##### Model ################ # TITLE:NFS 2004_10_27 # INFO:2004_10_27 # CONVERSION TYPE # GENE-PROTEIN:TPP_RAPID # METABOLIC:MM N_VAR ; 64; # num of variables(all) N_ALGEBR; 45; # num of variables(Algebraic Eq) #Y_START ; index; initial_value; tag #comment Y_START ; 1; 1.0811e-09; NR1.cyt # Y_START ; 2; 2.1760e-11; glnAP1.cyt # Y_START ; 3; 9.9944e-10; glnAp2.cyt # Y_START ; 4; 3.3448e-10; glnLp.cyt # Y_START ; 5; 1.3201e-08; NR1-P.cyt # Y_START ; 6; 9.0845e-13; NR2.cyt # Y_START ; 7; 6.5435e-11; NR2-P.cyt # Y_START ; 8; 4.9724e-10; P2.cyt # Y_START ; 9; 3.9254e-12; GlnK.cyt # Y_START ; 10; 1.9496e-11; P2-UMP.cyt # Y_START ; 11; 1.5233e-13; GlnK-UMP.cyt # Y_START ; 12; 8.5247e-13; UTUR.cyt # Y_START ; 13; 2.8024e-09; GS.cyt # Y_START ; 14; 3.6782e-10; GS-AMP.cyt # Y_START ; 15; 4.8327e-09; P1.cyt # Y_START ; 16; 9.9860e-10; En(GlnK).cyt # Y_START ; 17; 9.7877e-10; En(Nac).cyt # Y_START ; 18; 9.7824e-10; NR1:glnAP1.cyt # Y_START ; 19; 5.6130e-13; glnAp2:NR1-P:NR1-P:NR1-P:NR1-P.cyt # Y_START ; 20; 6.6552e-10; NR1:glnLp.cyt # Y_START ; 21; 3.6916e-07; UTUR:glutamine.cyt # Y_START ; 22; 2.8668e-07; UTUR:aKG.cyt # Y_START ; 23; 1.4084e-11; P2:P1.cyt # Y_START ; 24; 1.0057e-11; GS:AMP:P2:P1.cyt # Y_START ; 25; 1.1119e-13; GlnK:P1.cyt # Y_START ; 26; 7.9398e-14; GS:AMP:GlnK:P1.cyt # Y_START ; 27; 2.0991e-08; P2-UMP:P1.cyt # Y_START ; 28; 8.1923e-12; GS-AMP:AMP:P2-UMP:P1.cyt # Y_START ; 29; 1.6401e-10; GlnK-UMP:P1.cyt # Y_START ; 30; 6.4009e-14; GS-AMP:AMP:GlnK-UMP:P1.cyt # Y_START ; 31; 1.5256e-10; GlnK-UMP:UMP:UTUR:glutamine.cyt # Y_START ; 32; 3.1095e-11; NR2:P2.cyt # Y_START ; 33; 2.4548e-13; NR2:GlnK.cyt # Y_START ; 34; 1.5758e-08; NR1-P:P:NR2:P2.cyt # Y_START ; 35; 1.2440e-10; NR1-P:P:NR2:GlnK.cyt # Y_START ; 36; 1.3993e-12; NR1-P:En(GlnK).cyt # Y_START ; 37; 1.5901e-08; NR1:NR2-P.cyt # Y_START ; 38; 2.1233e-11; NR1-P:En(Nac).cyt # Y_START ; 39; 1.9526e-08; P2-UMP:UMP:UTUR:glutamine.cyt # Y_START ; 40; 1.9526e-08; P2:UMP:UTUR:aKG.cyt # Y_START ; 41; 1.5415e-10; GlnK:UMP:UTUR:aKG.cyt # Y_START ; 42; 1.2750e-10; NR1:acetly.cyt # Y_START ; 43; 1.5981e-08; NR2:ATP.cyt # Y_START ; 44; 3.3004e-13; NR2-P:ADP:P2.cyt # Y_START ; 45; 2.6055e-15; NR2-P:ADP:GlnK.cyt # Y_START ; 46; 2.3376e-04; glutamine.cyt # Y_START ; 47; 2.2917e-04; aKG.cyt # Y_START ; 48; 8.2392e-05; glutamate.cyt # Y_START ; 49; 1.0495e-12; mRNA(GlnK).cyt # Y_START ; 50; 3.0333e-09; nac.cyt # Y_START ; 51; 5.5801e-12; mRNA(GS).cyt # Y_START ; 52; 5.3082e-12; mRNA(nac).cyt # Y_START ; 53; 8.3758e-11; mRNA(NR1).cyt # Y_START ; 54; 8.3758e-11; mRNA(NR2).cyt # Y_START ; 55; 1.8753e-08; TNR1.cyt # Y_START ; 56; 2.9109e-08; TNR1-P.cyt # Y_START ; 57; 3.1895e-08; TNR2.cyt # Y_START ; 58; 1.5966e-08; TNR2-P.cyt # Y_START ; 59; 3.5837e-08; TP2.cyt # Y_START ; 60; 2.8292e-10; TGlnK.cyt # Y_START ; 61; 4.0544e-08; TP2-UMP.cyt # Y_START ; 62; 3.1679e-10; TGlnK-UMP.cyt # Y_START ; 63; 2.8125e-09; TGS.cyt # Y_START ; 64; 3.7608e-10; TGS-AMP.cyt # #PARAM;name;index;val;val_start;num_survey;D/R/S;change-val;GA_min;GA_max;tag #comment PARAM ;constantPlayer; 1; 1e-09;;0;D;;;; DNA(GlnK).cyt # PARAM ;constantPlayer; 2; 1e-06;;0;D;;;; acetly.cyt # PARAM ;constantPlayer; 3; 1;;0;D;;;; acetlyphospate.cyt # Not Used!! PARAM ;constantPlayer; 4; 0.01;;0;D;;;; ATP.cyt # PARAM ;constantPlayer; 5; 0.01;;0;D;;;; ADP.cyt # PARAM ;constantPlayer; 6; 1e-09;;0;D;;;; DNA(nac).cyt # PARAM ;constantPlayer; 7; 1e-09;;0;D;;;; DNA1(NR1).cyt # PARAM ;constantPlayer; 8; 1e-09;;0;D;;;; DNA2(NR1).cyt # PARAM ;constantPlayer; 9; 1e-09;;0;D;;;; DNA1(NR2).cyt # PARAM ;constantPlayer; 10; 1e-09;;0;D;;;; DNA2(NR2).cyt # PARAM ;constantPlayer; 11; 1e-09;;0;D;;;; DNA1(GS).cyt # PARAM ;constantPlayer; 12; 1e-09;;0;D;;;; DNA2(GS).cyt # PARAM ;constantPlayer; 13; 1;;0;D;;;; P.cyt # PARAM ;constantPlayer; 14; 0.01;;0;D;;;; UMP.cyt # PARAM ;constantPlayer; 15; 0.01;;0;D;;;; AMP.cyt # PARAM ;constantPlayer; 16; 1e-09;;0;D;;;; TglnAP1.cyt # PARAM ;constantPlayer; 17; 1e-09;;0;D;;;; TglnAp2.cyt # PARAM ;constantPlayer; 18; 1e-09;;0;D;;;; TglnLp.cyt # PARAM ;constantPlayer; 19; 6.952e-07;;0;D;;;; TUTUR.cyt # PARAM ;constantPlayer; 20; 2.602e-08;;0;D;;;; TP1.cyt # PARAM ;constantPlayer; 21; 1e-09;;0;D;;;; TEn(GlnK).cyt # PARAM ;constantPlayer; 22; 1e-09;;0;D;;;; TEn(Nac).cyt # PARAM ;constantPlayer; 23; 0.0001;;0;D;;;; NH3.cyt # PARAM ;constantPlayer; 24; 1e-07;;0;D;;;; GOGAT.cyt # PARAM ;constantPlayer; 25; 1e-07;;0;D;;;; GDH.cyt # PARAM ;constantPlayer; 26; 0.0001;;0;D;;;; Dummy.cyt # PARAM ;Kb ; 1;3.838822E+010;;0;D;;;; binding_constant_NR2:P2.cyt_NR1-P.cyt # PARAM ;Kb ; 2;3.838822E+010;;0;D;;;; binding_constant_NR2:GlnK.cyt_NR1-P.cyt # PARAM ;Kb ; 3;4.158426E+010;;0;D;;;; binding_constant_NR1.cyt_glnAP1.cyt # PARAM ;Kb ; 4;1.166109E+007;;0;D;;;; binding_constant_NR1-P.cyt_glnAp2.cyt # PARAM ;Kb ; 5;1.840484E+009;;0;D;;;; binding_constant_NR1.cyt_glnLp.cyt # PARAM ;Kb ; 6;1.369784E+010;;0;D;;;; binding_constant_UTUR:aKG.cyt_P2.cyt_UMP.cyt # PARAM ;Kb ; 7;1.369784E+010;;0;D;;;; binding_constant_UTUR:aKG.cyt_GlnK.cyt_UMP.cyt # PARAM ;Kb ; 8;1.852542E+009;;0;D;;;; binding_constant_UTUR.cyt_glutamine.cyt # PARAM ;Kb ; 9;1.467449E+009;;0;D;;;; binding_constant_UTUR.cyt_aKG.cyt # PARAM ;Kb ; 10;2.713008E+009;;0;D;;;; binding_constant_UTUR:glutamine.cyt_P2-UMP.cyt # PARAM ;Kb ; 11;2.713008E+009;;0;D;;;; binding_constant_UTUR:glutamine.cyt_GlnK-UMP.cyt # PARAM ;Kb ; 12;2.548103E+010;;0;D;;;; binding_constant_GlnK:P1.cyt_AMP.cyt_GS.cyt # PARAM ;Kb ; 13;2.548103E+010;;0;D;;;; binding_constant_P2:P1.cyt_AMP.cyt_GS.cyt # PARAM ;Kb ; 14;1.061055E+006;;0;D;;;; binding_constant_GlnK-UMP:P1.cyt_GS-AMP.cyt # PARAM ;Kb ; 15;1.061055E+006;;0;D;;;; binding_constant_P2-UMP:P1.cyt_GS-AMP.cyt # PARAM ;Kb ; 16;5.861139E+006;;0;D;;;; binding_constant_P1.cyt_P2.cyt # PARAM ;Kb ; 17;5.861139E+006;;0;D;;;; binding_constant_GlnK.cyt_P1.cyt # PARAM ;Kb ; 18;2.227830E+011;;0;D;;;; binding_constant_P1.cyt_P2-UMP.cyt # PARAM ;Kb ; 19;2.227830E+011;;0;D;;;; binding_constant_GlnK-UMP.cyt_P1.cyt # PARAM ;Kb ; 20;6.883653E+010;;0;D;;;; binding_constant_NR2.cyt_P2.cyt # PARAM ;Kb ; 21;6.883653E+010;;0;D;;;; binding_constant_GlnK.cyt_NR2.cyt # PARAM ;Kb ; 22;1.061449E+005;;0;D;;;; binding_constant_En(GlnK).cyt_NR1-P.cyt # PARAM ;Kb ; 23;2.247709E+011;;0;D;;;; binding_constant_NR1.cyt_NR2-P.cyt # PARAM ;Kb ; 24;1.643270E+006;;0;D;;;; binding_constant_En(Nac).cyt_NR1-P.cyt # PARAM ;Kb ; 25;1.179332E+005;;0;D;;;; binding_constant_NR1.cyt_acetly.cyt # PARAM ;Kb ; 26;1.759106E+006;;0;D;;;; binding_constant_ATP.cyt_NR2.cyt # PARAM ;Kb ; 27;1.014357E+009;;0;D;;;; binding_constant_P2.cyt_ADP.cyt_NR2-P.cyt # PARAM ;Kb ; 28;1.014357E+009;;0;D;;;; binding_constant_GlnK.cyt_ADP.cyt_NR2-P.cyt # PARAM ;kx ; 1; 7 ;;0;D;;;; reaction_rate_constant_NR2:P2.cyt_NR1-P.cyt # PARAM ;kx ; 2; 7 ;;0;D;;;; reaction_rate_constant_NR2:GlnK.cyt_NR1-P.cyt # PARAM ;kx ; 3; 0 ;;0;D;;;; reaction_rate_constant_NR1.cyt_P.cyt # PARAM ;kx ; 