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Molecule Parameter List for AI-extracellular

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

AI-extracellular 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	0	1	1

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

AI-extracellular acting as a Molecule in  Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
AI-extracellular	Quorum_ repressilator Accession No. : 69	Shared_Object_ Quorum_ repressilator Pathway No. : 298	0	3	No
Extracellular AI

AI-extracellular 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
AI_degradation	Quorum_ repressilator Accession No. : 69	Shared_Object_ Quorum_ repressilator Pathway No. : 298	3 (s^-1)	0 (s^-1)	-	-	Substrate AI-extracellular Product Degraded_AI
Degradation of autoinducer Garcia-Ojalvo, J et al. (2004) PNAS USA 101(30):10955-10960

AI-extracellular acting as a Product 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
AI_diffusion	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	2 (s^-1)	2 (s^-1)	Keq = 1(uM)	0.25sec	Substrate AI-1 Product AI-extracellular
Diffusion of the autoinducer from inside the cell to the outside and vice versa. Garcia-Ojalvo, J et al. (2004) PNAS USA 101(30):10955-10960