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<html>
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<table>
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<tr>
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<td><b><u>Reaction</u></b></td>
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<td><b><u>Rate Constant</u></b></td>
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</tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td><b> Constitutive Expression </b></td> <td> </td> </tr>
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<tr> <td> --> lacl4 </td> <td> 1E-10 </td> </tr>
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<tr> <td> --> tetR2 </td> <td> 1E-10 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td><b> Multimerization </b></td> <td> </td> </tr>
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<tr> <td> 2  lacI --> lacI2 </td> <td> 1.00E+09 </td> </tr>
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<tr> <td> lacI2 --> 2 lacI </td> <td> 10 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> 2 lacI2 --> lacI4 </td> <td> 1.00E+09 </td> </tr>
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<tr> <td> lacI4 --> 2 lacI2 </td> <td> 10 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> 2  tetR --> tetR2 </td> <td> 1.00E+09 </td> </tr>
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<tr> <td> tetR2 --> 2 tetR </td> <td> 10 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> 2  Enc --> Enc2 </td> <td> 100 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td><b> Encapsulation </b></td> <td> </td> </tr>
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<tr> <td> Enc2 + eCFPt --> Enc2:eCFPt </td> <td> 100 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td><b> Transcription</b> </td> <td> </td> </tr>
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<tr> <td> RNAp + BBa_R0010 + LacI_binding_site --> RNAp:BBa_R0010:LacI_binding_site </td> <td> 10000000 </td> </tr>
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<tr> <td> RNAp:BBa_R0010:LacI_binding_site --> RNAp + BBa_R0010 + LacI_binding_site </td> <td> 0.057 </td> </tr>
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<tr> <td> RNAp:BBa_R0010:LacI_binding_site --> RNAp:BBa_R0010:LacI_binding_site* </td> <td> 0.1 </td> </tr>
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<tr> <td> RNAp:BBa_R0010:LacI_binding_site* --> RNAp:DNA_eCFPt + BBa_R0010 + LacI_binding_site </td> <td> 30 </td> </tr>
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<tr> <td> RNAp:DNA_eCFPt --> RNAp + mRNA_eCFPt </td> <td> 0.035 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> RNAp + BBa_R0040 + TetR_1 + TetR_2 --> RNAp:BBa_R0040:TetR_1:TetR_2 </td> <td> 10000000 </td> </tr>
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<tr> <td> RNAp:BBa_R0040:TetR_1:TetR_2 --> RNAp + BBa_R0040 + TetR_1 + TetR_2 </td> <td> 0.057 </td> </tr>
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<tr> <td> RNAp:BBa_R0040:TetR_1:TetR_2 --> RNAp:BBa_R0040:TetR_1:TetR_2* </td> <td> 0.1 </td> </tr>
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<tr> <td> RNAp:BBa_R0040:TetR_1:TetR_2* --> RNAp:DNA_Enc + BBa_R0040 + TetR_1 + TetR_2 </td> <td> 30 </td> </tr>
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<tr> <td> RNAp:DNA_Enc --> RNAp + mRNA_Enc </td> <td> 0.0375 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td><b> Translation </b></td> <td> </td> </tr>
