//genesis // kkit Version 9 flat dumpfile // Original version saved on Tue Jun 10 10:15:34 2003 // Corrected version uploaded on Nov 12 2004 // Corrections made for reaction nomenclature. include kkit {argv 1} FASTDT = 0.0001 SIMDT = 0.001 CONTROLDT = 0.1 PLOTDT = 0.1 MAXTIME = 20 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1.6667e-21 VERSION = 9.0 setfield /file/modpath value /home2/bhalla/scripts/modules kparms //genesis initdump -version 3 -ignoreorphans 1 simobjdump table input output alloced step_mode stepsize x y z simobjdump xtree path script namemode sizescale simobjdump xcoredraw xmin xmax ymin ymax simobjdump xtext editable simobjdump xgraph xmin xmax ymin ymax overlay simobjdump xplot pixflags script fg ysquish do_slope wy simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \ link savename file version md5sum mod_save_flag x y z simobjdump kpool CoTotal CoInit Co n nInit nTotal nMin vol slave_enable notes \ xtree_fg_req xtree_textfg_req x y z simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \ keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \ trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z simobjdump xtab input output alloced step_mode stepsize notes editfunc \ xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \ xtree_textfg_req x y z simobjdump transport input output alloced step_mode stepsize dt delay clock \ kf xtree_fg_req xtree_textfg_req x y z simobjdump proto x y z simobjdump linkinfo xtree_fg_req xtree_textfg_req uplink downlink x y z simobjdump uplink xtree_fg_req xtree_textfg_req x y z simobjdump downlink xtree_fg_req xtree_textfg_req x y z simobjdump mirror notes xtree_fg_req x y z simobjdump calculator resetclock output_init simundump kpool /kinetics/CheA 0 1.13 1.13 3.1271 2645.5 955.98 955.98 0 846 \ 0 "" 47 black -102 -104 0 simundump kpool /kinetics/CheAp 0 0.569 0.569 0.038934 32.938 481.37 481.37 0 \ 846 0 "" 62 black -106 -49 0 simundump kpool /kinetics/CheB 0 1.62 1.62 1.926 1629.4 1370.5 1370.5 0 846 0 \ "" 15 black -127 11 0 simundump kpool /kinetics/CheBp 0 0.381 0.381 0.074982 63.435 322.33 322.33 0 \ 846 0 "" 0 black -212 22 0 simundump kreac /kinetics/Phosphotransfer 0 0.001182 0 "" 62 black -143 -26 0 simundump kpool /kinetics/CheYp 0 0.01 0.01 0.010386 8.7862 8.46 8.46 0 846 0 \ "" white black 4 -62 0 simundump kpool /kinetics/CheY 0 9.88 9.88 9.8912 8368 8358.5 8358.5 0 846 0 \ "" 41 black -78 -126 0 simundump kreac /kinetics/Phosphotransfer[1] 0 0.00031915 0 "" 62 black -36 \ -87 0 simundump kpool /kinetics/CheW 0 1.37 1.37 2.9907 2530.1 1159 1159 0 846 0 "" \ 5 black 17 -240 0 simundump kreac /kinetics/Complexing 0 0.0001182 1 "" 62 black -292 -259 0 simundump kpool /kinetics/TW 0 1.88 1.88 0.72738 615.37 1590.5 1590.5 0 846 0 \ "" 9 black -264 -257 0 simundump kpool /kinetics/CheZ 0 20 20 20 16920 16920 16920 0 846 0 "" 20 \ black 36 -75 0 simundump kreac /kinetics/Autophosphorylation 0 0.001 0 "" 62 black -165 -159 \ 0 simundump kreac /kinetics/Autodephosphorylation 0 1 0 "" 62 black -174 52 0 simundump kreac /kinetics/Autodephosphorylation[1] 0 0.037 0 "" 62 black -47 \ -58 0 simundump kreac /kinetics/Autophosphorylation[1] 0 8.948e-05 0 "" 62 black \ -167 -55 0 simundump kreac /kinetics/Autophosphorylation[2] 0 0 0 "" 62 black -36 -173 0 simundump kreac /kinetics/Dephosphorylation 0 0.00059102 0 "" 62 black 17 \ -113 0 simundump kreac /kinetics/Complexing[1] 0 0.0001182 1 "" 62 black -305 -380 0 simundump kpool /kinetics/Ni 0 0 0 0 0 0 0 0 846 0 "" white black -248 -343 0 simundump kreac /kinetics/Binding 0 1.182e-06 1 "" 62 black -207 -323 0 simundump kpool /kinetics/Tn 0 0 0 0 0 0 0 0 846 0 "" 43 black -172 -263 0 simundump kpool /kinetics/TnW 0 5 0 0 0 0 4230 0 846 0 "" 9 black -115 -300 0 simundump kreac /kinetics/Autophosphorylation[3] 0 0.001182 0 "" 62 black -64 \ -230 0 simundump kreac /kinetics/Binding[1] 0 0.001513 1 "" 62 black 179 -193 0 simundump kpool /kinetics/Ta 0 0 0 0.00014317 0.12112 0 0 0 846 0 "" 43 black \ 208 -261 0 simundump kreac /kinetics/Complexing[2] 0 0.0001182 1 "" 62 black 134 -169 0 simundump kpool /kinetics/TaW 0 0 0 6.005e-05 0.050802 0 0 0 846 0 "" 9 black \ 90 -100 0 simundump kreac /kinetics/Dephosphorylation[1] 0 0.1182 0 "" 62 black -11 \ -136 0 simundump kreac /kinetics/Binding[2] 0 0.00047281 1 "" 62 black -219 -217 0 simundump kpool /kinetics/TWA 0 0.212 0.212 0.74281 628.42 179.35 179.35 0 \ 846 0 "" 9 black -233 -101 0 simundump kreac /kinetics/Complexing[3] 0 0.10402 5.5 "" 62 black 