//genesis // kkit Version 11 flat dumpfile // Saved on Wed Feb 15 14:40:56 2006 include kkit {argv 1} FASTDT = 5e-05 SIMDT = 0.01 CONTROLDT = 0.1 PLOTDT = 20 MAXTIME = 30000 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 3e-18 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 simundump geometry /kinetics/geometry 0 3e-18 3 sphere "" white black 492 4 0 simundump kpool /kinetics/AI-extracellular 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry brown yellow 575 -18 0 simundump kpool /kinetics/Degraded_AI 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry 2 yellow 397 -18 0 simundump kreac /kinetics/AI_degradation 0 3 0 "" white yellow 479 -20 0 simundump doqcsinfo /kinetics/doqcsinfo 0 \ /home/harsha/DOQCS_DB_files/Upload_model_Dec2006/Quorum_repressilator/Quorum_repressilator.g \ Quorum_repressilator network " Sharat J. Vayttaden and Pragati Jain, NCBS" \ "Jordia Garcia-Ojalvo, Elowitz and Strogatz" \ "Modelling a synthetic multicellular clock: Repressilators coupled by quorum sensing" \ "E. Coli" "E.coli Expression, Transposon Tn10, Lambda phage Expression" \ "Cytosol, Extracellular" Qualitative \ " Garcia-Ojalvo J, Elowitz MB, Strogatz SH. Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10955-60. ( Peer-reviewed publication )" \ "Exact GENESIS implementation" "Approximates original data " 435 4 0 simundump group /kinetics/TetR 0 61 yellow x 0 0 "" TetR \ /home2/bhalla/scripts/modules/TetR_gene_0.g 0 0 0 311 1 0 simundump kreac /kinetics/TetR/TetR_degradation 0 0.005676 0 "" white 61 303 \ -13 0 simundump kpool /kinetics/TetR/TetR_operator 0 0 0.022222 0.022222 40 40 0 0 \ 1800 0 /kinetics/geometry 36 61 334 -8 0 simundump kenz /kinetics/TetR/TetR_operator/TetR_basal_transcription 0 0 0 0 \ 0 1800 1079.9 864 216 0 1 "" red 36 "" 334 -7 0 simundump kpool /kinetics/TetR/Nucleotides 0 0 0.00055555 0.00055555 0.99999 \ 0.99999 0 0 1800 4 /kinetics/geometry blue 61 323 -4 0 simundump kpool /kinetics/TetR/TetR-1 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 0 61 303 -11 0 simundump kpool /kinetics/TetR/TetR_operator_1st_bound 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 2 61 308 -8 0 simundump kenz /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription 0 0 \ 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 308 -6 0 simundump kpool /kinetics/TetR/TetR_operator_2nd_bound 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 46 61 282 -8 0 simundump kenz /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1 0 0 \ 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 46 "" 282 -7 0 simundump kpool /kinetics/TetR/Amino_Acids 0 0 0.00055555 0.00055555 0.99999 \ 0.99999 0 0 1800 4 /kinetics/geometry blue 61 303 -4 0 simundump kreac /kinetics/TetR/tetR_mRNA_degradation 0 0.00577 0 "" white 61 \ 313 -3 0 simundump kpool /kinetics/TetR/Degraded_tetR_mRNA 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry 1 61 316 -4 0 simundump kpool /kinetics/TetR/Degraded_TetR 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry 2 61 303 -15 0 simundump kreac /kinetics/TetR/TetR_operator_inhibition_reaction 0 0.55556 \ 224 "" white 61 319 -9 0 simundump kreac /kinetics/TetR/TetR_operator_inhibition_reaction[1] 0 0.55556 \ 9 "" white 61 313 -9 0 simundump kpool /kinetics/TetR/tetR_mRNA1 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 12 61 309 -4 0 simundump kenz /kinetics/TetR/tetR_mRNA1/tetR_translation 0 0 0 0 0 1800 \ 0.83494 0.668 0.167 0 1 "" red 12 "" 303 -6 0 simundump group /kinetics/LacI 0 yellow yellow x 0 0 "" LacI \ /home2/bhalla/scripts/modules/lac_gene_0.g 0 0 0 345 1 0 simundump kpool /kinetics/LacI/Nucleotides 0 0 0.00055555 0.00055555 0.99999 \ 0.99999 0 0 1800 4 /kinetics/geometry 6 yellow 358 -4 0 simundump kreac /kinetics/LacI/lac_mRNA_degradation 0 0.00577 0 "" white \ yellow 347 -3 0 simundump kpool /kinetics/LacI/Degraded_lac_mRNA 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry 1 yellow 351 -4 0 simundump kpool /kinetics/LacI/Lac_operator 0 0 0.022222 0.022222 40 40 0 0 \ 1800 0 /kinetics/geometry 36 yellow 358 -8 0 simundump kenz /kinetics/LacI/Lac_operator/Lac_basal_transcription 0 0 0 0 0 \ 1800 1079.9 864 216 0 1 "" red 36 "" 362 -7 0 simundump kpool /kinetics/LacI/Lac_operator_1st_bound 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 2 yellow 351 -8 0 simundump kenz /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription 0 0 0 \ 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 351 -6 0 simundump kpool /kinetics/LacI/Lac_operator_2nd_bound 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 52 yellow 344 -8 0 simundump kenz /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1 0 0 0 \ 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 344 -7 0 simundump kpool /kinetics/LacI/Lac-1 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 4 yellow 338 -11 0 simundump kreac /kinetics/LacI/Lac_degradation 0 0.005676 0 "" white yellow \ 338 -13 0 simundump kpool /kinetics/LacI/Degraded_lac 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry 2 yellow 338 -15 0 simundump kpool /kinetics/LacI/Amino_Acids 0 0 0.00055555 0.00055555 0.99999 \ 0.99999 0 0 1800 4 /kinetics/geometry 52 yellow 338 -4 0 simundump kreac /kinetics/LacI/Lac_operator_inhibition_reaction 0 0.55556 224 \ "" white yellow 354 -9 0 simundump kreac /kinetics/LacI/Lac_operator_inhibition_reaction[1] 0 0.55556 \ 9 "" white yellow 348 -9 0 simundump kpool /kinetics/LacI/lac_mRNA1 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 12 yellow 344 -4 0 simundump kenz /kinetics/LacI/lac_mRNA1/lac_translation 0 0 0 0 0 1800 \ 0.83494 0.668 0.167 0 1 "" red 12 "" 338 -6 0 simundump group /kinetics/Lambda-cl 0 15 yellow x 0 0 "" Lambda-cl \ /home2/bhalla/scripts/modules/yellow_0.g 0 0 0 386 1 0 simundump kpool /kinetics/Lambda-cl/Nucleotides 0 0 0.00055555 0.00055555 \ 0.99999 0.99999 0 0 1800 4 /kinetics/geometry 6 15 400 -4 0 simundump kpool /kinetics/Lambda-cl/Amino_Acids 0 0 0.00055555 0.00055555 \ 0.99999 0.99999 0 0 1800 4 /kinetics/geometry 52 15 379 -4 0 simundump kpool /kinetics/Lambda-cl/Lambda-cl-1 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 0 15 379 -11 0 simundump kpool /kinetics/Lambda-cl/Degraded_lambda-cl_mRNA 0 0 0 0 0 0 0 0 \ 1800 4 /kinetics/geometry 1 15 393 -4 0 simundump kpool /kinetics/Lambda-cl/Lambda-cl_operator 0 0 0.022222 0.022222 \ 40 40 0 0 1800 0 /kinetics/geometry 36 15 400 -8 0 simundump kenz /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription 0 \ 0 0 0 0 1800 1079.9 864 216 0 1 "" red 36 "" 400 -7 0 simundump kreac /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction 0 \ 0.55556 224 "" white 15 396 -9 0 simundump kreac /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] 0 \ 0.55556 9 "" white 15 390 -9 0 simundump kpool /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound 0 0 0 0 0 0 \ 0 0 1800 0 /kinetics/geometry 2 15 393 -8 0 simundump kenz /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription 0 \ 0 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 393 -6 0 simundump kpool /kinetics/Lambda-cl/Degraded_Lambda-cl 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry 2 15 379 -15 0 simundump kreac /kinetics/Lambda-cl/lambda-cl_mRNA_degradation 0 0.00577 0 "" \ white 15 389 -3 0 simundump kreac /kinetics/Lambda-cl/Lambda-cl_degradation 0 0.005676 0 "" \ white 15 379 -13 0 simundump kpool /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound 0 0 0 0 0 0 \ 0 0 1800 0 /kinetics/geometry 52 15 386 -8 0 simundump kenz /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1 0 \ 0 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 386 -7 0 simundump kpool /kinetics/Lambda-cl/lambda-cl_mRNA1 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 5 15 386 -4 0 simundump kenz /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation 0 0 \ 0 0 0 1800 0.83494 0.668 0.167 0 1 "" red 5 "" 379 -6 0 simundump group /kinetics/LacI_2nd_copy 0 yellow yellow x 0 0 "" \ LacI_2nd_copy /home2/bhalla/scripts/modules/lac_gene_0.g 0 0 0 423 1 0 simundump kpool /kinetics/LacI_2nd_copy/lac_mRNA 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 12 yellow 417 -4 0 simundump kenz /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation 0 0 0 0 0 \ 1800 0.83494 0.668 0.167 0 1 "" red 12 "" 411 -6 0 simundump kpool /kinetics/LacI_2nd_copy/Nucleotides 0 0 0.00055555 0.00055555 \ 0.99999 0.99999 0 0 1800 4 /kinetics/geometry 6 yellow 444 -4 0 simundump kreac /kinetics/LacI_2nd_copy/lac_mRNA_degradation 0 0.00577 0 "" \ white yellow 425 -3 0 simundump kpool /kinetics/LacI_2nd_copy/Degraded_lac_mRNA 0 0 0 0 0 0 0 0 \ 1800 4 /kinetics/geometry 1 yellow 429 -4 0 simundump kpool /kinetics/LacI_2nd_copy/Lac_operator 0 0 0.022222 0.022222 40 \ 40 0 0 1800 0 /kinetics/geometry 36 yellow 435 -8 0 simundump kenz /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription 0 \ 0 0 0 0 1800 1079.9 864 216 0 1 "" red 36 "" 436 -7 0 simundump kpool /kinetics/LacI_2nd_copy/Lac_operator_1st_bound 0 0 0 0 0 0 0 \ 0 1800 0 /kinetics/geometry 2 yellow 428 -8 0 simundump kenz /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription 0 \ 0 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 428 -6 0 simundump kpool /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound 0 0 0 0 0 0 0 \ 0 1800 0 /kinetics/geometry 52 yellow 422 -8 0 simundump kenz /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1 0 \ 0 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 422 -7 0 simundump kpool /kinetics/LacI_2nd_copy/Amino_Acids 0 0 0.00055555 0.00055555 \ 0.99999 0.99999 0 0 1800 4 /kinetics/geometry 52 yellow 411 -4 0 simundump kreac /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction 0 \ 0.55556 224 "" white yellow 432 -9 0 simundump kreac /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] 0 \ 0.55556 9 "" white yellow 426 -9 0 simundump kreac /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction 0 \ 1000 224 "" white yellow 406 -11 0 simundump kpool /kinetics/LacI_2nd_copy/Lac_operator_activator_bound 0 0 0 0 \ 0 0 0 0 1800 0 /kinetics/geometry 24 yellow 445 -8 0 simundump kenz /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription 0 \ 0 0 0 0 1800 99.992 80 20 0 1 "" red 24 "" 441 -6 0 simundump group /kinetics/LuxI 0 1 yellow x 0 0 "" LuxI \ /home2/bhalla/scripts/modules/yellow_0.g 0 0 0 470 1 0 simundump kpool /kinetics/LuxI/Nucleotides 0 0 0.00055555 0.00055555 0.99999 \ 0.99999 0 0 1800 4 /kinetics/geometry 