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Molecule Parameter List for LuxI_operator_1st_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
LuxI_operator_1st_bound participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1010011

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Quorum_
    repressilator
  • 69Network
    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_operator_1st_bound acting as a Molecule in  
    Quorum_repressilator Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    LuxI_operator_1st_bound
  • Quorum_
    repressilator

    Accession No. : 69
  • LuxI
    Pathway No. : 303
    03No
    This represents the promoter with one of its sites bound by the inhibitor. 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_operator_1st_bound acting as an Enzyme in  
    Quorum_repressilator Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
  • LuxI_operator_
    1st_bound
     /
  • LuxI_
    transcription
  • Quorum_
    repressilator

    Accession No. : 69
  • LuxI
    Pathway No. : 303
    0.00055560.00054Classical 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

    LuxI_operator_1st_bound 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.
    NameAccession NamePathway NameKfKbKdtauReagents
  • LuxI_operator_
    inhibitor_
    reaction[1]
  • Quorum_
    repressilator

    Accession No. : 69
  • LuxI
    Pathway No. : 303
    1000.01
    (uM^-1 s^-1)
    9
    (s^-1)
    Kd(bf) = 0.009(uM)-Substrate
    Lac-1
  • LuxI_operator_
    1st_bound


    Product
  • LuxI_operator_
    2nd_bound

  • This signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 9 /sec 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_operator_1st_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.
    NameAccession NamePathway NameKfKbKdtauReagents
  • LuxI_operator_
    inhibitor_
    reaction
  • Quorum_
    repressilator

    Accession No. : 69
  • LuxI
    Pathway No. : 303
    1000.01
    (uM^-1 s^-1)
    224
    (s^-1)
    Kd(bf) = 0.224(uM)-Substrate
    Lac-1
    LuxI_operator

    Product
  • LuxI_operator_
    1st_bound

  • This signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 224 /sec 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



    Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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