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Molecule Parameter List for lambda-cl_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 |
lambda-cl_mRNA1 acting as a Molecule in Quorum_repressilator Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | lambda-cl_mRNA1 | Quorum_
repressilator
Accession No. : 69 | Lambda-cl
Pathway No. : 301 | 0 | 3 | No | | The m-RNA transcribed by the Lcl operator Elowitz etal Nature 2000 Vol 403:335-338 |
lambda-cl_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 | lambda-cl_mRNA1 /
lambda-cl_
translation
| Quorum_
repressilator
Accession No. : 69 | Lambda-cl
Pathway No. : 301 | 0.000555595 | 0.167 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Amino_Acids
Product
Lambda-cl-1
| | Translation the lambda cl mRNA. Rates from Box 1 Elowitz, M. et al (2000) Nature 403:335-338 |
lambda-cl_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 | Lambda-cl_
operator /
Lambda-cl_
basal_
transcription
| Quorum_
repressilator
Accession No. : 69 | Lambda-cl
Pathway No. : 301 | 0.000555607 | 216 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Nucleotides
Product
lambda-cl_mRNA1
| | | Basal transcription of the Lambda cl gene. Rates from Fig 2 Garcia and Elowitz et al. (2004) PNAS 101:10955-60 | | 2 | Lambda-cl_
operator_1st_
bound /
Lambda-cl_
transcription
| Quorum_
repressilator
Accession No. : 69 | Lambda-cl
Pathway No. : 301 | 0.0005556 | 0.0005 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Nucleotides
Product
lambda-cl_mRNA1
| | | Transcription of the Lambda cl gene with only one of its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338 | | 3 | Lambda-cl_
operator_2nd_
bound /
Lambda-cl_
transcription1
| Quorum_
repressilator
Accession No. : 69 | Lambda-cl
Pathway No. : 301 | 0.0005556 | 0.0005 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
Nucleotides
Product
lambda-cl_mRNA1
| | | Transcription of the Lambda cl gene with both its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338 |
lambda-cl_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 | lambda-cl_mRNA_
degradation | Quorum_
repressilator
Accession No. : 69 | Lambda-cl
Pathway No. : 301 | 0.0058
(s^-1) | 0
(s^-1) | - | - | Substrate
lambda-cl_mRNA1
Product
Degraded_
lambda-cl_mRNA
| | This reaction denotes the degradation of the lambda cl 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
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