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Molecule Parameter List for Lac_operator_activator_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 |
| Lac_operator_activator_bound 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 | 1 | 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 |
Lac_operator_activator_bound acting as a Molecule in Quorum_repressilator Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | Lac_operator_activator_bound | Quorum_
repressilator
Accession No. : 69 | LacI_2nd_copy
Pathway No. : 302 | 0 | 3 | No | | This represents the promoter bound to the activator. |
Lac_operator_activator_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 | Lac_operator_
activator_bound /
Lac_active_
transcription
| Quorum_
repressilator
Accession No. : 69 | LacI_2nd_copy
Pathway No. : 302 | 0.0005556 | 20 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Nucleotides
Product
lac_mRNA
| | Lac transcription from the activator bound Lac gene. kcat is taken from Garcia & Elowitz et al. (2004) PNAS 101: 10955-60 |
Lac_operator_activator_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 | Lac_operator_
activation_
reaction | Quorum_
repressilator
Accession No. : 69 | LacI_2nd_copy
Pathway No. : 302 | 1000
(s^-1) | 224
(s^-1) | Keq = 0.224(uM) | 0.001sec | Substrate
2_LuxR-AI
Product
Lac_operator_
activator_bound
| | It signifies the binding of the activator with the operator Kf = 1 /nM/sec Kb = 224 /sec Used first binding rates for repressor from 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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