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Molecule Parameter List for Nucleotides

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

*Nucleotides* participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	5	0	0	16	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

Nucleotides acting as a Molecule in Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Nucleotides	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.0006	3	Yes

Nucleotides	Quorum_ repressilator Accession No. : 69	LacI Pathway No. : 300	0.0006	3	Yes

Nucleotides	Quorum_ repressilator Accession No. : 69	Lambda-cl Pathway No. : 301	0.0006	3	Yes

Nucleotides	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.0006	3	Yes

Nucleotides	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0.0006	3	Yes

Nucleotides acting as a Substrate for an Enzyme in Quorum_repressilator Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	TetR_operator / TetR_basal_ transcription	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.000555607	216	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product tetR_mRNA1
	Basal transcription of the Tet R gene. Rates from Fig 2 Garcia & Elowitz et al. (2004) PNAS Vol.101
2	TetR_operator_ 1st_bound / TetR_ transcription	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product tetR_mRNA1
	Transcription of the TetR gene with only one of its promoter sites activated. Rates from Box 1 Elowitz, M. et al (2000) Nature 403:335-338
3	TetR_operator_ 2nd_bound / TetR_ transcription1	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product tetR_mRNA1
	Transcription of the TetR gene with both its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
4	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
5	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
6	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
7	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
8	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
9	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
10	Lac_operator / Lac_basal_ transcription	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.000555607	216	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product lac_mRNA
	Basal transcription of the Lac gene. Rates from Fig 2 Garcia and Elowitz et al.(2004) PNAS 101: 10955-60
11	Lac_operator_ 1st_bound / Lac_ transcription	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product lac_mRNA
	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
12	Lac_operator_ 2nd_bound / Lac_ transcription1	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product lac_mRNA
	Transcription of the Lac gene with both its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403: 335-338
13	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
14	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
15	LuxI_operator_ 2nd_bound / LuxI_ transcription1	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
16	LuxI_operator / LuxI_basal_ transcription	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0.000555607	216	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product luxI_mRNA
	Basal transcription of the Lux I gene. 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

Nucleotides 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_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
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