Models
Simulation of Hertel et al. 2013
The SBML file representing the requested model is shown below. Click "SBML download" to save the file into your client file system. The SBML file can be used for further analysis of the model by using third party tools.
SBML download
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="M34">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.model/34/"/>
</annotation>
<listOfCompartments>
<compartment id="cytosol" size="1">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/9/"/>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species id="kaiA_mRNA" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1043/"/>
</annotation>
</species>
<species id="kaiBC_mRNA" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1044/"/>
</annotation>
</species>
<species id="KaiA" compartment="cytosol">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1040/"/>
</annotation>
</species>
<species id="KaiC6_U" compartment="cytosol">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1050/"/>
</annotation>
</species>
<species id="KaiC6_T" compartment="cytosol">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1050/"/>
</annotation>
</species>
<species id="KaiC6_S" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1050/"/>
</annotation>
</species>
<species id="KaiC6_D" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1050/"/>
</annotation>
</species>
<species id="KaiBC_U" compartment="cytosol">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1051/"/>
</annotation>
</species>
<species id="KaiBC_T" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1051/"/>
</annotation>
</species>
<species id="KaiBC_S" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1051/"/>
</annotation>
</species>
<species id="KaiBC_D" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1051/"/>
</annotation>
</species>
<species id="KaiC_U" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1042/"/>
</annotation>
</species>
<species id="KaiC_T" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1042/"/>
</annotation>
</species>
<species id="KaiC_S" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1042/"/>
</annotation>
</species>
<species id="KaiC_D" compartment="cytosol" initialConcentration="0">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1042/"/>
</annotation>
</species>
</listOfSpecies>
<listOfParameters>
<parameter id="k1_a" value="0.0117" constant="true"/>
<parameter id="k1_bc" value="0.4139" constant="true"/>
<parameter id="lambda" value="3.0378" constant="true"/>
<parameter id="k2_a" value="0.3497" constant="true"/>
<parameter id="k2_bc" value="0.0457" constant="true"/>
<parameter id="k3_a" value="0.0195" constant="true"/>
<parameter id="k3_bc" value="0.2996" constant="true"/>
<parameter id="k4_a" value="0.3278" constant="true"/>
<parameter id="k4_c" value="0.0162" constant="true"/>
<parameter id="ktuN" value="0.01" constant="true"/>
<parameter id="kdtN" value="0.13" constant="true"/>
<parameter id="kdsN" value="0" constant="true"/>
<parameter id="ksuN" value="0" constant="true"/>
<parameter id="kutN" value="0.22" constant="true"/>
<parameter id="ktdN" value="0" constant="true"/>
<parameter id="ksdN" value="0.34" constant="true"/>
<parameter id="kusN" value="0.12" constant="true"/>
<parameter id="ktuA" value="3.9" constant="true"/>
<parameter id="kdtA" value="0" constant="true"/>
<parameter id="kdsA" value="10.9" constant="true"/>
<parameter id="ksuA" value="0.6" constant="true"/>
<parameter id="kutA" value="0" constant="true"/>
<parameter id="ktdA" value="0.5" constant="true"/>
<parameter id="ksdA" value="0" constant="true"/>
<parameter id="kusA" value="0.6" constant="true"/>
<parameter id="KMj" value="3" constant="true"/>
<parameter id="KDAC" value="0.1" constant="true"/>
<parameter id="KDAS" value="8e-06" constant="true"/>
<parameter id="gammam" value="0.4" constant="true"/>
<parameter id="gammap" value="50000" constant="true"/>
<parameter id="cu" value="0" constant="true"/>
<parameter id="cs" value="1380" constant="true"/>
<parameter id="cd" value="2420" constant="true"/>
<parameter id="C_H" constant="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1050/"/>
</annotation>
</parameter>
<parameter id="C_B" constant="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1052/"/>
</annotation>
</parameter>
<parameter id="C_P" constant="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1042/"/>
</annotation>
</parameter>
<parameter id="Zz" constant="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1050/"/>
</annotation>
</parameter>
<parameter id="C_total" constant="false"/>
<parameter id="A2C6" constant="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1052/"/>
</annotation>
</parameter>
<parameter id="Af" constant="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1045/"/>
</annotation>
</parameter>
<parameter id="kut" constant="false"/>
<parameter id="kus" constant="false"/>
<parameter id="ksu" constant="false"/>
<parameter id="ktu" constant="false"/>
<parameter id="ktd" constant="false"/>
<parameter id="kdt" constant="false"/>
<parameter id="ksd" constant="false"/>
<parameter id="kds" constant="false"/>
<parameter id="CT" value="3.5" constant="true"/>
<parameter id="AT" value="0.6" constant="true"/>
</listOfParameters>
<listOfInitialAssignments>
<initialAssignment symbol="KaiA">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> 2 </cn>
<ci> AT </ci>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="KaiC6_U">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn> 0.998 </cn>
<ci> CT </ci>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="KaiC6_T">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn> 0.001 </cn>
<ci> CT </ci>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="KaiBC_U">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn> 0.001 </cn>
<ci> CT </ci>
</apply>
</math>
</initialAssignment>
</listOfInitialAssignments>
<listOfRules>
<assignmentRule variable="C_H">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> KaiC6_U </ci>
<ci> KaiC6_T </ci>
<ci> KaiC6_S </ci>
<ci> KaiC6_D </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="C_B">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> KaiBC_U </ci>
<ci> KaiBC_T </ci>
<ci> KaiBC_S </ci>