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<tr> <td> rib + mRNA_eCFPt --> rib:mRNA_eCFPt </td> <td> 100000 </td> </tr>
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<tr> <td> rib:mRNA_eCFPt --> rib:mRNA_eCFPt_1 + mRNA_eCFPt </td> <td> 33 </td> </tr>
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<tr> <td> rib:mRNA_eCFPt_1 --> rib + eCFPt </td> <td> 0.1154 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> rib + mRNA_Enc --> rib:mRNA_Enc </td> <td> 100000 </td> </tr>
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<tr> <td> rib:mRNA_Enc --> rib:mRNA_Enc_1 + mRNA_Enc </td> <td> 33 </td> </tr>
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<tr> <td> rib:mRNA_Enc_1 --> rib + Enc </td> <td> 0.1234 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td><b> Protein-DNA </b></td> <td> </td> </tr>
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<tr> <td> lacI4 + nsDNA --> lacI4:nsDNA </td> <td> 1000 </td> </tr>
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<tr> <td> lacI4:nsDNA --> lacI4 + nsDNA </td> <td> 1.6225 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> lacI4 + LacI_binding_site --> lacI4:LacI_binding_site </td> <td> 1.00E+09 </td> </tr>
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<tr> <td> lacI4:LacI_binding_site --> lacI4 + LacI_binding_site </td> <td> 0.005 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> tetR2 + nsDNA --> tetR2:nsDNA </td> <td> 1000 </td> </tr>
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<tr> <td> tetR2:nsDNA --> tetR2 + nsDNA </td> <td> 1.6225 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> tetR2 + TetR_1 --> tetR2:TetR_1 </td> <td> 1.00E+09 </td> </tr>
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<tr> <td> tetR2:TetR_1 --> tetR2 + TetR_1 </td> <td> 0.005 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> tetR2 + TetR_2 --> tetR2:TetR_2 </td> <td> 1.00E+09 </td> </tr>
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<tr> <td> tetR2:TetR_2 --> tetR2 + TetR_2 </td> <td> 0.005 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td><b> Protein - Effector - DNA </b></td> <td> </td> </tr>
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<tr> <td> lacI4 + IPTG --> lacI4:IPTG </td> <td> 50000000 </td> </tr>
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<tr> <td> lacI4:IPTG --> lacI4 + IPTG </td> <td> 0.1 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> lacI4:IPTG + LacI_binding_site --> lacI4:IPTG:LacI_binding_site </td> <td> 1.00E+09 </td> </tr>
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<tr> <td> lacI4:IPTG:LacI_binding_site --> lacI4:IPTG + LacI_binding_site </td> <td> 0.7 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> lacI4:LacI_binding_site + IPTG --> lacI4:IPTG:LacI_binding_site </td> <td> 1000000 </td> </tr>
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<tr> <td> lacI4:IPTG:LacI_binding_site --> lacI4:LacI_binding_site + IPTG </td> <td> 0.4 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> lacI4:IPTG + nsDNA --> lacI4:IPTG:nsDNA </td> <td> 1000 </td> </tr>
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<tr> <td> lacI4:IPTG:nsDNA --> lacI4:IPTG + nsDNA </td> <td> 1.6225 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> lacI4:nsDNA + IPTG --> lacI4:IPTG:nsDNA </td> <td> 1000 </td> </tr>
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<tr> <td> lacI4:IPTG:nsDNA --> lacI4:nsDNA + IPTG </td> <td> 1.6225 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> tetR2 + aTc --> tetR2:aTc </td> <td> 50000000 </td> </tr>
