<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
  <model name="AI2_LB">
    <listOfUnitDefinitions>
      <unitDefinition name="volume">
        <listOfUnits>
          <unit kind="dimensionless"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition name="substance">
        <listOfUnits>
          <unit kind="item"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
    <listOfCompartments>
      <compartment name="compartment" volume="1"/>
    </listOfCompartments>
    <listOfSpecies>
      <species name="Nutrients" compartment="compartment" initialAmount="28350"/>
      <species name="Met" compartment="compartment" initialAmount="2248"/>
      <species name="SAM" compartment="compartment" initialAmount="10000"/>
      <species name="SAH" compartment="compartment" initialAmount="320"/>
      <species name="Decarb_SAM" compartment="compartment" initialAmount="220"/>
      <species name="Putrescine" compartment="compartment" initialAmount="4400"/>
      <species name="Pfs_mRNA" compartment="compartment" initialAmount="32"/>
      <species name="pfs_gene" compartment="compartment" initialAmount="1"/>
      <species name="Pfs_prot" compartment="compartment" initialAmount="800"/>
      <species name="Adenine" compartment="compartment" initialAmount="596"/>
      <species name="SRH" compartment="compartment" initialAmount="300"/>
      <species name="LuxS_gene" compartment="compartment" initialAmount="1"/>
      <species name="LuxS_mRNA" compartment="compartment" initialAmount="16"/>
      <species name="LuxS_prot" compartment="compartment" initialAmount="400"/>
      <species name="DPD" compartment="compartment" initialAmount="300"/>
      <species name="Homocys" compartment="compartment" initialAmount="300"/>
      <species name="MTA" compartment="compartment" initialAmount="296"/>
      <species name="Spermidine" compartment="compartment" initialAmount="940"/>
      <species name="MTR" compartment="compartment" initialAmount="180"/>
      <species name="AI2_intra" compartment="compartment" initialAmount="60"/>
      <species name="AI2_extra" compartment="compartment" initialAmount="60"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter name="AI2_trans_r" value="0"/>
      <parameter name="AI2_phos_r" value="0"/>
      <parameter name="AI2_excret_r" value="0.25"/>
      <parameter name="AI2_syn_r" value="0.00067"/>
      <parameter name="AdoMet_r" value="0.962"/>
      <parameter name="DPD_deg_r" value="0.005"/>
      <parameter name="LuxS_mRNA_d" value="0.03"/>
      <parameter name="LuxS_prot_d" value="0.012"/>
      <parameter name="LuxS_transc" value="1.25"/>
      <parameter name="LuxS_transl" value="0.74"/>
      <parameter name="MTR_e" value="0.02"/>
      <parameter name="MTR_syn_r" value="2.21e-005"/>
      <parameter name="Met_recov" value="0.35"/>
      <parameter name="Methy_trans" value="0.15"/>
      <parameter name="Pfs_prot_d" value="0.003"/>
      <parameter name="Polyamine_uti" value="0.15"/>
      <parameter name="SAH_Hydro_r" value="0.00055"/>
      <parameter name="SAM_Dec" value="0.055"/>
      <parameter name="SRH_cleav" value="0.00224"/>
      <parameter name="SpeE_syn_r" value="4.03e-006"/>
      <parameter name="Spermi_uti" value="0.0208"/>
      <parameter name="b_reac_r" value="0.01"/>
      <parameter name="pfs_mRNA_d" value="0.022"/>
      <parameter name="pfs_transc" value="2.1"/>
      <parameter name="pfs_transl" value="0.54"/>
    </listOfParameters>
    <listOfReactions>
      <reaction name="bio_reac" reversible="false">
        <listOfReactants>
          <speciesReference species="Nutrients"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="Met"/>
        </listOfProducts>
        <kineticLaw formula="b_reac_r * Nutrients"/>
      </reaction>
      <reaction name="AdoMet" reversible="false">
        <listOfReactants>
          <speciesReference species="Met"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="SAM"/>
        </listOfProducts>
        <kineticLaw formula="AdoMet_r * Met"/>
      </reaction>
      <reaction name="MethyTrans" reversible="false">
        <listOfReactants>
          <speciesReference species="SAM"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="SAH"/>
        </listOfProducts>
        <kineticLaw formula="Methy_trans * SAM"/>
      </reaction>
      <reaction name="SAM_Decarb" reversible="false">
        <listOfReactants>
          <speciesReference species="SAM"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="Decarb_SAM"/>
        </listOfProducts>
        <kineticLaw formula="SAM_Dec * SAM"/>
      </reaction>
      <reaction name="SpeE_syn" reversible="false">
        <listOfReactants>
          <speciesReference species="Decarb_SAM"/>
          <speciesReference species="Putrescine"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="MTA"/>
          <speciesReference species="Spermidine"/>
        </listOfProducts>
        <kineticLaw formula="SpeE_syn_r * Decarb_SAM * Putrescine"/>
      </reaction>
      <reaction name="Spermi_util" reversible="false">
        <listOfReactants>
          <speciesReference species="Spermidine"/>
        </listOfReactants>
        <kineticLaw formula="Spermi_uti * Spermidine"/>
      </reaction>
      <reaction name="MTR_syn" reversible="false">
        <listOfReactants>
          <speciesReference species="MTA"/>
          <speciesReference species="Pfs_prot"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="MTR"/>
