31042"/> <rdf:li 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metaid="R_PLIPA1A140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1A140pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1A140pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.32"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102968"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pa140_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2tdecg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_dopa_e" fast="false" reversible="false" name="Dopamine exchange" metaid="R_EX_dopa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dopa_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dopa_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97758"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-372542"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-372542"/> <rdf:li 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<fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA1A180pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidate, n-C18:0) (periplasm)" metaid="R_PLIPA1A180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA1A180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA1A180pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.32"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102972"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09128"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference 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stoichiometry="1" constant="true"/> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ca2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3196"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACOAD3f" fast="false" reversible="true" name="Acyl-CoA dehydrogenase (octanoyl-CoA)" metaid="R_ACOAD3f" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOAD3f"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACOAD3f"/> <rdf:li 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</bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_occoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oc2coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0221"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACOAD2f" fast="false" reversible="true" name="Acyl-CoA dehydrogenase (hexanoyl-CoA)" metaid="R_ACOAD2f" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOAD2f"> <bqbiol:is 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fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOAD4f"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACOAD4f"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95298"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcacoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dc2coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0221"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACOAD6f" fast="false" reversible="true" name="Acyl-CoA dehydrogenase (tetradecanoyl-CoA)" metaid="R_ACOAD6f" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOAD6f"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACOAD6f"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.8.9"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.3.6"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.8.8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.8.7"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03990"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95300"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-77274"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-77274"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-77274"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-77274"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-77274"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-77274"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77274"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-77274"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-77274"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-77274"/> <rdf:li 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constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0221"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADH16pp" fast="false" reversible="false" name="NADH dehydrogenase (ubiquinone-8 & 3 protons) (periplasm)" metaid="R_NADH16pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADH16pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADH16pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.5.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101864"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08972"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml: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_p" 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_b2279"/> <fbc:geneProductRef fbc:geneProduct="G_b2277"/> <fbc:geneProductRef fbc:geneProduct="G_b2284"/> <fbc:geneProductRef fbc:geneProduct="G_b2282"/> <fbc:geneProductRef fbc:geneProduct="G_b2278"/> <fbc:geneProductRef fbc:geneProduct="G_b2288"/> <fbc:geneProductRef fbc:geneProduct="G_b2276"/> <fbc:geneProductRef fbc:geneProduct="G_b2287"/> <fbc:geneProductRef fbc:geneProduct="G_b2283"/> <fbc:geneProductRef fbc:geneProduct="G_b2281"/> <fbc:geneProductRef fbc:geneProduct="G_b2286"/> <fbc:geneProductRef fbc:geneProduct="G_b2280"/> <fbc:geneProductRef fbc:geneProduct="G_b2285"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADH18pp" fast="false" reversible="false" name="NADH dehydrogenase (demethylmenaquinone-8 & 3 protons) (periplasm)" metaid="R_NADH18pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADH18pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADH18pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.5.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101866"/> <rdf:li 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fbc:geneProduct="G_b2276"/> <fbc:geneProductRef fbc:geneProduct="G_b2287"/> <fbc:geneProductRef fbc:geneProduct="G_b2283"/> <fbc:geneProductRef fbc:geneProduct="G_b2281"/> <fbc:geneProductRef fbc:geneProduct="G_b2286"/> <fbc:geneProductRef fbc:geneProduct="G_b2280"/> <fbc:geneProductRef fbc:geneProduct="G_b2285"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_tartr__D_e" fast="false" reversible="false" name="D-tartrate exchange" metaid="R_EX_tartr__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_tartr__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tartr__D_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104722"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35199"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35200"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35202"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35201"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tartr__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GLYBt2pp" fast="false" reversible="false" name="Glycine betaine transport via proton symport (periplasm)" metaid="R_GLYBt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYBt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYBt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-29A"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100315"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05579"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08638"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyb_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyb_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1801"/> <fbc:geneProductRef fbc:geneProduct="G_b4111"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_5DGLCNt2rpp" fast="false" reversible="true" name="5-Dehydro-D-gluconate transport via proton symport, reversible (periplasm)" metaid="R_5DGLCNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_5DGLCNt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/5DGLCNt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-228"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95066"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28820"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28822"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28821"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28819"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08011"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5dglcn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5dglcn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4265"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALCTNt2pp" fast="false" reversible="false" name="D-galactonate transport via proton symport (periplasm)" metaid="R_GALCTNt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALCTNt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALCTNt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-16"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99960"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29836"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29838"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29837"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29835"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08578"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10160"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galctn__D_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_galctn__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3691"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALCTNLtex" fast="false" reversible="true" name="L-galactonate transport via diffusion (extracellular to periplasm)" metaid="R_GALCTNLtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALCTNLtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALCTNLtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99959"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08577"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galctn__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_galctn__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_galctn__L_e" fast="false" reversible="false" name="L-Galactonate exchange" metaid="R_EX_galctn__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_galctn__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_galctn__L_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99959"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08577"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galctn__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_DSERt2pp" fast="false" reversible="false" name="D-serine transport in via proton symport (periplasm)" metaid="R_DSERt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DSERt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DSERt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5130"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97798"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05649"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08372"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__D_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4208"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_hom__L_e" fast="false" reversible="false" name="L-Homoserine exchange" metaid="R_EX_hom__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_hom__L_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_hom__L_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100678"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08723"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hom__L_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_ALAt4pp" fast="false" reversible="false" name="L-alanine transport in via sodium symport (periplasm)" metaid="R_ALAt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALAt4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALAt4pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-125"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95692"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29286"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29283"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29285"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29284"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08102"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05215"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0007"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LYSt3pp" fast="false" reversible="false" name="L-lysine transport out via proton antiport (cytoplasm to periplasm)" metaid="R_LYSt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LYSt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYSt3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101267"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05305"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08855"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13343"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lys__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2923"/> <fbc:geneProductRef fbc:geneProduct="G_b0874"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_KDUI" fast="false" reversible="false" name="5-keto-4-deoxyuronate isomerase" metaid="R_KDUI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_KDUI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/KDUI"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dt5hsu_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dkdglcn_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2843"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_tungs_e" fast="false" reversible="true" name="Tungstate exchange" metaid="R_EX_tungs_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_tungs_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tungs_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104979"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32842"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32841"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32840"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32839"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09334"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tungs_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_CA2t3pp" fast="false" reversible="false" name="Calcium (Ca+2) transport out via proton antiport (periplasm)" metaid="R_CA2t3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CA2t3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CA2t3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96437"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05514"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08185"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ca2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ca2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1216"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CTBTCAL2" fast="false" reversible="false" name="Crotonobetaine-CoA Ligase" metaid="R_CTBTCAL2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CTBTCAL2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CTBTCAL2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96937"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30081"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30079"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30080"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30082"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ctbt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ctbtcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0037"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_OBTFL" fast="false" reversible="false" name="2-Oxobutanoate formate lyase" metaid="R_OBTFL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OBTFL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OBTFL"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:KETOBUTFORMLY-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.54"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06987"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102135"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28055"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28056"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28057"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28054"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04794"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2obut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0902"/> <fbc:geneProductRef fbc:geneProduct="G_b0903"/> </fbc:and> <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_b0902"/> <fbc:geneProductRef fbc:geneProduct="G_b3114"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADH17pp" fast="false" reversible="false" name="NADH dehydrogenase (menaquinone-8 & 3 protons) (periplasm)" metaid="R_NADH17pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADH17pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADH17pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.5.3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101865"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08973"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="3" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2279"/> <fbc:geneProductRef fbc:geneProduct="G_b2277"/> <fbc:geneProductRef fbc:geneProduct="G_b2284"/> <fbc:geneProductRef fbc:geneProduct="G_b2282"/> <fbc:geneProductRef fbc:geneProduct="G_b2278"/> <fbc:geneProductRef fbc:geneProduct="G_b2288"/> <fbc:geneProductRef fbc:geneProduct="G_b2276"/> <fbc:geneProductRef fbc:geneProduct="G_b2287"/> <fbc:geneProductRef fbc:geneProduct="G_b2283"/> <fbc:geneProductRef fbc:geneProduct="G_b2281"/> <fbc:geneProductRef fbc:geneProduct="G_b2286"/> <fbc:geneProductRef fbc:geneProduct="G_b2280"/> <fbc:geneProductRef fbc:geneProduct="G_b2285"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FA161ACPHi" fast="false" reversible="false" name="Fatty-acyl-ACP hydrolase" metaid="R_FA161ACPHi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FA161ACPHi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FA161ACPHi"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.14"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99103"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0404"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_BGLA1" fast="false" reversible="false" name="6-phospho-beta-glucosidase" metaid="R_BGLA1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BGLA1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BGLA1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96242"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_6pgg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1734"/> <fbc:geneProductRef fbc:geneProduct="G_b2716"/> <fbc:geneProductRef fbc:geneProduct="G_b3721"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FA141ACPHi" fast="false" reversible="false" name="Fatty-acyl-ACP hydrolase" metaid="R_FA141ACPHi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FA141ACPHi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FA141ACPHi"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.14"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99093"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0404"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_THRt2pp" fast="false" reversible="false" name="L-threonine efflux transport via proton antiport (periplasm)" metaid="R_THRt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THRt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-0244"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104851"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28997"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28998"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28996"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28995"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13940#2"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13747"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09304"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_thr__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thr__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0813"/> <fbc:geneProductRef fbc:geneProduct="G_b3823"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARGt3pp" fast="false" reversible="false" name="L-arginine transport out via proton antiport (cytoplasm to periplasm)" metaid="R_ARGt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARGt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARGt3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95954"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13228"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08154"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arg__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2923"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FA160ACPHi" fast="false" reversible="false" name="Fatty-acyl-ACP hydrolase" metaid="R_FA160ACPHi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FA160ACPHi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FA160ACPHi"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.14"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99097"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0404"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALDtex" fast="false" reversible="true" name="D-Malate transport via diffusion (extracellular to periplasm)" metaid="R_MALDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101341"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08864"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mal__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mal__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_OROTtex" fast="false" reversible="true" name="Orotate transport via diffusion (extracellular to periplasm)" metaid="R_OROTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OROTtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OROTtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102230"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10908"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09050"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_orot_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_orot_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_crn__D_e" fast="false" reversible="false" name="D-carnitine exchange" metaid="R_EX_crn__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_crn__D_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_crn__D_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96904"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35067"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35068"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35070"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35069"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_crn__D_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GDPMNP" fast="false" reversible="false" name="GDP-mannose phyrophosphatase" metaid="R_GDPMNP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GDPMNP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GDPMNP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5108"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.21"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00881"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100092"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27981"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27980"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27978"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27979"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00639"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gdpmann_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_man1p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2467"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_OPHHX3" fast="false" reversible="false" name="2-Octaprenylphenol hydroxylase (anaerobic)" metaid="R_OPHHX3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OPHHX3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OPHHX3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102204"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09045"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2oph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="3" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2ohph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="2" constant="true"/> </listOfProducts> </reaction> <reaction id="R_AMMQLT8" fast="false" reversible="false" name="S-adenosylmethione:2-demthylmenaquinole methyltransferase (menaquinone 8)" metaid="R_AMMQLT8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMMQLT8"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMMQLT8"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ADOMET-DMK-METHYLTRANSFER-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.163"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95819"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30064"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30063"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30066"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30065"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08130"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3833"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FA120ACPHi" fast="false" reversible="false" name="Fatty-acyl-ACP hydrolase" metaid="R_FA120ACPHi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FA120ACPHi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FA120ACPHi"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99087"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0404"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FA80ACPHi" fast="false" reversible="false" name="Fatty-acyl-ACP hydrolase" metaid="R_FA80ACPHi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FA80ACPHi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FA80ACPHi"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99125"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0404"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FA140ACPHi" fast="false" reversible="false" name="Fatty-acyl-ACP hydrolase" metaid="R_FA140ACPHi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FA140ACPHi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FA140ACPHi"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.14"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99089"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0404"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PPAt4pp" fast="false" reversible="false" name="Na+/Propionate symporter (periplasm)" metaid="R_PPAt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PPAt4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPAt4pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103093"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ppa_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1015"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_OROTt2_2pp" fast="false" reversible="false" name="Orotate transport via proton symport (2 H) (periplasm)" metaid="R_OROTt2_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OROTt2_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OROTt2_2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-121C"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102229"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29349"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29348"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29347"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29350"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09049"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_orot_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_orot_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3528"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALDt2_2pp" fast="false" reversible="false" name="D-Malate transport via proton symport (2 H) (periplasm)" metaid="R_MALDt2_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALDt2_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALDt2_2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-451"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101340"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28715"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28716"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28718"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28717"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08863"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_mal__D_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mal__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3528"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FA100ACPHi" fast="false" reversible="false" name="Fatty-acyl-ACP hydrolase" metaid="R_FA100ACPHi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FA100ACPHi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FA100ACPHi"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.21"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99086"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dca_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0404"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CRNDCAL2" fast="false" reversible="false" name="D-Carnitine-CoA Ligase" metaid="R_CRNDCAL2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNDCAL2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNDCAL2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96901"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30544"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30543"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30546"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30545"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08260"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_crn__D_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_crnDcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0037"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_5DGLCNtex" fast="false" reversible="true" name="5-Dehydro-D-gluconate transport via diffusion (extracellular to periplasm)" metaid="R_5DGLCNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_5DGLCNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/5DGLCNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95067"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08012"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5dglcn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5dglcn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_LalaDgluMdapDala_e" fast="false" reversible="false" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine exchange" metaid="R_EX_LalaDgluMdapDala_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_LalaDgluMdapDala_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_LalaDgluMdapDala_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95051"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08009"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDgluMdapDala_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_5dglcn_e" fast="false" reversible="false" name="5-Dehydro-D-gluconate exchange" metaid="R_EX_5dglcn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_5dglcn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_5dglcn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95067"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08012"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5dglcn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_DTARTD" fast="false" reversible="false" name="D(-)-tartrate dehydratase" metaid="R_DTARTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DTARTD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DTARTD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:D--TARTRATE-DEHYDRATASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.81"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00340"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97802"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18289"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18291"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18290"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18292"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/820"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tartr__D_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4122"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CRNCAL2" fast="false" reversible="false" name="Carnitine-CoA Ligase" metaid="R_CRNCAL2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNCAL2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNCAL2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96895"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_crncoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0037"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CHLt2pp" fast="false" reversible="false" name="Choline transport via proton symport (periplasm)" metaid="R_CHLt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CHLt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHLt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-99"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96692"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28843"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28845"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28846"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28844"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09692"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08213"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_chol_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_chol_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0314"/> <fbc:geneProductRef fbc:geneProduct="G_b1801"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYt4pp" fast="false" reversible="false" name="Glycine transport in via sodium symport (periplasm)" metaid="R_GLYt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYt4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYt4pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100351"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08661"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10537"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gly_p" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0007"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2E161pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylethanolamine, n-C16:1) (periplasm)" metaid="R_PLIPA2E161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2E161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2E161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103000"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe161_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1agpe161_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2E180pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylethanolamine, n-C18:0) (periplasm)" metaid="R_PLIPA2E180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2E180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2E180pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143296"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe180_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1agpe180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRULYSE" fast="false" reversible="true" name="Fructoselysine 3-epimerase" metaid="R_FRULYSE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRULYSE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRULYSE"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-4841"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99654"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28391"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28390"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28392"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28393"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08531"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_psclys_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_frulys_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4474"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FRULYSt2pp" fast="false" reversible="false" name="Fructoselysine transport via proton symport (periplasm)" metaid="R_FRULYSt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FRULYSt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRULYSt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99656"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08533"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_frulys_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_frulys_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3370"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_LalaDgluMdap_e" fast="false" reversible="false" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate exchange" metaid="R_EX_LalaDgluMdap_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_LalaDgluMdap_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_LalaDgluMdap_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94971"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08004"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDgluMdap_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_psclys_e" fast="false" reversible="false" name="Psicoselysine exchange" metaid="R_EX_psclys_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_psclys_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_psclys_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-418"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103228"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28450"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28453"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28451"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28452"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09196"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_psclys_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_TUNGStex" fast="false" reversible="true" name="Tungstate transport via diffusion (extracellular to periplasm)" metaid="R_TUNGStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TUNGStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TUNGStex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104979"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32842"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32841"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32840"/> <rdf:li rdf:resource="http://identifiers.org/rhea/32839"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09334"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tungs_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tungs_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2G120pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylglycerol, n-C12:0) (periplasm)" metaid="R_PLIPA2G120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2G120pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2G120pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103003"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg120_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1agpg120_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PLIPA2G180pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylglycerol, n-C18:0) (periplasm)" metaid="R_PLIPA2G180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PLIPA2G180pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2G180pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103008"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pg180_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1agpg180_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1A161pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C16:1) (periplasm)" metaid="R_LPLIPAL1A161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1A161pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1A161pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101145"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1hdec9eg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL1A160pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C16:0) (periplasm)" metaid="R_LPLIPAL1A160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL1A160pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1A160pp"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101144"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08799"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_1hdecg3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0494"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSCLYSt2pp" fast="false" reversible="false" name="Psicoselysine transport via proton symport (periplasm)" metaid="R_PSCLYSt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSCLYSt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSCLYSt2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103227"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09195"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_psclys_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_psclys_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3370"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LYSt2pp" fast="false" reversible="false" name="L-lysine transport in via proton symport (periplasm)" metaid="R_LYSt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LYSt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYSt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-58"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101266"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28913"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28914"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28911"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28912"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09740"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08854"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09674"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lys__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2156"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_COBALT2tpp" fast="false" reversible="false" name="Cobalt transport in via permease (no H+)" metaid="R_COBALT2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_COBALT2tpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/COBALT2tpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-141A"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96821"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28579"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28580"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28581"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28578"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12148"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08241"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08242"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10474"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cobalt2_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cobalt2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3040"/> <fbc:geneProductRef fbc:geneProduct="G_b3816"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_OXCDC" fast="false" reversible="false" name="Oxalyl-CoA decarboxylase" metaid="R_OXCDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OXCDC"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OXCDC"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:OXALYL-COA-DECARBOXYLASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.8"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01908"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102239"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19335"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19336"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19333"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19334"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1962"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01395"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oxalcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_forcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2373"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2A140" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C14:0)" metaid="R_LPLIPAL2A140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2A140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2A140"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101163"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2tdecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2A160" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C16:0)" metaid="R_LPLIPAL2A160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2A160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2A160"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101165"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08820"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2hdecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2A161" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C16:1)" metaid="R_LPLIPAL2A161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2A161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2A161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101166"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2hdec9eg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LPLIPAL2A180" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C18:0)" metaid="R_LPLIPAL2A180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LPLIPAL2A180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL2A180"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101167"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08822"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2odecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3825"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYt2pp" fast="false" reversible="false" name="Glycine transport in via proton symport (periplasm)" metaid="R_GLYt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-62B"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100368"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28901"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28902"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28900"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28899"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08660"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09748"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05582"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gly_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gly_c" stoichiometry="1" 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rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95704"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29446"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29444"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29445"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29443"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13939#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05496"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08101"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4208"/> <fbc:geneProductRef fbc:geneProduct="G_b4130"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_anhgm_e" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid exchange" metaid="R_EX_anhgm_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_anhgm_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_anhgm_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95839"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08135"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_anhgm_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_BALAt2pp" fast="false" reversible="false" name="Beta-alanine transport in via proton symport (periplasm)" metaid="R_BALAt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BALAt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BALAt2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5201"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96212"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29460"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29459"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29462"/> <rdf:li 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constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_galctn__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4356"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GALCTLO" fast="false" reversible="false" name="L-galactonate oxidoreductase" metaid="R_GALCTLO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GALCTLO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALCTLO"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5229"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.M8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99956"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30184"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30186"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30185"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30183"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08575"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_galctn__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_tagur_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4358"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_THYMt3pp" fast="false" reversible="false" name="Thymine transport out via proton antiport (periplasm)" metaid="R_THYMt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THYMt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THYMt3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104854"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09308"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09656"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_thym_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thym_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_CLt3_2pp" fast="false" reversible="false" name="Chloride transport out via proton antiport (2:1) (periplasm)" metaid="R_CLt3_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLt3_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLt3_2pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2501"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96796"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29569"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29567"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29568"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29570"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08233"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cl_p" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cl_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0155"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_ppal_e" fast="false" reversible="false" name="Propanal exchange" metaid="R_EX_ppal_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ppal_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ppal_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103071"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09169"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09170"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ppal_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_POR5" fast="false" reversible="true" name="Pyruvate synthase" metaid="R_POR5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_POR5"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/POR5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103064"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_flxso_c" stoichiometry="2" 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_flxr_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1378"/> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1378"/> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_HACD8" fast="false" reversible="true" name="3-hydroxyacyl-CoA dehydrogenase (3-oxooctadecanoyl-CoA), peroxisomal" metaid="R_HACD8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HACD8"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HACD8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.35"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100549"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08700"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ohodcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3hodcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3846"/> <fbc:geneProductRef fbc:geneProduct="G_b2341"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CTECOAI8" fast="false" reversible="true" name="3-cis-2-trans-enoyl-CoA isomerase" metaid="R_CTECOAI8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CTECOAI8"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CTECOAI8"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.3.8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96942"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_odecoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_od2coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3846"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CTECOAI6" fast="false" reversible="true" name="3-cis-2-trans-enoyl-CoA isomerase" metaid="R_CTECOAI6" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CTECOAI6"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CTECOAI6"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.3.8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96940"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tdecoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_td2coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3846"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MTHTHFSs" fast="false" reversible="false" name="(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran synthesis (spontaneous)" metaid="R_MTHTHFSs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MTHTHFSs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MTHTHFSs"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-10017"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101756"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35161"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35162"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35159"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35160"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mdhdhf_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mththf_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SELGTHR" fast="false" reversible="false" name="Selenate glutathione reductase" metaid="R_SELGTHR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SELGTHR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SELGTHR"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12864"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09367"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104318"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-2408556"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-2408553"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34906"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34903"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34904"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34905"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gthrd_c" stoichiometry="4" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_slnt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dgslnt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="3" constant="true"/> </listOfProducts> </reaction> <reaction id="R_SELGTHR3" fast="false" reversible="false" name="Selenate glutathione reductase III" metaid="R_SELGTHR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SELGTHR3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SELGTHR3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104320"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gslnt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_seln_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_EX_slnt_e" fast="false" reversible="true" name="Selenite exchange" metaid="R_EX_slnt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_slnt_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_slnt_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104325"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34894"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34891"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34893"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34892"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_slnt_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_MALCOAMT" fast="false" reversible="false" name="Malonyl-CoA methyltransferase" metaid="R_MALCOAMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALCOAMT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALCOAMT"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101337"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34900"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34899"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34902"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34901"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malcoame_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0777"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSCLYStex" fast="false" reversible="true" name="Psicoselysine transporter via diffusion (extracellular)" metaid="R_PSCLYStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSCLYStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSCLYStex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-418"/> <rdf:li 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reversible="true" name="Thymine transport via diffusion (extracellular to periplasm)" metaid="R_THYMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THYMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THYMtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-524"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104853"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09309"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_thym_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_thym_p" 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(Fe+2) transport out via proton antiport (periplasm)" metaid="R_FE2t3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE2t3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE2t3pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99506"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29441"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29439"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29442"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29440"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08474"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3915"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MN2t3pp" fast="false" reversible="false" name="Manganese (Mn+2) transport out via proton antiport (periplasm)" metaid="R_MN2t3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MN2t3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MN2t3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101669"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08946"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mn2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mn2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3915"/> <fbc:geneProductRef fbc:geneProduct="G_b0752"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MG2t3_2pp" fast="false" reversible="true" name="Magnesium (Mg+2) transport in/out via proton antiport (periplasm)" metaid="R_MG2t3_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MG2t3_2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MG2t3_2pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101508"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08921"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mg2_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_p" stoichiometry="2" constant="true"/> <speciesReference species="M_mg2_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_CD2tpp" fast="false" reversible="false" name="Cadmium (+2) transport in via permease (no H+)" metaid="R_CD2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CD2tpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CD2tpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-10"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96499"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28709"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28708"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28707"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28710"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13041"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08198"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08197"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cd2_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cd2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3040"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ETHAt2pp" fast="false" reversible="false" name="Ethanolamine transport in via proton symport" metaid="R_ETHAt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description 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sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3abcpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.30-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.30"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99525"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12335#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12332#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12334#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12333#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05195"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08477"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe3_p" 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_fe3_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 id="R_THRA" fast="false" reversible="false" name="Threonine aldolase" metaid="R_THRA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THRA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRA"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THREONINE-ALDOLASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.48"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00751"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104833"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19625"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19626"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19627"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19628"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00541"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_thr__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2551"/> <fbc:geneProductRef fbc:geneProduct="G_b0870"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_OGMEACPS" fast="false" reversible="false" name="3-Oxo-glutaryl-[ACP] methyl ester synthase" metaid="R_OGMEACPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OGMEACPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li 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fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OGMEACPR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OGMEACPR"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102160"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ogmeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hgmeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_OPMEACPS" fast="false" reversible="false" name="3-Oxo-pimeloyl-[ACP] methyl ester synthase" metaid="R_OPMEACPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OPMEACPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OPMEACPS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102208"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gmeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_opmeACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2323"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPAabctex" fast="false" reversible="false" name="Lipid A transport via ABC system (periplasm to extracellular)" metaid="R_LIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPAabctex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPAabctex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101083"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lipa_p" 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_lipa_e" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4262"/> <fbc:geneProductRef fbc:geneProduct="G_b4261"/> <fbc:geneProductRef fbc:geneProduct="G_b3199"/> <fbc:geneProductRef fbc:geneProduct="G_b3201"/> <fbc:geneProductRef fbc:geneProduct="G_b3200"/> <fbc:geneProductRef fbc:geneProduct="G_b0054"/> <fbc:geneProductRef fbc:geneProduct="G_b0641"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DGUNC" fast="false" reversible="false" name="Diguanylate cyclase" metaid="R_DGUNC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DGUNC"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DGUNC"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97353"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtp_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdigmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1341"/> <fbc:geneProductRef fbc:geneProduct="G_b1794"/> <fbc:geneProductRef fbc:geneProduct="G_b1535"/> <fbc:geneProductRef fbc:geneProduct="G_b1025"/> <fbc:geneProductRef fbc:geneProduct="G_b1490"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_XYLK2" fast="false" reversible="false" name="L-xylulokinase" metaid="R_XYLK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_XYLK2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYLK2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:LYXK-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.53"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01901"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138925"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18871"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18872"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18869"/> <rdf:li rdf:resource="http://identifiers.org/rhea/18870"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01389"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xylu__L_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_xu5p__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0063"/> <fbc:geneProductRef fbc:geneProduct="G_b3580"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLDBRAN2" fast="false" reversible="false" name="Glycogen debranching enzyme (bglycogen -> glycogen)" metaid="R_GLDBRAN2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLDBRAN2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLDBRAN2"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.18"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100155"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08605"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_bglycogen_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glycogen_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3431"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LALADGLUtex" fast="false" reversible="true" name="L-alanyl-D-glutamate transport via diffusion (extracellular to periplasm)" metaid="R_LALADGLUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LALADGLUtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LALADGLUtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101003"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35127"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35128"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35129"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35130"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDglu_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDglu_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_S2FE2SR" fast="false" reversible="false" name="SUF [2Fe-2S] regeneration" metaid="R_S2FE2SR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_S2FE2SR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/S2FE2SR"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104149"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2fe1s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufbcd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufsesh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="5" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufbcd_2fe2s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufse_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1680"/> <fbc:geneProductRef fbc:geneProduct="G_b1679"/> <fbc:geneProductRef fbc:geneProduct="G_b1682"/> <fbc:geneProductRef fbc:geneProduct="G_b1681"/> <fbc:geneProductRef fbc:geneProduct="G_b1683"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CDGUNPD" fast="false" reversible="false" name="3,5-cyclic-nucleotide phosphodiesterase" metaid="R_CDGUNPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CDGUNPD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDGUNPD"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96524"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdigmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5pg35pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2503"/> <fbc:geneProductRef fbc:geneProduct="G_b1489"/> <fbc:geneProductRef fbc:geneProduct="G_b3525"/> <fbc:geneProductRef fbc:geneProduct="G_b1285"/> <fbc:geneProductRef fbc:geneProduct="G_b0315"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACACT8r" fast="false" reversible="true" name="Acetyl-CoA acyltransferase (hexadecanoyl-CoA), (r)" metaid="R_ACACT8r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACACT8r"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACACT8r"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95204"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35282"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35280"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35279"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35281"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08767"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3ohodcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pmtcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2342"/> <fbc:geneProductRef fbc:geneProduct="G_b3845"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LALALGLUtpp" fast="false" reversible="false" name="L-alanyl-L-glutamate transport in via proton symport (periplasm)" metaid="R_LALALGLUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LALALGLUtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LALALGLUtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101006"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35131"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35132"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35133"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35134"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaLglu_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaLglu_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1634"/> <fbc:geneProductRef fbc:geneProduct="G_b3496"/> <fbc:geneProductRef fbc:geneProduct="G_b4130"/> <fbc:geneProductRef fbc:geneProduct="G_b0709"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CTECOAI7" fast="false" reversible="true" name="3-cis-2-trans-enoyl-CoA isomerase" metaid="R_CTECOAI7" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CTECOAI7"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CTECOAI7"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.3.8"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96941"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hdcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hdd2coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3846"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLIPAabctex" fast="false" reversible="false" name="Cold lipid A transport via ABC system (periplasm to extracellular)" metaid="R_CLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLIPAabctex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLIPAabctex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96766"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lipa_cold_p" 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_lipa_cold_e" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4262"/> <fbc:geneProductRef fbc:geneProduct="G_b4261"/> <fbc:geneProductRef fbc:geneProduct="G_b3199"/> <fbc:geneProductRef fbc:geneProduct="G_b3201"/> <fbc:geneProductRef fbc:geneProduct="G_b3200"/> <fbc:geneProductRef fbc:geneProduct="G_b0054"/> <fbc:geneProductRef fbc:geneProduct="G_b0641"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_3AMACHYD" fast="false" reversible="false" name="3-aminoacrylate hydrolase" metaid="R_3AMACHYD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3AMACHYD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3AMACHYD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6452"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09983"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94854"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34948"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34947"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34950"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34949"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3amac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_msa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1009"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_K2L4Aabctex" fast="false" reversible="false" name="KDO(2)-lipid IV A transport via ABC system (periplasm to extracellular)" metaid="R_K2L4Aabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_K2L4Aabctex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/K2L4Aabctex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100900"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_kdo2lipid4_p" 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_kdo2lipid4_e" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4262"/> <fbc:geneProductRef fbc:geneProduct="G_b4261"/> <fbc:geneProductRef fbc:geneProduct="G_b3199"/> <fbc:geneProductRef fbc:geneProduct="G_b3201"/> <fbc:geneProductRef fbc:geneProduct="G_b3200"/> <fbc:geneProductRef fbc:geneProduct="G_b0054"/> <fbc:geneProductRef fbc:geneProduct="G_b0641"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FDH4pp" fast="false" reversible="false" name="Formate dehydrogenase (quinone-8) (periplasm)" metaid="R_FDH4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FDH4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FDH4pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99478"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29077#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29075#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29078#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29076#1"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_for_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3893"/> <fbc:geneProductRef fbc:geneProduct="G_b3894"/> <fbc:geneProductRef fbc:geneProduct="G_b3892"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1474"/> <fbc:geneProductRef fbc:geneProduct="G_b1476"/> <fbc:geneProductRef fbc:geneProduct="G_b1475"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FDH5pp" fast="false" reversible="false" name="Formate Dehydrogenase (menaquinone-8) (periplasm)" metaid="R_FDH5pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FDH5pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FDH5pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99480"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_for_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1474"/> <fbc:geneProductRef fbc:geneProduct="G_b1476"/> <fbc:geneProductRef fbc:geneProduct="G_b1475"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3893"/> <fbc:geneProductRef fbc:geneProduct="G_b3894"/> <fbc:geneProductRef fbc:geneProduct="G_b3892"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACPPAT140" fast="false" reversible="false" name="Acyl-(acyl carrier protein):phosphate acyltransferase (C14:0)" metaid="R_ACPPAT140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACPPAT140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACPPAT140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95396"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcap_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b1090"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_APG3PAT140" fast="false" reversible="false" name="Acyl-phosphate:glycerol-3-phosphate acyltransferase (C14:0)" metaid="R_APG3PAT140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APG3PAT140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APG3PAT140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95870"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1tdecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3059"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LDGUNPD" fast="false" reversible="false" name="Linear diguanylate phosphodiesterase" metaid="R_LDGUNPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LDGUNPD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LDGUNPD"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101036"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5pg35pg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gmp_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1285"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MPTAT" fast="false" reversible="false" name="Molybdopterin adenylyltransferase" metaid="R_MPTAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MPTAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MPTAT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-8344"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.75"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09726"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101730"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31333"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31334"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31332"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31331"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mpt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mptamp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0009"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_APG3PAT141" fast="false" reversible="false" name="Acyl-phosphate:glycerol-3-phosphate acyltransferase (C14:1)" metaid="R_APG3PAT141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APG3PAT141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APG3PAT141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95871"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdceap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1tdec7eg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3059"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MOADSUx" fast="false" reversible="false" name="MoaD sulfuration (nadh, assumed)" metaid="R_MOADSUx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MOADSUx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOADSUx"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101682"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_iscssh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_moadamp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_iscs_c" stoichiometry="1" constant="true"/> <speciesReference species="M_moadcosh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0784"/> <fbc:geneProductRef fbc:geneProduct="G_b2530"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HPPtex" fast="false" reversible="true" name="3-hydroxypropionate transport via diffusion (extracellular to periplasm)" metaid="R_3HPPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HPPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HPPtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-465"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94904"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34951"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34953"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34952"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34954"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hpp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3hpp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CMtpp" fast="false" reversible="false" name="Chloramphenicol transport via TolC system" metaid="R_CMtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CMtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CMtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96809"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cm_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cm_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b2470"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b0462"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FUSAtpp" fast="false" reversible="false" name="Fusidic acid transport via TolC system" metaid="R_FUSAtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FUSAtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FUSAtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99718"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fusa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fusa_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b0462"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b2470"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_APG3PAT181" fast="false" reversible="false" name="Acyl-phosphate:glycerol-3-phosphate acyltransferase (C18:1)" metaid="R_APG3PAT181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APG3PAT181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APG3PAT181"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95875"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdceap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1odec11eg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3059"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_APH140" fast="false" reversible="false" name="Acylphosphatase (C14:0)" metaid="R_APH140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APH140"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APH140"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95877"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0968"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_APH160" fast="false" reversible="false" name="Acylphosphatase (C16:0)" metaid="R_APH160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APH160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APH160"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95879"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0968"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_OPMEACPD" fast="false" reversible="false" name="3-Oxo-pimeloyl-[ACP] methyl ester dehydratase" metaid="R_OPMEACPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OPMEACPD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OPMEACPD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-11481"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.59"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10121"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102206"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hpmeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_epmeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EPMEACPR" fast="false" reversible="false" name="Enoylpimeloyl-[ACP] methyl ester reductase" metaid="R_EPMEACPR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EPMEACPR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EPMEACPR"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.10"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10122"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97945"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_epmeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pmeACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RFAMPtex" fast="false" reversible="true" name="Rifampin transport via diffusion (extracellular to periplasm)" metaid="R_RFAMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RFAMPtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RFAMPtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104014"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35234"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35231"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35232"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35233"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_rfamp_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_rfamp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MINCYCtex" fast="false" reversible="true" name="Minocycline transport via diffusion (extracellular to periplasm)" metaid="R_MINCYCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MINCYCtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MINCYCtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101582"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35168"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35167"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35169"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35170"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mincyc_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mincyc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_AOXSr2" fast="false" reversible="false" name="8-amino-7-oxononanoate synthase" metaid="R_AOXSr2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AOXSr2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AOXSr2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-11484"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.47"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10124"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95855"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pimACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_8aonn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0776"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MINCYCtpp" fast="false" reversible="false" name="Minocycline transport via TolC system" metaid="R_MINCYCtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MINCYCtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MINCYCtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101583"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mincyc_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mincyc_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b2470"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b0462"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MEOHtrpp" fast="false" reversible="true" name="Methanol reversible transport via diffusion (periplasm)" metaid="R_MEOHtrpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MEOHtrpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MEOHtrpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-459"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101464"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34873"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34872"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34874"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34871"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10570"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_meoh_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_meoh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_LalaDglu_e" fast="false" reversible="false" name="L-alanine-D-glutamate exchange" metaid="R_EX_LalaDglu_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_LalaDglu_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_LalaDglu_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101003"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35127"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35128"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35129"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35130"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDglu_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_SCYSDS" fast="false" reversible="false" name="SUF Cysteine desulfuration" metaid="R_SCYSDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SCYSDS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SCYSDS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104298"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufse_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufsesh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1680"/> <fbc:geneProductRef fbc:geneProduct="G_b1679"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DOXRBCNtex" fast="false" reversible="true" name="Doxorubicin transport via diffusion (extracellular to periplasm)" metaid="R_DOXRBCNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DOXRBCNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DOXRBCNtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97760"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35079"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35081"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35080"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35082"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_doxrbcn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_doxrbcn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DOXRBCNtpp" fast="false" reversible="false" name="Doxorubicin transport via TolC system" metaid="R_DOXRBCNtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DOXRBCNtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DOXRBCNtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97761"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_doxrbcn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_doxrbcn_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b0462"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b2470"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_S2FE2SS" fast="false" reversible="false" name="SUF [2Fe-2S] Synthesis" metaid="R_S2FE2SS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_S2FE2SS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/S2FE2SS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104150"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufbcd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufsesh_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="7" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufbcd_2fe2s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufse_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1680"/> <fbc:geneProductRef fbc:geneProduct="G_b1683"/> <fbc:geneProductRef fbc:geneProduct="G_b1681"/> <fbc:geneProductRef fbc:geneProduct="G_b1682"/> <fbc:geneProductRef fbc:geneProduct="G_b1679"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_S4FE4SR" fast="false" reversible="false" name="SUF [4Fe-4S] Reduction" metaid="R_S4FE4SR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_S4FE4SR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/S4FE4SR"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104171"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_sufbcd_2fe2s2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufbcd_4fe4s_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1682"/> <fbc:geneProductRef fbc:geneProduct="G_b1681"/> <fbc:geneProductRef fbc:geneProduct="G_b1683"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CCGS" fast="false" reversible="false" name="7-cyano-7-carbaguanine synthase" metaid="R_CCGS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CCGS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CCGS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12093"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.4.20"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09978"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96492"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27985"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27984"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27983"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27982"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cdg_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_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_preq0_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0444"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SELtex" fast="false" reversible="true" name="Selenate transport via diffusion (extracellular to periplasm)" metaid="R_SELtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SELtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SELtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104327"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34889"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34887"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34888"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34890"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sel_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_sel_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SELR" fast="false" reversible="false" name="Selenate reductase" metaid="R_SELR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SELR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SELR"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104323"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34939"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34940"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34942"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34941"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sel_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/> <speciesReference species="M_slnt_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1589"/> <fbc:geneProductRef fbc:geneProduct="G_b1590"/> <fbc:geneProductRef fbc:geneProduct="G_b1588"/> <fbc:geneProductRef fbc:geneProduct="G_b1587"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_OGMEACPD" fast="false" reversible="false" name="3-Oxo-glutaryl-[ACP] methyl ester dehydratase" metaid="R_OGMEACPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OGMEACPD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OGMEACPD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-11477"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.59"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10117"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102159"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_hgmeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_egmeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0180"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EGMEACPR" fast="false" reversible="false" name="Enoylglutaryl-[ACP] methyl ester reductase" metaid="R_EGMEACPR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EGMEACPR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EGMEACPR"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.10"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10118"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97906"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_egmeACP_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_gmeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1288"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_OPMEACPR" fast="false" reversible="false" name="3-Oxo-pimeloyl-[ACP] methyl ester reductase" metaid="R_OPMEACPR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OPMEACPR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OPMEACPR"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102207"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_opmeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hpmeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PMEACPE" fast="false" reversible="false" name="Pimeloyl-[ACP] methyl ester esterase" metaid="R_PMEACPE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PMEACPE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PMEACPE"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-11483"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.85"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09725"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103041"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pmeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_meoh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pimACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3412"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ETOHtrpp" fast="false" reversible="true" name="Ethanol reversible transport via diffusion (periplasm)" metaid="R_ETOHtrpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ETOHtrpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ETOHtrpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-546"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97980"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35269"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35267"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35270"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35268"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09683"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08428"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09764"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_etoh_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_etoh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_REPHACCOAI" fast="false" reversible="true" name="Ring 1,2-epoxyphenylacetyl-CoA isomerase (oxepin-CoA forming)" metaid="R_REPHACCOAI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_REPHACCOAI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/REPHACCOAI"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103993"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_rephaccoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2oxpaccoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1394"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACPPAT141" fast="false" reversible="false" name="Acyl-(acyl carrier protein):phosphate acyltransferase (C14:1)" metaid="R_ACPPAT141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACPPAT141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACPPAT141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95397"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdceap_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b1090"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACPPAT161" fast="false" reversible="false" name="Acyl-(acyl carrier protein):phosphate acyltransferase (C16:1)" metaid="R_ACPPAT161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACPPAT161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACPPAT161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95399"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdceap_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b1090"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACPPAT180" fast="false" reversible="false" name="Acyl-(acyl carrier protein):phosphate acyltransferase (C18:0)" metaid="R_ACPPAT180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACPPAT180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACPPAT180"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95400"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcap_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b1090"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_APG3PAT160" fast="false" reversible="false" name="Acyl-phosphate:glycerol-3-phosphate acyltransferase (C16:0)" metaid="R_APG3PAT160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APG3PAT160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APG3PAT160"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95872"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1hdecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3059"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_APG3PAT161" fast="false" reversible="false" name="Acyl-phosphate:glycerol-3-phosphate acyltransferase (C16:1)" metaid="R_APG3PAT161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APG3PAT161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APG3PAT161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95873"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdceap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1hdec9eg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3059"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MEOHtex" fast="false" reversible="true" name="Methanol transport via diffusion (extracellular to periplasm)" metaid="R_MEOHtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MEOHtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MEOHtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-459"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101464"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34873"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34872"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34874"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34871"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10570"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_meoh_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_meoh_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_5mtr_e" fast="false" reversible="false" name="5-Methylthio-D-ribose exchange" metaid="R_EX_5mtr_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_5mtr_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_5mtr_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-461"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95091"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34955"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34958"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34956"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34957"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5mtr_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_APG3PAT180" fast="false" reversible="false" name="Acyl-phosphate:glycerol-3-phosphate