cy3sabiork-SupplementaryFile-S1
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Kinetic entry 14792 SBML for query http://sabiork.h-its.org/sabioRestWebServices/kineticLaws/14792

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Filename: cy3sabiork-SupplementaryFile-S1.xml  Download

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<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model id="cy3sabiork_S1" name="SABIOmdl10Jun2016824">
<notes><body xmlns="http://www.w3.org/1999/xhtml">
<p>
This model has been created with the help of the SABIO-RK Database
(http://sabio.h-its.org/) 
 (c) 2005-2016 HITS gGmbH http://www.h-its.org

</p><br/>
To cite SABIO-RK Database, please use
"http://www.ncbi.nlm.nih.gov/pubmed/22102587"
<br/>
SABIO-RK - database for biochemical reaction kinetics. Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, Algaa E, Weidemann A, Sauer-Danzwith H, Mir S, Krebs O, Bittkowski M, Wetsch E, Rojas I, Mueller W. Nucleic Acids Res. 2012;40(Database issue)790-6
</body></notes>
      <listOfFunctionDefinitions>
      <functionDefinition id="KL_14792" sboTerm="SBO:0000029">
        <math xmlns="http://www.w3.org/1998/Math/MathML">        
          <lambda>
            <bvar>
              <ci> E </ci>
            </bvar>
            <bvar>
              <ci> kcat </ci>
            </bvar>
            <bvar>
              <ci> A </ci>
            </bvar>
            <bvar>
              <ci> kcat_Km </ci>
            </bvar>
            <bvar>
              <ci> Km </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <apply>
                  <times/>
                  <ci> E </ci>
                  <ci> kcat </ci>
                </apply>
                <ci> A </ci>
              </apply>
              <apply>
                <plus/>
                <ci> Km </ci>
                <ci> A </ci>
              </apply>
            </apply>
          </lambda>
        </math>
      </functionDefinition>
    </listOfFunctionDefinitions>
    <listOfUnitDefinitions>
      <unitDefinition id="swedgeone" name="s^(-1)">
        <listOfUnits>
          <unit scale="0" exponent="-1" multiplier="1" kind="second"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="Mwedgeoneswedgeone" name="M^(-1)*s^(-1)">
        <listOfUnits>
          <unit scale="0" exponent="1" multiplier="1" kind="litre"/>
          <unit scale="0" exponent="-1" multiplier="1" kind="mole"/>
          <unit scale="0" exponent="-1" multiplier="1" kind="second"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="M" name="M">
        <listOfUnits>
          <unit scale="0" exponent="-1" multiplier="1" kind="litre"/>
          <unit scale="0" exponent="1" multiplier="1" kind="mole"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
    <listOfCompartments>
      <compartment id="compart_cytosol" constant="true" name="cytosol"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="SPC_1661_cytosol" initialConcentration="1" constant="false" hasOnlySubstanceUnits="false" name="D-Galactose" metaid="META_SPC_1661_cytosol" boundaryCondition="false" compartment="compart_cytosol">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
            <rdf:Description rdf:about="#META_SPC_1661_cytosol">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:4139"/>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:12936"/>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00124"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
</species>
      <species id="SPC_34_cytosol" initialConcentration="1" constant="false" hasOnlySubstanceUnits="false" name="ATP" metaid="META_SPC_34_cytosol" boundaryCondition="false" compartment="compart_cytosol">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
            <rdf:Description rdf:about="#META_SPC_34_cytosol">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15422"/>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:30616"/>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00002"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
</species>
      <species id="SPC_35_cytosol" initialConcentration="1" constant="false" hasOnlySubstanceUnits="false" name="ADP" metaid="META_SPC_35_cytosol" boundaryCondition="false" compartment="compart_cytosol">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
            <rdf:Description rdf:about="#META_SPC_35_cytosol">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16761"/>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00008"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
</species>
      <species id="SPC_1381_cytosol" initialConcentration="1" constant="false" hasOnlySubstanceUnits="false" name="alpha-D-Galactose 1-phosphate" metaid="META_SPC_1381_cytosol" boundaryCondition="false" compartment="compart_cytosol">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
