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Molecule Parameter List for Lac-1

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
Lac-1 participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000250

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

    Lac-1 acting as a Molecule in  
    Quorum_repressilator Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    Lac-1
  • Quorum_
    repressilator

    Accession No. : 69
  • LacI
    Pathway No. : 300
    03No
    Lac translated from lac m-RNA Derived from Figure 1(c) stochastic version Elowitz, M. et al. (2000) Nature 403:335-338

    Lac-1 acting as a Product of an Enzyme in  
    Quorum_repressilator Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1lac_mRNA1  /
    lac_translation
  • Quorum_
    repressilator

    Accession No. : 69
  • LacI
    Pathway No. : 300
    0.0005555950.1674Classical 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
    2lac_mRNA  /
    lac_translation
  • Quorum_
    repressilator

    Accession No. : 69
  • LacI_2nd_copy
    Pathway No. : 302
    0.0005555950.1674Classical 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-1 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
    1
  • TetR_operator_
    inhibition_
    reaction
  • Quorum_
    repressilator

    Accession No. : 69
  • TetR
    Pathway No. : 299
    1000.01
    (uM^-1 s^-1)
    224
    (s^-1)
    Kd(bf) = 0.224(uM)-Substrate
    Lac-1
    TetR_operator

    Product
  • TetR_operator_
    1st_bound

  •   It signifies the first binding of the repressor with the operator Kf = 1 /nM/sec Kb = 224 /sec Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
    2
  • TetR_operator_
    inhibition_
    reaction[1]
  • Quorum_
    repressilator

    Accession No. : 69
  • TetR
    Pathway No. : 299
    1000.01
    (uM^-1 s^-1)
    9
    (s^-1)
    Kd(bf) = 0.009(uM)-Substrate
    Lac-1
  • TetR_operator_
    1st_bound


    Product
  • TetR_operator_
    2nd_bound

  •   It signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 9 /sec Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
    3Lac_degradation
  • Quorum_
    repressilator

    Accession No. : 69
  • LacI
    Pathway No. : 300
    0.0057
    (s^-1)
    0
    (s^-1)
    --Substrate
    Lac-1

    Product
    Degraded_lac
      This reaction denotes the degradation of Lac, Kf is chosen from a random gaussian distribution. Ref: Fig 2 Garcia & Elowitz et al (2004) PNAS 101(30) 10955-60
    4
  • 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
    5
  • 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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