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Molecule Parameter List for tetR_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

*tetR_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.

tetR_mRNA acting as a Molecule in Repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
tetR_mRNA	Repressilator Accession No. : 68	TetR_gene Pathway No. : 297	0	3	No
The mRNA transcribed by the TetR operator Elowitz, M, et al. (2000) Nature 403:335-338

tetR_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
tetR_mRNA / tetR_ translation	Repressilator Accession No. : 68	TetR_gene Pathway No. : 297	0.000555595	0.167	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Amino_Acids Product TetR
Translation of the tetR mRNA. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338

tetR_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	TetR_operator / TetR_basal_ transcription	Repressilator Accession No. : 68	TetR_gene Pathway No. : 297	0.0005556	0.5	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product tetR_mRNA
	Basal transcription of the Tet R gene. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
2	TetR_operator_ 1st_bound / TetR_ transcription	Repressilator Accession No. : 68	TetR_gene Pathway No. : 297	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product tetR_mRNA
	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	Repressilator Accession No. : 68	TetR_gene Pathway No. : 297	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product tetR_mRNA
	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_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
tetR_mRNA_ degradation	Repressilator Accession No. : 68	TetR_gene Pathway No. : 297	0.0058 (s^-1)	0 (s^-1)	-	-	Substrate tetR_mRNA 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

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