            <rdf:Description rdf:about="#META_SPC_1381_cytosol">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:17973"/>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00446"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
</species>
      <species id="ENZ_77023_cytosol" initialConcentration="1" constant="false" hasOnlySubstanceUnits="false" name="galactokinase(Enzyme) wildtype His-tagged" metaid="META_ENZ_77023_cytosol" boundaryCondition="false" compartment="compart_cytosol">
        <annotation bqbiol="http://biomodels.net/biology-qualifiers/" rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#/">
<sbrk:sabiork xmlns:sbrk="http://sabiork.h-its.org">
<sbrk:modifierType>Modifier-Catalyst</sbrk:modifierType>
</sbrk:sabiork>                  <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
            <rdf:Description rdf:about="#META_ENZ_77023_cytosol">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P51570"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
</species>
    </listOfSpecies>
    <listOfReactions>
      <reaction id="REAC_0" metaid="META_REAC_0" reversible="true" fast="false">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
            <rdf:Description rdf:about="#META_REAC_0">
              <bqbiol:isVersionOf>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.6"/>
                </rdf:Bag>
              </bqbiol:isVersionOf>
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01092"/>
                </rdf:Bag>
              </bqbiol:is>
              <bqbiol:hasTaxon>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/taxonomy/9606"/>
                </rdf:Bag>
              </bqbiol:hasTaxon>
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/sabiork.reaction/1354"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference constant="true" species="SPC_1661_cytosol" sboTerm="SBO:0000015" stoichiometry="1"/>
          <speciesReference constant="true" species="SPC_34_cytosol" sboTerm="SBO:0000015" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference constant="true" species="SPC_35_cytosol" sboTerm="SBO:0000011" stoichiometry="1"/>
          <speciesReference constant="true" species="SPC_1381_cytosol" sboTerm="SBO:0000011" stoichiometry="1"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="ENZ_77023_cytosol" sboTerm="SBO:0000460"/>
        </listOfModifiers>
        <kineticLaw metaid="META_KL_14792" sboTerm="SBO:0000029">
          <annotation sbrk="http://sabiork.h-its.org" bqbiol="http://biomodels.net/biology-qualifiers/" rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#/">
<sbrk:sabiork xmlns:sbrk="http://sabiork.h-its.org">
<sbrk:kineticLawID>14792</sbrk:kineticLawID>
<sbrk:experimentalConditions>
<sbrk:pH>
<sbrk:startValuepH>8.0</sbrk:startValuepH>
</sbrk:pH>
<sbrk:temperature>
<sbrk:startValueTemperature>37.0</sbrk:startValueTemperature>
<sbrk:temperatureUnit>°C</sbrk:temperatureUnit>
</sbrk:temperature>
<sbrk:buffer> 20 mM Hepes, 150 mM NaCl, 5 mM MgCl2, 1 mM KCl, 10% (v/v) glycerrol, 1 mM NADH, 1 mM dithiothreitol, 400 µM phosphoenolpyrovate, 7.5 U pyrovate kinase, 10 U lactate dehydrogenase</sbrk:buffer>
</sbrk:experimentalConditions>
</sbrk:sabiork>
                      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
              <rdf:Description rdf:about="#META_KL_14792">
                <bqbiol:isDescribedBy>
                  <rdf:Bag>
                    <rdf:li rdf:resource="http://identifiers.org/pubmed/12694189"/>
                  </rdf:Bag>
                </bqbiol:isDescribedBy>
                <bqbiol:isDescribedBy>
                  <rdf:Bag>
                    <rdf:li rdf:resource="http://identifiers.org/sabiork.kineticrecord/14792"/>
                  </rdf:Bag>
                </bqbiol:isDescribedBy>
              </rdf:Description>
            </rdf:RDF>
          </annotation>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <ci> KL_14792 </ci>
              <ci> ENZ_77023_cytosol </ci>
              <ci> kcat </ci>
              <ci> SPC_34_cytosol </ci>
              <ci> kcat_Km_SPC_34_cytosol </ci>
              <ci> Km_SPC_34_cytosol </ci>
            </apply>
          </math>
                  <listOfLocalParameters>
            <localParameter id="kcat" name="kcat" value="8.7" sboTerm="SBO:0000025" units="swedgeone"/>
            <localParameter id="kcat_Km_SPC_34_cytosol" name="kcat_Km_ATP" value="260000" sboTerm="SBO:0000302" units="Mwedgeoneswedgeone"/>
            <localParameter id="Km_SPC_34_cytosol" name="Km_ATP" value="3.4E-5" sboTerm="SBO:0000027" units="M"/>
          </listOfLocalParameters>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>
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Created: 18th Jul 2016 at 16:27

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Version 1 (earliest) Created 18th Jul 2016 at 16:27 by Matthias König

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