6 1 483 -4 0 simundump kpool /kinetics/LuxI/luxI_mRNA 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 5 1 469 -4 0 simundump kenz /kinetics/LuxI/luxI_mRNA/luxI_translation 0 0 0 0 0 1800 \ 0.83494 0.668 0.167 0 1 "" red 5 "" 460 -6 0 simundump kreac /kinetics/LuxI/luxI_mRNA_degradation 0 0.00577 0 "" white 1 \ 472 -3 0 simundump kreac /kinetics/LuxI/AI_degradation 0 0.2 0 "" white 1 462 -13 0 simundump kpool /kinetics/LuxI/LuxR 0 0 0.055555 0.055555 99.999 99.999 0 0 \ 1800 4 /kinetics/geometry 12 1 454 -7 0 simundump kreac /kinetics/LuxI/LuxR_binding_autoinducer 0 0.0027778 0.1 "" \ white 1 454 -10 0 simundump kpool /kinetics/LuxI/LuxR-AI 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 51 1 446 -11 0 simundump kpool /kinetics/LuxI/AI-1 0 0 0 0 0 0 0 0 1800 0 /kinetics/geometry \ 4 1 462 -11 0 simundump kreac /kinetics/LuxI/AI_diffusion 0 2 2 "" white 1 478 -11 0 simundump kpool /kinetics/LuxI/Degraded_luxI_mRNA 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry 1 1 476 -4 0 simundump kreac /kinetics/LuxI/LuxR-AI_complex_dimerization 0 0.001 0.1 "" \ white 1 431 -10 0 simundump kpool /kinetics/LuxI/Amino_Acids 0 0 0.00055555 0.00055555 0.99999 \ 0.99999 0 0 1800 4 /kinetics/geometry 52 1 462 -4 0 simundump kpool /kinetics/LuxI/LuxI_operator_1st_bound 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 2 1 476 -8 0 simundump kenz /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription 0 0 \ 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 2 "" 476 -6 0 simundump kpool /kinetics/LuxI/LuxI_operator_2nd_bound 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 52 1 469 -8 0 simundump kenz /kinetics/LuxI/LuxI_operator_2nd_bound/LuxI_transcription1 0 0 \ 0 0 0 1800 0.0024998 0.002 0.0005 0 1 "" red 52 "" 469 -7 0 simundump kpool /kinetics/LuxI/LuxI_operator 0 0 0.022222 0.022222 40 40 0 0 \ 1800 0 /kinetics/geometry 36 1 483 -8 0 simundump kenz /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription 0 0 0 0 \ 0 1800 1079.9 864 216 0 1 "" red 36 "" 483 -7 0 simundump kreac /kinetics/LuxI/LuxR-AI_degradation 0 0.2 0 "" white 1 446 -13 \ 0 simundump kpool /kinetics/LuxI/Degraded_AI 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry 2 1 462 -15 0 simundump kpool /kinetics/LuxI/Degraded_LuxR-AI 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry 2 1 446 -15 0 simundump kreac /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] 0 0.55556 \ 9 "" white 1 473 -9 0 simundump kreac /kinetics/LuxI/LuxI_operator_inhibitor_reaction 0 0.55556 224 \ "" white 1 480 -9 0 simundump kpool /kinetics/LuxI/LuxI 0 0 0 0 0 0 0 0 1800 0 /kinetics/geometry \ blue 1 491 -11 0 simundump kreac /kinetics/LuxI/LuxI_degradation 0 25 0 "" white 1 486 -13 0 simundump kpool /kinetics/LuxI/degraded_LuxI 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry blue 1 488 -15 0 simundump kreac /kinetics/LuxI/AI_form 0 0.01 0 "" 1 1 484 -10 0 simundump kpool /kinetics/LuxI/2_LuxR-AI 0 0 0 0 0 0 0 0 1800 0 \ /kinetics/geometry 62 1 428 -11 0 simundump kpool /kinetics/LuxI/Degraded_2_LuxR-AI 0 0 0 0 0 0 0 0 1800 4 \ /kinetics/geometry 2 1 425 -15 0 simundump kreac /kinetics/LuxI/2_LuxR-AI_degradation 0 0.2 0 "" white 1 428 \ -13 0 simundump xgraph /graphs/conc1 0 0 30000 0.00011999 111.74 0 simundump xgraph /graphs/conc2 0 0 30000 0 1 0 simundump xplot /graphs/conc1/lambda-cl_mRNA1.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 5 0 0 1 simundump xgraph /moregraphs/conc3 0 0 30000 0 1 0 simundump xgraph /moregraphs/conc4 0 0 30000 0 1 0 simundump xcoredraw /edit/draw 0 280 577 -22 7 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 \ "Cleaned up version of a single cell." \ "Repressilator coupled to quorum sensing mechanism:" \ "A synthetic oscillatory network of transcriptional regulators " \ "coupled to quorum sensing module." \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" addmsg /kinetics/LuxI/AI_diffusion /kinetics/AI-extracellular REAC B A addmsg /kinetics/AI_degradation /kinetics/AI-extracellular REAC A B addmsg /kinetics/AI_degradation /kinetics/Degraded_AI REAC B A addmsg /kinetics/AI-extracellular /kinetics/AI_degradation SUBSTRATE n addmsg /kinetics/Degraded_AI /kinetics/AI_degradation PRODUCT n addmsg /kinetics/TetR/TetR-1 /kinetics/TetR/TetR_degradation SUBSTRATE n addmsg /kinetics/TetR/Degraded_TetR /kinetics/TetR/TetR_degradation PRODUCT n addmsg /kinetics/TetR/TetR_operator_inhibition_reaction /kinetics/TetR/TetR_operator REAC A B addmsg /kinetics/TetR/TetR_operator /kinetics/TetR/TetR_operator/TetR_basal_transcription ENZYME n addmsg /kinetics/TetR/Nucleotides /kinetics/TetR/TetR_operator/TetR_basal_transcription SUBSTRATE n addmsg /kinetics/TetR/TetR_operator/TetR_basal_transcription /kinetics/TetR/Nucleotides REAC sA B addmsg /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription /kinetics/TetR/Nucleotides REAC sA B addmsg /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1 /kinetics/TetR/Nucleotides REAC sA B addmsg /kinetics/TetR/tetR_mRNA1/tetR_translation /kinetics/TetR/TetR-1 MM_PRD pA addmsg /kinetics/TetR/TetR_degradation /kinetics/TetR/TetR-1 REAC A B addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] /kinetics/TetR/TetR-1 REAC A B addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction /kinetics/TetR/TetR-1 REAC A B addmsg /kinetics/TetR/TetR_operator_inhibition_reaction[1] /kinetics/TetR/TetR_operator_1st_bound REAC A B addmsg /kinetics/TetR/TetR_operator_inhibition_reaction /kinetics/TetR/TetR_operator_1st_bound REAC B A addmsg /kinetics/TetR/TetR_operator_1st_bound /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription ENZYME n addmsg /kinetics/TetR/Nucleotides /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription SUBSTRATE n addmsg /kinetics/TetR/TetR_operator_inhibition_reaction[1] /kinetics/TetR/TetR_operator_2nd_bound REAC B A addmsg /kinetics/TetR/TetR_operator_2nd_bound /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1 ENZYME n addmsg /kinetics/TetR/Nucleotides /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1 SUBSTRATE n addmsg /kinetics/TetR/tetR_mRNA1/tetR_translation /kinetics/TetR/Amino_Acids REAC sA B addmsg /kinetics/TetR/tetR_mRNA1 /kinetics/TetR/tetR_mRNA_degradation SUBSTRATE n addmsg /kinetics/TetR/Degraded_tetR_mRNA /kinetics/TetR/tetR_mRNA_degradation PRODUCT n addmsg /kinetics/TetR/tetR_mRNA_degradation /kinetics/TetR/Degraded_tetR_mRNA REAC B A addmsg /kinetics/TetR/TetR_degradation /kinetics/TetR/Degraded_TetR REAC B A addmsg /kinetics/TetR/TetR_operator_1st_bound /kinetics/TetR/TetR_operator_inhibition_reaction PRODUCT n addmsg /kinetics/TetR/TetR_operator /kinetics/TetR/TetR_operator_inhibition_reaction SUBSTRATE n addmsg /kinetics/LacI/Lac-1 /kinetics/TetR/TetR_operator_inhibition_reaction SUBSTRATE n addmsg /kinetics/TetR/TetR_operator_2nd_bound /kinetics/TetR/TetR_operator_inhibition_reaction[1] PRODUCT n addmsg /kinetics/TetR/TetR_operator_1st_bound /kinetics/TetR/TetR_operator_inhibition_reaction[1] SUBSTRATE n addmsg /kinetics/LacI/Lac-1 /kinetics/TetR/TetR_operator_inhibition_reaction[1] SUBSTRATE n addmsg /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1 /kinetics/TetR/tetR_mRNA1 MM_PRD pA addmsg /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription /kinetics/TetR/tetR_mRNA1 MM_PRD pA addmsg /kinetics/TetR/TetR_operator/TetR_basal_transcription /kinetics/TetR/tetR_mRNA1 MM_PRD pA addmsg /kinetics/TetR/tetR_mRNA_degradation /kinetics/TetR/tetR_mRNA1 REAC A B addmsg /kinetics/TetR/tetR_mRNA1 /kinetics/TetR/tetR_mRNA1/tetR_translation ENZYME n addmsg /kinetics/TetR/Amino_Acids /kinetics/TetR/tetR_mRNA1/tetR_translation SUBSTRATE n addmsg /kinetics/LacI/Lac_operator/Lac_basal_transcription /kinetics/LacI/Nucleotides REAC sA B addmsg /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1 /kinetics/LacI/Nucleotides REAC sA B addmsg /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription /kinetics/LacI/Nucleotides REAC sA B addmsg /kinetics/LacI/lac_mRNA1 /kinetics/LacI/lac_mRNA_degradation SUBSTRATE n addmsg /kinetics/LacI/Degraded_lac_mRNA /kinetics/LacI/lac_mRNA_degradation PRODUCT n addmsg /kinetics/Lambda-cl/Nucleotides /kinetics/LacI/lac_mRNA_degradation PRODUCT n addmsg /kinetics/LacI/lac_mRNA_degradation /kinetics/LacI/Degraded_lac_mRNA REAC B A addmsg /kinetics/LacI/Lac_operator_inhibition_reaction /kinetics/LacI/Lac_operator REAC A B addmsg /kinetics/LacI/Lac_operator /kinetics/LacI/Lac_operator/Lac_basal_transcription ENZYME n addmsg /kinetics/LacI/Nucleotides /kinetics/LacI/Lac_operator/Lac_basal_transcription SUBSTRATE n addmsg /kinetics/LacI/Lac_operator_inhibition_reaction /kinetics/LacI/Lac_operator_1st_bound REAC B A addmsg /kinetics/LacI/Lac_operator_inhibition_reaction[1] /kinetics/LacI/Lac_operator_1st_bound REAC A B addmsg /kinetics/LacI/Lac_operator_1st_bound /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription ENZYME n addmsg /kinetics/LacI/Nucleotides /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription SUBSTRATE n addmsg /kinetics/LacI/Lac_operator_inhibition_reaction[1] /kinetics/LacI/Lac_operator_2nd_bound REAC B A addmsg /kinetics/LacI/Lac_operator_2nd_bound /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1 ENZYME n addmsg /kinetics/LacI/Nucleotides /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1 SUBSTRATE n addmsg /kinetics/LacI/Lac_degradation /kinetics/LacI/Lac-1 REAC A B addmsg /kinetics/LacI/lac_mRNA1/lac_translation /kinetics/LacI/Lac-1 MM_PRD pA addmsg /kinetics/TetR/TetR_operator_inhibition_reaction /kinetics/LacI/Lac-1 REAC A B addmsg /kinetics/TetR/TetR_operator_inhibition_reaction[1] /kinetics/LacI/Lac-1 REAC A B addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] /kinetics/LacI/Lac-1 REAC A B addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction /kinetics/LacI/Lac-1 REAC A B addmsg /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation /kinetics/LacI/Lac-1 MM_PRD pA addmsg /kinetics/LacI/Degraded_lac /kinetics/LacI/Lac_degradation PRODUCT n addmsg /kinetics/LacI/Lac-1 /kinetics/LacI/Lac_degradation SUBSTRATE n addmsg /kinetics/LacI/Lac_degradation /kinetics/LacI/Degraded_lac REAC B A addmsg /kinetics/LacI/lac_mRNA1/lac_translation /kinetics/LacI/Amino_Acids REAC sA B addmsg /kinetics/LacI/Lac_operator /kinetics/LacI/Lac_operator_inhibition_reaction SUBSTRATE n addmsg /kinetics/LacI/Lac_operator_1st_bound /kinetics/LacI/Lac_operator_inhibition_reaction PRODUCT n addmsg /kinetics/Lambda-cl/Lambda-cl-1 /kinetics/LacI/Lac_operator_inhibition_reaction SUBSTRATE n addmsg /kinetics/LacI/Lac_operator_1st_bound /kinetics/LacI/Lac_operator_inhibition_reaction[1] SUBSTRATE n addmsg /kinetics/LacI/Lac_operator_2nd_bound /kinetics/LacI/Lac_operator_inhibition_reaction[1] PRODUCT n addmsg /kinetics/Lambda-cl/Lambda-cl-1 /kinetics/LacI/Lac_operator_inhibition_reaction[1] SUBSTRATE n addmsg /kinetics/LacI/Lac_operator/Lac_basal_transcription /kinetics/LacI/lac_mRNA1 MM_PRD pA addmsg /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1 /kinetics/LacI/lac_mRNA1 MM_PRD pA addmsg /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription /kinetics/LacI/lac_mRNA1 MM_PRD pA addmsg /kinetics/LacI/lac_mRNA_degradation /kinetics/LacI/lac_mRNA1 REAC A B addmsg /kinetics/LacI/lac_mRNA1 /kinetics/LacI/lac_mRNA1/lac_translation ENZYME n addmsg /kinetics/LacI/Amino_Acids /kinetics/LacI/lac_mRNA1/lac_translation SUBSTRATE n addmsg /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1 /kinetics/Lambda-cl/Nucleotides REAC sA B addmsg /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription /kinetics/Lambda-cl/Nucleotides REAC sA B addmsg /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription /kinetics/Lambda-cl/Nucleotides REAC sA B addmsg /kinetics/LacI/lac_mRNA_degradation /kinetics/Lambda-cl/Nucleotides REAC B A addmsg /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation /kinetics/Lambda-cl/Amino_Acids REAC sA B addmsg /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation /kinetics/Lambda-cl/Lambda-cl-1 MM_PRD pA addmsg /kinetics/LacI/Lac_operator_inhibition_reaction /kinetics/Lambda-cl/Lambda-cl-1 REAC A B addmsg /kinetics/LacI/Lac_operator_inhibition_reaction[1] /kinetics/Lambda-cl/Lambda-cl-1 REAC A B addmsg /kinetics/Lambda-cl/Lambda-cl_degradation /kinetics/Lambda-cl/Lambda-cl-1 REAC A B addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] /kinetics/Lambda-cl/Lambda-cl-1 REAC A B addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction /kinetics/Lambda-cl/Lambda-cl-1 REAC A B addmsg /kinetics/Lambda-cl/lambda-cl_mRNA_degradation /kinetics/Lambda-cl/Degraded_lambda-cl_mRNA REAC B A addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction /kinetics/Lambda-cl/Lambda-cl_operator REAC A B addmsg /kinetics/Lambda-cl/Lambda-cl_operator /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription ENZYME n addmsg /kinetics/Lambda-cl/Nucleotides /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription SUBSTRATE n addmsg /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction PRODUCT n addmsg /kinetics/Lambda-cl/Lambda-cl_operator /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction SUBSTRATE n addmsg /kinetics/TetR/TetR-1 /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction SUBSTRATE n addmsg /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] PRODUCT n addmsg /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] SUBSTRATE n addmsg /kinetics/TetR/TetR-1 /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] SUBSTRATE n addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound REAC A B addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound REAC B A addmsg /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription ENZYME n addmsg /kinetics/Lambda-cl/Nucleotides /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription SUBSTRATE n addmsg /kinetics/Lambda-cl/Lambda-cl_degradation /kinetics/Lambda-cl/Degraded_Lambda-cl REAC B A addmsg /kinetics/Lambda-cl/lambda-cl_mRNA1 /kinetics/Lambda-cl/lambda-cl_mRNA_degradation SUBSTRATE n addmsg /kinetics/Lambda-cl/Degraded_lambda-cl_mRNA /kinetics/Lambda-cl/lambda-cl_mRNA_degradation PRODUCT n addmsg /kinetics/Lambda-cl/Lambda-cl-1 /kinetics/Lambda-cl/Lambda-cl_degradation SUBSTRATE n addmsg /kinetics/Lambda-cl/Degraded_Lambda-cl /kinetics/Lambda-cl/Lambda-cl_degradation PRODUCT n addmsg /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1] /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound REAC B A addmsg /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1 ENZYME n addmsg /kinetics/Lambda-cl/Nucleotides /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1 SUBSTRATE n addmsg /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1 /kinetics/Lambda-cl/lambda-cl_mRNA1 MM_PRD pA addmsg /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription /kinetics/Lambda-cl/lambda-cl_mRNA1 MM_PRD pA addmsg /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription /kinetics/Lambda-cl/lambda-cl_mRNA1 MM_PRD pA addmsg /kinetics/Lambda-cl/lambda-cl_mRNA_degradation /kinetics/Lambda-cl/lambda-cl_mRNA1 REAC A B addmsg /kinetics/Lambda-cl/lambda-cl_mRNA1 /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation ENZYME n addmsg /kinetics/Lambda-cl/Amino_Acids /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/lac_mRNA_degradation /kinetics/LacI_2nd_copy/lac_mRNA REAC A B addmsg /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription /kinetics/LacI_2nd_copy/lac_mRNA MM_PRD pA addmsg /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription /kinetics/LacI_2nd_copy/lac_mRNA MM_PRD pA addmsg /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1 /kinetics/LacI_2nd_copy/lac_mRNA MM_PRD pA addmsg /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription /kinetics/LacI_2nd_copy/lac_mRNA MM_PRD pA addmsg /kinetics/LacI_2nd_copy/lac_mRNA /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation ENZYME n addmsg /kinetics/LacI_2nd_copy/Amino_Acids /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription /kinetics/LacI_2nd_copy/Nucleotides REAC sA B addmsg /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription /kinetics/LacI_2nd_copy/Nucleotides REAC sA B addmsg /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1 /kinetics/LacI_2nd_copy/Nucleotides REAC sA B addmsg /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription /kinetics/LacI_2nd_copy/Nucleotides REAC sA B addmsg /kinetics/LacI_2nd_copy/lac_mRNA /kinetics/LacI_2nd_copy/lac_mRNA_degradation SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/Degraded_lac_mRNA /kinetics/LacI_2nd_copy/lac_mRNA_degradation PRODUCT n addmsg /kinetics/LacI_2nd_copy/lac_mRNA_degradation /kinetics/LacI_2nd_copy/Degraded_lac_mRNA REAC B A addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction /kinetics/LacI_2nd_copy/Lac_operator REAC A B addmsg /kinetics/LacI_2nd_copy/Nucleotides /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/Lac_operator /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription ENZYME n addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction /kinetics/LacI_2nd_copy/Lac_operator_1st_bound REAC B A addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] /kinetics/LacI_2nd_copy/Lac_operator_1st_bound REAC A B addmsg /kinetics/LacI_2nd_copy/Nucleotides /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/Lac_operator_1st_bound /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription ENZYME n addmsg /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound REAC B A addmsg /kinetics/LacI_2nd_copy/Nucleotides /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1 SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1 ENZYME n addmsg /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation /kinetics/LacI_2nd_copy/Amino_Acids REAC sA B addmsg /kinetics/LacI_2nd_copy/Lac_operator /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/Lac_operator_1st_bound /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction PRODUCT n addmsg /kinetics/Lambda-cl/Lambda-cl-1 /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/Lac_operator_1st_bound /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] PRODUCT n addmsg /kinetics/Lambda-cl/Lambda-cl-1 /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1] SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/Lac_operator_activator_bound /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction PRODUCT n addmsg /kinetics/LuxI/2_LuxR-AI /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction SUBSTRATE n addmsg /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction /kinetics/LacI_2nd_copy/Lac_operator_activator_bound REAC B A addmsg /kinetics/LacI_2nd_copy/Lac_operator_activator_bound /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription ENZYME n addmsg /kinetics/LacI_2nd_copy/Nucleotides /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription SUBSTRATE n addmsg /kinetics/LuxI/LuxI_operator_2nd_bound/LuxI_transcription1 /kinetics/LuxI/Nucleotides REAC sA B addmsg /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription /kinetics/LuxI/Nucleotides REAC sA B addmsg /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription /kinetics/LuxI/Nucleotides REAC sA B addmsg /kinetics/LuxI/LuxI_operator_2nd_bound/LuxI_transcription1 /kinetics/LuxI/luxI_mRNA MM_PRD pA addmsg /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription /kinetics/LuxI/luxI_mRNA MM_PRD pA addmsg /kinetics/LuxI/luxI_mRNA_degradation /kinetics/LuxI/luxI_mRNA REAC A B addmsg /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription /kinetics/LuxI/luxI_mRNA MM_PRD pA addmsg /kinetics/LuxI/Amino_Acids /kinetics/LuxI/luxI_mRNA/luxI_translation SUBSTRATE n addmsg /kinetics/LuxI/luxI_mRNA /kinetics/LuxI/luxI_mRNA/luxI_translation ENZYME n addmsg /kinetics/LuxI/luxI_mRNA /kinetics/LuxI/luxI_mRNA_degradation SUBSTRATE n addmsg /kinetics/LuxI/Degraded_luxI_mRNA /kinetics/LuxI/luxI_mRNA_degradation PRODUCT n addmsg /kinetics/LuxI/AI-1 /kinetics/LuxI/AI_degradation SUBSTRATE n addmsg /kinetics/LuxI/Degraded_AI /kinetics/LuxI/AI_degradation PRODUCT n addmsg /kinetics/LuxI/LuxR_binding_autoinducer /kinetics/LuxI/LuxR REAC A B addmsg /kinetics/LuxI/AI-1 /kinetics/LuxI/LuxR_binding_autoinducer SUBSTRATE n addmsg /kinetics/LuxI/LuxR-AI /kinetics/LuxI/LuxR_binding_autoinducer PRODUCT n addmsg /kinetics/LuxI/LuxR /kinetics/LuxI/LuxR_binding_autoinducer SUBSTRATE n addmsg /kinetics/LuxI/LuxR_binding_autoinducer /kinetics/LuxI/LuxR-AI REAC B A addmsg /kinetics/LuxI/LuxR-AI_complex_dimerization /kinetics/LuxI/LuxR-AI REAC A B addmsg /kinetics/LuxI/LuxR-AI_complex_dimerization /kinetics/LuxI/LuxR-AI REAC A B addmsg /kinetics/LuxI/LuxR-AI_degradation /kinetics/LuxI/LuxR-AI REAC A B addmsg /kinetics/LuxI/AI_diffusion /kinetics/LuxI/AI-1 REAC A B addmsg /kinetics/LuxI/AI_degradation /kinetics/LuxI/AI-1 REAC A B addmsg /kinetics/LuxI/LuxR_binding_autoinducer /kinetics/LuxI/AI-1 REAC A B addmsg /kinetics/LuxI/AI_form /kinetics/LuxI/AI-1 REAC B A addmsg /kinetics/LuxI/AI-1 /kinetics/LuxI/AI_diffusion SUBSTRATE n addmsg /kinetics/AI-extracellular /kinetics/LuxI/AI_diffusion PRODUCT n addmsg /kinetics/LuxI/luxI_mRNA_degradation /kinetics/LuxI/Degraded_luxI_mRNA REAC B A addmsg /kinetics/LuxI/LuxR-AI /kinetics/LuxI/LuxR-AI_complex_dimerization SUBSTRATE n addmsg /kinetics/LuxI/2_LuxR-AI /kinetics/LuxI/LuxR-AI_complex_dimerization PRODUCT n addmsg /kinetics/LuxI/LuxR-AI /kinetics/LuxI/LuxR-AI_complex_dimerization SUBSTRATE n addmsg /kinetics/LuxI/luxI_mRNA/luxI_translation /kinetics/LuxI/Amino_Acids REAC sA B addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] /kinetics/LuxI/LuxI_operator_1st_bound REAC A B addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction /kinetics/LuxI/LuxI_operator_1st_bound REAC B A addmsg /kinetics/LuxI/LuxI_operator_1st_bound /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription ENZYME n addmsg /kinetics/LuxI/Nucleotides /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription SUBSTRATE n addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] /kinetics/LuxI/LuxI_operator_2nd_bound REAC B A addmsg /kinetics/LuxI/LuxI_operator_2nd_bound /kinetics/LuxI/LuxI_operator_2nd_bound/LuxI_transcription1 ENZYME n addmsg /kinetics/LuxI/Nucleotides /kinetics/LuxI/LuxI_operator_2nd_bound/LuxI_transcription1 SUBSTRATE n addmsg /kinetics/LuxI/LuxI_operator_inhibitor_reaction /kinetics/LuxI/LuxI_operator REAC A B addmsg /kinetics/LuxI/Nucleotides /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription SUBSTRATE n addmsg /kinetics/LuxI/LuxI_operator /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription ENZYME n addmsg /kinetics/LuxI/LuxR-AI /kinetics/LuxI/LuxR-AI_degradation SUBSTRATE n addmsg /kinetics/LuxI/Degraded_LuxR-AI /kinetics/LuxI/LuxR-AI_degradation PRODUCT n addmsg /kinetics/LuxI/AI_degradation /kinetics/LuxI/Degraded_AI REAC B A addmsg /kinetics/LuxI/LuxR-AI_degradation /kinetics/LuxI/Degraded_LuxR-AI REAC B A addmsg /kinetics/LuxI/LuxI_operator_2nd_bound /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] PRODUCT n addmsg /kinetics/LuxI/LuxI_operator_1st_bound /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] SUBSTRATE n addmsg /kinetics/LacI/Lac-1 /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1] SUBSTRATE n addmsg /kinetics/LuxI/LuxI_operator /kinetics/LuxI/LuxI_operator_inhibitor_reaction SUBSTRATE n addmsg /kinetics/LuxI/LuxI_operator_1st_bound /kinetics/LuxI/LuxI_operator_inhibitor_reaction PRODUCT n addmsg /kinetics/LacI/Lac-1 /kinetics/LuxI/LuxI_operator_inhibitor_reaction SUBSTRATE n addmsg /kinetics/LuxI/luxI_mRNA/luxI_translation /kinetics/LuxI/LuxI MM_PRD pA addmsg /kinetics/LuxI/AI_form /kinetics/LuxI/LuxI REAC A B addmsg /kinetics/LuxI/LuxI_degradation /kinetics/LuxI/LuxI REAC A B addmsg /kinetics/LuxI/LuxI /kinetics/LuxI/LuxI_degradation SUBSTRATE n addmsg /kinetics/LuxI/degraded_LuxI /kinetics/LuxI/LuxI_degradation PRODUCT n addmsg /kinetics/LuxI/LuxI_degradation /kinetics/LuxI/degraded_LuxI REAC B A addmsg /kinetics/LuxI/LuxI /kinetics/LuxI/AI_form SUBSTRATE n addmsg /kinetics/LuxI/AI-1 /kinetics/LuxI/AI_form PRODUCT n addmsg /kinetics/LuxI/LuxR-AI_complex_dimerization /kinetics/LuxI/2_LuxR-AI REAC B A addmsg /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction /kinetics/LuxI/2_LuxR-AI REAC A B addmsg /kinetics/LuxI/2_LuxR-AI_degradation /kinetics/LuxI/2_LuxR-AI REAC A B addmsg /kinetics/LuxI/2_LuxR-AI_degradation /kinetics/LuxI/Degraded_2_LuxR-AI REAC B A addmsg /kinetics/LuxI/2_LuxR-AI /kinetics/LuxI/2_LuxR-AI_degradation SUBSTRATE n addmsg /kinetics/LuxI/Degraded_2_LuxR-AI /kinetics/LuxI/2_LuxR-AI_degradation PRODUCT n addmsg /kinetics/Lambda-cl/lambda-cl_mRNA1 /graphs/conc1/lambda-cl_mRNA1.Co PLOT Co *lambda-cl_mRNA1.Co *5 enddump // End of dump call /kinetics/AI-extracellular/notes LOAD \ "Extracellular AI" call /kinetics/Degraded_AI/notes LOAD \ "Degradation product of autoinducer" call /kinetics/AI_degradation/notes LOAD \ "Degradation of autoinducer" \ "Garcia-Ojalvo, J et al. (2004)" \ "PNAS USA 101(30):10955-10960" call /kinetics/doqcsinfo/notes LOAD \ "This model represents a single cell with the repressilator circuit, which is part of a" \ "population of similar cells. The repressilator circuit is a network of three proteins," \ "i.e. LacI, TetR, Lambda-cI. " \ "The single repressilator model is at accession number 68 in the" \ "DOQCS database. " \ "In the current model, the LacI is coupled with LuxI which forms an" \ "Autoinducer(AI) protein, which couples to LuxR which activates LacI. The AI protein" \ "difffuses across the cell membrane so that the population of cells can interact." \ "" \ "The lifetime ratio is the ratio between the mRNA and protein lifetimes. This" \ "ratio in different cells is chosen from a random gaussian distribution of mean" \ "1 and standard deviation 0.05. The lifetime ratio of this example cell is 0.9837" call /kinetics/TetR/notes LOAD \ "This is a group of reactions resulting in the production" \ "of Tet R" \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/TetR/TetR_degradation/notes LOAD \ "This reaction denotes the degradation of TetR, " \ "" \ "kf is chosen from a