acyltransferase (C18:0)" metaid="R_APG3PAT180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APG3PAT180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APG3PAT180"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95874"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1odecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3059"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ICYSDS" fast="false" reversible="false" name="ISC Cysteine desulfuration" metaid="R_ICYSDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ICYSDS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ICYSDS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100790"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_iscs_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_iscssh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2530"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MECDPDH5" fast="false" reversible="false" name="2C-methyl-D-erythritol 2,4 cyclodiphosphate dehydratase" metaid="R_MECDPDH5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MECDPDH5"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MECDPDH5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101450"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2mecdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2mb4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2515"/> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2515"/> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CDGR" fast="false" reversible="false" name="7-cyano-7-deazaguanine reductase" metaid="R_CDGR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CDGR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDGR"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-4022"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.7.1.13"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07605"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96521"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13410"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13411"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13412"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13409"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13537"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="2" constant="true"/> <speciesReference species="M_preq0_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="2" constant="true"/> <speciesReference species="M_preq1_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2794"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RNTR1c2" fast="false" reversible="false" name="Ribonucleoside-triphosphate reductase (ATP) (flavodoxin)" metaid="R_RNTR1c2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RNTR1c2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNTR1c2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104072"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_datp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3924"/> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> <fbc:geneProductRef fbc:geneProduct="G_b4237"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3924"/> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> <fbc:geneProductRef fbc:geneProduct="G_b4237"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_RNTR2c2" fast="false" reversible="false" name="Ribonucleoside-triphosphate reductase (GTP) (flavodoxin)" metaid="R_RNTR2c2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RNTR2c2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNTR2c2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104075"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dgtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3924"/> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> <fbc:geneProductRef fbc:geneProduct="G_b4237"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3924"/> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> <fbc:geneProductRef fbc:geneProduct="G_b4237"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_I4FE4SR" fast="false" reversible="false" name="ISC [4Fe-4S] Reduction" metaid="R_I4FE4SR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_I4FE4SR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/I4FE4SR"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100770"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_iscu_2fe2s2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_iscu_4fe4s_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2529"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_S2FE2ST" fast="false" reversible="false" name="SUF [2Fe-2S] Transfer" metaid="R_S2FE2ST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_S2FE2ST"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/S2FE2ST"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104152"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> <speciesReference species="M_sufbcd_2fe2s_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2fe2s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufbcd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1682"/> <fbc:geneProductRef fbc:geneProduct="G_b1681"/> <fbc:geneProductRef fbc:geneProduct="G_b1684"/> <fbc:geneProductRef fbc:geneProduct="G_b1683"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_BMOCOS" fast="false" reversible="false" name="Bis-molybdenum cofactor synthase" metaid="R_BMOCOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BMOCOS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BMOCOS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138144"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_moco_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mptamp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_bmoco_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0827"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_BWCOS" fast="false" reversible="false" name="Tungsten bispterin cofactor synthase" metaid="R_BWCOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BWCOS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BWCOS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138151"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mptamp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_wco_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_bwco_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0827"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RNTR3c2" fast="false" reversible="false" name="Ribonucleoside-triphosphate reductase (CTP) (flavodoxin)" metaid="R_RNTR3c2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RNTR3c2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNTR3c2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104078"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3924"/> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> <fbc:geneProductRef fbc:geneProduct="G_b4237"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3924"/> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> <fbc:geneProductRef fbc:geneProduct="G_b4237"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_RNTR4c2" fast="false" reversible="false" name="Ribonucleoside-triphosphate reductase (UTP) (flavodoxin)" metaid="R_RNTR4c2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RNTR4c2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNTR4c2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104081"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dutp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3924"/> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> <fbc:geneProductRef fbc:geneProduct="G_b4237"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3924"/> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> <fbc:geneProductRef fbc:geneProduct="G_b4237"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> <fbc:geneProductRef fbc:geneProduct="G_b4238"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_BWCOGDS1" fast="false" reversible="false" name="Tungsten bispterin guanine dinucleotide synthase (single GDP)" metaid="R_BWCOGDS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BWCOGDS1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BWCOGDS1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96356"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_bwco_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_bwco1gdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3857"/> <fbc:geneProductRef fbc:geneProduct="G_b3856"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3857"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_BWCOGDS2" fast="false" reversible="false" name="Tungsten bispterin guanine dinucleotide synthase" metaid="R_BWCOGDS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BWCOGDS2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BWCOGDS2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96357"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_bwco1gdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_bwcogdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3857"/> <fbc:geneProductRef fbc:geneProduct="G_b3856"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3857"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FLDR2" fast="false" reversible="false" name="Flavodoxin reductase (NADPH)" metaid="R_FLDR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FLDR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FLDR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99599"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3924"/> <fbc:geneProductRef fbc:geneProduct="G_b2895"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3924"/> <fbc:geneProductRef fbc:geneProduct="G_b0684"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CDGS" fast="false" reversible="false" name="7-deaza-7-carboxyguanine synthase" metaid="R_CDGS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CDGS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDGS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6575"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.99.3"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10002"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96522"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27974"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27976"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27977"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27975"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cph4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cdg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_5MTRtpp" fast="false" reversible="false" name="5-Methylthio-D-ribose transport via proton symport (periplasm)" metaid="R_5MTRtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_5MTRtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/5MTRtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95090"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05481"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5mtr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5mtr_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_TTRCYCtex" fast="false" reversible="true" name="Tetracycline transport via diffusion (extracellular to periplasm)" metaid="R_TTRCYCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TTRCYCtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TTRCYCtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104976"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35242"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35240"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35241"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35239"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ttrcyc_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ttrcyc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHNPTE" fast="false" reversible="true" name="Dihydroneopterin epimerase" metaid="R_DHNPTE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHNPTE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHNPTE"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138236"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhnpt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhmpt_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3058"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHMPTR" fast="false" reversible="false" name="Dihydromonapterin reductase" metaid="R_DHMPTR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHMPTR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHMPTR"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97405"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhmpt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thmnp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1606"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NOVBCNtpp" fast="false" reversible="false" name="Novobiocin transport via TolC system" metaid="R_NOVBCNtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NOVBCNtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NOVBCNtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102009"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_novbcn_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_novbcn_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b2470"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b0462"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CMtex" fast="false" reversible="true" name="Chloramphenicol transport via diffusion (extracellular to periplasm)" metaid="R_CMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CMtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96808"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35288"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35290"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35287"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35289"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cm_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cm_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TTRCYCtpp" fast="false" reversible="false" name="Tetracycline transport via TolC system" metaid="R_TTRCYCtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TTRCYCtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TTRCYCtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104977"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ttrcyc_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttrcyc_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b2470"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b0462"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_LALALGLUtex" fast="false" reversible="true" name="L-alanyl-L-glutamate transport via diffusion (extracellular to periplasm)" metaid="R_LALALGLUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LALALGLUtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LALALGLUtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101005"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35136"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35137"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35138"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35135"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaLglu_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaLglu_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CBMD" fast="false" reversible="false" name="Carbamate deaminase" metaid="R_CBMD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CBMD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CBMD"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5222"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.104"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.110"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07316"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96481"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15652"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15651"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15649"/> <rdf:li rdf:resource="http://identifiers.org/rhea/15650"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05064"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cbm_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LALADGLUtpp" fast="false" reversible="false" name="L-alanyl-D-glutamate transport in via proton symport (periplasm)" metaid="R_LALADGLUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LALADGLUtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LALADGLUtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101004"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35123"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35126"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35125"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35124"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaDglu_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_LalaDglu_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0709"/> <fbc:geneProductRef fbc:geneProduct="G_b1634"/> <fbc:geneProductRef fbc:geneProduct="G_b3496"/> <fbc:geneProductRef fbc:geneProduct="G_b4130"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_I2FE2SS" fast="false" reversible="false" name="ISC [2Fe-2S] Synthesis" metaid="R_I2FE2SS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_I2FE2SS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/I2FE2SS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100767"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_iscssh_c" stoichiometry="2" constant="true"/> <speciesReference species="M_iscu_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="6" constant="true"/> <speciesReference species="M_iscs_c" stoichiometry="2" constant="true"/> <speciesReference species="M_iscu_2fe2s_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2530"/> <fbc:geneProductRef fbc:geneProduct="G_b2529"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_I2FE2ST" fast="false" reversible="false" name="ISC [2Fe-2S] Transfer" metaid="R_I2FE2ST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_I2FE2ST"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/I2FE2ST"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100769"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> <speciesReference species="M_iscu_2fe2s_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2fe2s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_iscu_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2529"/> <fbc:geneProductRef fbc:geneProduct="G_b2528"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FESR" fast="false" reversible="false" name="Iron-sulfur cluster repair" metaid="R_FESR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FESR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FESR"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99587"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3fe4s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4fe4s_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4209"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_OXCOAHDH" fast="false" reversible="false" name="Oxepin-CoA hydrolase/ 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (NADP+)" metaid="R_OXCOAHDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OXCOAHDH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OXCOAHDH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6511"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102240"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34875"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34876"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34877"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34878"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2oxpaccoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3oxdhscoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1387"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHACOAH" fast="false" reversible="true" name="2,3-dehydroadipyl-CoA hydratase" metaid="R_DHACOAH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHACOAH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHACOAH"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.17"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97357"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34864"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34866"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34863"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34865"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23dhacoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3hadpcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1393"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_I2FE2SS2" fast="false" reversible="false" name="ISC [2Fe-2S] Synthesis II" metaid="R_I2FE2SS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_I2FE2SS2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/I2FE2SS2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100768"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_iscssh_c" stoichiometry="2" constant="true"/> <speciesReference species="M_iscu_2fe2s_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="6" constant="true"/> <speciesReference species="M_iscs_c" stoichiometry="2" constant="true"/> <speciesReference species="M_iscu_2fe2s2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2530"/> <fbc:geneProductRef fbc:geneProduct="G_b2529"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_MSAR" fast="false" reversible="false" name="Malonic semialdehyde reductase" metaid="R_MSAR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MSAR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MSAR"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-8974"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.298"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.-"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09289"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101737"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26439"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26438"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26441"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26440"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/12224"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_msa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3hpp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1008"/> <fbc:geneProductRef fbc:geneProduct="G_b1539"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_I4FE4ST" fast="false" reversible="false" name="ISC [4Fe-4S] Transfer" metaid="R_I4FE4ST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_I4FE4ST"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/I4FE4ST"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100771"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> <speciesReference species="M_iscu_4fe4s_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4fe4s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_iscu_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2529"/> <fbc:geneProductRef fbc:geneProduct="G_b2528"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_S4FE4ST" fast="false" reversible="false" name="SUF [4Fe-4S] Transfer" metaid="R_S4FE4ST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_S4FE4ST"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/S4FE4ST"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104172"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> <speciesReference species="M_sufbcd_4fe4s_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4fe4s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufbcd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1682"/> <fbc:geneProductRef fbc:geneProduct="G_b1681"/> <fbc:geneProductRef fbc:geneProduct="G_b1684"/> <fbc:geneProductRef fbc:geneProduct="G_b1683"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_THFAT" fast="false" reversible="false" name="Tetrahydrofolate aminomethyltransferase" metaid="R_THFAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THFAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THFAT"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.2.10"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02300"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99614"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34770"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34769"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34768"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34767"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2262"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01652"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5fthf_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2551"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FOMETRi" fast="false" reversible="false" name="Aminomethyltransferase" metaid="R_FOMETRi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation 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<speciesReference species="M_5fthf_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2912"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SLNTtex" fast="false" reversible="true" name="Selenite transport via diffusion (extracellular to periplasm)" metaid="R_SLNTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SLNTtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SLNTtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104325"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34894"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34891"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34893"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34892"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_slnt_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_slnt_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_S2FE2SS2" fast="false" reversible="false" name="SUF [2Fe-2S] Synthesis II" metaid="R_S2FE2SS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_S2FE2SS2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/S2FE2SS2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104151"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufbcd_2fe2s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufsesh_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="7" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufbcd_2fe2s2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sufse_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1680"/> <fbc:geneProductRef fbc:geneProduct="G_b1683"/> <fbc:geneProductRef fbc:geneProduct="G_b1681"/> <fbc:geneProductRef fbc:geneProduct="G_b1682"/> <fbc:geneProductRef fbc:geneProduct="G_b1679"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_BTS5" fast="false" reversible="false" name="Biotin synthase" metaid="R_BTS5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BTS5"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BTS5"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96344"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2fe2s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dtbt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2fe1s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_btn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dad_5_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0775"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SELGTHR2" fast="false" reversible="false" name="Selenate glutathione reductase II" metaid="R_SELGTHR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SELGTHR2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SELGTHR2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104319"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dgslnt_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_gslnt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_EX_LalaLglu_e" fast="false" reversible="false" name="L-alanine-L-glutamate exchange" metaid="R_EX_LalaLglu_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_LalaLglu_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_LalaLglu_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101005"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35136"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35137"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35138"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35135"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_LalaLglu_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GDPTPDP" fast="false" reversible="false" name="Guanosine 3'-diphosphate 5'-triphosphate 3'-diphosphatase" metaid="R_GDPTPDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GDPTPDP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GDPTPDP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6427"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.7.2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100094"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33058"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33057"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33056"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33055"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gdptp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3650"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPOS" fast="false" reversible="false" name="Lipoate synthase" metaid="R_LIPOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPOS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPOS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101090"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4fe4s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octapb_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2fe2s_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dad_5_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_lipopb_c" stoichiometry="1" constant="true"/> <speciesReference species="M_met__L_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0628"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_COLIPAKpp" fast="false" reversible="false" name="Lipid A core kinase (periplasm)" metaid="R_COLIPAKpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_COLIPAKpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/COLIPAKpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96842"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_colipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_colipap_p" stoichiometry="1" constant="true"/> <speciesReference species="M_udcpp_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2174"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACPPAT120" fast="false" reversible="false" name="Acyl-(acyl carrier protein):phosphate acyltransferase (C12:0)" metaid="R_ACPPAT120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACPPAT120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACPPAT120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95395"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ddcap_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b1090"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HPPtpp" fast="false" reversible="false" name="3-hydroxypropionate transport via proton symport (periplasm)" metaid="R_3HPPtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HPPtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HPPtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94905"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hpp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3hpp_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_MPTSS" fast="false" reversible="false" name="Molybdopterin synthase sulfurylase" metaid="R_MPTSS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MPTSS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MPTSS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101736"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_moadcoo_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_moadamp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0826"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CPMPS" fast="false" reversible="false" name="Cyclic pyranopterin monophosphate synthase" metaid="R_CPMPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPMPS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPMPS"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.99.18"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142714"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cpmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0783"/> <fbc:geneProductRef fbc:geneProduct="G_b0781"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPOCT" fast="false" reversible="false" name="Lipoyl(octanoyl) transferase" metaid="R_LIPOCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPOCT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPOCT"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101089"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octapb_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0630"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPATPT" fast="false" reversible="false" name="Lipoate-ATP adenylate transferase" metaid="R_LIPATPT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPATPT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPATPT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-8654"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.1.20"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.63"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07770"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101081"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12914"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12915"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12916"/> <rdf:li