          <speciesReference species="Adenine"/>
          <speciesReference species="Pfs_prot"/>
        </listOfProducts>
        <kineticLaw formula="MTR_syn_r * Pfs_prot * MTA"/>
      </reaction>
      <reaction name="MTR_excret" reversible="false">
        <listOfReactants>
          <speciesReference species="MTR"/>
        </listOfReactants>
        <kineticLaw formula="MTR_e * MTR"/>
      </reaction>
      <reaction name="Polyamine_util" reversible="false">
        <listOfReactants>
          <speciesReference species="Adenine"/>
        </listOfReactants>
        <kineticLaw formula="Polyamine_uti * Adenine"/>
      </reaction>
      <reaction name="Pfs_prot_deg" reversible="false">
        <listOfReactants>
          <speciesReference species="Pfs_prot"/>
        </listOfReactants>
        <kineticLaw formula="Pfs_prot_d * Pfs_prot"/>
      </reaction>
      <reaction name="pfs_translation" reversible="false">
        <listOfReactants>
          <speciesReference species="Pfs_mRNA"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="Pfs_prot"/>
          <speciesReference species="Pfs_mRNA"/>
        </listOfProducts>
        <kineticLaw formula="pfs_transl * Pfs_mRNA"/>
      </reaction>
      <reaction name="Pfs_mRNA_deg" reversible="false">
        <listOfReactants>
          <speciesReference species="Pfs_mRNA"/>
        </listOfReactants>
        <kineticLaw formula="pfs_mRNA_d * Pfs_mRNA"/>
      </reaction>
      <reaction name="pfs_transcription" reversible="false">
        <listOfReactants>
          <speciesReference species="pfs_gene"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="Pfs_mRNA"/>
          <speciesReference species="pfs_gene"/>
        </listOfProducts>
        <kineticLaw formula="pfs_transc"/>
      </reaction>
      <reaction name="SAH_Hydro" reversible="false">
        <listOfReactants>
          <speciesReference species="SAH"/>
          <speciesReference species="Pfs_prot"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="SRH"/>
          <speciesReference species="Adenine"/>
          <speciesReference species="Pfs_prot"/>
        </listOfProducts>
        <kineticLaw formula="SAH_Hydro_r * SAH * Pfs_prot"/>
      </reaction>
      <reaction name="SRH_cleave" reversible="false">
        <listOfReactants>
          <speciesReference species="LuxS_prot"/>
          <speciesReference species="SRH"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="LuxS_prot"/>
          <speciesReference species="Homocys"/>
          <speciesReference species="DPD"/>
        </listOfProducts>
        <kineticLaw formula="SRH_cleav * LuxS_prot * SRH"/>
      </reaction>
      <reaction name="Met_recover" reversible="false">
        <listOfReactants>
          <speciesReference species="Homocys"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="Met"/>
        </listOfProducts>
        <kineticLaw formula="Met_recov * Homocys"/>
      </reaction>
      <reaction name="DPD_deg" reversible="false">
        <listOfReactants>
          <speciesReference species="DPD"/>
        </listOfReactants>
        <kineticLaw formula="DPD_deg_r * DPD"/>
      </reaction>
      <reaction name="LuxS_prot_deg" reversible="false">
        <listOfReactants>
          <speciesReference species="LuxS_prot"/>
        </listOfReactants>
        <kineticLaw formula="LuxS_prot_d * LuxS_prot"/>
      </reaction>
      <reaction name="LuxS_translation" reversible="false">
        <listOfReactants>
          <speciesReference species="LuxS_mRNA"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="LuxS_prot"/>
          <speciesReference species="LuxS_mRNA"/>
        </listOfProducts>
        <kineticLaw formula="LuxS_transl * LuxS_mRNA"/>
      </reaction>
      <reaction name="LuxS_mRNA_deg" reversible="false">
        <listOfReactants>
          <speciesReference species="LuxS_mRNA"/>
        </listOfReactants>
        <kineticLaw formula="LuxS_mRNA_d * LuxS_mRNA"/>
      </reaction>
      <reaction name="LuxS_transcription" reversible="false">
        <listOfReactants>
          <speciesReference species="LuxS_gene"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="LuxS_gene"/>
          <speciesReference species="LuxS_mRNA"/>
        </listOfProducts>
        <kineticLaw formula="LuxS_transc"/>
      </reaction>
      <reaction name="AI2_syn" reversible="false">
        <listOfReactants>
          <speciesReference species="DPD"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="AI2_intra"/>
        </listOfProducts>
        <kineticLaw formula="AI2_syn_r * DPD"/>
      </reaction>
      <reaction name="AI2_excret" reversible="false">
        <listOfReactants>
          <speciesReference species="AI2_intra"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="AI2_extra"/>
        </listOfProducts>
        <kineticLaw formula="AI2_excret_r * AI2_intra"/>
      </reaction>
      <reaction name="AI2_trans" reversible="false">
        <listOfReactants>
          <speciesReference species="AI2_extra"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="AI2_intra"/>
        </listOfProducts>
        <kineticLaw formula="AI2_trans_r * AI2_extra"/>
      </reaction>
      <reaction name="AI2_phos" reversible="false">
        <listOfReactants>
          <speciesReference species="AI2_intra"/>
        </listOfReactants>
        <kineticLaw formula="AI2_phos_r * AI2_intra"/>
      </reaction>
    </listOfReactions>
  </model>
</sbml>
