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Molecule Parameter List for LuxI_operator_1st_bound | 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 |
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 |
LuxI_operator_1st_bound acting as a Molecule in Quorum_repressilator Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | LuxI_operator_1st_bound | Quorum_
repressilator
Accession No. : 69 | LuxI
Pathway No. : 303 | 0 | 3 | No | | This represents the promoter with one of its sites bound by the inhibitor. Garcia-Ojalvo, J. et al. (2004) PNAS USA 101(30):10955-10960 As described for components of the Repressilator by Elowitz, M. et al. (2000) Nature 403:335-338 |
LuxI_operator_1st_bound acting as an Enzyme in Quorum_repressilator Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | LuxI_operator_
1st_bound /
LuxI_
transcription
| Quorum_
repressilator
Accession No. : 69 | LuxI
Pathway No. : 303 | 0.0005556 | 0.0005 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Nucleotides
Product
luxI_mRNA
| | Transcription of the LuxI gene with only one of its promoter sites activated. Garcia-Ojalvo, J. et al (2004) PNAS USA 101(30):10955-10960 As described for components of the Repressilator in Box 1 Elowitz, M. et al. (2000) Nature 403:335-338 |
LuxI_operator_1st_bound 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 | LuxI_operator_
inhibitor_
reaction[1] | Quorum_
repressilator
Accession No. : 69 | LuxI
Pathway No. : 303 | 1000.01
(uM^-1 s^-1) | 9
(s^-1) | Kd(bf) = 0.009(uM) | - | Substrate
Lac-1
LuxI_operator_
1st_bound
Product
LuxI_operator_
2nd_bound
| | This signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 9 /sec Garcia-Ojalvo, J. et al. (2004) PNAS USA 101(30):10955-10960 As described for components of the Repressilator in Box 1 Elowitz, M. et al. (2000) Nature 403:335-338 |
LuxI_operator_1st_bound 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 | LuxI_operator_
inhibitor_
reaction | Quorum_
repressilator
Accession No. : 69 | LuxI
Pathway No. : 303 | 1000.01
(uM^-1 s^-1) | 224
(s^-1) | Kd(bf) = 0.224(uM) | - | Substrate
Lac-1
LuxI_operator
Product
LuxI_operator_
1st_bound
| | This signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 224 /sec Garcia-Ojalvo, J. et al. (2004) PNAS USA 101(30):10955-10960 As described for components of the Repressilator in Box 1 Elowitz, M. et al. (2000) Nature 403:335-338 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details. |
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