// DOQCS : http://doqcs.ncbs.res.in/
// Accession Name = Chemotaxis
// Accession Number = 57
// Transcriber = Sharat J. Vayttaden, NCBS
// Developer = Dennis Bray, Robert B. Bourret and, Melvin I. Simon, Cambridge and Caltech
// Species = E. Coli
// Tissue = -
// Cell Compartment = Cell membrane + cytosol
// Notes = Reactions feeding into TnWa, TaWA and TWA are scaled by 10 Binding reaction of Tar with Aspartate has been scaled by 10 Phosphotransfer from CheAp to CheY has Kb = 0.263/sec/uM instead of 0.2/sec/uM used in BCT1.1.
All remaining parameters are from the .BCT files for BCT1.1 provided by Matthew Levin from the Computational Biology Group in the Department of Zoology at the University of Cambridge.
The June 2003 version of the BCT program is BCT4.3 and is available at the computational biology site of the Zoology department at Cambridge University.
Citation: Bray et al. Mol.Biol.Cell (1993) 4(5): 469-482.
//genesis
// kkit Version 11 flat dumpfile
// Saved on Fri Dec 9 11:26:58 2005
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 = 11.0
setfield /file/modpath value /home2/bhalla/scripts/modules
kparms
//genesis
initdump -version 3 -ignoreorphans 1
simobjdump doqcsinfo filename accessname accesstype transcriber developer \
citation species tissue cellcompartment methodology sources \
model_implementation model_validation x y z
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 geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \
z
simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \
geomname 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 calculator resetclock output_init
simundump geometry /kinetics/geometry 0 1.41e-18 3 sphere "" white black 145 \
56 0
simundump kpool /kinetics/CheA 0 0 1.13 1.13 955.98 955.98 0 0 846 0 \
/kinetics/geometry 47 black -102 -104 0
simundump kpool /kinetics/CheAp 0 0 0.569 0.569 481.37 481.37 0 0 846 0 \
/kinetics/geometry 62 black -106 -49 0
simundump kpool /kinetics/CheB 0 0 1.62 1.62 1370.5 1370.5 0 0 846 0 \
/kinetics/geometry 15 black -127 11 0
simundump kpool /kinetics/CheBp 0 0 0.381 0.381 322.33 322.33 0 0 846 0 \
/kinetics/geometry 0 black -212 22 0
simundump kreac /kinetics/Phosphotransfer 0 0.001182 0 "" 62 black -143 -26 0
simundump kpool /kinetics/CheYp 0 0 0.01 0.01 8.46 8.46 0 0 846 0 \
/kinetics/geometry white black 4 -62 0
simundump kpool /kinetics/CheY 0 0 9.88 9.88 8358.5 8358.5 0 0 846 0 \
/kinetics/geometry 41 black -78 -126 0
simundump kreac /kinetics/Phosphotransfer[1] 0 0.00031087 0 "" 62 black -36 \
-87 0
simundump kpool /kinetics/CheW 0 0 1.37 1.37 1159 1159 0 0 846 0 \
/kinetics/geometry 5 black 17 -240 0
simundump kreac /kinetics/Complexing 0 0.0001182 1 "" 62 black -292 -259 0
simundump kpool /kinetics/TW 0 0 1.88 1.88 1590.5 1590.5 0 0 846 0 \
/kinetics/geometry 9 black -264 -257 0
simundump kpool /kinetics/CheZ 0 0 20 20 16920 16920 0 0 846 0 \
/kinetics/geometry 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 /kinetics/geometry 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 /kinetics/geometry 43 \
black -172 -263 0
simundump kpool /kinetics/TnW 0 0 0 0 0 0 0 0 846 0 /kinetics/geometry 9 \
black -115 -300 0
simundump kreac /kinetics/Autophosphorylation[3] 0 0.001182 0 "" 62 black -40 \
-262 0
simundump kreac /kinetics/Binding[1] 0 0.01513 10 "" 62 black 179 -193 0
simundump kpool /kinetics/Ta 0 0 0 0 0 0 0 0 846 0 /kinetics/geometry 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 0 0 0 0 0 846 0 /kinetics/geometry 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 0.0047281 10 "" 62 black -219 -217 0
