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Molecule Parameter List for Degraded_AI

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

Degraded_AI participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	2	0	0	0	0	0	2

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

Degraded_AI acting as a Molecule in  Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Degraded_AI	Quorum_ repressilator Accession No. : 69	Shared_Object_ Quorum_ repressilator Pathway No. : 298	0	3	Yes
Degradation product of autoinducer
Degraded_AI	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0	3	Yes
Degradation product of autoinducer.

Degraded_AI 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
1	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
2	AI_degradation	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0.2 (s^-1)	0 (s^-1)	-	-	Substrate AI-1 Product Degraded_AI
	Degradation of autoinducer. kf = 0.2, McMillen et al (2002) PNAS 99(2): 679-84