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Molecule Parameter List for Degraded_TetR

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
Degraded_TetR participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000001

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

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

    Accession No. : 69
  • TetR
    Pathway No. : 299
    03Yes
    Degradation product of TetR protein

    Degraded_TetR 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
  • TetR_
    degradation
  • Quorum_
    repressilator

    Accession No. : 69
  • TetR
    Pathway No. : 299
    0.0057
    (s^-1)
    0
    (s^-1)
    --Substrate
    TetR-1

    Product
    Degraded_TetR
    This reaction denotes the degradation of TetR, kf is chosen from a random gaussian distribution. Ref: Fig 2 Garcia and Elowitz et al. (2004) PNAS 101(30) 10955 - 60



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