rdf:resource="http://identifiers.org/rhea/12913"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07584"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lipoate_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_lipoamp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4386"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LIPAMPL" fast="false" reversible="false" name="Lipoyl-adenylate protein ligase" metaid="R_LIPAMPL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LIPAMPL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LIPAMPL"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101080"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lipoamp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lipopb_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4386"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALDD19xr" fast="false" reversible="true" name="Aldehyde dehydrogenase (phenylacetaldehyde, NAD)" metaid="R_ALDD19xr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALDD19xr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALDD19xr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PHENDEHYD-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.5"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.39"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02536"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95743"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21392"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21395"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21394"/> <rdf:li rdf:resource="http://identifiers.org/rhea/21393"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/2456"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01840"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pacald_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pac_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1385"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MMM" fast="false" reversible="false" name="Methylmalonyl-CoA mutase" metaid="R_MMM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MMM"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MMM"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101660"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mmcoa__S_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2917"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MOGDS" fast="false" reversible="false" name="Molybdopterin guanine dinucleotide synthase" metaid="R_MOGDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MOGDS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOGDS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138629"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_moco_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mocogdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3857"/> <fbc:geneProductRef fbc:geneProduct="G_b3856"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3857"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CPH4S" fast="false" reversible="false" name="6-carboxy-5,6,7,8-tetrahydropterin synthase" metaid="R_CPH4S" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPH4S"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPH4S"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5507"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.50"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09959"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95095"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27969"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27968"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27967"/> <rdf:li rdf:resource="http://identifiers.org/rhea/27966"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ahdt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cph4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2765"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_WCOS" fast="false" reversible="false" name="Tungsten pterin cofactor synthase" metaid="R_WCOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_WCOS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/WCOS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138920"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mptamp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tungs_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_wco_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0827"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RFAMPtpp" fast="false" reversible="false" name="Rifampin transport via TolC system" metaid="R_RFAMPtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RFAMPtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RFAMPtpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104015"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_rfamp_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rfamp_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b0462"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0463"/> <fbc:geneProductRef fbc:geneProduct="G_b3035"/> <fbc:geneProductRef fbc:geneProduct="G_b2470"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SHCHCS3" fast="false" reversible="false" name="2-succinyl-6-hydroxy-2,4-cyclohexadiene 1-carboxylate synthase" metaid="R_SHCHCS3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description 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species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2263"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_VPAMTr" fast="false" reversible="true" name="Valine-pyruvate aminotransferase" metaid="R_VPAMTr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_VPAMTr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/VPAMTr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:VALINE-PYRUVATE-AMINOTRANSFER-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.66"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01215"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105217"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22915"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22914"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22912"/> <rdf:li rdf:resource="http://identifiers.org/rhea/22913"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00904"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3mob_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3572"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACOLIPAabctex" fast="false" reversible="false" name="Arabinose modified core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" metaid="R_ACOLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOLIPAabctex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACOLIPAabctex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95378"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_acolipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acolipa_e" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4262"/> <fbc:geneProductRef fbc:geneProduct="G_b4261"/> <fbc:geneProductRef fbc:geneProduct="G_b3199"/> <fbc:geneProductRef fbc:geneProduct="G_b3201"/> <fbc:geneProductRef fbc:geneProduct="G_b3200"/> <fbc:geneProductRef fbc:geneProduct="G_b0054"/> <fbc:geneProductRef fbc:geneProduct="G_b0641"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PYK4" fast="false" reversible="false" name="Pyruvate kinase(4)" metaid="R_PYK4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PYK4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYK4"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.40"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00572"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103373"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00411"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cdp_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_ctp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1854"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADPHXD" fast="false" reversible="false" name="NADPHX dehydratase" metaid="R_NADPHXD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADPHXD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADPHXD"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadphx__S_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4167"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADHHR" fast="false" reversible="false" name="NADH hydratase" metaid="R_NADHHR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADHHR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADHHR"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadhx__R_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> <fbc:geneProductRef fbc:geneProduct="G_b1779"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ECA4COLIPAabctex" fast="false" reversible="false" name="Enterobacterial common antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" metaid="R_ECA4COLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ECA4COLIPAabctex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ECA4COLIPAabctex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97871"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_eca4colipa_p" 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_eca4colipa_e" 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_b4262"/> <fbc:geneProductRef fbc:geneProduct="G_b4261"/> <fbc:geneProductRef fbc:geneProduct="G_b3199"/> <fbc:geneProductRef fbc:geneProduct="G_b3201"/> <fbc:geneProductRef fbc:geneProduct="G_b3200"/> <fbc:geneProductRef fbc:geneProduct="G_b0054"/> <fbc:geneProductRef fbc:geneProduct="G_b0641"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_ttrcyc_e" fast="false" reversible="false" name="Tetracycline exchange" metaid="R_EX_ttrcyc_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_ttrcyc_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ttrcyc_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104976"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35242"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35240"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35241"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35239"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ttrcyc_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_COLIPAPabctex" fast="false" reversible="false" name="Core oligosaccharide lipid A diphosphate transport via ABC system (periplasm to extracellular)" metaid="R_COLIPAPabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_COLIPAPabctex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/COLIPAPabctex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96843"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_colipap_p" 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_colipap_e" 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_b4262"/> <fbc:geneProductRef fbc:geneProduct="G_b4261"/> <fbc:geneProductRef fbc:geneProduct="G_b3199"/> <fbc:geneProductRef fbc:geneProduct="G_b3201"/> <fbc:geneProductRef fbc:geneProduct="G_b3200"/> <fbc:geneProductRef fbc:geneProduct="G_b0054"/> <fbc:geneProductRef fbc:geneProduct="G_b0641"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADPHXE" fast="false" reversible="true" name="NADPHX epimerase" metaid="R_NADPHXE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADPHXE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADPHXE"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nadphx__R_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadphx__S_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4167"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALAtpp" fast="false" reversible="false" name="L-alanine export via facilited diffusion" metaid="R_ALAtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALAtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALAtpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ala__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2670"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CH4tex" fast="false" reversible="true" name="Methane Transport(extracellular via diffusion)" metaid="R_CH4tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CH4tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CH4tex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ch4_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ch4_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_EX_mincyc_e" fast="false" reversible="false" name="Minocycline exchange" metaid="R_EX_mincyc_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_mincyc_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mincyc_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101582"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35168"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35167"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35169"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35170"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mincyc_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_TARTRDtex" fast="false" reversible="true" name="D-tartrate transport via diffusion (extracellular to periplasm)" metaid="R_TARTRDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TARTRDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TARTRDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104722"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35199"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35200"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35202"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35201"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tartr__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tartr__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DM_4crsol_c" fast="false" reversible="false" name="Sink needed to allow p-Cresol to leave system" metaid="R_DM_4crsol_c" sboTerm="SBO:0000628" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DM_4crsol_c"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DM_4crsol_c"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-500"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96888"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35071"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35072"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35074"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35073"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4crsol_c" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_3OXCOAT" fast="false" reversible="false" name="3-oxoadipyl-CoA thiolase" metaid="R_3OXCOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3OXCOAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OXCOAT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-3641"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.16"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.174"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00829"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94967"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19482"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19483"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19481"/> <rdf:li rdf:resource="http://identifiers.org/rhea/19484"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1170"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00598"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oxadpcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1397"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_BTNt2ipp" fast="false" reversible="false" name="Biotin transport via proton symport (periplasm)" metaid="R_BTNt2ipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BTNt2ipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BTNt2ipp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96334"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09693"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_btn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_btn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_URACPAH" fast="false" reversible="false" name="Peroxyureidoacrylate hydrolase" metaid="R_URACPAH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_URACPAH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URACPAH"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6460"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.110"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09947"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105143"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31592"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31594"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31593"/> <rdf:li rdf:resource="http://identifiers.org/rhea/31591"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uracp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cbm_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_poaac_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1011"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_BTNtex" fast="false" reversible="true" name="Biotin transport via diffusion (extracellular to periplasm)" metaid="R_BTNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BTNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BTNtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-240"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96333"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28459"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28461"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28460"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28458"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_btn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_btn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHBSZ3FEabcpp" fast="false" reversible="false" name="23dhbsz3 Fe III transport via ABC system periplasm" metaid="R_DHBSZ3FEabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHBSZ3FEabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHBSZ3FEabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97371"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fe3dhbzs3_p" 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_fe3dhbzs3_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_b0588"/> <fbc:geneProductRef fbc:geneProduct="G_b0589"/> <fbc:geneProductRef fbc:geneProduct="G_b0590"/> <fbc:geneProductRef fbc:geneProduct="G_b0592"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE3DHBZS3R" fast="false" reversible="false" name="Fe(III)-(2,3-dihydroxybenzoylserine)3 reductase via NADPH" metaid="R_FE3DHBZS3R" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3DHBZS3R"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3DHBZS3R"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3dhbzs3_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23dhbzs3_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3070"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DXYLONtpp" fast="false" reversible="true" name="D-xylonate reversible tranposrt (periplasm)" metaid="R_DXYLONtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DXYLONtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DXYLONtpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dxylnt_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dxylnt_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_DXYLTD" fast="false" reversible="true" name="D-xylonate dehydratase" metaid="R_DXYLTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DXYLTD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DXYLTD"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dxylnt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2ddara_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0269"/> <fbc:geneProductRef fbc:geneProduct="G_b4297"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_2DDARAA" fast="false" reversible="true" name="2-dehydro-3-deoxy-D-arabinonate Aldolase" metaid="R_2DDARAA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2DDARAA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2DDARAA"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2ddara_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gcald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4298"/> <fbc:geneProductRef fbc:geneProduct="G_b0268"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_2DGLCptspp" fast="false" reversible="false" name="2-Deoxy-D-glucose transport via PEP:Pyr PTS (periplasm)" metaid="R_2DGLCptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2DGLCptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2DGLCptspp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dglc_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2doxg6p_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_b1817"/> <fbc:geneProductRef fbc:geneProduct="G_b1819"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b1818"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_2DGULRGx" fast="false" reversible="false" name="2-Dehydro-L-gulonate reductase to gluconate (NADH)" metaid="R_2DGULRGx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2DGULRGx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2DGULRGx"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94785"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dhguln_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glcn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3553"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2DGULRGy" fast="false" reversible="false" name="2-Dehydro-L-gulonate reductase to gluconate (NADPH)" metaid="R_2DGULRGy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2DGULRGy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2DGULRGy"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94786"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dhguln_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_glcn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3553"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AP4AS" fast="false" reversible="false" name="Ap4A synthetase" metaid="R_AP4AS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AP4AS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AP4AS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5208"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95858"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34936"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34935"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34938"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34937"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ap4a_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4129"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARBTptspp" fast="false" reversible="false" name="Arbutin transport via PEP:Pyr PTS (periplasm)" metaid="R_ARBTptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBTptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95932"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34944"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34945"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34946"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34943"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05501"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbt_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arbt6p_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_b3722"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2715"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARBTtex" fast="false" reversible="false" name="Arbutin transport via diffusion (extracellular to periplasm)" metaid="R_ARBTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARBTtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95933"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35024"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35025"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35023"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35026"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbt_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_arbt_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_arbt_e" fast="false" reversible="false" name="Arbutin exchange" metaid="R_EX_arbt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_arbt_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_arbt_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95933"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35024"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35025"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35023"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35026"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_arbt_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_GNP" fast="false" reversible="false" name="Phosphogluconate phosphatase" metaid="R_GNP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GNP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GNP"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glcn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3715"/> <fbc:geneProductRef fbc:geneProduct="G_b2690"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALLTAMH2" fast="false" reversible="false" name="Allantoate amidinohydrolase" metaid="R_ALLTAMH2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALLTAMH2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALLTAMH2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_alltt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_urdgci_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0516"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_UGCIAMH" fast="false" reversible="false" name="Ureidoglycine aminohydrolase" metaid="R_UGCIAMH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_UGCIAMH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UGCIAMH"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_urdgci_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_urdglyc_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0515"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DMSOtpp" fast="false" reversible="true" name="Dimethyl sulfoxide transport via diffusion (periplasm)" metaid="R_DMSOtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DMSOtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DMSOtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-273"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97533"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29700"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29701"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29702"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29699"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08358"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dmso_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dmso_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_POAACR" fast="false" reversible="false" name="Peroxyaminoacrylate reductase" metaid="R_POAACR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_POAACR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/POAACR"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103056"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_poaac_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3amac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1010"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PYDXtex" fast="false" reversible="true" name="Pyridoxal transport via diffusion (extracellular)" metaid="R_PYDXtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PYDXtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYDXtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-214"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103370"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28462"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28465"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28463"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28464"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12666"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pydx_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pydx_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PYDXtpp" fast="false" reversible="false" name="Pyridoxal import" metaid="R_PYDXtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PYDXtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYDXtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-214"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103370"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28462"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28465"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28463"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28464"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12666"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pydx_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pydx_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_SUCASPtpp" fast="false" reversible="true" name="Succinate:aspartate antiporter (periplasm)" metaid="R_SUCASPtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SUCASPtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCASPtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-106A"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104611"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29343"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29345"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29344"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29346"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asp__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4138"/> <fbc:geneProductRef fbc:geneProduct="G_b4123"/> <fbc:geneProductRef fbc:geneProduct="G_b0621"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_METGLCUR" fast="false" reversible="false" name="1-O-Methyl-Beta-D-glucuronidase" metaid="R_METGLCUR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METGLCUR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METGLCUR"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_metglcur_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glcur_c" stoichiometry="1" constant="true"/> <speciesReference species="M_meoh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1617"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACOAD1fr" fast="false" reversible="false" name="Acyl-CoA dehydrogenase (butanoyl-CoA)" metaid="R_ACOAD1fr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOAD1fr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACOAD1fr"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_b2coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1695"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_23DOGULNt4pp" fast="false" reversible="false" name="Na+/ 2,3-Dioxo-L-gulonate symport (periplasm)" metaid="R_23DOGULNt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_23DOGULNt4pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/23DOGULNt4pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_23doguln_p" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23doguln_c" stoichiometry="1" constant="true"/> <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3577"/> <fbc:geneProductRef fbc:geneProduct="G_b3579"/> <fbc:geneProductRef fbc:geneProduct="G_b3578"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FE3DCITexs" fast="false" reversible="false" name="Dicitrate Fe(III) binding (spontaneous)" metaid="R_FE3DCITexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FE3DCITexs"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3DCITexs"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cit_e" stoichiometry="2" constant="true"/> <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe3dcit_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SUCMALtpp" fast="false" reversible="true" name="Succinate:malate antiporter (periplasm)" metaid="R_SUCMALtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SUCMALtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCMALtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-106B"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97456"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29329"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29327"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29328"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29330"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09767"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mal__L_p" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b4138"/> <fbc:geneProductRef fbc:geneProduct="G_b4123"/> <fbc:geneProductRef fbc:geneProduct="G_b0621"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PYDXNtex" fast="false" reversible="true" name="Pyridoxine transport via diffusion (extracellular)" metaid="R_PYDXNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PYDXNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYDXNtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-205"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103364"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28472"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28470"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28473"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28471"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13097"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pydxn_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pydxn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FEENTERES" fast="false" reversible="false" name="Enterochelin Esterase (Fe containing)" metaid="R_FEENTERES" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEENTERES"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEENTERES"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_feenter_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fe3dhbzs3_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0585"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PYDXNtpp" fast="false" reversible="false" name="Pyridoxine import" metaid="R_PYDXNtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation 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species="M_pydxn_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_FEENTERR4" fast="false" reversible="false" name="Fe-enterobactin