simundump kpool /kinetics/TWA 0 0 0.212 0.212 179.35 179.35 0 0 846 0 \
/kinetics/geometry 9 black -233 -101 0
simundump kreac /kinetics/Complexing[3] 0 1.0402 55 "" 62 black 19 -41 0
simundump kpool /kinetics/MYpYp 0 0 0.000366 0.000366 0.30964 0.30964 0 0 846 \
0 /kinetics/geometry 23 black 2 53 0
simundump kpool /kinetics/MYpYpYp 0 0 0.000447 0.000447 0.37816 0.37816 0 0 \
846 0 /kinetics/geometry 18 black -7 39 0
simundump kpool /kinetics/MYpYpYpYp 0 0 0.00151 0.00151 1.2775 1.2775 0 0 846 \
0 /kinetics/geometry 62 black -22 20 0
simundump kreac /kinetics/Complexing[4] 0 3.3688 66.4 "" 62 black 10 -26 0
simundump kreac /kinetics/Complexing[5] 0 8.2033 51 "" 62 black 92 33 0
simundump kreac /kinetics/Complexing[6] 0 23.723 55 "" 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 0 1.55 1.55 1311.3 1311.3 0 0 846 0 \
/kinetics/geometry 50 black -272 -102 0
simundump kreac /kinetics/Complexing[7] 0 0.0047281 10 "" 62 black -299 -44 0
simundump kpool /kinetics/TnA 0 0 0 0 0 0 0 0 846 0 /kinetics/geometry 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 0.0047281 10 "" 62 black -75 -325 0
simundump kpool /kinetics/TnWA 0 0 0 0 0 0 0 0 846 0 /kinetics/geometry 62 \
black -29 -327 0
simundump kreac /kinetics/Binding[5] 0 0.0047281 10 "" 62 black -70 -294 0
simundump kreac /kinetics/Binding[6] 0 0.0047281 10 "" 62 black 71 -158 0
simundump kpool /kinetics/TaWA 0 0 0 0 0 0 0 0 846 0 /kinetics/geometry 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 0 0 0 0 0 846 0 /kinetics/geometry 50 \
black 69 -270 0
simundump kreac /kinetics/Complexing[9] 0 0.0047281 10 "" 62 black 129 -109 0
simundump kpool /kinetics/Denominator 0 0 0 0.010006 8.4651 0 0 0 846 0 \
/kinetics/geometry 62 black -100 72 0
simundump kpool /kinetics/Bias 0 0 0.768 0.768 649.73 649.73 0 0 846 0 \
/kinetics/geometry 0 black -96 110 0
simundump kpool /kinetics/Aspartate 0 0 0 0 0 0 0 0 846 4 /kinetics/geometry \
white black 159 -131 0
simundump kpool /kinetics/MYp 0 0 0.000953 0.000953 0.80624 0.80624 0 0 846 0 \
/kinetics/geometry 56 black 10 64 0
simundump kpool /kinetics/Motor 0 0 0.00673 0.00673 5.6936 5.6936 0 0 846 0 \
/kinetics/geometry 18 black 23 76 0
simundump kpool /kinetics/Numerator 0 0 0 0.007683 6.4998 0 0 0 846 0 \
/kinetics/geometry 46 black -30 128 0
simundump kpool /kinetics/CW_rotation 0 0 0 0.001957 1.6557 0 0 0 846 0 \
/kinetics/geometry 1 black -104 44 0
simundump kpool /kinetics/WA 0 0 1.55 1.55 1311.3 1311.3 0 0 846 0 \
/kinetics/geometry 9 black -109 -484 0
simundump kpool /kinetics/Tar 0 0 1.37 1.37 1159 1159 0 0 846 0 \
/kinetics/geometry 24 black -347 -196 0
simundump kreac /kinetics/Binding[9] 0 0.0047281 10 "" 62 black -291 -132 0
simundump kreac /kinetics/Binding[10] 0 0.0047281 10 "" 62 black -142 -428 0
simundump kreac /kinetics/Binding[11] 0 0.0047281 10 "" 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 doqcsinfo /kinetics/doqcsinfo 0 db57.g Chemotaxis pathway \
" Sharat J. Vayttaden, NCBS" \
" Dennis Bray, Robert B. Bourret and, Melvin I. Simon, Cambridge and Caltech" \
"citation here" "E. Coli-" - " Cell membrane + cytosol" Qualitative \
"Bray et al. Mol.Biol.Cell (1993) 4(5): 469-482. ( peer-reviewed publication )" \
"Mathematically equivalent" "Replicates original data " 148 91 0
simundump xgraph /graphs/conc1 0 0 45 0.68 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 1.1248e-07 0 1
simundump xplot /graphs/conc1/Bias.Co[2] 0 0 nil 0 0 0 1
simundump xplot /graphs/conc1/Bias.Co[3] 0 0 nil 0 0 0 1
