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Molecule Parameter List for lambda-cl_mRNA

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_mRNA 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
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_mRNA acting as a Molecule in  Repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
lambda-cl_mRNA	Repressilator Accession No. : 68	Lambda-cl_gene Pathway No. : 295	0	3	No
The m-RNA transcribed by the Lcl operator Elowitz etal Nature 2000 Vol 403:335-338

lambda-cl_mRNA acting as 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_mRNA 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
1	Lambda-cl_ operator  / Lambda-cl_ basal_ transcription	Repressilator Accession No. : 68	Lambda-cl_gene Pathway No. : 295	0.0005556	0.5	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product lambda-cl_mRNA
	Basal transcription of the Lambda cl gene. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
2	Lambda-cl_ operator_1st_ bound  / Lambda-cl_ transcription	Repressilator Accession No. : 68	Lambda-cl_gene Pathway No. : 295	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product lambda-cl_mRNA
	Transcription of the Lambda cl gene with only one of its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
3	Lambda-cl_ operator_2nd_ bound  / Lambda-cl_ transcription1	Repressilator Accession No. : 68	Lambda-cl_gene Pathway No. : 295	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product lambda-cl_mRNA
	Transcription of the Lambda cl gene with both its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338

lambda-cl_mRNA 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
lambda-cl_mRNA_ degradation	Repressilator Accession No. : 68	Lambda-cl_gene Pathway No. : 295	0.0058 (s^-1)	0 (s^-1)	-	-	Substrate lambda-cl_mRNA Product Degraded_ lambda-cl_mRNA
This reaction denotes the degradation of the lambda cl m-RNA, the half life of which is two minutes. t1/2 = 0.693/k where k denotes kf