Mercurial > repos > tduigou > straindesign_simulate_deletion
diff test-data/butanol.xml @ 0:14747c55330c draft
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
| author | tduigou |
|---|---|
| date | Mon, 15 May 2023 14:05:52 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/butanol.xml Mon May 15 14:05:52 2023 +0000 @@ -0,0 +1,496 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false"> + <model metaid="meta_butanol" id="butanol" fbc:strict="true"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit kind="mole" exponent="1" scale="-3" multiplier="1"/> + <unit kind="gram" exponent="-1" scale="0" multiplier="1"/> + <unit kind="second" exponent="-1" scale="0" multiplier="3600"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <fbc:listOfObjectives fbc:activeObjective="obj"> + <fbc:objective fbc:id="obj" fbc:type="maximize"> + <fbc:listOfFluxObjectives> + <fbc:fluxObjective fbc:reaction="R_EX_1btol_e" fbc:coefficient="0.5"/> + </fbc:listOfFluxObjectives> + </fbc:objective> + </fbc:listOfObjectives> + <listOfCompartments> + <compartment id="c" name="cytosol" constant="true"/> + <compartment id="p" name="periplasm" constant="true"/> + <compartment id="e" name="extracellular space" constant="true"/> + </listOfCompartments> + <listOfSpecies> + <species metaid="meta_M_co2_e" sboTerm="SBO:0000247" id="M_co2_e" name="CO2 CO2" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="CO2"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_co2_e"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/co2"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:CARBON-DIOXIDE"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:23011"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:3283"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:48829"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:16526"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13283"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13285"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13284"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13282"/> + <rdf:li rdf:resource="https://identifiers.org/envipath/650babc9-9d68-4b73-9332-11972ca26f7b/compound/2ec3da94-5f50-4525-81b1-5607c5c7a3d3"/> + <rdf:li rdf:resource="https://identifiers.org/envipath/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05f60af4-0a3f-4ead-9a29-33bb0f123379"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB01967"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/CURLTUGMZLYLDI-UHFFFAOYSA-N"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00011"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.drug/D00004"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM13"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/29376"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/5668565"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/189480"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1132345"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/113528"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1237009"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/159751"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/389536"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/159942"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/1266"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00011"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_glc__D_e" sboTerm="SBO:0000247" id="M_glc__D_e" name="D-Glucose" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C6H12O6"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_glc__D_e"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/glc__D"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:Glucopyranose"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:12965"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:20999"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:4167"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:17634"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB00122"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB06564"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/WQZGKKKJIJFFOK-GASJEMHNSA-N"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00031"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.drug/D00009"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM41"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/1406"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/1407"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd26821"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00027"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_b2coa_c" sboTerm="SBO:0000247" id="M_b2coa_c" name="Crotonoyl-CoA" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-4" fbc:chemicalFormula="C25H36N7O17P3S"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_b2coa_c"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/b2coa"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:CROTONYL-COA"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:3928"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:11531"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:15473"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:36926"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:57332"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:23408"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:14031"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:14032"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13921"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:41612"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:58669"/> + <rdf:li rdf:resource="https://identifiers.org/envipath/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c0e5f008-6d8b-4b94-a265-03d19ff197f4"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB62466"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB02009"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB59627"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/KFWWCMJSYSSPSK-PAXLJYGASA-J"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00877"/> + <rdf:li rdf:resource="https://identifiers.org/lipidmaps/LMFA07050307"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM214"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/71045"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/77313"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/2174"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00650"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_btcoa_c" sboTerm="SBO:0000247" id="M_btcoa_c" name="Gamma-butyrobetainyl-CoA" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3" fbc:chemicalFormula="C28H46N8O17P3S"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_btcoa_c"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/btcoa"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:GAMMA-BUTYROBETAINYL-COA"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:61513"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:61517"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/QAMRRBGWSPTAEJ-SVHODSNWSA-K"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C20749"/> + <rdf:li rdf:resource="https://identifiers.org/lipidmaps/LMFA07050321"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM5762"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd15412"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_btal_c" sboTerm="SBO:0000247" id="M_btal_c" name="Butanal C4H8O" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C4H8O"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_btal_c"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/btal"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:BUTANAL"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:22938"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:3233"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:15743"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13923"/> + <rdf:li rdf:resource="https://identifiers.org/envipath/650babc9-9d68-4b73-9332-11972ca26f7b/compound/242f8a4e-2a91-4c5f-a129-d044d115b969"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB03543"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/ZTQSAGDEMFDKMZ-UHFFFAOYSA-N"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C01412"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM1017"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/2281"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd01011"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_nad_c" sboTerm="SBO:0000247" id="M_nad_c" name="Deamino-NAD+" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2" fbc:chemicalFormula="C21H24N6O15P2"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_nad_c"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/nad"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:DEAMIDO-NAD"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:14104"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:58437"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:14103"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:4340"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:14105"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:18304"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:23567"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB01179"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/SENPVEZBRZQVST-HISDBWNOSA-L"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00857"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM309"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/8938090"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/200499"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/197256"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/1349"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00638"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_nadh_c" sboTerm="SBO:0000247" id="M_nadh_c" name="Nicotinamide adenine dinucleotide - reduced" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2" fbc:chemicalFormula="C21H27N7O14P2"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_nadh_c"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/nadh"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:NADH"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13395"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:21902"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:7423"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:44216"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:57945"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:16908"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13396"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB01487"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/BOPGDPNILDQYTO-NNYOXOHSSA-L"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00004"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM10"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/192305"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/73473"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/29362"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/194697"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/38"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00004"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_h_c" sboTerm="SBO:0000247" id="M_h_c" name="H+" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="H"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_h_c"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/h"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:PROTON"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:5584"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13357"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:15378"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:10744"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB59597"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/GPRLSGONYQIRFK-UHFFFAOYSA-N"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00080"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM1"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/2000349"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425978"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/74722"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/428040"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/427899"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/428548"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/156540"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/70106"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425969"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1132304"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/5668577"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1470067"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/163953"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/193465"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/113529"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/351626"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425999"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/194688"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/374900"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/2872447"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/372511"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/39"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00067"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_h_e" sboTerm="SBO:0000247" id="M_h_e" name="H+" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="H"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_h_e"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/h"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:PROTON"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:5584"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13357"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:15378"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:10744"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB59597"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/GPRLSGONYQIRFK-UHFFFAOYSA-N"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00080"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM1"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/2000349"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425978"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/74722"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/428040"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/427899"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/428548"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/156540"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/70106"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425969"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1132304"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/5668577"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1470067"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/163953"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/193465"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/113529"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/351626"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425999"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/194688"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/374900"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/2872447"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/372511"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/39"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00067"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_h_p" sboTerm="SBO:0000247" id="M_h_p" name="H+" compartment="p" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="H"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_h_p"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/h"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:PROTON"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:5584"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13357"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:15378"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:10744"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB59597"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/GPRLSGONYQIRFK-UHFFFAOYSA-N"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00080"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM1"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/2000349"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425978"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/74722"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/428040"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/427899"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/428548"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/156540"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/70106"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425969"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1132304"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/5668577"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1470067"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/163953"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/193465"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/113529"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/351626"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425999"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/194688"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/374900"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/2872447"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/372511"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/39"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00067"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_1btol_c" id="M_1btol_c" name="butan1ol" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C4H10O"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_1btol_c"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:22936"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_1btol_p" id="M_1btol_p" name="butan1ol" compartment="p" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C4H10O"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_1btol_p"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:22936"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_1btol_e" id="M_1btol_e" name="butan1ol" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C4H10O"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_1btol_e"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:22936"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-1000"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="1000"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0"/> + </listOfParameters> + <listOfReactions> + <reaction metaid="meta_R_EX_1btol_e" sboTerm="SBO:0000627" id="R_EX_1btol_e" name="butan1ol exchange" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_1btol_e" stoichiometry="1" constant="true"/> + </listOfReactants> + </reaction> + <reaction id="R_ButCoaDeh" name="Butyryl-CoA dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_b2coa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButanalDeh" name="Butanal dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButanolDeh" name="Butanol dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1btol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButOlTrP" name="1-Butanol transporter (periplasm)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_1btol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1btol_p" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButOlTrE" name="1-Butanol transporter (extracellular)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_1btol_p" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1btol_e" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + </listOfReactions> + <groups:listOfGroups> + <groups:group metaid="meta_rp_pathway" groups:id="rp_pathway" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="meta_rp_pathway"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="R_ButCoaDeh"/> + <groups:member groups:idRef="R_ButanalDeh"/> + <groups:member groups:idRef="R_ButanolDeh"/> + <groups:member groups:idRef="R_ButOlTrP"/> + <groups:member groups:idRef="R_ButOlTrE"/> + <groups:member groups:idRef="R_EX_1btol_e"/> + </groups:listOfMembers> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>