simundump xplot /graphs/conc1/Bias.Co[4] 0 0 nil 0 0 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 " 23 0 0 1
simundump xplot /moregraphs/conc3/MYp.Co 3 524288 \
"delete_plot.w ; edit_plot.D " 56 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 " 18 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 \
"Reactions feeding into TnWA, TaWA and TWA scaled by 10" \
"Binding reaction of Tar with Aspartate scaled by 10" \
"Motor and Yp reactions scaled by 10" \
"Phosphotransfer from CheAp to CheY has Kb = 0.263/sec/uM " \
"instead of 0.2/sec/uM used in BCT1.1 All remaining parameters" \
"as in .BCT files for BCT1.1 provided by Matthew Levin" \
"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/Division /graphs/conc1/Bias.Co[2] PLOT output *Bias.Co *0
addmsg /kinetics/Division /graphs/conc1/Bias.Co[3] PLOT output *Bias.Co *0
addmsg /kinetics/Division /graphs/conc1/Bias.Co[4] 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 *23
addmsg /kinetics/MYp /moregraphs/conc3/MYp.Co PLOT Co *MYp.Co *56
addmsg /kinetics/MYpYpYpYp /moregraphs/conc4/MYpYpYpYp.Co PLOT Co *MYpYpYpYp.Co *62
addmsg /kinetics/MYpYpYp /moregraphs/conc4/MYpYpYp.Co PLOT Co *MYpYpYp.Co *18
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" \
"Rates used here are 10 times that stated, to allow for " \
"faster time courses seen during the drop of bias" \
"on removal of stimulus."
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" \
"Rates used here are 10 times that stated, to allow for" \
"faster time courses seen during the drop of bias " \
"on removal of stimulus."
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" \
"Rates used here are 10 times that stated, to allow for" \
"faster time courses seen during the drop of bias on" \
"removal of stimulus. " \
"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" \
"Rates used here are 10 times that stated, to allow for" \
"faster time courses seen during the drop of bias" \
"on removal of stimulus." \
"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" \
"Rates used here are 10 time that stated, to allow for" \
"faster time courses seen during the drop of bias" \
"on removal of stimulus." \
"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" \
"Rates used here are 10 times that stated, to allow for " \
"faster time courses seen during the drop of bias " \
"on removal of stimulus."
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" \
"Rates used here are 10 times that stated, to allow for" \
"faster time courses seen during the drop of bias on" \
"removal of stimulus." \
"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" \
"Rates used here are 10 times that stated, to allow for" \
"faster time courses seen during the drop of bias on " \
"removal of stimulus." \
"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"
call /kinetics/doqcsinfo/notes LOAD \
"Reactions feeding into TnWa, TaWA and TWA are scaled by 10 Binding reaction of Tar with Aspartate has been scaled by 10\ Phosphotransfer from CheAp to CheY has Kb = 0.263/sec/uM instead of 0.2/sec/uM used in BCT1.1.
All remaining parameters are\ from the .BCT files for BCT1.1. All remaining parameters are from the .BCT files for BCT1.1 provided by Matthew Levin from the Computational Biology Group in the Department of Zoology at the University of Cambridge. The June 2003 version of the BCT program is BCT4.3 and is available at the computational biology site of the Zoology department at Cambridge University.
Citation: Bray et al. Mol.Biol.Cell (1993) 4(5): 469-482."
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