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Molecule Parameter List for luxI_mRNA

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

luxI_mRNA 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	3	1	0

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

luxI_mRNA acting as a Molecule in  Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
luxI_mRNA	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0	3	No
The m-RNA transcribed by the luxI operator Garcia-Ojalvo, J. et al. (2004) PNAS USA 101(30):10955-10960 As described for components of the Repressilator by Elowitz, M. et al. (2000) Nature 403:335-338

luxI_mRNA 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
luxI_mRNA / luxI_ translation	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0.000555595	0.167	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Amino_Acids Product LuxI
Rates from Box 1 Elowitz et al (2003) Nature 403:335-338

luxI_mRNA 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	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
2	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
3	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

luxI_mRNA 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
luxI_mRNA_ degradation	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0.0058 (s^-1)	0 (s^-1)	-	-	Substrate luxI_mRNA Product Degraded_luxI_ mRNA
This reaction denotes the degradation of the luxI m-RNA, the half life of which is two minutes. t1/2 = 0.693/k where k denotes kf Garcia-Ojalvo, J. et al. (2004) PNAS USA 101(30):10955-10960 As described for components of the Repressilator by Elowitz, M. et al. (2000) Nature 403:335-338