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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
lambda-cl_mRNA1 participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1010310

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

    lambda-cl_mRNA1 acting as a Molecule in  
    Quorum_repressilator Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    lambda-cl_mRNA1
  • Quorum_
    repressilator

    Accession No. : 69
  • Lambda-cl
    Pathway No. : 301
    03No
    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 NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    lambda-cl_mRNA1 /
  • lambda-cl_
    translation
  • Quorum_
    repressilator

    Accession No. : 69
  • Lambda-cl
    Pathway No. : 301
    0.0005555950.1674Classical 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 NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1
  • Lambda-cl_
    operator
      /
  • Lambda-cl_
    basal_
    transcription
  • Quorum_
    repressilator

    Accession No. : 69
  • Lambda-cl
    Pathway No. : 301
    0.0005556072164Classical 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
    0.00055560.00054Classical 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
    0.00055560.00054Classical 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.
    NameAccession NamePathway NameKfKbKdtauReagents
  • 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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