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Molecule Parameter List for tetR_mRNA1

The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network. The text color of a molecule is highlighted by color.

Statistics

tetR_mRNA1 participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	1	0	1	0	3	1	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Quorum_ repressilator	69	Network	Shared_Object_Quorum_repressilator,  TetR,  LacI,   Lambda-cl,  LacI_2nd_copy,  LuxI
This model represents a single cell with the repressilator circuit, which is part of a population of similar cells. The repressilator circuit is a network of three proteins, i.e. LacI, TetR, Lambda-cI. The single repressilator model is at accession number 68 in the DOQCS database. In the current model, the LacI is coupled with LuxI which forms an Autoinducer(AI) protein, which couples to LuxR which activates LacI. The AI protein difffuses across the cell membrane so that the population of cells can interact. The lifetime ratio is the ratio between the mRNA and protein lifetimes. This ratio in different cells is chosen from a random gaussian distribution of mean 1 and standard deviation 0.05. The lifetime ratio of this example cell is 0.9837

tetR_mRNA1 acting as a Molecule in  Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
tetR_mRNA1	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0	3	No
The mRNA transcribed by the TetR operator Elowitz, M, et al. (2000) Nature 403:335-338

tetR_mRNA1 acting as an Enzyme in  Quorum_repressilator Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
tetR_mRNA1 / tetR_ translation	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.000555595	0.167	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Amino_Acids Product TetR-1
Translation of the tetR mRNA. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338

tetR_mRNA1 acting as a Product of an Enzyme in  Quorum_repressilator Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	TetR_operator  / TetR_basal_ transcription	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.000555607	216	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product tetR_mRNA1
	Basal transcription of the Tet R gene. Rates from Fig 2 Garcia & Elowitz et al. (2004) PNAS Vol.101
2	TetR_operator_ 1st_bound  / TetR_ transcription	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product tetR_mRNA1
	Transcription of the TetR gene with only one of its promoter sites activated. Rates from Box 1 Elowitz, M. et al (2000) Nature 403:335-338
3	TetR_operator_ 2nd_bound  / TetR_ transcription1	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product tetR_mRNA1
	Transcription of the TetR gene with both its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338

tetR_mRNA1 acting as a Substrate in a reaction in  Quorum_repressilator Network

Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.

Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
tetR_mRNA_ degradation	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.0058 (s^-1)	0 (s^-1)	-	-	Substrate tetR_mRNA1 Product Degraded_tetR_ mRNA
This reaction denotes the degradation of the tetR m-RNA, the half life of which is two minutes. t1/2 = 0.693/k where k denotes kf Elowitz, M. et al. (2000) Nature 403:335-338