19 -41 0 simundump kpool /kinetics/MYpYp 0 0.000366 0.000366 0.00042419 0.35887 \ 0.30964 0.30964 0 846 0 "" 24 black 2 53 0 simundump kpool /kinetics/MYpYpYp 0 0.000447 0.000447 0.00059701 0.50507 \ 0.37816 0.37816 0 846 0 "" 17 black -7 39 0 simundump kpool /kinetics/MYpYpYpYp 0 0.00151 0.00151 0.0022606 1.9125 1.2775 \ 1.2775 0 846 0 "" 62 black -22 20 0 simundump kreac /kinetics/Complexing[4] 0 0.33688 6.64 "" 62 black 10 -26 0 simundump kreac /kinetics/Complexing[5] 0 0.82033 5.1 "" 62 black 1 -5 0 simundump kreac /kinetics/Complexing[6] 0 2.3723 5.5 "" 62 black -14 6 0 simundump kreac /kinetics/Binding[3] 0 5.9102e-05 1 "" 62 black -251 -160 0 simundump kpool /kinetics/TA 0 1.55 1.55 0.55113 466.25 1311.3 1311.3 0 846 0 \ "" 50 black -272 -102 0 simundump kreac /kinetics/Complexing[7] 0 0.00047281 1 "" 62 black -299 -44 0 simundump kpool /kinetics/TnA 0 0 0 0 0 0 0 0 846 0 "" 50 black -115 -260 0 simundump kreac /kinetics/Binding[4] 0 5.9102e-05 1 "" 62 black -146 -214 0 simundump kreac /kinetics/Complexing[8] 0 0.00047281 1 "" 62 black -75 -325 0 simundump kpool /kinetics/TnWA 0 0 0 0 0 0 0 0 846 0 "" 62 black -29 -327 0 simundump kreac /kinetics/Binding[5] 0 0.00047281 1 "" 62 black -70 -294 0 simundump kreac /kinetics/Binding[6] 0 0.00047281 1 "" 62 black 71 -158 0 simundump kpool /kinetics/TaWA 0 0 0 6.5383e-05 0.055314 0 0 0 846 0 "" 9] \ black 62 -222 0 simundump kreac /kinetics/Binding[7] 0 5.9102e-05 1 "" 62 black 128 -247 0 simundump kpool /kinetics/TaA 0 0 0 5.0232e-05 0.042496 0 0 0 846 0 "" 50 \ black 69 -270 0 simundump kreac /kinetics/Complexing[9] 0 0.00047281 1 "" 62 black 129 -109 0 simundump kpool /kinetics/Denominator 0 0.010006 0 0.010006 8.4647 0 8.4647 0 \ 846 0 "" 62 black -100 72 0 simundump kpool /kinetics/Bias 0 0.768 0.768 0.768 649.73 649.73 649.73 0 846 \ 0 "" 0 black -96 110 0 simundump kpool /kinetics/Aspartate 0 0 0 0 0 0 0 0 846 4 "" white black 159 \ -131 0 simundump kpool /kinetics/MYp 0 0.000953 0.000953 0.00095611 0.80887 0.80624 \ 0.80624 0 846 0 "" 55 black 10 64 0 simundump kpool /kinetics/Motor 0 0.00673 0.00673 0.0057676 4.8794 5.6936 \ 5.6936 0 846 0 "" 18 black 23 76 0 simundump kpool /kinetics/Numerator 0 0.007683 0 0.0067238 5.6883 0 5.6883 0 \ 846 0 "" 46 black -30 128 0 simundump kpool /kinetics/CW_rotation 0 0.001957 0 0.0028576 2.4175 0 2.4175 \ 0 846 0 "" 1 black -104 44 0 simundump kpool /kinetics/WA 0 1.55 1.55 0.55113 466.25 1311.3 1311.3 0 846 0 \ "" 9 black -109 -484 0 simundump kpool /kinetics/Tar 0 1.37 1.37 2.9908 2530.2 1159 1159 0 846 0 "" \ 24 black -347 -196 0 simundump kreac /kinetics/Binding[9] 0 0.00047281 1 "" 62 black -291 -132 0 simundump kreac /kinetics/Binding[10] 0 0.00047281 1 "" 62 black -142 -428 0 simundump kreac /kinetics/Binding[11] 0 0.00047281 1 "" 62 black 118 -302 0 simundump calculator /kinetics/Division 0 0 1 simundump kreac /kinetics/Complexing[10] 0 5.9102e-05 1 "" 62 black -242 -34 \ 0 simundump xgraph /graphs/conc1 0 0 45 0.14934 1 0 simundump xgraph /graphs/conc2 0 0 45 0.00073069 0.054934 0 simundump xplot /graphs/conc1/Bias.Co 0 0 nil 0 0 0 1 simundump xplot /graphs/conc1/Bias.Co[1] 0 0 nil 0 1.6105e-05 0 1 simundump xplot /graphs/conc2/Motor.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 18 0 0 1 simundump xgraph /moregraphs/conc3 0 0 45 9.789 9.9067 0 simundump xgraph /moregraphs/conc4 0 0 45 0.016921 3.1898 0 simundump xplot /moregraphs/conc3/MYpYp.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 24 0 0 1 simundump xplot /moregraphs/conc3/MYp.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 55 0 0 1 simundump xplot /moregraphs/conc4/MYpYpYpYp.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 62 0 0 1 simundump xplot /moregraphs/conc4/MYpYpYp.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 17 0 0 1 simundump xcoredraw /edit/draw 0 -349 210 -486 130 simundump xtree /edit/draw/tree 0 \ /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ "edit_elm.D ; drag_from_edit.w " auto 0.6 simundump xtext /file/notes 0 1 xtextload /file/notes \ "All parameters are from .BCT files for BCT1.1 " \ "provided by Matthew Levin" \ "Bias doesn't reach 0.7, there is a shift in the rise and fall" \ "of the bias in response to the 5 sec 1uM Aspartate pulse" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "The current version of the BCT program is BCT4.3 and is available " \ "at http://www.zoo.cam.ac.uk/comp-cell/Chemotaxis.html" \ "" addmsg /kinetics/Phosphotransfer /kinetics/CheA REAC B A addmsg /kinetics/Phosphotransfer[1] /kinetics/CheA REAC B A addmsg /kinetics/Binding[6] /kinetics/CheA REAC A B addmsg /kinetics/Binding[7] /kinetics/CheA REAC A B addmsg /kinetics/Autophosphorylation /kinetics/CheA REAC A B addmsg /kinetics/Binding[5] /kinetics/CheA REAC A B addmsg /kinetics/Complexing[10] /kinetics/CheA REAC A B addmsg /kinetics/Binding[2] /kinetics/CheA REAC A B addmsg /kinetics/Autophosphorylation[1] /kinetics/CheA REAC A B addmsg /kinetics/Autophosphorylation[3] /kinetics/CheA REAC A B addmsg /kinetics/Binding[4] /kinetics/CheA REAC A B addmsg /kinetics/Binding[3] /kinetics/CheA REAC A B addmsg /kinetics/Phosphotransfer /kinetics/CheAp REAC A B addmsg /kinetics/Phosphotransfer[1] /kinetics/CheAp REAC A B addmsg /kinetics/Autophosphorylation /kinetics/CheAp REAC B A addmsg /kinetics/Autophosphorylation[1] /kinetics/CheAp REAC B A addmsg /kinetics/Autophosphorylation[3] /kinetics/CheAp REAC B A addmsg /kinetics/Phosphotransfer /kinetics/CheB REAC A B addmsg /kinetics/Autodephosphorylation /kinetics/CheB REAC B A addmsg /kinetics/Phosphotransfer /kinetics/CheBp REAC B A addmsg /kinetics/Autodephosphorylation /kinetics/CheBp REAC A B addmsg /kinetics/CheAp /kinetics/Phosphotransfer SUBSTRATE n addmsg /kinetics/CheBp /kinetics/Phosphotransfer PRODUCT n addmsg /kinetics/CheA /kinetics/Phosphotransfer PRODUCT n addmsg /kinetics/CheB /kinetics/Phosphotransfer SUBSTRATE n addmsg /kinetics/Phosphotransfer[1] /kinetics/CheYp REAC B A addmsg /kinetics/Autophosphorylation[2] /kinetics/CheYp REAC B A addmsg /kinetics/Dephosphorylation /kinetics/CheYp REAC A B addmsg /kinetics/Dephosphorylation[1] /kinetics/CheYp REAC A B addmsg /kinetics/Complexing[3] /kinetics/CheYp REAC A B addmsg /kinetics/Complexing[4] /kinetics/CheYp REAC A B addmsg /kinetics/Complexing[5] /kinetics/CheYp REAC A B addmsg /kinetics/Complexing[6] /kinetics/CheYp REAC A B addmsg /kinetics/Autodephosphorylation[1] /kinetics/CheY REAC B A addmsg /kinetics/Phosphotransfer[1] /kinetics/CheY REAC A B addmsg /kinetics/Dephosphorylation /kinetics/CheY REAC B A addmsg /kinetics/Dephosphorylation[1] /kinetics/CheY REAC B A addmsg /kinetics/CheAp /kinetics/Phosphotransfer[1] SUBSTRATE n addmsg /kinetics/CheY /kinetics/Phosphotransfer[1] SUBSTRATE n addmsg /kinetics/CheYp /kinetics/Phosphotransfer[1] PRODUCT n addmsg /kinetics/CheA /kinetics/Phosphotransfer[1] PRODUCT n addmsg /kinetics/Complexing /kinetics/CheW REAC A B addmsg /kinetics/Complexing[7] /kinetics/CheW REAC A B addmsg /kinetics/Complexing[10] /kinetics/CheW REAC A B addmsg /kinetics/Complexing[1] /kinetics/CheW REAC A B addmsg /kinetics/Complexing[8] /kinetics/CheW REAC A B addmsg /kinetics/Complexing[9] /kinetics/CheW REAC A B addmsg /kinetics/Complexing[2] /kinetics/CheW REAC A B addmsg /kinetics/CheW /kinetics/Complexing SUBSTRATE n addmsg /kinetics/TW /kinetics/Complexing PRODUCT n addmsg /kinetics/Tar /kinetics/Complexing SUBSTRATE n addmsg /kinetics/Complexing /kinetics/TW REAC B A addmsg /kinetics/Binding[2] /kinetics/TW REAC A B addmsg /kinetics/Dephosphorylation /kinetics/CheZ REAC A B addmsg /kinetics/Dephosphorylation /kinetics/CheZ REAC B A addmsg /kinetics/CheA /kinetics/Autophosphorylation SUBSTRATE n addmsg /kinetics/CheAp /kinetics/Autophosphorylation PRODUCT n addmsg /kinetics/CheBp /kinetics/Autodephosphorylation SUBSTRATE n addmsg /kinetics/CheB /kinetics/Autodephosphorylation PRODUCT n addmsg /kinetics/CheYp /kinetics/Autodephosphorylation[1] SUBSTRATE n addmsg /kinetics/CheY /kinetics/Autodephosphorylation[1] PRODUCT n addmsg /kinetics/TWA /kinetics/Autophosphorylation[1] SUBSTRATE n addmsg /kinetics/CheAp /kinetics/Autophosphorylation[1] PRODUCT n addmsg /kinetics/CheA /kinetics/Autophosphorylation[1] SUBSTRATE n addmsg /kinetics/CheYp /kinetics/Autophosphorylation[2] PRODUCT n addmsg /kinetics/CheYp /kinetics/Dephosphorylation SUBSTRATE n addmsg /kinetics/CheZ /kinetics/Dephosphorylation SUBSTRATE n addmsg /kinetics/CheY /kinetics/Dephosphorylation PRODUCT n addmsg /kinetics/Tn /kinetics/Complexing[1] SUBSTRATE n addmsg /kinetics/TnW /kinetics/Complexing[1] PRODUCT n addmsg /kinetics/CheW /kinetics/Complexing[1] SUBSTRATE n addmsg /kinetics/Binding /kinetics/Ni REAC A B addmsg /kinetics/Ni /kinetics/Binding SUBSTRATE n addmsg /kinetics/Tn /kinetics/Binding PRODUCT n addmsg /kinetics/Tar /kinetics/Binding SUBSTRATE n addmsg /kinetics/Complexing[1] /kinetics/Tn REAC A B addmsg /kinetics/Binding /kinetics/Tn REAC B A addmsg /kinetics/Binding[4] /kinetics/Tn REAC A B addmsg /kinetics/Binding[10] /kinetics/Tn REAC A B addmsg /kinetics/Complexing[1] /kinetics/TnW REAC B A addmsg /kinetics/Binding[5] /kinetics/TnW REAC A B addmsg /kinetics/TnWA /kinetics/Autophosphorylation[3] SUBSTRATE n addmsg /kinetics/CheA /kinetics/Autophosphorylation[3] SUBSTRATE n addmsg /kinetics/CheAp /kinetics/Autophosphorylation[3] PRODUCT n addmsg /kinetics/Ta /kinetics/Binding[1] PRODUCT n addmsg /kinetics/Aspartate /kinetics/Binding[1] SUBSTRATE n addmsg /kinetics/Tar /kinetics/Binding[1] SUBSTRATE n addmsg /kinetics/Binding[1] /kinetics/Ta REAC B A addmsg /kinetics/Complexing[2] /kinetics/Ta REAC A B addmsg /kinetics/Binding[7] /kinetics/Ta REAC A B addmsg /kinetics/Binding[11] /kinetics/Ta REAC A B addmsg /kinetics/Ta /kinetics/Complexing[2] SUBSTRATE n addmsg /kinetics/TaW /kinetics/Complexing[2] PRODUCT n addmsg /kinetics/CheW /kinetics/Complexing[2] SUBSTRATE n addmsg /kinetics/Complexing[2] /kinetics/TaW REAC B A addmsg /kinetics/Binding[6] /kinetics/TaW REAC A B addmsg /kinetics/CheYp /kinetics/Dephosphorylation[1] SUBSTRATE n addmsg /kinetics/CheY /kinetics/Dephosphorylation[1] PRODUCT n addmsg /kinetics/TaWA /kinetics/Dephosphorylation[1] SUBSTRATE n addmsg /kinetics/TW /kinetics/Binding[2] SUBSTRATE n addmsg /kinetics/TWA /kinetics/Binding[2] PRODUCT n addmsg /kinetics/CheA /kinetics/Binding[2] SUBSTRATE n addmsg /kinetics/Binding[2] /kinetics/TWA REAC B A addmsg /kinetics/Autophosphorylation[1] /kinetics/TWA REAC A B addmsg /kinetics/Complexing[7] /kinetics/TWA REAC B A addmsg /kinetics/Binding[9] /kinetics/TWA REAC B A addmsg /kinetics/Autophosphorylation[1] /kinetics/TWA REAC B A addmsg /kinetics/CheYp /kinetics/Complexing[3] SUBSTRATE n addmsg /kinetics/Motor /kinetics/Complexing[3] SUBSTRATE n addmsg /kinetics/MYp /kinetics/Complexing[3] PRODUCT n addmsg /kinetics/Complexing[4] /kinetics/MYpYp REAC B A addmsg /kinetics/Complexing[5] /kinetics/MYpYp REAC A B addmsg /kinetics/Complexing[5] /kinetics/MYpYpYp REAC B A addmsg /kinetics/Complexing[6] /kinetics/MYpYpYp REAC A B addmsg /kinetics/Complexing[6] /kinetics/MYpYpYpYp REAC B A addmsg /kinetics/CheYp /kinetics/Complexing[4] SUBSTRATE n addmsg /kinetics/MYpYp /kinetics/Complexing[4] PRODUCT n addmsg /kinetics/MYp /kinetics/Complexing[4] SUBSTRATE n addmsg /kinetics/CheYp /kinetics/Complexing[5] SUBSTRATE n addmsg /kinetics/MYpYp /kinetics/Complexing[5] SUBSTRATE n addmsg /kinetics/MYpYpYp /kinetics/Complexing[5] PRODUCT n addmsg /kinetics/CheYp /kinetics/Complexing[6] SUBSTRATE n addmsg /kinetics/MYpYpYp /kinetics/Complexing[6] SUBSTRATE n addmsg /kinetics/MYpYpYpYp /kinetics/Complexing[6] PRODUCT n addmsg /kinetics/TA /kinetics/Binding[3] PRODUCT n addmsg /kinetics/Tar /kinetics/Binding[3] SUBSTRATE n addmsg /kinetics/CheA /kinetics/Binding[3] SUBSTRATE n addmsg /kinetics/Binding[3] /kinetics/TA REAC B A addmsg /kinetics/Complexing[7] /kinetics/TA REAC A B addmsg /kinetics/TA /kinetics/Complexing[7] SUBSTRATE n addmsg /kinetics/CheW /kinetics/Complexing[7] SUBSTRATE n addmsg /kinetics/TWA /kinetics/Complexing[7] PRODUCT n addmsg /kinetics/Binding[4] /kinetics/TnA REAC B A addmsg /kinetics/Complexing[8] /kinetics/TnA REAC A B addmsg /kinetics/Tn /kinetics/Binding[4] SUBSTRATE n addmsg /kinetics/TnA /kinetics/Binding[4] PRODUCT n addmsg /kinetics/CheA /kinetics/Binding[4] SUBSTRATE n addmsg /kinetics/TnA /kinetics/Complexing[8] SUBSTRATE n addmsg /kinetics/TnWA /kinetics/Complexing[8] PRODUCT n addmsg /kinetics/CheW /kinetics/Complexing[8] SUBSTRATE n addmsg /kinetics/Complexing[8] /kinetics/TnWA REAC B A addmsg /kinetics/Binding[5] /kinetics/TnWA REAC B A addmsg /kinetics/Binding[10] /kinetics/TnWA REAC B A addmsg /kinetics/Autophosphorylation[3] /kinetics/TnWA REAC A B addmsg /kinetics/Autophosphorylation[3] /kinetics/TnWA REAC B A addmsg /kinetics/TnW /kinetics/Binding[5] SUBSTRATE n addmsg /kinetics/TnWA /kinetics/Binding[5] PRODUCT n addmsg /kinetics/CheA /kinetics/Binding[5] SUBSTRATE n addmsg /kinetics/TaW /kinetics/Binding[6] SUBSTRATE n addmsg /kinetics/CheA /kinetics/Binding[6] SUBSTRATE n addmsg /kinetics/TaWA /kinetics/Binding[6] PRODUCT n addmsg /kinetics/Binding[6] /kinetics/TaWA REAC B A addmsg /kinetics/Dephosphorylation[1] /kinetics/TaWA REAC A B addmsg /kinetics/Complexing[9] /kinetics/TaWA REAC B A addmsg /kinetics/Binding[11] /kinetics/TaWA REAC B A addmsg /kinetics/Dephosphorylation[1] /kinetics/TaWA REAC B A addmsg /kinetics/Ta /kinetics/Binding[7] SUBSTRATE n addmsg /kinetics/CheA /kinetics/Binding[7] SUBSTRATE n addmsg /kinetics/TaA /kinetics/Binding[7] PRODUCT n addmsg /kinetics/Binding[7] /kinetics/TaA REAC B A addmsg /kinetics/Complexing[9] /kinetics/TaA REAC A B addmsg /kinetics/TaA /kinetics/Complexing[9] SUBSTRATE n addmsg /kinetics/TaWA /kinetics/Complexing[9] PRODUCT n addmsg /kinetics/CheW /kinetics/Complexing[9] SUBSTRATE n addmsg /kinetics/MYpYp /kinetics/Denominator SUMTOTAL n nInit addmsg /kinetics/MYpYpYp /kinetics/Denominator SUMTOTAL n nInit addmsg /kinetics/MYpYpYpYp /kinetics/Denominator SUMTOTAL n nInit addmsg /kinetics/MYp /kinetics/Denominator SUMTOTAL n nInit addmsg /kinetics/Motor /kinetics/Denominator SUMTOTAL n nInit addmsg /kinetics/Binding[1] /kinetics/Aspartate REAC A B addmsg /kinetics/Complexing[3] /kinetics/MYp REAC B A addmsg /kinetics/Complexing[4] /kinetics/MYp REAC A B addmsg /kinetics/Complexing[3] /kinetics/Motor REAC A B addmsg /kinetics/MYp /kinetics/Numerator SUMTOTAL n nInit addmsg /kinetics/Motor /kinetics/Numerator SUMTOTAL n nInit addmsg /kinetics/MYpYpYpYp /kinetics/CW_rotation SUMTOTAL n nInit addmsg /kinetics/MYpYpYp /kinetics/CW_rotation SUMTOTAL n nInit addmsg /kinetics/Complexing[10] /kinetics/WA REAC B A addmsg /kinetics/Binding[9] /kinetics/WA REAC A B addmsg /kinetics/Binding[10] /kinetics/WA REAC A B addmsg /kinetics/Binding[11] /kinetics/WA REAC A B addmsg /kinetics/Complexing /kinetics/Tar REAC A B addmsg /kinetics/Binding[3] /kinetics/Tar REAC A B addmsg /kinetics/Binding[9] /kinetics/Tar REAC A B addmsg /kinetics/Binding /kinetics/Tar REAC A B addmsg /kinetics/Binding[1] /kinetics/Tar REAC A B addmsg /kinetics/WA /kinetics/Binding[9] SUBSTRATE n addmsg /kinetics/Tar /kinetics/Binding[9] SUBSTRATE n addmsg /kinetics/TWA /kinetics/Binding[9] PRODUCT n addmsg /kinetics/Tn /kinetics/Binding[10] SUBSTRATE n addmsg /kinetics/TnWA /kinetics/Binding[10] PRODUCT n addmsg /kinetics/WA /kinetics/Binding[10] SUBSTRATE n addmsg /kinetics/Ta /kinetics/Binding[11] SUBSTRATE n addmsg /kinetics/TaWA /kinetics/Binding[11] PRODUCT n addmsg /kinetics/WA /kinetics/Binding[11] SUBSTRATE n addmsg /kinetics/Denominator /kinetics/Division DIVIDE Co addmsg /kinetics/Numerator /kinetics/Division MULTIPLY Co addmsg /kinetics/CheW /kinetics/Complexing[10] SUBSTRATE n addmsg /kinetics/CheA /kinetics/Complexing[10] SUBSTRATE n addmsg /kinetics/WA /kinetics/Complexing[10] PRODUCT n addmsg /kinetics/Division /graphs/conc1 PLOT output *Bias.Co *0 addmsg /kinetics/Division /graphs/conc1/Bias.Co PLOT output *Bias.Co *0 addmsg /kinetics/Division /graphs/conc1/Bias.Co[1] PLOT output *Bias.Co *0 addmsg /kinetics/Motor /graphs/conc2/Motor.Co PLOT Co *Motor.Co *18 addmsg /kinetics/MYpYp /moregraphs/conc3/MYpYp.Co PLOT Co *MYpYp.Co *24 addmsg /kinetics/MYp /moregraphs/conc3/MYp.Co PLOT Co *MYp.Co *55 addmsg /kinetics/MYpYpYpYp /moregraphs/conc4/MYpYpYpYp.Co PLOT Co *MYpYpYpYp.Co *62 addmsg /kinetics/MYpYpYp /moregraphs/conc4/MYpYpYp.Co PLOT Co *MYpYpYp.Co *17 enddump // End of dump call /kinetics/CheA/notes LOAD \ "CheA = 1.13e-06 M = 1.13 uM" \ "As per Signal in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "CheA = 4250 molecules per cell" \ "As per Enzyme entry 4 in 1ENZ.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/CheAp/notes LOAD \ "CheAp = 5.69e-07 M = 5.69e-1 uM" \ "As per Signal entry 17 in 1SIG_B.BCT" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/CheB/notes LOAD \ "CheB = 1.62e-06 M = 1.62 uM" \ "As per Signal 18 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "CheB = 1700 molecules per cell" \ "As per Enzyme entry 2 in 1ENZ.BCT provided by " \ "" \ "Cell volume = 1.41e-15 L" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 1 pp.474" call /kinetics/CheBp/notes LOAD \ "CheBp = 3.81e-07 M = 3.81e-1 uM" \ "As per Signal entry 19 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Phosphotransfer/notes LOAD \ "Phosphotransfer from CheAp to CheB" \ "" \ "Kf = 1 * 10e6 /sec/M = 1 /sec/uM" \ "Kb = 0 /sec/M" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 2 pp.475 Reaction Scheme 9" call /kinetics/CheYp/notes LOAD \ "CheYp = 1.24e-07 M = 1.24e-01 uM" \ "As per Signal 22 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "CheYp = 1e-08 M = 1e-2 uM" \ "As per Set_Yp configuration in 1CONFIG.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/CheY/notes LOAD \ "CheY = 9.88e-06 M = 9.88 uM" \ "As per Signal 21 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "CheY = 8500 molecules per cell" \ "As per Enzyme entry 5 in 1ENZ.