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<tr> <td> tetR2:aTc --> tetR2 + aTc </td> <td> 0.1 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> tetR2:aTc + TetR_1 --> tetR2:aTc:TetR_1 </td> <td> 1.00E+09 </td> </tr>
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<tr> <td> tetR2:aTc:TetR_1 --> tetR2:aTc + TetR_1 </td> <td> 0.7 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> tetR2:TetR_1 + aTc --> tetR2:aTc:TetR_1 </td> <td> 1000000 </td> </tr>
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<tr> <td> tetR2:aTc:TetR_1 --> tetR2:TetR_1 + aTc </td> <td> 0.4 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> tetR2:aTc + TetR_2 --> tetR2:aTc:TetR_2 </td> <td> 1.00E+09 </td> </tr>
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<tr> <td> tetR2:aTc:TetR_2 --> tetR2:aTc + TetR_2 </td> <td> 0.7 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> tetR2:TetR_2 + aTc --> tetR2:aTc:TetR_2 </td> <td> 1000000 </td> </tr>
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<tr> <td> tetR2:aTc:TetR_2 --> tetR2:TetR_2 + aTc </td> <td> 0.4 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> tetR2:aTc + nsDNA --> tetR2:aTc:nsDNA </td> <td> 1000 </td> </tr>
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<tr> <td> tetR2:aTc:nsDNA --> tetR2:aTc + nsDNA </td> <td> 1.6225 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> tetR2:nsDNA + aTc --> tetR2:aTc:nsDNA </td> <td> 1000 </td> </tr>
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<tr> <td> tetR2:aTc:nsDNA --> tetR2:nsDNA + aTc </td> <td> 1.6225 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td><b> Degradation</b> </td> <td> </td> </tr>
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<tr> <td> lacI4 --> </td> <td> 0.000289 </td> </tr>
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<tr> <td> tetR2 --> </td> <td> 0.000289 </td> </tr>
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<tr> <td> mRNA_eCFPt --> </td> <td> 0.0015 </td> </tr>
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<tr> <td> mRNA_Enc --> </td> <td> 0.0015 </td> </tr>
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<tr> <td> eCFPt --> </td> <td> 0.000289 </td> </tr>
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<tr> <td> Enc2 --> </td> <td> 0.000289 </td> </tr>
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<tr> <td> Enc2:eCFPt --> </td> <td> 0.000289 </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td> </td> <td> </td> </tr>
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<tr> <td><b> Dilution</b> </td> <td> </td> </tr>
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<tr> <td> lacI4:nsDNA --> nsDNA </td> <td> 0.000193 </td> </tr>
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<tr> <td> tetR2:nsDNA --> nsDNA </td> <td> 0.000193 </td> </tr>
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<tr> <td> lacI4:IPTG --> IPTG </td> <td> 0.000289 </td> </tr>
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<tr> <td> tetR2:aTc --> aTc </td> <td> 0.000289 </td> </tr>
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<tr> <td> lacI4:IPTG:nsDNA --> IPTG + nsDNA </td> <td> 0.000193 </td> </tr>
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<tr> <td> tetR2:aTc:nsDNA --> aTc + nsDNA </td> <td> 0.000193 </td> </tr>
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</table>
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</html>