reduction via nadph" metaid="R_FEENTERR4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FEENTERR4"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEENTERR4"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_feenter_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_enter_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3070"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACPPAT160" fast="false" reversible="false" name="Acyl-(acyl carrier protein):phosphate acyltransferase (C16:0)" metaid="R_ACPPAT160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACPPAT160"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACPPAT160"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95398"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdcap_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b1090"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DXYLONtex" fast="false" reversible="true" name="D-xylonate transport via diffusion (extracellular)" metaid="R_DXYLONtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DXYLONtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DXYLONtex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dxylnt_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dxylnt_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PYDAMtex" fast="false" reversible="true" name="Pyridoxamine transport via diffusion (extracellular)" metaid="R_PYDAMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PYDAMtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYDAMtex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-213"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103358"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28468"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28467"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28469"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28466"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pydam_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pydam_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PYDAMtpp" fast="false" reversible="false" name="Pyridoxamine import" metaid="R_PYDAMtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PYDAMtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYDAMtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-213"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103358"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28468"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28467"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28469"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28466"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pydam_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pydam_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_PSURItex" fast="false" reversible="true" name="Pseudouridine transport via diffusion (extracellular to periplasm)" metaid="R_PSURItex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSURItex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSURItex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_psuri_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_psuri_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ALR2x" fast="false" reversible="false" name="Aldose reductase (methylglyoxal) (nadh)" metaid="R_ALR2x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ALR2x"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALR2x"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mthgxl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acetol_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1771"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_OMPHHXy" fast="false" reversible="false" name="2-octaprenyl-6-methoxyphenol hydroxylase (NADPH)" metaid="R_OMPHHXy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OMPHHXy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OMPHHXy"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2omph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2ombzl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2907"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CHLt3pp" fast="false" reversible="false" name="Choline transport via proton antiport (periplasm)" metaid="R_CHLt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CHLt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHLt3pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_chol_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_chol_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0543"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_13PPDH2" fast="false" reversible="true" name="1,3-propanediol dehydrogenase" metaid="R_13PPDH2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_13PPDH2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/13PPDH2"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hppnl_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_13ppd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3011"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TARTt2_3pp" fast="false" reversible="false" name="D-tartrate transport via proton symport (3 H) (periplasm)" metaid="R_TARTt2_3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TARTt2_3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TARTt2_3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104725"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="3" constant="true"/> <speciesReference species="M_tartr__D_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> <speciesReference species="M_tartr__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4123"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SUCTARTtpp" fast="false" reversible="true" name="Succinate:D-tartrate antiporter (periplasm)" metaid="R_SUCTARTtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SUCTARTtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCTARTtpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-499"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104642"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34763"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34764"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34765"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34766"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tartr__D_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/> <speciesReference species="M_tartr__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4123"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_APCS" fast="false" reversible="false" name="Aminopropylcadaverine synthase" metaid="R_APCS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APCS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APCS"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5217"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R08359"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95867"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33387"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33389"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33390"/> <rdf:li rdf:resource="http://identifiers.org/rhea/33388"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/14104"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12049"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_15dap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ametam_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5mta_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_na15dap_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0121"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CHTBSptspp" fast="false" reversible="false" name="Chitobiose transport via PEP:Pyr PTS (periplasm)" metaid="R_CHTBSptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CHTBSptspp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHTBSptspp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138170"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_chtbs_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_chtbs6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1738"/> <fbc:geneProductRef fbc:geneProduct="G_b1737"/> <fbc:geneProductRef fbc:geneProduct="G_b1736"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2415"/> <fbc:geneProductRef fbc:geneProduct="G_b2416"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYBt3pp" fast="false" reversible="false" name="Glycine betaine transport via proton antiport (periplasm)" metaid="R_GLYBt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYBt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYBt3pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyb_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyb_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0543"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AI2tpp" fast="false" reversible="false" name="Quorum signal AI-2 exporter" metaid="R_AI2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AI2tpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AI2tpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mththf_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mththf_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1601"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACPPAT181" fast="false" reversible="false" name="Acyl-(acyl carrier protein):phosphate acyltransferase (C18:1)" metaid="R_ACPPAT181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACPPAT181"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACPPAT181"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95401"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octeACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdceap_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1094"/> <fbc:geneProductRef fbc:geneProduct="G_b1090"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_Ftpp" fast="false" reversible="false" name="F- efflux transport" metaid="R_Ftpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_Ftpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/Ftpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_f_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_f_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0624"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SQVOSI" fast="false" reversible="false" name="Sulfoquinovose isomerase" metaid="R_SQVOSI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SQVOSI"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SQVOSI"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sq_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_sf_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3880"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_6D6SPA" fast="false" reversible="false" name="6-deoxy-6-sulfofructose-1-phosphate aldolase" metaid="R_6D6SPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_6D6SPA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/6D6SPA"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sfp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sla_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3881"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CHTBStex" fast="false" reversible="true" name="Chitobiose transport via diffusion (extracellular to periplasm)" metaid="R_CHTBStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CHTBStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHTBStex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138171"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_chtbs_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_chtbs_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0681"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_TRPtipp" fast="false" reversible="false" name="L-tryptophan transport out (periplasm)" metaid="R_TRPtipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TRPtipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TRPtipp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_trp__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_trp__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1473"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TYRtipp" fast="false" reversible="false" name="L-tyrosine transport out (periplasm)" metaid="R_TYRtipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TYRtipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TYRtipp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_tyr__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1473"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ThDPAT" fast="false" reversible="false" name="ThDP adenylyl transferase" metaid="R_ThDPAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ThDPAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ThDPAT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5291"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105006"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35246"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35244"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35243"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35245"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thmpp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_athtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_GHBDHx" fast="false" reversible="true" name="Gamma-hydroxybutyrate dehydrogenase (NADH)" metaid="R_GHBDHx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GHBDHx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GHBDHx"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:4-HYDROXYBUTYRATE-DEHYDROGENASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.61"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01644"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100140"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23948"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23950"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23951"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23949"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1781"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01201"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sucsal_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ghb_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3882"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHPStr" fast="false" reversible="false" name="2,3-dihydroxypropane 1-sulfonate transporter" metaid="R_DHPStr" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHPStr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHPStr"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhps_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhps_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3877"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SQtr" fast="false" reversible="false" name="Sulfoquinovose transporter" metaid="R_SQtr" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SQtr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SQtr"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sq_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_sq_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3876"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHPStex" fast="false" reversible="true" name="2,3-dihydroxypropane 1-sulfonate transport via diffusion" metaid="R_DHPStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHPStex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHPStex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhps_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhps_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3875"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_APPLDHr" fast="false" reversible="true" name="Aminopropanol dehydrogenase reversible" metaid="R_APPLDHr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APPLDHr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APPLDHr"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:AMINOPROPDEHYDROG-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.37"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.75"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03759"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95894"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16520"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16519"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16517"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16518"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02667"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_aact_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_appl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3945"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SPMDt3pp" fast="false" reversible="false" name="Spermidine transport out via proton antiport (periplasm)" metaid="R_SPMDt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SPMDt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SPMDt3pp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-266"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104497"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28737"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28738"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28736"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28735"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05652"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_spmd_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1600"/> <fbc:geneProductRef fbc:geneProduct="G_b1599"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_FMNtex" fast="false" reversible="true" name="FMN transport, outer membrane" metaid="R_FMNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FMNtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FMNtex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fmn_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fmn_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_APH141" fast="false" reversible="false" name="Acylphosphatase (C14:1)" metaid="R_APH141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APH141"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APH141"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95878"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdceap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0968"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_dxylnt_e" fast="false" reversible="false" name="D-Xylonate exchange" metaid="R_EX_dxylnt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dxylnt_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dxylnt_e"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dxylnt_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_AI2K" fast="false" reversible="false" name="Autoinducer-2 kinase" metaid="R_AI2K" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AI2K"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AI2K"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dhptd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dhptdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1511"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PHEtipp" fast="false" reversible="false" name="L-phenylalanine transport out (periplasm)" metaid="R_PHEtipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PHEtipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PHEtipp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_phe__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_phe__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1473"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_G2PP" fast="false" reversible="false" name="Glycerol-2-phosphate phosphatase" metaid="R_G2PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_G2PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G2PP"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLYCEROL-2-PHOSPHATASE-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.19"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01043"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99852"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13106"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13108"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13107"/> <rdf:li rdf:resource="http://identifiers.org/rhea/13105"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1325"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00766"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glyc2p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2533"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_MALt3pp" fast="false" reversible="false" name="L-malate transport out via proton antiport (periplasm)" metaid="R_MALt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MALt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALt3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101373"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mal__L_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_CITt3pp" fast="false" reversible="false" name="Citrate transport out via proton antiport (periplasm)" metaid="R_CITt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CITt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CITt3pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96747"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cit_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_APH161" fast="false" reversible="false" name="Acylphosphatase (C16:1)" metaid="R_APH161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APH161"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APH161"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95880"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdceap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0968"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHNPA2r" fast="false" reversible="true" name="Dihydroneopterin aldolase reversible" metaid="R_DHNPA2r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHNPA2r"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHNPA2r"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:H2NEOPTERINALDOL-RXN"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.25"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03504"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR125603"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10541"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10540"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10542"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10543"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/3293"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02504"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhnpt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_6hmhpt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gcald_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3058"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_QUIN2tpp" fast="false" reversible="true" name="Quinate transport (periplasm)" metaid="R_QUIN2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_QUIN2tpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/QUIN2tpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103397"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35197"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35195"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35196"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35198"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12452"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_quin_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_quin_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_GLYC2Pabcpp" fast="false" reversible="false" name="Sn-Glycerol 2-phosphate transport via ABC system (periplasm)" metaid="R_GLYC2Pabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYC2Pabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYC2Pabcpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100318"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34761#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34759#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34760#1"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34762#1"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc2p_p" 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_glyc2p_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_b3450"/> <fbc:geneProductRef fbc:geneProduct="G_b3453"/> <fbc:geneProductRef fbc:geneProduct="G_b3451"/> <fbc:geneProductRef fbc:geneProduct="G_b3452"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CRNDtex" fast="false" reversible="true" name="D-carnitine transport via diffusion (extracellular to periplasm)" metaid="R_CRNDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CRNDtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNDtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96904"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35067"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35068"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35070"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35069"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_crn__D_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_crn__D_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SHGO" fast="false" reversible="false" name="S-2-hydroxyglutarate oxidase" metaid="R_SHGO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SHGO"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SHGO"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_S2hglut_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2660"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLBtex" fast="false" reversible="true" name="Cellobiose transport transport via diffusion extracellular to periplasm " metaid="R_CLBtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLBtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLBtex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96760"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cellb_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cellb_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACOXT" fast="false" reversible="true" name="Acetyl-CoA:oxalate CoA-transferase" metaid="R_ACOXT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOXT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACOXT"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oxa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oxalcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2371"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_mththf_e" fast="false" reversible="false" name="(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran exchange" metaid="R_EX_mththf_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> 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<rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2HESR"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dtgcl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mercpeth_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2989"/> <fbc:geneProductRef fbc:geneProduct="G_b2302"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_CHOLID" fast="false" reversible="false" name="7-?-hydroxysteroid dehydrogenase" metaid="R_CHOLID" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> 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metaid="R_CHOLATEtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CHOLATEtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHOLATEtpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cholate_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cholate_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4337"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADHXD" fast="false" reversible="false" name="NADHX dehydratase" metaid="R_NADHXD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADHXD"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADHXD"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadhx__S_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4167"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADPHHR" fast="false" reversible="false" name="NADPH hydratase" metaid="R_NADPHHR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADPHHR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADPHHR"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadphx__R_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> <fbc:geneProductRef fbc:geneProduct="G_b1779"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADPHHS" fast="false" reversible="false" name="NADPH hydratase" metaid="R_NADPHHS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADPHHS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADPHHS"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadphx__S_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1779"/> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_4ABZGLUH" fast="false" reversible="true" name="P-aminobenzoyl-glutamate hydrolase" metaid="R_4ABZGLUH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_4ABZGLUH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4ABZGLUH"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4abzglu_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4abz_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1337"/> <fbc:geneProductRef fbc:geneProduct="G_b1338"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_4ABZGLUtr" fast="false" reversible="true" name="P-aminobenzoyl glutamate:H+ symporter" metaid="R_4ABZGLUtr" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_4ABZGLUtr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4ABZGLUtr"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4abzglu_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4abzglu_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1336"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADHHS" fast="false" reversible="false" name="NADH hydratase" metaid="R_NADHHS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADHHS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADHHS"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadhx__S_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> <fbc:geneProductRef fbc:geneProduct="G_b1779"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_APH180" fast="false" reversible="false" name="Acylphosphatase (C18:0)" metaid="R_APH180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APH180"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APH180"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95881"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ocdcap_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0968"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_NADHXE" fast="false" reversible="true" name="NADHX epimerase" metaid="R_NADHXE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_NADHXE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADHXE"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nadhx__S_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadhx__R_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4167"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SELabcpp" fast="false" reversible="false" name="Selenatenate transport via ABC system (periplasm)" metaid="R_SELabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SELabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SELabcpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sel_p" 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"/> <speciesReference species="M_sel_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2423"/> <fbc:geneProductRef fbc:geneProduct="G_b2422"/> <fbc:geneProductRef fbc:geneProduct="G_b2425"/> <fbc:geneProductRef fbc:geneProduct="G_b2424"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2423"/> <fbc:geneProductRef fbc:geneProduct="G_b2422"/> <fbc:geneProductRef fbc:geneProduct="G_b3917"/> <fbc:geneProductRef fbc:geneProduct="G_b2424"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PHDA" fast="false" reversible="false" name="Phenylhydantoinase" metaid="R_PHDA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PHDA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PHDA"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5phdt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5phua_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2873"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TEO2M" fast="false" reversible="false" name="Tellurite methyltransferase" metaid="R_TEO2M" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> 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fbc:geneProduct="G_b2264"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHNCOAS" fast="false" reversible="false" name="1,4-dihydroxy-2-napthoyl-CoA synthase" metaid="R_DHNCOAS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHNCOAS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHNCOAS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97412"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sbzcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference 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rdf:resource="http://identifiers.org/ec-code/1.3.1.84"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00919"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102415"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26456"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26455"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26454"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26457"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1239"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00668"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppcoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_prpncoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3253"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PYK6" fast="false" reversible="false" name="RE2954" metaid="R_PYK6" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PYK6"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYK6"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dtdp_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_dttp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1854"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHNCOAT" fast="false" reversible="false" name="1,4-dihydroxy-2-napthoyl-CoA thioesterase" metaid="R_DHNCOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHNCOAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHNCOAT"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97413"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_14dhncoa_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_dhna_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1686"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FADt" fast="false" reversible="false" name="FAD transporter, periplasm" metaid="R_FADt" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FADt"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FADt"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fad_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1985"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_HPACOAT" fast="false" reversible="false" name="Hydroxyphenylacetyl-CoA thioesterase" metaid="R_HPACOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HPACOAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HPACOAT"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_34dphacoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_34dhpha_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_b1396"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PUACGAMtr" fast="false" reversible="false" name="Transport of poly-?