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Phosphotransfer[1]/notes LOAD \ "Phosphotransfer from CheAp to CheY" \ "" \ "Kf = 2 * 10e+05 /sec/M = 0.2 /sec/uM" \ "Kb = 0 /sec/M" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 2 pp.475 Reaction Scheme 5" call /kinetics/CheW/notes LOAD \ "CheW = 1.37 uM " \ "As per Signal 5 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "CheW = 4250 molecules per cell" \ "As per Enzyme entry 3 in 1ENZ.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Complexing/notes LOAD \ "Tar and CheW complex formation" \ "" \ "Kf = 1 * 10e5 /sec/M = 0.1 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 3" call /kinetics/TW/notes LOAD \ "Tar-CheW complex" \ "TW = 1.88e-06 M = 1.88 uM" \ "As per Signal entry 3 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/CheZ/notes LOAD \ "CheZ = 2.00e-05 M = 20 uM" \ "As per Signal 20 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "CheZ = 17000 molecules per cell" \ "As per Enzyme entry 6 in 1ENZ.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Autophosphorylation/notes LOAD \ "Autophosphorylation of CheA by ATP" \ "" \ "Kf = 0.001 /sec" \ "Kb = 0 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 2 pp.475 Reaction Scheme 1" call /kinetics/Autodephosphorylation/notes LOAD \ "Autodephosphorylation of CheBp" \ "" \ "Kf = 1 /sec" \ "Kb = 0 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 2 pp.475 Reaction Scheme 10" call /kinetics/Autodephosphorylation[1]/notes LOAD \ "Autodephosphorylation of CheYp" \ "" \ "Kf = 3.7*10e-02 /sec" \ "Kb = 0 /sec" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 2 pp.475 Reaction Scheme 7 " call /kinetics/Autophosphorylation[1]/notes LOAD \ "TWA stimulated autophosphorylation of CheA " \ "TWA is complex of Tar, CheW and CheA" \ "Kf = 7.57*10e+04 /sec/M = 0.0757 /sec/uM" \ "As per Reaction 9 in 1REACT.BCT provided by Matthew Levin" \ "" \ "Kf = 5.9*10e+4 /sec/M = 0.059 /sec/uM" \ "Kb = 0 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 2 pp.475 Reaction Scheme 2" call /kinetics/Autophosphorylation[2]/notes LOAD \ "Autophosphorylation of CheY" \ "Paper says reaction not applicable " \ "Table 2 pp.475 Reaction Scheme 6" \ "" \ "kf = 0/sec" \ "kb = 0/sec " \ "As per Reaction 14 in 1REACT.BCT provided by Matthew Levin" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Dephosphorylation/notes LOAD \ "CheZ stimulated dephosphorylation of CheYp" \ "" \ "Kf = 5*10e+05 /sec/M = 0.5 /sec/uM" \ "Kb = 0 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 2 pp.475 Reaction Scheme 8" call /kinetics/Complexing[1]/notes LOAD \ "Complex formation of Ni bound Tar and CheW" \ "Kf = 1 * 10e5 /sec/M = 0.1 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482; " \ "Table 3 pp.476 Reaction Scheme 3 " \ " " \ "Footnote states that ligands do not have any effect" \ "on the formation of the Tar-Chew-CheA complex so same rates" \ "are used for Aspartate or Ni associated Tar complexes." call /kinetics/Ni/notes LOAD \ "Ni = 0.0 uM" \ "As per Signal 1 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Binding/notes LOAD \ "Binding of Tar and Ni" \ "" \ "Kf = 1 * 10e+03 /sec/M = 0.001 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 2" call /kinetics/Tn/notes LOAD \ "Ni bound Tar" \ "Ni-Tar = 0 M" \ "As per Signal 4 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/TnW/notes LOAD \ "Nickel bound Tar and CheW complex" \ "TnW = 0.0 uM" \ "As per Signal 8 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Autophosphorylation[3]/notes LOAD \ "TnWA stimulated autophosphorylation of CheA " \ "TnWA is complex of Tar, CheW, CheA and Ni" \ "Kf = 1*10e+06 /sec/M = 1 /sec/uM" \ "Kb = 0 /sec" \ "As per Reaction 10 in 1REACT.BCT provided by Matthew Levin" \ " " \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 2 pp.475, Reaction scheme 3" call /kinetics/Binding[1]/notes LOAD \ "Binding of Aspartate with Tar" \ "Kd = 0.78 uM Dunten and Koshland, 1991" \ "" \ "Kf = 1.28e+06 /sec/M = 1.28 /sec/uM here scaled by 5" \ "As per Reaction 0 in 1REACT.BCT provided by Matthew Levin" \ "" \ "Kf = 1.0e+06 /sec/M = 1 /sec/uM; Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 1" call /kinetics/Ta/notes LOAD \ "Aspartate bound Tar" \ "Ta = 0.0 M" \ "As per Signal 3 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Complexing[2]/notes LOAD \ "Complex formation of aspartate bound Tar and CheW" \ "Kf = 1 * 10e+05 /sec/M = 0.1 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482;" \ "Table 3 pp.476 Reaction Scheme 3" \ "" \ "Footnote states that ligands