4; 0 ;;0;D;;;; reaction_rate_constant_NR2-P.cyt # PARAM ;kx ; 5; 7 ;;0;D;;;; reaction_rate_constant_UTUR:aKG.cyt_P2.cyt_UMP.cyt # PARAM ;kx ; 6; 7 ;;0;D;;;; reaction_rate_constant_UTUR:aKG.cyt_GlnK.cyt_UMP.cyt # PARAM ;kx ; 7; 7 ;;0;D;;;; reaction_rate_constant_UTUR:glutamine.cyt_P2-UMP.cyt # PARAM ;kx ; 8; 7 ;;0;D;;;; reaction_rate_constant_UTUR:glutamine.cyt_GlnK-UMP.cyt # PARAM ;kx ; 9; 7 ;;0;D;;;; reaction_rate_constant_GlnK:P1.cyt_AMP.cyt_GS.cyt # PARAM ;kx ; 10; 7 ;;0;D;;;; reaction_rate_constant_P2:P1.cyt_AMP.cyt_GS.cyt # PARAM ;kx ; 11; 7 ;;0;D;;;; reaction_rate_constant_GlnK-UMP:P1.cyt_GS-AMP.cyt # PARAM ;kx ; 12; 7 ;;0;D;;;; reaction_rate_constant_P2-UMP:P1.cyt_GS-AMP.cyt # PARAM ;kx ; 13; 7 ;;0;D;;;; reaction_rate_constant_NR1:NR2-P.cyt # PARAM ;kx ; 14; 7 ;;0;D;;;; reaction_rate_constant_NR1:acetly.cyt # PARAM ;kx ; 15; 7 ;;0;D;;;; reaction_rate_constant_NR2:ATP.cyt # PARAM ;kx ; 16; 7 ;;0;D;;;; reaction_rate_constant_P2.cyt_ADP.cyt_NR2-P.cyt # PARAM ;kx ; 17; 7 ;;0;D;;;; reaction_rate_constant_GlnK.cyt_ADP.cyt_NR2-P.cyt # PARAM ;kp ; 1; 20 ;;0;D;;;; translation_rate_constant_mRNA(GlnK).cyt # PARAM ;kp ; 2; 20 ;;0;D;;;; translation_rate_constant_mRNA(nac).cyt # PARAM ;kp ; 3; 20 ;;0;D;;;; translation_rate_constant_mRNA(NR1).cyt # PARAM ;kp ; 4; 20 ;;0;D;;;; translation_rate_constant_mRNA(NR2).cyt # PARAM ;kp ; 5; 20 ;;0;D;;;; translation_rate_constant_mRNA(GS).cyt # PARAM ;kpd ; 1; 0.035 ;;0;D;;;; decomposition_rate_constant_NR1.cyt # PARAM ;kpd ; 2; 0.035 ;;0;D;;;; decomposition_rate_constant_NR1-P.cyt # PARAM ;kpd ; 3; 0.035 ;;0;D;;;; decomposition_rate_constant_NR2.cyt # PARAM ;kpd ; 4; 0.035 ;;0;D;;;; decomposition_rate_constant_NR2-P.cyt # PARAM ;kpd ; 5; 0.035 ;;0;D;;;; decomposition_rate_constant_GlnK.cyt # PARAM ;kpd ; 6; 0.035 ;;0;D;;;; decomposition_rate_constant_GlnK-UMP.cyt # PARAM ;kpd ; 7; 0.035 ;;0;D;;;; decomposition_rate_constant_GS.cyt # PARAM ;kpd ; 8; 0.035 ;;0;D;;;; decomposition_rate_constant_GS-AMP.cyt # PARAM ;kpd ; 9; 0.035 ;;0;D;;;; decomposition_rate_constant_nac.cyt # PARAM ;kpd ; 10; 0.035 ;;0;D;;;; decomposition_rate_constant_NR1:glnAP1.cyt # PARAM ;kpd ; 11; 0.035 ;;0;D;;;; decomposition_rate_constant_glnAp2:NR1-P:NR1-P:NR1-P:NR1-P.cyt # PARAM ;kpd ; 12; 0.035 ;;0;D;;;; decomposition_rate_constant_NR1:glnLp.cyt # PARAM ;kpd ; 13; 0.035 ;;0;D;;;; decomposition_rate_constant_P2:P1.cyt # Not Used!! PARAM ;kpd ; 14; 0.035 ;;0;D;;;; decomposition_rate_constant_GS:AMP:P2:P1.cyt # PARAM ;kpd ; 15; 0.035 ;;0;D;;;; decomposition_rate_constant_GlnK:P1.cyt # PARAM ;kpd ; 16; 0.035 ;;0;D;;;; decomposition_rate_constant_GS:AMP:GlnK:P1.cyt # PARAM ;kpd ; 17; 0.035 1;;0;D;;;; decomposition_rate_constant_P2-UMP:P1.cyt # Not Used!! PARAM ;kpd ; 18; 0.035 ;;0;D;;;; decomposition_rate_constant_GS-AMP:AMP:P2-UMP:P1.cyt # PARAM ;kpd ; 19; 0.035 ;;0;D;;;; decomposition_rate_constant_GlnK-UMP:P1.cyt # PARAM ;kpd ; 20; 0.035 ;;0;D;;;; decomposition_rate_constant_GS-AMP:AMP:GlnK-UMP:P1.cyt # PARAM ;kpd ; 21; 0.035 ;;0;D;;;; decomposition_rate_constant_GlnK-UMP:UMP:UTUR:glutamine.cyt # PARAM ;kpd ; 22; 0.035 ;;0;D;;;; decomposition_rate_constant_NR2:P2.cyt # PARAM ;kpd ; 23; 0.035 ;;0;D;;;; decomposition_rate_constant_NR2:GlnK.cyt # PARAM ;kpd ; 24; 0.035 ;;0;D;;;; decomposition_rate_constant_NR1-P:P:NR2:P2.cyt # PARAM ;kpd ; 25; 0.035 ;;0;D;;;; decomposition_rate_constant_NR1-P:P:NR2:GlnK.cyt # PARAM ;kpd ; 26; 0.035 ;;0;D;;;; decomposition_rate_constant_NR1-P:En(GlnK).cyt # PARAM ;kpd ; 27; 0.035 ;;0;D;;;; decomposition_rate_constant_NR1:NR2-P.cyt # PARAM ;kpd ; 28; 0.035 ;;0;D;;;; decomposition_rate_constant_NR1-P:En(Nac).cyt # PARAM ;kpd ; 29; 0.035 ;;0;D;;;; decomposition_rate_constant_GlnK:UMP:UTUR:aKG.cyt # PARAM ;kpd ; 30; 0.035 ;;0;D;;;; decomposition_rate_constant_NR1:acetly.cyt # PARAM ;kpd ; 31; 0.035 ;;0;D;;;; decomposition_rate_constant_NR2:ATP.cyt # PARAM ;kpd ; 32; 0.035 ;;0;D;;;; decomposition_rate_constant_NR2-P:ADP:P2.cyt # PARAM ;kpd ; 33; 0.035 ;;0;D;;;; decomposition_rate_constant_NR2-P:ADP:GlnK.cyt # PARAM ;km ; 1; 0.09 ;;0;D;;;; transcription_rate_constant_NR1-P:En(GlnK).cyt_DNA(GlnK).cyt # PARAM ;km ; 2; 0.03 ;;0;D;;;; transcription_rate_constant_NR1-P:En(Nac).cyt_DNA(nac).cyt # PARAM ;km ; 3; 0.03 ;;0;D;;;; transcription_rate_constant_glnAp2:NR1-P:NR1-P:NR1-P:NR1-P.cyt_DNA1(NR1).cyt # PARAM ;km ; 4; 0.03 ;;0;D;;;; transcription_rate_constant_NR1:glnLp.cyt_DNA2(NR1).cyt # PARAM ;km ; 5; 0.03 ;;0;D;;;; transcription_rate_constant_NR1:glnLp.cyt_DNA1(NR2).cyt # PARAM ;km ; 6; 0.03 ;;0;D;;;; transcription_rate_constant_glnAp2:NR1-P:NR1-P:NR1-P:NR1-P.cyt_DNA2(NR2).cyt # PARAM ;km ; 7; 0.03 ;;0;D;;;; transcription_rate_constant_glnAp2:NR1-P:NR1-P:NR1-P:NR1-P.cyt_DNA1(GS).cyt # PARAM ;km ; 8; 0.03 ;;0;D;;;; transcription_rate_constant_NR1:glnAP1.cyt_DNA2(GS).cyt # PARAM ;kmd ; 1; 0.12 ;;0;D;;;; decomposition_rate_constant_mRNA(GlnK).cyt # PARAM ;kmd ; 2; 0.12 ;;0;D;;;; decomposition_rate_constant_mRNA(GS).cyt # PARAM ;kmd ; 3; 0.12 ;;0;D;;;; decomposition_rate_constant_mRNA(nac).cyt # PARAM ;kmd ; 4; 0.12 ;;0;D;;;; decomposition_rate_constant_mRNA(NR1).cyt # PARAM ;kmd ; 5; 0.12 ;;0;D;;;; decomposition_rate_constant_mRNA(NR2).cyt # PARAM ;Q ; 1; 9e+09;;0;D;;;; reaction_rate_constant_GS.cyt_NH3.cyt_glutamate.cyt_MM # PARAM ;Q ; 2; 5e+06;;0;D;;;; reaction_rate_constant_GOGAT.cyt_aKG.cyt_glutamine.cyt_MM # PARAM ;Q ; 3; 1.25e+07;;0;D;;;; reaction_rate_constant_GDH.cyt_NH3.cyt_aKG.cyt_MM # PARAM ;Q ; 4; 1;;0;D;;;; reaction_rate_constant_Dummy.cyt_MM # PARAM ;Q ; 5; 0.026;;0;D;;;; reaction_rate_constant_glutamine.cyt_MM # PARAM ;Q ; 6; 0.22;;0;D;;;; reaction_rate_constant_glutamate.cyt_MM # PARAM ;Q ; 7; 1.2;;0;D;;;; reaction_rate_constant_aKG.cyt_MM # PARAM ;Kmich ; 1; 0.03;;0;D;;;; Michaelis_constant(glutamate.cyt)_GS.cyt_NH3.cyt_glutamate.cyt_MM # PARAM ;Kmich ; 2; 0.03;;0;D;;;; Michaelis_constant(NH3.cyt)_GS.cyt_NH3.cyt_glutamate.cyt_MM # PARAM ;Kmich ; 3; 0.03;;0;D;;;; Michaelis_constant(glutamine.cyt)_GOGAT.cyt_aKG.cyt_glutamine.cyt_MM # PARAM ;Kmich ; 4; 0.03;;0;D;;;; Michaelis_constant(aKG.cyt)_GOGAT.cyt_aKG.cyt_glutamine.cyt_MM # PARAM ;Kmich ; 5; 0.001;;0;D;;;; Michaelis_constant(aKG.cyt)_GDH.cyt_NH3.cyt_aKG.cyt_MM # PARAM ;Kmich ; 6; 0.03;;0;D;;;; Michaelis_constant(NH3.cyt)_GDH.cyt_NH3.cyt_aKG.cyt_MM # PARAM ;Kmich ; 7; 0.01;;0;D;;;; Michaelis_constant(Dummy.cyt)_Dummy.cyt_MM # PARAM ;Kmich ; 8; 0.03;;0;D;;;; Michaelis_constant(glutamine.cyt)_glutamine.cyt_MM # PARAM ;Kmich ; 9; 0.03;;0;D;;;; Michaelis_constant(glutamate.cyt)_glutamate.cyt_MM # PARAM ;Kmich ; 10; 0.03;;0;D;;;; Michaelis_constant(aKG.cyt)_aKG.cyt_MM # #T_EVENT ; name; index; time; value; #comment T_EVENT ;constantPlayer; 23; 1000; 0.00002;# NH3.cyt ######## Don't edit the following lines. ###### PARAM_NAME ;constantPlayer # PARAM_NAME ;Kb # PARAM_NAME ;kx # PARAM_NAME ;kp # PARAM_NAME ;kpd # PARAM_NAME ;km # PARAM_NAME ;kmd # PARAM_NAME ;Q # PARAM_NAME ;Kmich #