-1,6-N-acetyl-D-glucosamine (poly-?-1,6-N-acetyl-D-glucosamine synthase)" metaid="R_PUACGAMtr" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PUACGAMtr"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PUACGAMtr"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_puacgam_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_puacgam_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1021"/> <fbc:geneProductRef fbc:geneProduct="G_b1022"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DC6PDA" fast="false" reversible="false" name="Chito-oligosaccharide mono-deacetylase" metaid="R_DC6PDA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DC6PDA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DC6PDA"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_chtbs6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mchtbs6p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1733"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_5DGLCNR" fast="false" reversible="false" name="5-dehydro-D-gluconate reductase" metaid="R_5DGLCNR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_5DGLCNR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/5DGLCNR"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14367"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.69"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01740"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95065"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23937"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23939"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23936"/> <rdf:li rdf:resource="http://identifiers.org/rhea/23938"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01278"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_5dglcn_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_glcn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4266"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PIt2rpp" fast="false" reversible="false" name="Phosphate reversible transport via symport (periplasm)" metaid="R_PIt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PIt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PIt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-114"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102872"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29939"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29941"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29940"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29942"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05312"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09833"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09811"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09872"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09723"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09120"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_p" 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_b3493"/> <fbc:geneProductRef fbc:geneProduct="G_b2987"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FADtex" fast="false" reversible="true" name="FAD transport, outer membrane" metaid="R_FADtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FADtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FADtex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fad_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fad_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_AI2abcpp" fast="false" reversible="false" name="Autoinducer-2 ABC transporter" metaid="R_AI2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AI2abcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AI2abcpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mththf_p" 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_mththf_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1516"/> <fbc:geneProductRef fbc:geneProduct="G_b1513"/> <fbc:geneProductRef fbc:geneProduct="G_b1515"/> <fbc:geneProductRef fbc:geneProduct="G_b1514"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAI2I" fast="false" reversible="false" name="Phospho-AI-2 isomerase" metaid="R_PAI2I" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAI2I"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAI2I"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhptdp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhptdd_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1518"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_4HBZt3pp" fast="false" reversible="false" name="4-hydroxybenzoate transport out via antiporter" metaid="R_4HBZt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_4HBZt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4HBZt3pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4hbz_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4hbz_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3240"/> <fbc:geneProductRef fbc:geneProduct="G_b3241"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CURR" fast="false" reversible="false" name="NADPH-dependent curcumin reductase" metaid="R_CURR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CURR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CURR"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cur_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_dhcur_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1449"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LKDRA" fast="false" reversible="true" name="2-keto-3-deoxy-L-rhamnonate aldolase" metaid="R_LKDRA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LKDRA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LKDRA"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lkdr_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_lald__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2245"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LEUt2rpp" fast="false" reversible="false" name="L-leucine reversible transport via proton symport (periplasm)" metaid="R_LEUt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LEUt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LEUt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101055"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05243"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08785"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11119"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13340"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_leu__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0401"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LCTStpp" fast="false" reversible="false" name="Lactose transport via proton symport (periplasm)" metaid="R_LCTStpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LCTStpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LCTStpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101025"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28869"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28868"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28870"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28867"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10169"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08781"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_lcts_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lcts_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0343"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ILEt3pp" fast="false" reversible="false" name="L-isoleucine transport out via proton antiport (periplasm)" metaid="R_ILEt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ILEt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ILEt3pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ile__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4141"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_METNA" fast="false" reversible="true" name="L-amino acid N-acyltransferase" metaid="R_METNA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METNA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METNA"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acmet_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_b1448"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_METt3pp" fast="false" reversible="false" name="L-methionine tranport out via proton antiport (periplasm)" metaid="R_METt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METt3pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_met__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1798"/> <fbc:geneProductRef fbc:geneProduct="G_b4141"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FESD1s" fast="false" reversible="false" name="Iron-sulfur cluster damage (peroxide, spontaneous)" metaid="R_FESD1s" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FESD1s"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FESD1s"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99585"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4fe4s_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3fe4s_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe3_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GSNt3pp" fast="false" reversible="false" name="Guanosine transport out via proton antiport (periplasm)" metaid="R_GSNt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GSNt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GSNt3pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gsn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gsn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3662"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CLtipp" fast="false" reversible="false" name="Chloride ion transport in via diffusion (periplasm)" metaid="R_CLtipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CLtipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CLtipp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cl_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cl_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1592"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_5DKGR" fast="false" reversible="true" name="5-keto-D-gluconate 5-reductase" metaid="R_5DKGR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_5DKGR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/5DKGR"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_glcn_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_5dglcn_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_b2842"/> <fbc:geneProductRef fbc:geneProduct="G_b4266"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_XYHDL" fast="false" reversible="false" name="?-D-xyloside xylohydrolase" metaid="R_XYHDL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_XYHDL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYHDL"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_iprimv_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/> <speciesReference species="M_xyl__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3656"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_2DGLCtex" fast="false" reversible="true" name="2-Deoxy-D-glucose transport via diffusion (extracellular)" metaid="R_2DGLCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2DGLCtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2DGLCtex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dglc_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2dglc_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_E4PP" fast="false" reversible="false" name="Erythrose-4-phosphate phosphatase" metaid="R_E4PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_E4PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/E4PP"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_erthrs_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0822"/> <fbc:geneProductRef fbc:geneProduct="G_b2293"/> <fbc:geneProductRef fbc:geneProduct="G_b2690"/> <fbc:geneProductRef fbc:geneProduct="G_b3826"/> <fbc:geneProductRef fbc:geneProduct="G_b1727"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PUACGAMS" fast="false" reversible="true" name="Poly-?-1,6-N-acetyl-D-glucosamine synthase" metaid="R_PUACGAMS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PUACGAMS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PUACGAMS"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_puacgam_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_uacgam_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1021"/> <fbc:geneProductRef fbc:geneProduct="G_b1022"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_PItpp" fast="false" reversible="false" name="Phosphate export via facillated diffusion (periplasm)" metaid="R_PItpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PItpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PItpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4020"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RU5PP" fast="false" reversible="false" name="Ribulose-5-Phosphate Phosphatase" metaid="R_RU5PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RU5PP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RU5PP"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rbl__D_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2293"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_doxrbcn_e" fast="false" reversible="false" name="Doxorubicin exchange" metaid="R_EX_doxrbcn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_doxrbcn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_doxrbcn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97760"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35079"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35081"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35080"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35082"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_doxrbcn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_6D6SFK" fast="false" reversible="false" name="6-deoxy-6-sulfofructose kinase" metaid="R_6D6SFK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_6D6SFK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/6D6SFK"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sf_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_sfp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3883"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3SLAR" fast="false" reversible="false" name="3-sulfolactaldehyde reductase" metaid="R_3SLAR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3SLAR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3SLAR"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sla_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dhps_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3882"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_LEUt3pp" fast="false" reversible="false" name="L-leucine transport out via proton antiport (periplasm)" metaid="R_LEUt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_LEUt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LEUt3pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_leu__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1798"/> <fbc:geneProductRef fbc:geneProduct="G_b4141"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_INSt3pp" fast="false" reversible="false" name="Inosine transport out via proton antiport (perisplasm)" metaid="R_INSt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_INSt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INSt3pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ins_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ins_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3662"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_INDOLEt2rpp" fast="false" reversible="false" name="Indole transport via proton symport, reversible (periplasm)" metaid="R_INDOLEt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_INDOLEt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INDOLEt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-142"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100835"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29228"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29227"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29230"/> <rdf:li rdf:resource="http://identifiers.org/rhea/29229"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08750"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10176"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_indole_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_indole_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3161"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SQtex" fast="false" reversible="true" name="Sulphoquinovose transport via diffusion" metaid="R_SQtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SQtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SQtex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sq_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_sq_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3875"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ILEt2rpp" fast="false" reversible="false" name="L-isoleucine reversible transport via proton symport (periplasm)" metaid="R_ILEt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ILEt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ILEt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100822"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13322"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05244"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08746"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ile__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0401"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_GLYtpp" fast="false" reversible="true" name="Glycine transport via facillitated diffusion" metaid="R_GLYtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GLYtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYtpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gly_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3927"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_dhps_e" fast="false" reversible="false" name="2,3-Dihydroxypropane-1-sulfonate exchange" metaid="R_EX_dhps_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_dhps_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dhps_e"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhps_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_MOX" fast="false" reversible="false" name="Malate oxidase" metaid="R_MOX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MOX"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOX"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.5.4"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00360"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101715"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10513"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10512"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10515"/> <rdf:li rdf:resource="http://identifiers.org/rhea/10514"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00264"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_URATEtex" fast="false" reversible="true" name="Uric acid transport" metaid="R_URATEtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_URATEtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URATEtex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_urate_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_urate_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_cs1_e" fast="false" reversible="false" name="Cesium ion exchange" metaid="R_EX_cs1_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cs1_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cs1_e"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cs1_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_fusa_e" fast="false" reversible="false" name="Fusidic acid exchange" metaid="R_EX_fusa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_fusa_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fusa_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99717"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35106"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35105"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35104"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35103"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fusa_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_CBL1tonex" fast="false" reversible="false" name="Cob(1)alamin transport via ton system (extermal)" metaid="R_CBL1tonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CBL1tonex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CBL1tonex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96472"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cbl1_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cbl1_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1252"/> <fbc:geneProductRef fbc:geneProduct="G_b3005"/> <fbc:geneProductRef fbc:geneProduct="G_b3006"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3966"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_CBItonex" fast="false" reversible="false" name="Cobinamide transport via ton system (extermal)" metaid="R_CBItonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CBItonex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CBItonex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96468"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cbi_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cbi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1252"/> <fbc:geneProductRef fbc:geneProduct="G_b3005"/> <fbc:geneProductRef fbc:geneProduct="G_b3006"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3966"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ARHGDx" fast="false" reversible="true" name="(R)-alpha-hydroxyglutarate dehydrogenase" metaid="R_ARHGDx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ARHGDx"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARHGDx"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_r2hglut_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_nadh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2913"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CPL" fast="false" reversible="false" name="Carbon-phosphorous lyase" metaid="R_CPL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CPL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPL"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_prpmn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ch4_c" stoichiometry="1" constant="true"/> <speciesReference species="M_prcp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4098"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_mepn_e" fast="false" reversible="false" name="Methylphosphonic acid exchange" metaid="R_EX_mepn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_mepn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mepn_e"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mepn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PSURItpp" fast="false" reversible="false" name="Pseudouridine transport via permease" metaid="R_PSURItpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation 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<rdf:Description rdf:about="#R_FE3DCITR5"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3DCITR5"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fe3dcit_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cit_c" stoichiometry="4" constant="true"/> <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3070"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CH4t2pp" fast="false" reversible="false" name="Methane Transport(periplasm)" metaid="R_CH4t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CH4t2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CH4t2pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ch4_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ch4_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_EX_cm_e" fast="false" reversible="false" name="Chloramphenicol exchange" metaid="R_EX_cm_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_cm_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cm_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96808"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35288"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35290"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35287"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35289"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cm_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_4HTHRA" fast="false" reversible="true" name="4-hydroxy-L-threonine aldolase" metaid="R_4HTHRA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" 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fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_novbcn_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_novbcn_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102008"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35178"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35176"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35175"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35177"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_novbcn_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_I2FE2SR" fast="false" reversible="false" name="ISC [2Fe-2S] 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stoichiometry="1" constant="true"/> <speciesReference species="M_iscu_2fe2s_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2529"/> <fbc:geneProductRef fbc:geneProduct="G_b2530"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_GAPP" fast="false" reversible="false" name="Glyceraldehyde-3-phosphate phosphatase" metaid="R_GAPP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_GAPP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GAPP"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyald_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1727"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_TYRL" fast="false" reversible="false" name="Tyrosine lyase" metaid="R_TYRL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_TYRL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TYRL"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-11319"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.99.19"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104993"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26361"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26363"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26362"/> <rdf:li rdf:resource="http://identifiers.org/rhea/26364"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4crsol_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dad_5_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dhgly_c" stoichiometry="1" 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</rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_metglcur_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_metglcur_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1616"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_METGLCURtex" fast="false" reversible="true" name="1-O-methyl-Beta-D-glucuronate via diffusion (extracellular)" metaid="R_METGLCURtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_METGLCURtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METGLCURtex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_metglcur_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_metglcur_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_INOSTO" fast="false" reversible="true" name="Myo-Inositol:oxygen oxidoreductase" metaid="R_INOSTO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation 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<listOfReactants> <speciesReference species="M_inost_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glcur_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3488"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_THZPSN3" fast="false" reversible="false" name="Thiazole phosphate synthesis" metaid="R_THZPSN3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THZPSN3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THZPSN3"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104861"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dhgly_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dxyl5p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_iscssh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4mpetz_c" stoichiometry="1" constant="true"/> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> <speciesReference species="M_iscs_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0423"/> <fbc:geneProductRef fbc:geneProduct="G_b3990"/> <fbc:geneProductRef fbc:geneProduct="G_b2530"/> <fbc:geneProductRef fbc:geneProduct="G_b3992"/> <fbc:geneProductRef fbc:geneProduct="G_b4407"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_HPYRP" fast="false" reversible="false" name="3-phosphohydroxypyruvate phosphatase" metaid="R_HPYRP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HPYRP"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HPYRP"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3php_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hpyr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1813"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PSURIK" fast="false" reversible="false" name="Pseudouridine kinase" metaid="R_PSURIK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PSURIK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSURIK"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_psuri_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_psd5p_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2166"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FMNt" fast="false" reversible="false" name="FMN transporter, periplasm" metaid="R_FMNt" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FMNt"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FMNt"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_fmn_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1985"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AI2tex" fast="false" reversible="true" name="Ai2 transport, outer membrane" metaid="R_AI2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AI2tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AI2tex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mththf_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mththf_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_PAI2T" fast="false" reversible="false" name="3-hydroxy-2,4-pentadione 5-phosphate thiolase" metaid="R_PAI2T" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PAI2T"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAI2T"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dhptdd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1517"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CUt2pp" fast="false" reversible="false" name="Copper transport out via permease (no H+)" metaid="R_CUt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CUt2pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CUt2pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cu_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cu_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3291"/> <fbc:geneProductRef fbc:geneProduct="G_b0465"/> <fbc:geneProductRef fbc:geneProduct="G_b1330"/> <fbc:geneProductRef fbc:geneProduct="G_b0577"/> <fbc:geneProductRef fbc:geneProduct="G_b4159"/> <fbc:geneProductRef fbc:geneProduct="G_b2924"/> <fbc:geneProductRef fbc:geneProduct="G_b0808"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_Ftex" fast="false" reversible="true" name="Fluoride transport via diffusion" metaid="R_Ftex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_Ftex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/Ftex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_f_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_f_e" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_APG3PAT120" fast="false" reversible="false" name="Acyl-phosphate:glycerol-3-phosphate acyltransferase (C12:0)" metaid="R_APG3PAT120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APG3PAT120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APG3PAT120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95869"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ddcap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_1ddecg3p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b3059"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CYSItex" fast="false" reversible="true" name="L