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Molecule Parameter List for Degraded_TetR

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_TetR 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	0	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

Degraded_TetR acting as a Molecule in  Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Degraded_TetR	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0	3	Yes
Degradation product of TetR protein

Degraded_TetR 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
TetR_ degradation	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.0057 (s^-1)	0 (s^-1)	-	-	Substrate TetR-1 Product Degraded_TetR
This reaction denotes the degradation of TetR, kf is chosen from a random gaussian distribution. Ref: Fig 2 Garcia and Elowitz et al. (2004) PNAS 101(30) 10955 - 60