<ci> KaiBC_D </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="C_P">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> KaiC_U </ci>
<ci> KaiC_T </ci>
<ci> KaiC_S </ci>
<ci> KaiC_D </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="Zz">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> KaiC6_T </ci>
<ci> KaiC6_D </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="C_total">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> C_P </ci>
<ci> C_H </ci>
<ci> C_B </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="A2C6">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<divide/>
<apply>
<plus/>
<ci> KaiA </ci>
<apply>
<divide/>
<ci> C_total </ci>
<cn type="integer"> 6 </cn>
</apply>
<ci> KDAC </ci>
</apply>
<cn type="integer"> 2 </cn>
</apply>
<apply>
<root/>
<degree>
<cn type="integer"> 2 </cn>
</degree>
<apply>
<minus/>
<apply>
<divide/>
<apply>
<power/>
<apply>
<plus/>
<ci> KaiA </ci>
<apply>
<divide/>
<ci> C_total </ci>
<cn type="integer"> 6 </cn>
</apply>
<ci> KDAC </ci>
</apply>
<cn type="integer"> 2 </cn>
</apply>
<cn type="integer"> 4 </cn>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci> KaiA </ci>
<ci> C_total </ci>
</apply>
<cn type="integer"> 6 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="Af">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<minus/>
<ci> KaiA </ci>
<ci> A2C6 </ci>
</apply>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<divide/>
<ci> C_H </ci>
<ci> KMj </ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<cn type="integer"> 1 </cn>
<ci> KDAS </ci>
</apply>
<apply>
<divide/>
<ci> KaiBC_S </ci>
<cn type="integer"> 6 </cn>
</apply>
<apply>
<power/>
<apply>
<divide/>
<ci> KaiBC_S </ci>
<ci> C_B </ci>
</apply>
<cn type="integer"> 5 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="kut">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> kutN </ci>
<apply>
<times/>
<ci> kutA </ci>
<ci> Af </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="kus">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> kusN </ci>
<apply>
<times/>
<ci> kusA </ci>
<ci> Af </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="ksu">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> ksuN </ci>
<apply>
<times/>
<ci> ksuA </ci>
<ci> Af </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="ktu">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> ktuN </ci>
<apply>
<times/>
<ci> ktuA </ci>
<ci> Af </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="ktd">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> ktdN </ci>
<apply>
<times/>
<ci> ktdA </ci>
<ci> Af </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="kdt">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> kdtN </ci>
<apply>
<times/>
<ci> kdtA </ci>
<ci> Af </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="ksd">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> ksdN </ci>
<apply>
<times/>
<ci> ksdA </ci>
<ci> Af </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="kds">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> kdsN </ci>
<apply>
<times/>
<ci> kdsA </ci>
<ci> Af </ci>
</apply>
</apply>
</math>
</assignmentRule>
</listOfRules>
<listOfReactions>
<reaction id="R626" name="KaiA_mRNA transcription" reversible="true">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/663/"/>
</annotation>
<listOfProducts>
<speciesReference species="kaiA_mRNA" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> k1_a </ci>
</math>
</kineticLaw>
</reaction>
<reaction id="R627" name="kaiA_mRNA degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/667/"/>
</annotation>
<listOfReactants>
<speciesReference species="kaiA_mRNA" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k3_a </ci>
<ci> kaiA_mRNA </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R628" name="KaiA translation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/665/"/>
</annotation>
<listOfProducts>
<speciesReference species="KaiA" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="kaiA_mRNA"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k2_a </ci>
<ci> kaiA_mRNA </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R629" name="KaiA degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/670/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiA" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_a </ci>
<ci> KaiA </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R630" name="kaiBC_mRNA transcription" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/664/"/>
</annotation>
<listOfProducts>
<speciesReference species="kaiBC_mRNA" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="KaiC6_U"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k1_bc </ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<ci> lambda </ci>
<ci> Zz </ci>
</apply>
</apply>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<ci> Zz </ci>
</apply>
</apply>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<ci> KaiC6_U </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R631" name="kaiBC_mRNA degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/668/"/>
</annotation>
<listOfReactants>
<speciesReference species="kaiBC_mRNA" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k3_bc </ci>
<ci> kaiBC_mRNA </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R632" name="KaiC6_T dephosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/652/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_T" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_U" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kut </ci>
<ci> KaiC6_T </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R633" name="KaiC6_S dephosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/651/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_S" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_U" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kus </ci>
<ci> KaiC6_S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R634" name="KaiC6_U serine phosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/651/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_U" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_S" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> ksu </ci>
