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Reaction List for pathway LuxI (Pathway Number 303)

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 reactions is not considered.
  Name KfKbKdtauSubstrateProduct
1 2_LuxR-AI_
degradation		0.2
(s^-1)		0
(s^-1)		--2_LuxR-AI
  • Degraded_2_
    LuxR-AI
    •   Degradation of the dimer of the complex between Lux R and autoinducer. kf = 0.2, McMillen et al (2002) PNAS 99(2) 679-84
    2 AI_degradation0.2
    (s^-1)    		0
    (s^-1)    		--AI-1
    		Degraded_AI
      Degradation of autoinducer. kf = 0.2, McMillen et al (2002) PNAS 99(2): 679-84
    3 AI_diffusion2
    (s^-1)    		2
    (s^-1)    		Keq = 1(uM)0.25secAI-1
  • AI-extracellular
    •   Diffusion of the autoinducer from inside the cell to the outside and vice versa. Garcia-Ojalvo, J et al. (2004) PNAS USA 101(30):10955-10960
    4 AI_form0.01
    (s^-1)    		0
    (s^-1)    		--LuxI
    		AI-1
      Formation of Autoinducer The forward rate has taken from PNAS 101: 10955-60 by Garcia & Elowitz et al (2004)
    5 LuxI_
    degradation    		25
    (s^-1)    		0
    (s^-1)    		--LuxI
    		degraded_LuxI
      This reaction denotes degradation of LuxI, kf = 25, McMillen et al (2002) PNAS 99(2): 679-84
    6 luxI_mRNA_
    degradation    		0.0058
    (s^-1)    		0
    (s^-1)    		--luxI_mRNA
  • Degraded_luxI_
    mRNA
    •   This reaction denotes the degradation of the luxI m-RNA, the half life of which is two minutes. t1/2 = 0.693/k where k denotes kf 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
    7 LuxI_operator_
    inhibitor_
    reaction    		1000.01
    (uM^-1 s^-1)    		224
    (s^-1)    		Kd(bf) = 0.224(uM)-LuxI_operator
    Lac-1
  • 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
    8 LuxI_operator_
    inhibitor_
    reaction[1]    		1000.01
    (uM^-1 s^-1)    		9
    (s^-1)    		Kd(bf) = 0.009(uM)-
  • LuxI_operator_
    1st_bound
    Lac-1
  • 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
    9 LuxR-AI_
    complex_
    dimerization    		1.8
    (uM^-1 s^-1)    		0.1
    (s^-1)    		Keq = 0.0556(uM)-LuxR-AI
    LuxR-AI
    		2_LuxR-AI
      Dimerization of the complex between Lux R and the autoinducer protein Kf = 1.8e+18 /sec/M = 1.8 /sec/uM McMillen, M. et al. (2002) PNAS USA 99(2):679-684
    10 LuxR-AI_
    degradation    		0.2
    (s^-1)    		0
    (s^-1)    		--LuxR-AI
  • Degraded_
    LuxR-AI
    •   Degradation of autoinducer complexed to LuxR, kf = 0.2, McMillen et al (2002) PNAS 99(2) 679 - 84
    11 LuxR_binding_
    autoinducer    		5
    (uM^-1 s^-1)    		0.1
    (s^-1)    		Kd(bf) = 0.02(uM)-AI-1
    LuxR
    		LuxR-AI
      Binding of Lux R to the autoinducer protein Kf = 5e+06 /M = 5 /uM McMillen, M. et al. (2002) PNAS USA 99(2): 679-84
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