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