<ci> KaiC6_U </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R635" name="KaiC6_U threnine phosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/652/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_U" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_T" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> ktu </ci>
<ci> KaiC6_U </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R636" name="KaiC6_D serine dephoshorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/651/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_D" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_T" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> ktd </ci>
<ci> KaiC6_D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R637" name="KaiC6_T serine phosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/651/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_T" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_D" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kdt </ci>
<ci> KaiC6_T </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R638" name="KaiC6_D threonine dephoshorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/652/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_D" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_S" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> ksd </ci>
<ci> KaiC6_D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R639" name="KaiC6_S threonine phosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/652/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_S" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_D" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kds </ci>
<ci> KaiC6_S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R640" name="KaiC6_U degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/669/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_U" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiC6_U </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R641" name="KaiC6_T degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/669/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_T" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiC6_T </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R642" name="KaiC6_S degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/669/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_S" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiC6_S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R643" name="KaiC6_D degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/669/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_D" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiC6_D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R644" name="KaiC6_U dissociation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_U" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC_U" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammam </ci>
<ci> KaiC6_U </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R645" name="KaiC6_T dissociation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_T" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC_T" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammam </ci>
<ci> KaiC6_T </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R646" name="KaiC6_S dissociation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_S" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC_S" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammam </ci>
<ci> KaiC6_S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R647" name="KaiC6_D dissociation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_D" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC_D" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammam </ci>
<ci> KaiC6_D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R648" name="KaiC6_U assembly" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC_U" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_U" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammap </ci>
<ci> KaiC_U </ci>
<apply>
<power/>
<ci> C_P </ci>
<cn type="integer"> 5 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R649" name="KaiC6_T assembly" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC_T" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_T" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammap </ci>
<ci> KaiC_T </ci>
<apply>
<power/>
<ci> C_P </ci>
<cn type="integer"> 5 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R650" name="KaiC6_S assembly" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC_S" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_S" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammap </ci>
<ci> KaiC_S </ci>
<apply>
<power/>
<ci> C_P </ci>
<cn type="integer"> 5 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R651" name="KaiC6_D assembly" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC_D" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_D" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammap </ci>
<ci> KaiC_D </ci>
<apply>
<power/>
<ci> C_P </ci>
<cn type="integer"> 5 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R652" name="KaiBC_U to KaiC6_U exchange" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/657/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_U" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC6_U" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cu </ci>
<ci> KaiBC_U </ci>
<apply>
<power/>
<apply>
<divide/>
<ci> KaiBC_U </ci>
<ci> C_B </ci>
</apply>
<cn type="integer"> 5 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R653" name="KaiC6_S to KaiBC_S exchange" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/657/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_S" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiBC_S" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cs </ci>
<ci> KaiC6_S </ci>
<apply>
<power/>
<apply>
<divide/>
<ci> KaiC6_S </ci>
<ci> C_H </ci>
</apply>
<cn type="integer"> 5 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R654" name="KaiC6_D to KaiBC_D exchange" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/657/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC6_D" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiBC_D" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cd </ci>
<ci> KaiC6_D </ci>
<apply>
<power/>
<apply>
