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view test-data/lycopene_CrtEBI_from_selenzy.xml @ 0:ae16d7ce27d1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
author tduigou
date Tue, 28 Mar 2023 12:08:32 +0000
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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">
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                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]&gt;&gt;[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H].O=P(O)(O)OP(=O)(O)O.O=P(O)(O)OP(=O)(O)O"/>
                <brsynth:rp2_transfo_id value="TRS_0_1_9"/>
                <brsynth:rule_ids>
                  <brsynth:RR-02-b25156a335e3e30f-16-F/>
                </brsynth:rule_ids>
                <brsynth:tmpl_rxn_ids>
                  <brsynth:MNXR111250/>
                  <brsynth:MNXR111499/>
                  <brsynth:MNXR113543/>
                  <brsynth:MNXR118024/>
                  <brsynth:MNXR139549/>
                </brsynth:tmpl_rxn_ids>
                <brsynth:rule_score value="0.5683242688496836"/>
                <brsynth:idx_in_path value="2"/>
                <brsynth:selenzy_P21683>
                  <brsynth:score value="91.9"/>
                  <brsynth:target_ID value="553"/>
                </brsynth:selenzy_P21683>
                <brsynth:selenzy_P21684>
                  <brsynth:score value="74.885"/>
                  <brsynth:target_ID value="553"/>
                </brsynth:selenzy_P21684>
                <brsynth:fba_biomass>
                  <brsynth:value value="0.0"/>
                  <brsynth:units value="gDW / gDW / hour"/>
                </brsynth:fba_biomass>
                <brsynth:fba_fraction>
                  <brsynth:value value="0.5493228602383673"/>
                  <brsynth:units value="milimole / gDW / hour"/>
                </brsynth:fba_fraction>
                <brsynth:thermo_dG0_prime>
                  <brsynth:value value="-119.13360567395966"/>
                  <brsynth:error value="11.000567449695142"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG0_prime>
                <brsynth:thermo_dGm_prime>
                  <brsynth:value value="-153.36328074340173"/>
                  <brsynth:error value="11.000567449695142"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dGm_prime>
                <brsynth:thermo_dG_prime>
                  <brsynth:value value="-119.13360567395966"/>
                  <brsynth:error value="11.000567449695142"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG_prime>
                <brsynth:thermo_dG>
                  <brsynth:value value="-1501.0650763644926"/>
                  <brsynth:error value="11.000567449695142"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
          <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
        </listOfProducts>
      </reaction>
      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
            <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21683"/>
                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21685"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.31"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
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                <brsynth:rp2_transfo_id value="TRS_0_0_1"/>
                <brsynth:rule_ids>
                  <brsynth:RR-02-bdf7d8715e2e4d93-16-F/>
                </brsynth:rule_ids>
                <brsynth:tmpl_rxn_ids>
                  <brsynth:MNXR113128/>
                </brsynth:tmpl_rxn_ids>
                <brsynth:rule_score value="0.7486085128675456"/>
                <brsynth:idx_in_path value="3"/>
                <brsynth:selenzy_P21685>
                  <brsynth:score value="81.82"/>
                  <brsynth:target_ID value="553"/>
                </brsynth:selenzy_P21685>
                <brsynth:selenzy_P21683>
                  <brsynth:score value="63.183"/>
                  <brsynth:target_ID value="553"/>
                </brsynth:selenzy_P21683>
                <brsynth:fba_biomass>
                  <brsynth:value value="0.0"/>
                  <brsynth:units value="gDW / gDW / hour"/>
                </brsynth:fba_biomass>
                <brsynth:fba_fraction>
                  <brsynth:value value="0.5493228602383673"/>
                  <brsynth:units value="milimole / gDW / hour"/>
                </brsynth:fba_fraction>
                <brsynth:thermo_dG0_prime>
                  <brsynth:value value="1191.8613577748536"/>
                  <brsynth:error value="44.93683979991009"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG0_prime>
                <brsynth:thermo_dGm_prime>
                  <brsynth:value value="1191.8613577748536"/>
                  <brsynth:error value="44.93683979991009"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dGm_prime>
                <brsynth:thermo_dG_prime>
                  <brsynth:value value="1191.8613577748536"/>
                  <brsynth:error value="44.93683979991009"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG_prime>
                <brsynth:thermo_dG>
                  <brsynth:value value="329.6284950676197"/>
                  <brsynth:error value="44.93683979991009"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
          <speciesReference species="MNXM8975" stoichiometry="4" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="MNXM24" stoichiometry="4" constant="true"/>
          <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
        </listOfProducts>
      </reaction>
    </listOfReactions>
    <groups:listOfGroups>
      <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" 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="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                <brsynth:fba_biomass>
                  <brsynth:value value="0.7638744755010175"/>
                  <brsynth:units value="gDW / gDW / hour"/>
                </brsynth:fba_biomass>
                <brsynth:fba_fraction>
                  <brsynth:value value="0.5493228602383673"/>
                  <brsynth:units value="milimole / gDW / hour"/>
                </brsynth:fba_fraction>
                <brsynth:thermo_dG0_prime>
                  <brsynth:value value="-471.6056149411652"/>
                  <brsynth:error value="47.748437579463356"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG0_prime>
                <brsynth:thermo_dGm_prime>
                  <brsynth:value value="-522.9501275453283"/>
                  <brsynth:error value="47.748437579463356"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dGm_prime>
                <brsynth:thermo_dG_prime>
                  <brsynth:value value="-471.6056149411652"/>
                  <brsynth:error value="47.748437579463356"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG_prime>
                <brsynth:thermo_dG>
                  <brsynth:value value="-3052.5744369123167"/>
                  <brsynth:error value="47.748437579463356"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG>
                <brsynth:global_score value="0.9892438888549804"/>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="rxn_1"/>
          <groups:member groups:idRef="rxn_2"/>
          <groups:member groups:idRef="rxn_3"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" 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="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="CMPD_0000000001"/>
          <groups:member groups:idRef="CMPD_0000000003"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" 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="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
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          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="CMPD_0000000001"/>
          <groups:member groups:idRef="TARGET_0000000001"/>
          <groups:member groups:idRef="CMPD_0000000003"/>
          <groups:member groups:idRef="MNXM100"/>
          <groups:member groups:idRef="MNXM83"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" 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/">
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              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
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        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="MNXM24"/>
          <groups:member groups:idRef="MNXM11"/>
          <groups:member groups:idRef="MNXM8975"/>
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      </groups:group>
      <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" 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="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
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        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="MNXM100"/>
          <groups:member groups:idRef="MNXM83"/>
          <groups:member groups:idRef="MNXM11"/>
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      </groups:group>
      <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" 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="#a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
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          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="MNXM24"/>
          <groups:member groups:idRef="MNXM8975"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" 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="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="TARGET_0000000001"/>
          <groups:member groups:idRef="MNXM24"/>
          <groups:member groups:idRef="MNXM8975"/>
        </groups:listOfMembers>
      </groups:group>
    </groups:listOfGroups>
  </model>
</sbml>