Mercurial > repos > tduigou > get_sbml_model

comparison test-data/e_coli_core.xml @ 6:9b5947d48192 draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 87a863d4074543870caef1116b8e9be58005dcdd
author tduigou
date Mon, 28 Aug 2023 14:24:48 +0000
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5:80c32f0cb716 6:9b5947d48192
1 <?xml version='1.0' encoding='UTF-8'?>
2 <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">
3 <model fbc:strict="true" id="e_coli_core">
4 <listOfUnitDefinitions>
5 <unitDefinition id="mmol_per_gDW_per_hr">
6 <listOfUnits>
7 <unit kind="mole" scale="-3" multiplier="1" exponent="1"/>
8 <unit kind="gram" scale="0" multiplier="1" exponent="-1"/>
9 <unit kind="second" scale="0" multiplier="3600" exponent="-1"/>
10 </listOfUnits>
11 </unitDefinition>
12 </listOfUnitDefinitions>
13 <fbc:listOfObjectives fbc:activeObjective="obj">
14 <fbc:objective fbc:id="obj" fbc:type="maximize">
15 <fbc:listOfFluxObjectives>
16 <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ecoli_core_w_GAM" fbc:coefficient="1"/>
17 </fbc:listOfFluxObjectives>
18 </fbc:objective>
19 </fbc:listOfObjectives>
20 <listOfParameters>
21 <parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
22 <parameter value="1000" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
23 <parameter value="0" id="cobra_0_bound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
24 <parameter id="R_ATPM_lower_bound" value="8.39" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>
25 <parameter id="R_EX_glc__D_e_lower_bound" value="-10" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>
26 </listOfParameters>
27 <listOfCompartments>
28 <compartment id="e" name="extracellular space" constant="true"/>
29 <compartment id="c" name="cytosol" constant="true"/>
30 </listOfCompartments>
31 <listOfSpecies>
32 <species id="M_glc__D_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="D-Glucose" metaid="M_glc__D_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C6H12O6">
33 <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
34 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
35 <rdf:Description rdf:about="#M_glc__D_e">
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37 <rdf:Bag>
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39 <rdf:li rdf:resource="http://identifiers.org/biocyc/META:Glucopyranose"/>
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54 </rdf:Bag>
55 </bqbiol:is>
56 </rdf:Description>
57 </rdf:RDF>
58 </sbml:annotation>
59 </species>
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6217 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.2.15"/>
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6225 <rdf:li rdf:resource="http://identifiers.org/sabiork/71"/>
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6234 <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
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6238 <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
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6243 <fbc:geneProductRef fbc:geneProduct="G_b2296"/>
6244 <fbc:geneProductRef fbc:geneProduct="G_b1849"/>
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6259 <rdf:li rdf:resource="http://identifiers.org/rhea/23072"/>
6260 <rdf:li rdf:resource="http://identifiers.org/rhea/23075"/>
6261 <rdf:li rdf:resource="http://identifiers.org/rhea/23074"/>
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6276 <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/>
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6280 <fbc:geneProductRef fbc:geneProduct="G_b3956"/>
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6292 <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01325"/>
6293 <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95386"/>
6294 <rdf:li rdf:resource="http://identifiers.org/rhea/10230"/>
6295 <rdf:li rdf:resource="http://identifiers.org/rhea/10229"/>
6296 <rdf:li rdf:resource="http://identifiers.org/rhea/10231"/>
6297 <rdf:li rdf:resource="http://identifiers.org/rhea/10228"/>
6298 <rdf:li rdf:resource="http://identifiers.org/sabiork/268"/>
6299 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00974"/>
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6309 <speciesReference species="M_acon_C_c" stoichiometry="1" constant="true"/>
6310 <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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6313 <fbc:or>
6314 <fbc:geneProductRef fbc:geneProduct="G_b0118"/>
6315 <fbc:geneProductRef fbc:geneProduct="G_b1276"/>
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6327 <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01900"/>
6328 <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95387"/>
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6330 <rdf:li rdf:resource="http://identifiers.org/rhea/22144"/>
6331 <rdf:li rdf:resource="http://identifiers.org/rhea/22146"/>
6332 <rdf:li rdf:resource="http://identifiers.org/rhea/22147"/>
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6349 <fbc:geneProductRef fbc:geneProduct="G_b1276"/>
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6362 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.34"/>
6363 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.20"/>
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6365 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.8"/>
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6369 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.40"/>
6370 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.9"/>
6371 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.23"/>
6372 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.22"/>
6373 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.54"/>
6374 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.1"/>
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6378 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.50"/>
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6381 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.4"/>
6382 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.35"/>
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6393 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.51"/>
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6416 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.47"/>
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6418 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.36"/>
6419 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.21"/>
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6421 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.18"/>
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6426 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.4.7"/>
6427 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.46"/>
6428 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.41"/>
6429 <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.49"/>
6430 <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00086"/>
6431 <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96131"/>
6432 <rdf:li rdf:resource="http://identifiers.org/rhea/13066"/>
6433 <rdf:li rdf:resource="http://identifiers.org/rhea/13065"/>
6434 <rdf:li rdf:resource="http://identifiers.org/rhea/13068"/>
6435 <rdf:li rdf:resource="http://identifiers.org/rhea/13067"/>
6436 <rdf:li rdf:resource="http://identifiers.org/sabiork/75"/>
6437 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11300"/>
6438 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09694"/>
6439 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00062"/>
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6451 <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
6452 <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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6467 <rdf:li rdf:resource="http://identifiers.org/rhea/18618"/>
6468 <rdf:li rdf:resource="http://identifiers.org/rhea/18617"/>
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6471 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00247"/>
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6483 <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
6484 <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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6487 <fbc:geneProductRef fbc:geneProduct="G_b3403"/>
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6510 <listOfProducts>
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6540 <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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7230 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09772"/>
7231 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08350"/>
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7304 <rdf:li rdf:resource="http://identifiers.org/rhea/10167"/>
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7317 <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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7320 <fbc:geneProductRef fbc:geneProduct="G_b2779"/>
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7400 <fbc:geneProductRef fbc:geneProduct="G_b0723"/>
7401 <fbc:geneProductRef fbc:geneProduct="G_b0724"/>
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7452 <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
7453 <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/>
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7458 <fbc:geneProductRef fbc:geneProduct="G_b0729"/>
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7516 <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
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7520 <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
7521 <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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8665 <fbc:geneProductRef fbc:geneProduct="G_b1611"/>
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9415 <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101037"/>
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9429 <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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9434 <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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9439 <fbc:geneProductRef fbc:geneProduct="G_b1380"/>
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9467 <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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9591 <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/>
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9627 <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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9630 <fbc:geneProductRef fbc:geneProduct="G_b1479"/>
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9665 <fbc:geneProductRef fbc:geneProduct="G_b2463"/>
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9698 <fbc:geneProductRef fbc:geneProduct="G_b2279"/>
9699 <fbc:geneProductRef fbc:geneProduct="G_b2280"/>
9700 <fbc:geneProductRef fbc:geneProduct="G_b2281"/>
9701 <fbc:geneProductRef fbc:geneProduct="G_b2282"/>
9702 <fbc:geneProductRef fbc:geneProduct="G_b2283"/>
9703 <fbc:geneProductRef fbc:geneProduct="G_b2284"/>
9704 <fbc:geneProductRef fbc:geneProduct="G_b2285"/>
9705 <fbc:geneProductRef fbc:geneProduct="G_b2286"/>
9706 <fbc:geneProductRef fbc:geneProduct="G_b2287"/>
9707 <fbc:geneProductRef fbc:geneProduct="G_b2288"/>
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9725 <rdf:li rdf:resource="http://identifiers.org/rhea/11695"/>
9726 <rdf:li rdf:resource="http://identifiers.org/rhea/11694"/>
9727 <rdf:li rdf:resource="http://identifiers.org/rhea/11693"/>
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9736 <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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9747 <fbc:geneProductRef fbc:geneProduct="G_b1603"/>
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9775 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-444416"/>
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9779 <rdf:li rdf:resource="http://identifiers.org/rhea/28747"/>
9780 <rdf:li rdf:resource="http://identifiers.org/sabiork/11683"/>
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9783 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05466"/>
9784 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08987"/>
9785 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08986"/>
9786 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09736"/>
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9814 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09641"/>
9815 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/>
9816 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/>
9817 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09032"/>
9818 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09734"/>
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9825 <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/>
9826 </listOfReactants>
9827 <listOfProducts>
9828 <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
9829 </listOfProducts>
9830 <fbc:geneProductAssociation>
9831 <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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9834 <reaction id="R_PDH" fast="false" reversible="false" name="Pyruvate dehydrogenase" metaid="R_PDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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9843 <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.4"/>
9844 <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.51"/>
9845 <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.4.1"/>
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9850 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-71397"/>
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9854 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71397"/>
9855 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-71397"/>
9856 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-71397"/>
9857 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-71397"/>
9858 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-71397"/>
9859 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-71397"/>
9860 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-71397"/>
9861 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71397"/>
9862 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-71397"/>
9863 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-71397"/>
9864 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-71397"/>
9865 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-71397"/>
9866 <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-71397"/>
9867 <rdf:li rdf:resource="http://identifiers.org/rhea/28043"/>
9868 <rdf:li rdf:resource="http://identifiers.org/rhea/28045"/>
9869 <rdf:li rdf:resource="http://identifiers.org/rhea/28044"/>
9870 <rdf:li rdf:resource="http://identifiers.org/rhea/28042"/>
9871 <rdf:li rdf:resource="http://identifiers.org/sabiork/523"/>
9872 <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00154"/>
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9880 <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
9881 <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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9884 <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
9885 <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
9886 <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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9890 <fbc:geneProductRef fbc:geneProduct="G_b0114"/>
9891 <fbc:geneProductRef fbc:geneProduct="G_b0115"/>
9892 <fbc:geneProductRef fbc:geneProduct="G_b0116"/>
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9895 </reaction>
9896 </listOfReactions>
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