cystine transport via diffusion extracellular to periplasm " metaid="R_CYSItex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CYSItex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYSItex"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-507"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97004"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cysi__L_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cysi__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_SERtpp" fast="false" reversible="false" name="L-serine export via facilitated transport" metaid="R_SERtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SERtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SERtpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ser__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1533"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_QUINDHyi" fast="false" reversible="false" name="Quinate dehydrogenase (NADP)" metaid="R_QUINDHyi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_QUINDHyi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/QUINDHyi"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_quin_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3dhq_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1692"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHCURR" fast="false" reversible="false" name="NADPH-dependent dihydrocurcumin reductase" metaid="R_DHCURR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHCURR"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHCURR"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhcur_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thcur_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1449"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_RHMND" fast="false" reversible="true" name="L-rhamnonate dehydratase" metaid="R_RHMND" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_RHMND"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RHMND"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_rhmn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_lkdr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2247"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_3HBZCT" fast="false" reversible="false" name="3-hydroxybenzoyl-CoA thioesterase" metaid="R_3HBZCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HBZCT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HBZCT"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hbzcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3hbz_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0597"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CXSAMS" fast="false" reversible="false" name="Carboxy-S-adenosyl-L-methionine synthase" metaid="R_CXSAMS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CXSAMS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CXSAMS"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pphn_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cxsam_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_phpyr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1870"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_2dglc_e" fast="false" reversible="false" name="2-Deoxy-D-glucose exchange" metaid="R_EX_2dglc_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_2dglc_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_2dglc_e"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2dglc_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_THRt2rpp" fast="false" reversible="false" name="L-threonine reversible transport via proton symport (periplasm)" metaid="R_THRt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_THRt2rpp"> <bqbiol:is 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rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-71"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104352"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28888"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28887"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28889"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28890"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/13941#1"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09714"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09246"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05307"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2796"/> <fbc:geneProductRef fbc:geneProduct="G_b3116"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHGLYH" fast="false" reversible="false" name="Dehydroglycine Hydratase" metaid="R_DHGLYH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHGLYH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHGLYH"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhgly_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glx_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_PNSPA" fast="false" reversible="false" name="Purine Nucleoside Phorphoramidase" metaid="R_PNSPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PNSPA"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PNSPA"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_gmplys_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nalme_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1103"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_4HTHRK" fast="false" reversible="false" name="4-Hydroxy-L-threonine kinase" metaid="R_4HTHRK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_4HTHRK"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4HTHRK"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6564"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95023"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28788"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28790"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28789"/> <rdf:li rdf:resource="http://identifiers.org/rhea/28787"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4hthr_c" stoichiometry="1" constant="true"/> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_phthr_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0003"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_ACOAD1f" fast="false" reversible="false" name="Acyl-CoA dehydrogenase (butanoyl-CoA)" metaid="R_ACOAD1f" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ACOAD1f"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACOAD1f"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.3"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.8.1"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.-"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.3.6"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.8.7"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01175"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95302"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-77319"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-77319"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-77319"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-77319"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-77319"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77319"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-77319"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-77319"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-77319"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-77319"/> <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-77319"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24006"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30733"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24007"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30734"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24005"/> <rdf:li rdf:resource="http://identifiers.org/rhea/24004"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30731"/> <rdf:li rdf:resource="http://identifiers.org/rhea/30732"/> <rdf:li rdf:resource="http://identifiers.org/sabiork/1412"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00872"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_b2coa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0221"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_AMPNTAT" fast="false" reversible="false" name="Aminoalkylphosphonate N-acetyltransferase" metaid="R_AMPNTAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_AMPNTAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMPNTAT"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ampnt_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acampnt_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4093"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_sq_e" fast="false" reversible="false" name="Sulphoquinovose exchange" metaid="R_EX_sq_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_sq_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_sq_e"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_sq_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_APH120" fast="false" reversible="false" name="Acylphosphatase (C12:0)" metaid="R_APH120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_APH120"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APH120"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95876"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_ddcap_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_ddca_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0968"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_URATEtpp" fast="false" reversible="false" name="Uric acid transporter" metaid="R_URATEtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_URATEtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URATEtpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_urate_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_urate_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2888"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_CS1tex" fast="false" reversible="true" name="Cesium transport via diffusion" metaid="R_CS1tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_CS1tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CS1tex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cs1_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_cs1_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_ADOCBLtonex" fast="false" reversible="false" name="Adenosylcobalimin transport via ton system (extermal)" metaid="R_ADOCBLtonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ADOCBLtonex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADOCBLtonex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95472"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08071"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_adocbl_e" stoichiometry="1" constant="true"/> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_adocbl_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1252"/> <fbc:geneProductRef fbc:geneProduct="G_b3005"/> <fbc:geneProductRef fbc:geneProduct="G_b3006"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3966"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_SQGH" fast="false" reversible="false" name="Sulfoquinovosidase" metaid="R_SQGH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SQGH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SQGH"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_sqg_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_glyc_c" stoichiometry="1" 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<speciesReference species="M_ura_p" stoichiometry="1" constant="true"/> </listOfProducts> </reaction> <reaction id="R_ASPtpp" fast="false" reversible="true" name="L-aspartate uptake via facillitated diffusion" metaid="R_ASPtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ASPtpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPtpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_asp__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef 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<reaction id="R_PETNT181pp" fast="false" reversible="false" name="Phosphoethanolamine transferase (c-C16:1)" metaid="R_PETNT181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PETNT181pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PETNT181pp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102500"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_lipa_p" stoichiometry="1" constant="true"/> <speciesReference species="M_pe181_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_12dgr181_p" stoichiometry="1" constant="true"/> 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reversible="false" name="2-Octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase (NADPHl)" metaid="R_OMMBLHXy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OMMBLHXy"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OMMBLHXy"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2ommbl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference 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</rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_fmn_p" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/> <speciesReference species="M_ribflv_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0383"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_4abzglu_e" fast="false" reversible="false" name="4-aminobenzoyl-glutamate exchange" metaid="R_EX_4abzglu_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_4abzglu_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_4abzglu_e"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4abzglu_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_rfamp_e" fast="false" reversible="false" name="Rifampin exchange" metaid="R_EX_rfamp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_rfamp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_rfamp_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104014"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35234"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35231"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35232"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35233"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_rfamp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_3HPADHi" fast="false" reversible="false" name="3-Hydroxypropanal Dehydrogenase" metaid="R_3HPADHi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_3HPADHi"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3HPADHi"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hppnl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3hpp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1300"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_4ABZGLUtex" fast="false" reversible="true" name="P-aminobenzoyl glutamate transport via diffusion (extracellular to periplasm)" metaid="R_4ABZGLUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_4ABZGLUtex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4ABZGLUtex"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4abzglu_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_4abzglu_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_QUIN2tex" fast="false" reversible="true" name="Quinate transport via diffusion (extracellular to periplasm)" metaid="R_QUIN2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_QUIN2tex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/QUIN2tex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103397"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35197"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35195"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35196"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35198"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12452"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_quin_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_quin_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b2215"/> <fbc:geneProductRef fbc:geneProduct="G_b1377"/> <fbc:geneProductRef fbc:geneProduct="G_b0241"/> <fbc:geneProductRef fbc:geneProduct="G_b0929"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_2HPTCOAT" fast="false" reversible="false" name="2-hydroxycyclohepta-1,4,6-triene-1-carboxyl-CoA thioesterase" metaid="R_2HPTCOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_2HPTCOAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/2HPTCOAT"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_2hptcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_2hptcl_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1400"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_metglcur_e" fast="false" reversible="false" name="1-O-methyl-Beta-D-glucuronate exchange" metaid="R_EX_metglcur_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_metglcur_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_metglcur_e"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_metglcur_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_EX_quin_e" fast="false" reversible="false" name="Quinate exchange" metaid="R_EX_quin_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_quin_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_quin_e"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103397"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35197"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35195"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35196"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35198"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12452"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_quin_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_MC6PH" fast="false" reversible="false" name="Monoacetylchitobiose-6-phosphate hydrolase" metaid="R_MC6PH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MC6PH"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MC6PH"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mchtbs6p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_acgam6p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gam_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1734"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_FORCT" fast="false" reversible="true" name="Formyl-CoA Transferase" metaid="R_FORCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FORCT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FORCT"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1382"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.8.3.16"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07290"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99616"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16546"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16545"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16547"/> <rdf:li rdf:resource="http://identifiers.org/rhea/16548"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05044"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_forcoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oxa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> <speciesReference species="M_oxalcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b2374"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_SLNTabcpp" fast="false" reversible="false" name="Selenite ABC transporter (periplasm)" metaid="R_SLNTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_SLNTabcpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SLNTabcpp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_slnt_p" 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"/> <speciesReference species="M_slnt_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2423"/> <fbc:geneProductRef fbc:geneProduct="G_b2422"/> <fbc:geneProductRef fbc:geneProduct="G_b2425"/> <fbc:geneProductRef fbc:geneProduct="G_b2424"/> </fbc:and> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2423"/> <fbc:geneProductRef fbc:geneProduct="G_b2422"/> <fbc:geneProductRef fbc:geneProduct="G_b3917"/> <fbc:geneProductRef fbc:geneProduct="G_b2424"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_VALt2rpp" fast="false" reversible="false" name="L-valine reversible transport via proton symport (periplasm)" metaid="R_VALt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_VALt2rpp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/VALt2rpp"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105188"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05669"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09707"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11190"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09374"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_val__L_p" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0401"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_DHPTDCs2" fast="false" reversible="false" name="4,5-dihydroxy-2,3-pentanedione cyclization (spontaneous)" metaid="R_DHPTDCs2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DHPTDCs2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHPTDCs2"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-10015"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97442"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35157"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35158"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35155"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35156"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_dhptd_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mdhdhf_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_VALt3pp" fast="false" reversible="false" name="L-valine transport out via proton antiport (periplasm)" metaid="R_VALt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_VALt3pp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/VALt3pp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_val__L_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b2683"/> <fbc:geneProductRef fbc:geneProduct="G_b2682"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4141"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MN2tipp" fast="false" reversible="false" name="Manganese transport in via permease (no H+)" metaid="R_MN2tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MN2tipp"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MN2tipp"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mn2_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_mn2_p" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1821"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_EX_3hpp_e" fast="false" reversible="false" name="3-Hydroxypropanoate exchange" metaid="R_EX_3hpp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_EX_3hpp_e"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_3hpp_e"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-465"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94904"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34951"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34953"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34952"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34954"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hpp_e" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PACCOAE" fast="false" reversible="false" name="Ring 1,2-phenylacetyl-CoA epoxidase (NADPH)" metaid="R_PACCOAE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PACCOAE"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PACCOAE"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102314"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_phaccoa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_rephaccoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1391"/> <fbc:geneProductRef fbc:geneProduct="G_b1388"/> <fbc:geneProductRef fbc:geneProduct="G_b1392"/> <fbc:geneProductRef fbc:geneProduct="G_b1389"/> <fbc:geneProductRef fbc:geneProduct="G_b1390"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_OXDHCOAT" fast="false" reversible="false" name="3-oxo-5,6-dehydrosuberyl-CoA thiolase" metaid="R_OXDHCOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OXDHCOAT"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OXDHCOAT"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.223"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102241"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34441"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34440"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34439"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34442"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3oxdhscoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_23dhacoa_c" stoichiometry="1" constant="true"/> <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1397"/> <fbc:geneProductRef fbc:geneProduct="G_b1394"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_HADPCOADH3" fast="false" reversible="true" name="3-hydroxyadipyl-CoA dehydrogenase (NAD+)" metaid="R_HADPCOADH3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_HADPCOADH3"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HADPCOADH3"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2044"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.35"/> <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.157"/> <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06941"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100555"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34851"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34852"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34853"/> <rdf:li rdf:resource="http://identifiers.org/rhea/34854"/> <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04750"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_3hadpcoa_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_oxadpcoa_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b1395"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_O16A4COLIPAabctex" fast="false" reversible="false" name="O16 antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" metaid="R_O16A4COLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_O16A4COLIPAabctex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16A4COLIPAabctex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102075"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o16a4colipa_p" 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_o16a4colipa_e" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b4262"/> <fbc:geneProductRef fbc:geneProduct="G_b4261"/> <fbc:geneProductRef fbc:geneProduct="G_b3199"/> <fbc:geneProductRef fbc:geneProduct="G_b3201"/> <fbc:geneProductRef fbc:geneProduct="G_b3200"/> <fbc:geneProductRef fbc:geneProduct="G_b0054"/> <fbc:geneProductRef fbc:geneProduct="G_b0641"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_COLIPAabctex" fast="false" reversible="false" name="Core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" metaid="R_COLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_COLIPAabctex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/COLIPAabctex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96845"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_colipa_p" 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_colipa_e" 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_b0641"/> <fbc:geneProductRef fbc:geneProduct="G_b3200"/> <fbc:geneProductRef fbc:geneProduct="G_b4262"/> <fbc:geneProductRef fbc:geneProduct="G_b3201"/> <fbc:geneProductRef fbc:geneProduct="G_b3199"/> <fbc:geneProductRef fbc:geneProduct="G_b0054"/> <fbc:geneProductRef fbc:geneProduct="G_b4261"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_ENLIPAabctex" fast="false" reversible="false" name="Phosphoethanolamine lipid A transport via ABC system (periplasm to extracellular)" metaid="R_ENLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_ENLIPAabctex"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ENLIPAabctex"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97922"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_enlipa_p" 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_enlipa_e" 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_b4262"/> <fbc:geneProductRef fbc:geneProduct="G_b4261"/> <fbc:geneProductRef fbc:geneProduct="G_b3199"/> <fbc:geneProductRef fbc:geneProduct="G_b3201"/> <fbc:geneProductRef fbc:geneProduct="G_b3200"/> <fbc:geneProductRef fbc:geneProduct="G_b0054"/> <fbc:geneProductRef fbc:geneProduct="G_b0641"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_DM_mththf_c" fast="false" reversible="false" name="Sink needed to allow (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran to leave system" metaid="R_DM_mththf_c" sboTerm="SBO:0000628" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_DM_mththf_c"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DM_mththf_c"/> <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-453"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR124017"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35148"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35147"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35149"/> <rdf:li rdf:resource="http://identifiers.org/rhea/35150"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_mththf_c" stoichiometry="1" constant="true"/> </listOfReactants> </reaction> <reaction id="R_PYROX" fast="false" reversible="false" name="Pyrimidine oxygenase" metaid="R_PYROX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_PYROX"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYROX"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103383"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> <speciesReference species="M_uracp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b1007"/> <fbc:geneProductRef fbc:geneProduct="G_b1012"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_BMOGDS1" fast="false" reversible="false" name="Bis-molybdopterin guanine dinucleotide synthase (single GDP)" metaid="R_BMOGDS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BMOGDS1"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BMOGDS1"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96315"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_bmoco_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_bmoco1gdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:geneProductRef fbc:geneProduct="G_b3857"/> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3857"/> <fbc:geneProductRef fbc:geneProduct="G_b3856"/> </fbc:and> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_MPTS" fast="false" reversible="false" name="Molybdopterin synthase" metaid="R_MPTS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MPTS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MPTS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143253"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_cpmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_moadcosh_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="5" constant="true"/> <speciesReference species="M_moadcoo_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mpt_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b0785"/> <fbc:geneProductRef fbc:geneProduct="G_b0784"/> </fbc:and> </fbc:geneProductAssociation> </reaction> <reaction id="R_MOCOS" fast="false" reversible="false" name="Molybdenum cofactor synthase" metaid="R_MOCOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_MOCOS"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOCOS"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138626"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_mobd_c" stoichiometry="1" constant="true"/> <speciesReference species="M_mptamp_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_moco_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b0827"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_BMOGDS2" fast="false" reversible="false" name="Bis-molybdopterin guanine dinucleotide synthase" metaid="R_BMOGDS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_BMOGDS2"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BMOGDS2"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96316"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_bmoco1gdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_bmocogdp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> <fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3857"/> <fbc:geneProductRef fbc:geneProduct="G_b3856"/> </fbc:and> <fbc:geneProductRef fbc:geneProduct="G_b3857"/> </fbc:or> </fbc:geneProductAssociation> </reaction> <reaction id="R_FESD2s" fast="false" reversible="false" name="Iron-sulfur cluster damage (nitrous oxide, spontaneous)" metaid="R_FESD2s" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_FESD2s"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FESD2s"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99586"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_4fe4s_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> <speciesReference species="M_no_c" stoichiometry="2" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3fe4s_c" stoichiometry="2" constant="true"/> <speciesReference species="M_fe3_c" stoichiometry="2" constant="true"/> <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> <speciesReference species="M_n2o_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_s0001"/> </fbc:geneProductAssociation> </reaction> <reaction id="R_OCTNLL" fast="false" reversible="false" name="Octanoate non-lipoylated apo domain ligase" metaid="R_OCTNLL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="#R_OCTNLL"> <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OCTNLL"/> <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102155"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </sbml:annotation> <listOfReactants> <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octa_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octapb_c" stoichiometry="1" constant="true"/> <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_b4386"/> </fbc:geneProductAssociation> </reaction> </listOfReactions> </model> </sbml>