<divide/>
<ci> KaiC6_D </ci>
<ci> C_H </ci>
</apply>
<cn type="integer"> 5 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R655" name="KaiBC_U degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_U" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiBC_U </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R656" name="KaiBC_T degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_T" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiBC_T </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R657" name="KaiBC_D degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_D" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiBC_D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R658" name="KaiBC_S degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_S" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiBC_S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R659" name="KaiBC_U dissociation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_U" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC_U" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammam </ci>
<ci> KaiBC_U </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R660" name="KaiBC_T dissociation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/653/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_T" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC_T" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammam </ci>
<ci> KaiBC_T </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R661" name="KaiBC_S dissociation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/657/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_S" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC_S" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammam </ci>
<ci> KaiBC_S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R662" name="KaiBC_D dissociation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/657/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_D" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiC_D" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> gammam </ci>
<ci> KaiBC_D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R663" name="KaiBC_U threonine phosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/652/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_U" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiBC_T" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> ktuN </ci>
<ci> KaiBC_U </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R664" name="KaiBC_U serine phosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/651/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_U" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiBC_S" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> ksuN </ci>
<ci> KaiBC_U </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R665" name="KaiBC_T dephosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/652/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_T" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiBC_U" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kutN </ci>
<ci> KaiBC_T </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R666" name="KaiBC_S dephoshporylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/651/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_S" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiBC_U" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kusN </ci>
<ci> KaiBC_S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R667" name="KaiBC_S threonine phosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/652/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_S" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiBC_D" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kdsN </ci>
<ci> KaiBC_S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R668" name="KaiBC_D serine dephosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/651/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_D" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiBC_S" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> ksdN </ci>
<ci> KaiBC_D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R669" name="KaiBC_T serine phosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/651/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_T" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiBC_D" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kdtN </ci>
<ci> KaiBC_T </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R670" name="KaiBC_D threonine dephosphorylation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/652/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiBC_D" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="KaiBC_T" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> ktdN </ci>
<ci> KaiBC_D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R671" name="KaiC_U degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/669/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC_U" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiC_U </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R672" name="KaiC_T degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/669/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC_T" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiC_T </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R673" name="KaiC_S degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/669/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC_S" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiC_S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R674" name="KaiC_D degradation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/669/"/>
</annotation>
<listOfReactants>
<speciesReference species="KaiC_D" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4_c </ci>
<ci> KaiC_D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R675" name="KaiC translation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/666/"/>
</annotation>
<listOfProducts>
<speciesReference species="KaiC_U" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="kaiBC_mRNA"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k2_bc </ci>
<ci> kaiBC_mRNA </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI