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Molecule Parameter List for tetR_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
tetR_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

    tetR_mRNA1 acting as a Molecule in  
    Quorum_repressilator Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    tetR_mRNA1
  • Quorum_
    repressilator

    Accession No. : 69
  • TetR
    Pathway No. : 299
    03No
    The mRNA transcribed by the TetR operator Elowitz, M, et al. (2000) Nature 403:335-338

    tetR_mRNA1 acting as an Enzyme in  
    Quorum_repressilator Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    tetR_mRNA1 /
  • tetR_
    translation
  • Quorum_
    repressilator

    Accession No. : 69
  • TetR
    Pathway No. : 299
    0.0005555950.1674Classical Michaelis-Menten
    V = Etot.S.Kcat/Km+S
    Substrate
    Amino_Acids

    Product
    TetR-1
    Translation of the tetR mRNA. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403:335-338

    tetR_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
    1TetR_operator  /
  • TetR_basal_
    transcription
  • Quorum_
    repressilator

    Accession No. : 69
  • TetR
    Pathway No. : 299
    0.0005556072164Classical 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
    0.00055560.00054Classical 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
    0.00055560.00054Classical 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

    tetR_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
  • tetR_mRNA_
    degradation
  • Quorum_
    repressilator

    Accession No. : 69
  • TetR
    Pathway No. : 299
    0.0058
    (s^-1)
    0
    (s^-1)
    --Substrate
    tetR_mRNA1

    Product
  • Degraded_tetR_
    mRNA

  • This reaction denotes the degradation of the tetR 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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