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Molecule Parameter List for Lambda-cl-1

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

Lambda-cl-1 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	0	0	1	5	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

Lambda-cl-1 acting as a Molecule in  Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Lambda-cl-1	Quorum_ repressilator Accession No. : 69	Lambda-cl Pathway No. : 301	0	3	No
Lambda-cl translated from lcl m-RNA Derived from Figure 1(c) stochastic version Elowitz, M. et al. (2000) Nature 403:335-338

Lambda-cl-1 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
lambda-cl_mRNA1  / lambda-cl_ translation	Quorum_ repressilator Accession No. : 69	Lambda-cl Pathway No. : 301	0.000555595	0.167	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Amino_Acids Product Lambda-cl-1
Translation the lambda cl mRNA. Rates from Box 1 Elowitz, M. et al (2000) Nature 403:335-338

Lambda-cl-1 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
1	Lac_operator_ inhibition_ reaction	Quorum_ repressilator Accession No. : 69	LacI Pathway No. : 300	1000.01 (uM^-1 s^-1)	224 (s^-1)	Kd(bf) = 0.224(uM)	-	Substrate Lac_operator Lambda-cl-1 Product Lac_operator_ 1st_bound
	It signifies the first binding of the repressor with the operator Kf = 1 /nM/sec Kb = 224 /sec Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
2	Lac_operator_ inhibition_ reaction[1]	Quorum_ repressilator Accession No. : 69	LacI Pathway No. : 300	1000.01 (uM^-1 s^-1)	9 (s^-1)	Kd(bf) = 0.009(uM)	-	Substrate Lac_operator_ 1st_bound Lambda-cl-1 Product Lac_operator_ 2nd_bound
	It signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 9 /sec Box 1 Elowitz, M. et al (2000) Nature 403:335-338
3	Lambda-cl_ degradation	Quorum_ repressilator Accession No. : 69	Lambda-cl Pathway No. : 301	0.0057 (s^-1)	0 (s^-1)	-	-	Substrate Lambda-cl-1 Product Degraded_ Lambda-cl
	This reaction denotes the degradation of Lambda cl, kf is chosen from a random gaussian distribution. Ref: Fig 2 Garcia & Elowitz et al. (2004) PNAS 101(30) 10955 - 60
4	Lac_operator_ inhibition_ reaction	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	1000.01 (uM^-1 s^-1)	224 (s^-1)	Kd(bf) = 0.224(uM)	-	Substrate Lac_operator Lambda-cl-1 Product Lac_operator_ 1st_bound
	It signifies the first binding of the repressor with the operator Kf = 1 /nM/sec Kb = 224 /sec Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
5	Lac_operator_ inhibition_ reaction[1]	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	1000.01 (uM^-1 s^-1)	9 (s^-1)	Kd(bf) = 0.009(uM)	-	Substrate Lac_operator_ 1st_bound Lambda-cl-1 Product Lac_operator_ 2nd_bound
	It signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 9 /sec Box 1 Elowitz, M. et al (2000) Nature 403:335-338