Mercurial > repos > tduigou > straindesign_simulate_deletion
view test-data/butanol.xml @ 2:6b3e0996185f draft default tip
planemo upload for repository https://github.com/brsynth/straindesign commit 628dbf7f95517f13542059ac4a9de58da440f1c6
| author | tduigou |
|---|---|
| date | Tue, 23 Jul 2024 19:26:22 +0000 |
| parents | 14747c55330c |
| children |
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<?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" 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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>