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Molecule Parameter List for lac_mRNA1 | 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_mRNA1 acting as a Molecule in Quorum_repressilator Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | lac_mRNA1 | Quorum_
repressilator
Accession No. : 69 | LacI
Pathway No. : 300 | 0 | 3 | No | | The m-RNA transcribed by the lac operator Elowitz, M. et al. (2000) Nature 403:335-338 |
lac_mRNA1 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_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 |
lac_mRNA1 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_operator /
Lac_basal_
transcription
| Quorum_
repressilator
Accession No. : 69 | LacI
Pathway No. : 300 | 0.000555607 | 216 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Nucleotides
Product
lac_mRNA1
| | | Basal transcription of the Lac gene. Rates from Fig2 Garcia & Elowitz et al. (2004) PNAS 101:10955-60 | | 2 | Lac_operator_
1st_bound /
Lac_
transcription
| Quorum_
repressilator
Accession No. : 69 | LacI
Pathway No. : 300 | 0.0005556 | 0.0005 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Nucleotides
Product
lac_mRNA1
| | | Transcription of the lac gene with only one of its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) N Nature 403: 335-338 | | 3 | Lac_operator_
2nd_bound /
Lac_
transcription1
| Quorum_
repressilator
Accession No. : 69 | LacI
Pathway No. : 300 | 0.0005556 | 0.0005 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Nucleotides
Product
lac_mRNA1
| | | Transcription of the Lac gene with both its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403: 335-338 |
lac_mRNA1 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 | lac_mRNA_
degradation | Quorum_
repressilator
Accession No. : 69 | LacI
Pathway No. : 300 | 0.0058
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
lac_mRNA1
Product
Degraded_lac_
mRNA
Nucleotides
| | This reaction denotes the degradation of the lac m-RNA, the half life of which is two minutes. t1/2 = 0.693/k where k denotes kf 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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