Mercurial > repos > tduigou > get_sbml_model
changeset 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 |
| parents | 8dc4d3964ab5 |
| children | 6a2871e89352 |
| files | get_infos.py get_sbml_model.xml model.sbml |
| diffstat | 3 files changed, 169932 insertions(+), 43 deletions(-) [+] |
line wrap: on
line diff
--- a/get_infos.py Mon Sep 04 14:19:43 2023 +0000 +++ b/get_infos.py Fri Sep 29 09:03:09 2023 +0000 @@ -5,7 +5,86 @@ from requests import get as r_get -def entry_point(): +def get_biomass_rxn(sbml_doc): + ''' + Returns the biomass reaction of the model + + Parameters + ---------- + sbml_doc: libsbml.SBMLDocument + SBML model + + Returns + ------- + biomass_rxn: libsbml.Reaction + Biomass reaction + ''' + reactions = sbml_doc.getModel().getListOfReactions() + # Search for 'biomass' keyword in reaction name + for rxn in reactions: + if 'biomass' in rxn.getName().lower(): + return rxn + # Search for 'biomass' keyword in products + # AND not in reactants + for rxn in reactions: + in_reactants = False + for reac in rxn.getListOfReactants(): + if 'biomass' in reac.getSpecies().lower(): + in_reactants = True + break + if not in_reactants: + for prod in rxn.getListOfProducts(): + if 'biomass' in prod.getSpecies().lower(): + return rxn + return None + + +def get_taxon_id(hostid): + ''' + Returns the taxonomy ID of the host organism + + Parameters + ---------- + hostid: str + Extended name of the host organism + + Returns + ------- + taxid: str + Taxonomy ID of the host organism + ''' + taxid = get_taxon_id(hostid) + hostname = '' + # Extended Name + server = 'http://bigg.ucsd.edu/api/v2/models/' + ext = hostid + r = r_get(server+ext, headers={ "Content-Type" : "application/json"}) + if not r.ok: + print(f"Warning: unable to retrieve host name for id {hostid}") + else: + try: + hostname = r.json()["organism"] + except KeyError: + print(f"Warning: unable to retrieve host name for id {hostid}") + if not hostname: + taxid = '' + else: + # TAXON ID + server = 'https://rest.ensembl.org' + ext = f'/taxonomy/id/{hostname}?' + r = r_get(server+ext, headers={ "Content-Type" : "application/json"}) + if not r.ok: + print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}") + else: + try: + taxid = r.json()["id"] + except KeyError: + print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}") + taxid = '' + return taxid + + +def args(): parser = ArgumentParser('Returns cell informations') parser.add_argument( 'infile', @@ -29,6 +108,11 @@ help='Path to store biomass reaction ID' ) parser.add_argument( + '--biomass-id', + type=str, + help='ID of biomass reaction' + ) + parser.add_argument( '--hostid', type=str, help='Extended name of the host organism' @@ -39,63 +123,57 @@ help='Path to store host taxonomy ID' ) params = parser.parse_args() + return params + + +def entry_point(): + + params = args() sbml_doc = readSBMLFromFile(params.infile) + compartments = sbml_doc.getModel().getListOfCompartments() + comp_str = '' + for comp in compartments: + comp_str += f'{comp.getId()}\t{comp.getName()}\n' if params.comp: - compartments = sbml_doc.getModel().getListOfCompartments() with open(params.comp, 'w') as f: f.write('#ID\tNAME\n') - for comp in compartments: - f.write(f'{comp.getId()}\t{comp.getName()}\n') + f.write(comp_str) + else: + print('Compartments:') + for comp in compartments: + print(f'{comp.getId()}\t{comp.getName()}'.replace('\n', ' | ')) + if params.biomass_id: + biomass_rxn = sbml_doc.getModel().getReaction(params.biomass_id) + else: + biomass_rxn = get_biomass_rxn(sbml_doc) + if not biomass_rxn: + print('Warning: unable to retrieve biomass reaction') + biomass_id = '' + else: + biomass_id = biomass_rxn.getId() if params.biomass: - reactions = sbml_doc.getModel().getListOfReactions() with open(params.biomass, 'w') as f: f.write('#ID\n') - for rxn in reactions: - if 'biomass' in rxn.getId().lower(): - f.write(f'{rxn.getId()}\n') + f.write(f'{biomass_id}\n') + else: + print(f'Biomass reaction ID: {biomass_id}') + + # Model from BiGG + if params.bigg: + taxid = get_taxon_id(params.hostid) + # Model from user + else: + taxid = params.hostid if params.taxid: - hostname = '' - - # Model from BiGG - if params.bigg: - # Extended Name - server = 'http://bigg.ucsd.edu/api/v2/models/' - ext = params.hostid - r = r_get(server+ext, headers={ "Content-Type" : "application/json"}) - if not r.ok: - print(f"Warning: unable to retrieve host name for id {params.hostid}") - else: - try: - hostname = r.json()["organism"] - except KeyError: - print(f"Warning: unable to retrieve host name for id {params.hostid}") - if not hostname: - taxid = '' - else: - # TAXON ID - server = 'https://rest.ensembl.org' - ext = f'/taxonomy/id/{hostname}?' - r = r_get(server+ext, headers={ "Content-Type" : "application/json"}) - if not r.ok: - print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}") - else: - try: - taxid = r.json()["id"] - except KeyError: - print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}") - taxid = '' - - # Model from user - else: - taxid = params.hostid - with open(params.taxid, 'w') as f: f.write('#ID\n') f.write(f'{taxid}\n') + else: + print(f'Taxonomy ID: {taxid}') if __name__ == "__main__":
--- a/get_sbml_model.xml Mon Sep 04 14:19:43 2023 +0000 +++ b/get_sbml_model.xml Fri Sep 29 09:03:09 2023 +0000 @@ -20,6 +20,7 @@ python '$__tool_directory__/'get_infos.py #if str($cond_src.from_src) == 'from_bigg' '$model' + --bigg --taxid '$taxid' #else '${cond_src.input_file}'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/model.sbml Fri Sep 29 09:03:09 2023 +0000 @@ -0,0 +1,169810 @@ +<?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 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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 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<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 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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 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rdf:resource="http://identifiers.org/bigg.reaction/RHCCE"/> + <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RIBOSYLHOMOCYSTEINASE-RXN"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/4.4.1.21"/> + <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01291"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104026"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/17754"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/17753"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/17756"/> + <rdf:li rdf:resource="http://identifiers.org/rhea/17755"/> + <rdf:li rdf:resource="http://identifiers.org/sabiork/6873"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn14169"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05958"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </sbml:annotation> + <listOfReactants> + <speciesReference species="M_rhcys_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_dhptd_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_b2687"/> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_EX_dha_e" fast="false" reversible="false" name="Dihydroxyacetone exchange" metaid="R_EX_dha_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_dha_e"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dha_e"/> + <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-559"/> + <rdf:li 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</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 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+ <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 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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 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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" 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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" 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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 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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"/> + 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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/"> + 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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" 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<fbc:geneProductRef fbc:geneProduct="G_b3417"/> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_EX_lcts_e" fast="false" reversible="false" name="Lactose exchange" metaid="R_EX_lcts_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_lcts_e"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_lcts_e"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101027"/> + <rdf:li 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> + 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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 rdf:resource="http://identifiers.org/bigg.reaction/EX_cbl1_e"/> + <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1565"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR123114"/> + <rdf:li 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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" 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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 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</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 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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"/> + 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xmlns:sbml="http://www.sbml.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" 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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> + 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</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 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<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 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<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"/> + 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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 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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 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</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> + 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xmlns:sbml="http://www.sbml.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"/> 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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 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xmlns:sbml="http://www.sbml.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"/> + 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xmlns:sbml="http://www.sbml.