do not have any effect" \ "on the formation of complexes so same rates are used for" \ "Aspartate or Ni associated Tar complexes." call /kinetics/TaW/notes LOAD \ "Aspartate bound Tar and CheW complex" \ "TaW = 0 M" \ "As per Signal 7 in 1SIG_B.BCT" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Dephosphorylation[1]/notes LOAD \ "TWA-aspartate stimulated dephosphorylation of CheYp" \ "" \ "Kf = 1 * 10e08 /sec/M = 100 /sec/uM" \ "Kb = 0 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 2 pp.475 Reaction Scheme 4" call /kinetics/Binding[2]/notes LOAD \ "Binding of TW and CheA" \ "Kd = 0.3 uM and therefore Kf also suggested as 0.3 /sec/uM" \ "Kf = 4*10e5 /sec/M = 0.4 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 6" call /kinetics/TWA/notes LOAD \ "Tar-CheW-CheA complex" \ "TWA = 2.12e-07 M = 2.12e-1 uM" \ "As per Signal entry 13 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Complexing[3]/notes LOAD \ "CheYp complexes with Flagellar Motor (M)" \ "" \ "Kf = 0.88/Set_Yp = 0.88/1e-08 /sec/M " \ " = 0.88e+2/sec/uM" \ "Kb = 5.5 /sec" \ "" \ "As per EXEC.C provided by Matthew Levin" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/MYpYp/notes LOAD \ "MYpYp = 3.66e-10 M = 3.66e-4 uM" \ "As per Signal 25 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "MYpYp is responsible for pause in rotation of flagella" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/MYpYpYp/notes LOAD \ "MYpYpYp = 4.47e-10 M = 4.47e-4 uM" \ "As per Signal 26 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/MYpYpYpYp/notes LOAD \ "MYpYpYpYp = 1.51e-09 M = 1.51e-3 uM" \ "As per Signal 27 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Complexing[4]/notes LOAD \ "CheYp complexes with MYp" \ "" \ "Kf = 2.85/Set_Yp = 2.85/1e-08 /sec/M " \ " = 2.85e+2/sec/uM" \ "Kb = 6.64 /sec" \ "" \ "As per EXEC.C provided by Matthew Levin" \ " " \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Complexing[5]/notes LOAD \ "CheYp complexes with MYpYp" \ "" \ "Kf = 6.94/Set_Yp = 6.94/1e-08 /sec/M " \ " = 6.94e+2 /sec/uM" \ "Kb = 5.1 /sec" \ "" \ "As per EXEC.C provided by Matthew Levin " \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Complexing[6]/notes LOAD \ "CheYp complexes with MYpYpYp" \ "" \ "Kf = 20.07/Set_Yp = 20.07/1e-08 /sec/M " \ " = 20.07e+2 /sec/uM" \ "Kb = 5.5 /sec" \ "" \ "As per EXEC.C provided by Matthew Levin" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Binding[3]/notes LOAD \ "Binding of T and CheA" \ "" \ "Kf = 0.05 /sec/uM as per Reaction 3 in 1REACT.BCT" \ "" \ "Kf = 1*10e+04 /sec/M = 0.01 /sec/uM " \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 4" call /kinetics/TA/notes LOAD \ "Tar-CheA complex" \ "TA = 1.55e-06 M = 1.55 uM" \ "" \ "As per Signal entry 9 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ " " \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Complexing[7]/notes LOAD \ "TA and CheW complex formation" \ "" \ "Kf = 4*10e+05 /sec/M = 0.4 /sec/uM" \ "Kb = 1 /sec" \ "Table 3 pp.476 Reaction Scheme 7" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/TnA/notes LOAD \ "Tar-Ni-CheA complex" \ "TnA = 0 M" \ "As per Signal 11 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ " " \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Binding[4]/notes LOAD \ "Binding of T-Ni and CheA" \ "Kf = 0.05 /sec/uM as per Reaction 3 in 1REACT.BCT" \ "Kf = 1*10e+04 /sec/M = 0.01 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 4" \ "Footnote states that ligands do not have any effect on the " \ "formation of complexes so same rates are used for " \ "Aspartate or Ni associated Tar complexes." call /kinetics/Complexing[8]/notes LOAD \ "TnA and CheW complex formation" \ "Kf = 4*10e+05 /sec/M = 0.4 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 7" \ " " \ "Footnote states that ligands do not have any effect " \ "on the formation of Tar-CheW-CheA complex so same rates" \ "are used for Aspartate or Ni associated Tar complexes." call /kinetics/TnWA/notes LOAD \ "Tar-Ni-CheW-CheA complex" \ "TnWA = 0 M" \ "As per Signal 15 in 1SIG.