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Molecule Parameter List for Amino_Acids

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

*Amino_Acids* participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	5	0	0	5	0	0	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

Amino_Acids acting as a Molecule in Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Amino_Acids	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.0006	3	Yes

Amino_Acids	Quorum_ repressilator Accession No. : 69	LacI Pathway No. : 300	0.0006	3	Yes

Amino_Acids	Quorum_ repressilator Accession No. : 69	Lambda-cl Pathway No. : 301	0.0006	3	Yes

Amino_Acids	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.0006	3	Yes

Amino_Acids	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0.0006	3	Yes

Amino_Acids acting as a Substrate for 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_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
2	lac_mRNA1 / lac_translation	Quorum_ repressilator Accession No. : 69	LacI Pathway No. : 300	0.000555595	0.167	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Amino_Acids Product Lac-1
	Translation of the lac mRNA. Rates from Box 1 Elowitz, M. et al (2000) Nature 403: 335-338
3	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
4	lac_mRNA / lac_translation	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.000555595	0.167	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Amino_Acids Product Lac-1
	Translation of the lac mRNA. Rates from Box 1 Elowitz, M. et al (2000) Nature 403: 335-338
5	luxI_mRNA / luxI_ translation	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0.000555595	0.167	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Amino_Acids Product LuxI
	Rates from Box 1 Elowitz et al (2003) Nature 403:335-338

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