Latest revision as of 20:03, 19 October 2009

Home The Team The Project Parts Submitted to the Registry Modeling Bioinformatics Notebook

Reaction Rate Constant
Constitutive Expression
--> lacl4 1E-10
--> tetR2 1E-10
Multimerization
2 lacI --> lacI2 1.00E+09
lacI2 --> 2 lacI 10
2 lacI2 --> lacI4 1.00E+09
lacI4 --> 2 lacI2 10
2 tetR --> tetR2 1.00E+09
tetR2 --> 2 tetR 10
2 Enc --> Enc2 100
Encapsulation
Enc2 + eCFPt --> Enc2:eCFPt 100
Transcription
RNAp + BBa_R0010 + LacI_binding_site --> RNAp:BBa_R0010:LacI_binding_site 10000000
RNAp:BBa_R0010:LacI_binding_site --> RNAp + BBa_R0010 + LacI_binding_site 0.057
RNAp:BBa_R0010:LacI_binding_site --> RNAp:BBa_R0010:LacI_binding_site* 0.1
RNAp:BBa_R0010:LacI_binding_site* --> RNAp:DNA_eCFPt + BBa_R0010 + LacI_binding_site 30
RNAp:DNA_eCFPt --> RNAp + mRNA_eCFPt 0.035
RNAp + BBa_R0040 + TetR_1 + TetR_2 --> RNAp:BBa_R0040:TetR_1:TetR_2 10000000
RNAp:BBa_R0040:TetR_1:TetR_2 --> RNAp + BBa_R0040 + TetR_1 + TetR_2 0.057
RNAp:BBa_R0040:TetR_1:TetR_2 --> RNAp:BBa_R0040:TetR_1:TetR_2* 0.1
RNAp:BBa_R0040:TetR_1:TetR_2* --> RNAp:DNA_Enc + BBa_R0040 + TetR_1 + TetR_2 30
RNAp:DNA_Enc --> RNAp + mRNA_Enc 0.0375
Translation
rib + mRNA_eCFPt --> rib:mRNA_eCFPt 100000
rib:mRNA_eCFPt --> rib:mRNA_eCFPt_1 + mRNA_eCFPt 33
rib:mRNA_eCFPt_1 --> rib + eCFPt 0.1154
rib + mRNA_Enc --> rib:mRNA_Enc 100000
rib:mRNA_Enc --> rib:mRNA_Enc_1 + mRNA_Enc 33
rib:mRNA_Enc_1 --> rib + Enc 0.1234
Protein-DNA
lacI4 + nsDNA --> lacI4:nsDNA 1000
lacI4:nsDNA --> lacI4 + nsDNA 1.6225
lacI4 + LacI_binding_site --> lacI4:LacI_binding_site 1.00E+09
lacI4:LacI_binding_site --> lacI4 + LacI_binding_site 0.005
tetR2 + nsDNA --> tetR2:nsDNA 1000
tetR2:nsDNA --> tetR2 + nsDNA 1.6225
tetR2 + TetR_1 --> tetR2:TetR_1 1.00E+09
tetR2:TetR_1 --> tetR2 + TetR_1 0.005
tetR2 + TetR_2 --> tetR2:TetR_2 1.00E+09
tetR2:TetR_2 --> tetR2 + TetR_2 0.005
Protein - Effector - DNA
lacI4 + IPTG --> lacI4:IPTG 50000000
lacI4:IPTG --> lacI4 + IPTG 0.1
lacI4:IPTG + LacI_binding_site --> lacI4:IPTG:LacI_binding_site 1.00E+09
lacI4:IPTG:LacI_binding_site --> lacI4:IPTG + LacI_binding_site 0.7
lacI4:LacI_binding_site + IPTG --> lacI4:IPTG:LacI_binding_site 1000000
lacI4:IPTG:LacI_binding_site --> lacI4:LacI_binding_site + IPTG 0.4
lacI4:IPTG + nsDNA --> lacI4:IPTG:nsDNA 1000
lacI4:IPTG:nsDNA --> lacI4:IPTG + nsDNA 1.6225
lacI4:nsDNA + IPTG --> lacI4:IPTG:nsDNA 1000
lacI4:IPTG:nsDNA --> lacI4:nsDNA + IPTG 1.6225
tetR2 + aTc --> tetR2:aTc 50000000
tetR2:aTc --> tetR2 + aTc 0.1
tetR2:aTc + TetR_1 --> tetR2:aTc:TetR_1 1.00E+09
tetR2:aTc:TetR_1 --> tetR2:aTc + TetR_1 0.7
tetR2:TetR_1 + aTc --> tetR2:aTc:TetR_1 1000000
tetR2:aTc:TetR_1 --> tetR2:TetR_1 + aTc 0.4
tetR2:aTc + TetR_2 --> tetR2:aTc:TetR_2 1.00E+09
tetR2:aTc:TetR_2 --> tetR2:aTc + TetR_2 0.7
tetR2:TetR_2 + aTc --> tetR2:aTc:TetR_2 1000000
tetR2:aTc:TetR_2 --> tetR2:TetR_2 + aTc 0.4
tetR2:aTc + nsDNA --> tetR2:aTc:nsDNA 1000
tetR2:aTc:nsDNA --> tetR2:aTc + nsDNA 1.6225
tetR2:nsDNA + aTc --> tetR2:aTc:nsDNA 1000
tetR2:aTc:nsDNA --> tetR2:nsDNA + aTc 1.6225
Degradation
lacI4 --> 0.000289
tetR2 --> 0.000289
mRNA_eCFPt --> 0.0015
mRNA_Enc --> 0.0015
eCFPt --> 0.000289
Enc2 --> 0.000289
Enc2:eCFPt --> 0.000289
Dilution
lacI4:nsDNA --> nsDNA 0.000193
tetR2:nsDNA --> nsDNA 0.000193
lacI4:IPTG --> IPTG 0.000289
tetR2:aTc --> aTc 0.000289
lacI4:IPTG:nsDNA --> IPTG + nsDNA 0.000193
tetR2:aTc:nsDNA --> aTc + nsDNA 0.000193

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