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Binding[5]/notes LOAD \ "Binding of TnW and CheA" \ "Kf = 4*10e+05 /sec/M = 0.4 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 6" \ "" \ "Footnote states that ligands do not have any effect on the" \ "formation of complexes so same rates are used for" \ "Aspartate or Ni associated tar complexes." call /kinetics/Binding[6]/notes LOAD \ "Binding of TaW and CheA" \ "Kf = 4*10e+05 /sec/M = 0.4 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 6" \ "" \ "Footnote states that ligands do not have any effect on " \ "the formation of the Tar-CheW-CheA complex so same rates" \ "are used for Aspartate or Ni associated Tar complexes." call /kinetics/TaWA/notes LOAD \ "Tar-CheW-CheA-Aspartate complex" \ "TaWA = 0 M" \ "As per Signal 14 in 1SIG_B.BCT provided by Matthew Levin" \ " " \ "Cell volume = 1.41e-15 L" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 1. pp.474" call /kinetics/Binding[7]/notes LOAD \ "Binding of Tar-Aspartate and CheA" \ "Kf = 0.05 /sec/uM as per Reaction 3 in 1REACT.BCT" \ "Kf = 1e+04 /sec/M = 0.01 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 4" \ "Footnote states that ligands do not have any effect" \ "on the formation of complexes so same rates are " \ "used for Aspartate or Ni associated Tar complexes." call /kinetics/TaA/notes LOAD \ "Tar-Asp-CheA complex" \ "TaA = 0 M" \ "As per Signal 10 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ " " \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Complexing[9]/notes LOAD \ "TaA and CheW complex formation" \ "Kf = 4*10e+05 /sec/M = 0.4 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 7" \ "" \ "Footnote states that ligands do not have any effect on " \ "the formation of the Tar-CheW-CheA complex so same rates" \ "are used for Aspartate or Ni associated Tar complexes" call /kinetics/Denominator/notes LOAD \ "Denominator value to calculate bias as stated on pp.471" \ "" \ " M + MYp" \ "Bias = ----------------------------------------" \ " M + MYp + MYpYp + MYpYpYp + MYpYpYpYp" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Bias/notes LOAD \ "Bias calculated as per formula stated on pp.471" \ "" \ " M + MYp" \ "Bias = ----------------------------------------" \ " M + MYp + MYpYp + MYpYpYp + MYpYpYpYp" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Initialy set to 0.7" call /kinetics/Aspartate/notes LOAD \ "Aspartate = 0.0 uM" \ "As per Signal 0 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/MYp/notes LOAD \ "MYp = 9.53*e-10 M = 9.53*e-4 uM" \ "As per Signal 24 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Motor/notes LOAD \ "Motor = 8.5 molecules per cell" \ "As per Enzyme entry 7 in 1ENZ.BCT provided by Matthew Levin" \ "" \ "Motor = 6.73e-9 M = 6.73e-3 uM" \ "As per Signal 23 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Numerator/notes LOAD \ "Numerator value to calculate bias as stated on pp.471" \ "" \ " M + MYp" \ "Bias = ----------------------------------------" \ " M + MYp + MYpYp + MYpYpYp + MYpYpYpYp" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/CW_rotation/notes LOAD \ "Sum total of MYpYpYp and MYpYpYpYp which is responsible for " \ "CW rotation of the flagella" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/WA/notes LOAD \ "CheW-CheA complex" \ "WA = 1.55e-6 M = 1.55 uM" \ "As per Signal 12 in 1SIG_B.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Tar/notes LOAD \ "Tar = 1.37e-06 M = 1.37 uM" \ "As per Signal 2 in 1SIG_B.BCT provided by Matthew Levin " \ "" \ "Tar = 4250 molecules per cell" \ "As per Enzyme entry 0 in 1ENZ.BCT provided by Matthew Levin" \ "" \ "Cell volume = 1.41e-15 L" \ "Table 1 pp.474" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" call /kinetics/Binding[9]/notes LOAD \ "Binding of Tar and CheW-CheA complex" \ "Kd = 2 uM and therefore Kf also suggested as 0.5 /sec/uM" \ "Kf = 4e+05 /sec/M = 0.4 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 8" call /kinetics/Binding[10]/notes LOAD \ "Binding of Tn and CheW-CheA complex" \ "Kf = 4e+05 /sec/M = 0.4 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 8" \ "" \ "Footnote states that ligands do not have any effect on" \ "the formation of complexes so same rates are used for" \ "Aspartate or Ni associated Tar complexes." call /kinetics/Binding[11]/notes LOAD \ "Binding of Ta and CheW-CheA complex" \ "Kf = 4e+05 /sec/M = 0.4 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 8" \ "" \ "Footnote states that ligands do not have any effect on the" \ "the formation of complexes so same rates are used for " \ "Aspartate or Ni associated Tar complexes." call /kinetics/Complexing[10]/notes LOAD \ "CheA and CheW complex formation" \ "Kf = 5*10e+04 /sec/M = 0.05 /sec/uM" \ "As per Reaction 4 in 1REACT.BCT provided by Matthew Levin" \ "" \ "Kf = 0.01 /sec/uM" \ "Kb = 1 /sec" \ "Bray et al 1993, Mol.Biol.Cell 4: 469-482" \ "Table 3 pp.476 Reaction Scheme 5" complete_loading