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Molecule Parameter List for Lac-1 | 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 |
Lac-1 acting as a Molecule in Quorum_repressilator Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | Lac-1 | Quorum_
repressilator
Accession No. : 69 | LacI
Pathway No. : 300 | 0 | 3 | No | | Lac translated from lac m-RNA Derived from Figure 1(c) stochastic version Elowitz, M. et al. (2000) Nature 403:335-338 |
Lac-1 acting as a Product of an Enzyme in Quorum_repressilator Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | lac_mRNA1 /
lac_translation | Quorum_
repressilator
Accession No. : 69 | LacI
Pathway No. : 300 | 0.000555595 | 0.167 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Amino_Acids
Product
Lac-1
| | | Translation of the lac mRNA. Rates from Box 1 Elowitz, M. et al (2000) Nature 403: 335-338 | | 2 | lac_mRNA /
lac_translation | Quorum_
repressilator
Accession No. : 69 | LacI_2nd_copy
Pathway No. : 302 | 0.000555595 | 0.167 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Amino_Acids
Product
Lac-1
| | | Translation of the lac mRNA. Rates from Box 1 Elowitz, M. et al (2000) Nature 403: 335-338 |
Lac-1 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 | | 1 | TetR_operator_
inhibition_
reaction | Quorum_
repressilator
Accession No. : 69 | TetR
Pathway No. : 299 | 1000.01
(uM^-1 s^-1) | 224
(s^-1) | Kd(bf) = 0.224(uM) | - | Substrate
Lac-1
TetR_operator
Product
TetR_operator_
1st_bound
| | | It signifies the first binding of the repressor with the operator Kf = 1 /nM/sec Kb = 224 /sec Box 1 Elowitz, M. et al. (2000) Nature 403:335-338 | | 2 | TetR_operator_
inhibition_
reaction[1] | Quorum_
repressilator
Accession No. : 69 | TetR
Pathway No. : 299 | 1000.01
(uM^-1 s^-1) | 9
(s^-1) | Kd(bf) = 0.009(uM) | - | Substrate
Lac-1
TetR_operator_
1st_bound
Product
TetR_operator_
2nd_bound
| | | It signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 9 /sec Box 1 Elowitz, M. et al. (2000) Nature 403:335-338 | | 3 | Lac_degradation | Quorum_
repressilator
Accession No. : 69 | LacI
Pathway No. : 300 | 0.0057
(s^-1) | 0
(s^-1) | - | - | Substrate
Lac-1
Product
Degraded_lac
| | | This reaction denotes the degradation of Lac, Kf is chosen from a random gaussian distribution. Ref: Fig 2 Garcia & Elowitz et al (2004) PNAS 101(30) 10955-60 | | 4 | 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 | | 5 | 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
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