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"/> + 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</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 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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> + 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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"/> + 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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" 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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" 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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 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</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 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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"/> + 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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 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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 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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 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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"/> + 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+ <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 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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" 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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 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+ <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> + 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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"> + 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<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 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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)" 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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)" 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<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" 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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"/> + 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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" 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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 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<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" 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xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3PEPTtex"/> + <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> + <listOfProducts> + <speciesReference species="M_LalaDgluMdap_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_12ppd__S_e" fast="false" reversible="false" 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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" 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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 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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"> 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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> + 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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" 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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"/> 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+ </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" 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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" 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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"/> + 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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_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 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xmlns:sbml="http://www.sbml.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"/> + 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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 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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" 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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 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<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 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xmlns:sbml="http://www.sbml.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"/> + 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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) 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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" 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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" 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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 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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 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xmlns:sbml="http://www.sbml.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 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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" 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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) 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+ </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> 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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" 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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"/> + 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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 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<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"/> + 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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> 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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 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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 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<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"/> + 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<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" 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</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" 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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> + 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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" 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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> + 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<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> + 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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_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"/> + 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</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 rdf:about="#R_ETHAt2pp"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ETHAt2pp"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97975"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08423"/> + <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05551"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </sbml:annotation> + <listOfReactants> + <speciesReference species="M_etha_p" 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+ </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 rdf:resource="http://identifiers.org/bigg.reaction/OGMEACPS"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102161"/> + </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_malcoame_c" 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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 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</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" 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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"/> + 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</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 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xmlns:sbml="http://www.sbml.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" 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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"/> + 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</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 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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"/> + 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<sbml:annotation xmlns:sbml="http://www.sbml.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> 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<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 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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_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 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<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" 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+ <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 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</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> + 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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 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<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" 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xmlns:sbml="http://www.sbml.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> + 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</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> + 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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> + 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</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"/> 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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"> + <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> + <rdf:Description rdf:about="#R_TEO2M"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TEO2M"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </sbml:annotation> + <listOfReactants> + <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_teo2_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_mteo2_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_b1430"/> + </fbc:geneProductAssociation> + </reaction> + <reaction id="R_PACOAT" fast="false" reversible="false" name="Phenylacetyl-CoA thioesterase" metaid="R_PACOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> + <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> + <rdf:Description rdf:about="#R_PACOAT"> + <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PACOAT"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </sbml:annotation> + <listOfReactants> + <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_phaccoa_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_pac_c" stoichiometry="1" constant="true"/> + </listOfProducts> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="G_b1396"/> + </fbc:geneProductAssociation> + </reaction> + <reaction 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</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" 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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 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<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" 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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>