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Molecule Parameter List for Lambda-cl

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* 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	3	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Repressilator	68	Network	Lambda-cl_gene, Lac_gene, TetR_gene
This is a network model termed as Repressilator in which LacI inhibit transcription of tetR which in turn inhibit transcription of Lambda phage. This model simulates the result as per the Fig 1c of the paper : Elowitz MB, Leibler S., Nature. 2000 Jan 20;403(6767):335-8.

Lambda-cl acting as a Molecule in Repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Lambda-cl	Repressilator Accession No. : 68	Lambda-cl_gene Pathway No. : 295	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 acting as a Product of an Enzyme in Repressilator Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
lambda-cl_mRNA / lambda-cl_ translation	Repressilator Accession No. : 68	Lambda-cl_gene Pathway No. : 295	0.000555595	0.167	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Amino_Acids Product Lambda-cl
Translation the lambda cl mRNA. Rates from Box 1 Elowitz, M. et al (2000) Nature 403:335-338

Lambda-cl acting as a Substrate in a reaction in 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	Lambda-cl_ degradation	Repressilator Accession No. : 68	Lambda-cl_gene Pathway No. : 295	0.0167 (s^-1)	0 (s^-1)	-	-	Substrate Lambda-cl Product Degraded_ Lambda-cl
	This reaction denotes the degradation of Lambda cl the half life of which is ten minutes. t1/2 = 0.693/k where k denotes kf Note: Rates had to scaled by approx 1.4 to get desired levels Elowitz, M. et al. (2000) Nature 403:335-338
2	Lac_operator_ inhibition_ reaction	Repressilator Accession No. : 68	Lac_gene Pathway No. : 296	1000.01 (uM^-1 s^-1)	224 (s^-1)	Kd(bf) = 0.224(uM)	-	Substrate Lac_operator Lambda-cl 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
3	Lac_operator_ inhibition_ reaction[1]	Repressilator Accession No. : 68	Lac_gene Pathway No. : 296	1000.01 (uM^-1 s^-1)	9 (s^-1)	Kd(bf) = 0.009(uM)	-	Substrate Lac_operator_ 1st_bound Lambda-cl 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

Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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