random gaussian distribution. " \ "Ref: Fig 2" \ "Garcia and Elowitz et al. (2004)" \ "PNAS 101(30) 10955 - 60" \ "" call /kinetics/TetR/TetR_operator/notes LOAD \ "The TetR operator under normal conditions" \ "drives transcription of TetR" \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/TetR/TetR_operator/TetR_basal_transcription/notes LOAD \ "Basal transcription of the Tet R gene." \ "" \ "Rates from Fig 2" \ "Garcia & Elowitz et al. (2004)" \ "PNAS Vol.101" call /kinetics/TetR/TetR-1/notes LOAD \ "TetR translated from tetR m-RNA" \ "Derived from Figure 1(c) stochastic version" \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/TetR/TetR_operator_1st_bound/notes LOAD \ "This represents the promoter " \ "with one of its sites bound by the inhibitor" \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/TetR/TetR_operator_1st_bound/TetR_transcription/notes LOAD \ "Transcription of the TetR gene " \ "with only one of its promoter sites activated." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al (2000)" \ "Nature 403:335-338" call /kinetics/TetR/TetR_operator_2nd_bound/notes LOAD \ "This represents the promoter " \ "with both of its sites bound by the inhibitor." \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/TetR/TetR_operator_2nd_bound/TetR_transcription1/notes LOAD \ "Transcription of the TetR gene " \ "with both its promoter sites activated." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/TetR/tetR_mRNA_degradation/notes LOAD \ "This reaction denotes the degradation of the tetR m-RNA," \ "the half life of which is two minutes." \ "t1/2 = 0.693/k where k denotes kf" \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/TetR/Degraded_tetR_mRNA/notes LOAD \ "Degradation product of tetR m-RNA" call /kinetics/TetR/Degraded_TetR/notes LOAD \ "Degradation product of TetR protein" call /kinetics/TetR/TetR_operator_inhibition_reaction/notes LOAD \ "It signifies the first binding of the repressor " \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 224 /sec" \ "" \ "Box 1 " \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/TetR/TetR_operator_inhibition_reaction[1]/notes LOAD \ "It signifies the second binding of the repressor" \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 9 /sec" \ "" \ "Box 1 " \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/TetR/tetR_mRNA1/notes LOAD \ "The mRNA transcribed by the TetR operator" \ "" \ "Elowitz, M, et al. (2000) " \ "Nature 403:335-338" call /kinetics/TetR/tetR_mRNA1/tetR_translation/notes LOAD \ "Translation of the tetR mRNA." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LacI/notes LOAD \ "This is a group of reactions resulting in the production" \ "of Lac." \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LacI/lac_mRNA_degradation/notes LOAD \ "This reaction denotes the degradation of the lac m-RNA," \ "the half life of which is two minutes." \ "t1/2 = 0.693/k where k denotes kf" \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LacI/Degraded_lac_mRNA/notes LOAD \ "Degradation product of lac m-RNA" call /kinetics/LacI/Lac_operator/notes LOAD \ "The Lac operator under normal conditions" \ "drives transcription of Lac" \ "" \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LacI/Lac_operator/Lac_basal_transcription/notes LOAD \ "Basal transcription of the Lac gene." \ "" \ "Rates from Fig2" \ "Garcia & Elowitz et al. (2004)" \ "PNAS 101:10955-60" \ "" call /kinetics/LacI/Lac_operator_1st_bound/notes LOAD \ "This represents the promoter " \ "with one of its sites bound by the inhibitor." \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LacI/Lac_operator_1st_bound/Lac_transcription/notes LOAD \ "Transcription of the lac gene " \ "with only one of its promoter sites activated." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al. (2000) N" \ "Nature 403: 335-338" call /kinetics/LacI/Lac_operator_2nd_bound/notes LOAD \ "This represents the promoter " \ "with both of its sites bound by the inhibitor." \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LacI/Lac_operator_2nd_bound/Lac_transcription1/notes LOAD \ "Transcription of the Lac gene " \ "with both its promoter sites activated." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al. (2000) " \ "Nature 403: 335-338" call /kinetics/LacI/Lac-1/notes LOAD \ "Lac translated from lac m-RNA" \ "Derived from Figure 1(c) stochastic version" \ "" \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LacI/Lac_degradation/notes LOAD \ "This reaction denotes the degradation of Lac, " \ "" \ "Kf is chosen from a random gaussian distribution. " \ "Ref: Fig 2" \ "Garcia & Elowitz et al (2004)" \ "PNAS 101(30) 10955-60" \ " " call /kinetics/LacI/Degraded_lac/notes LOAD \ "Degradation product of Lac protein" call /kinetics/LacI/Lac_operator_inhibition_reaction/notes LOAD \ "It signifies the first binding of the repressor" \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 224 /sec" \ "" \ "Box 1 " \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LacI/Lac_operator_inhibition_reaction[1]/notes LOAD \ "It signifies the second binding of the repressor" \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 9 /sec" \ "" \ "Box 1 " \ "Elowitz, M. et al (2000)" \ "Nature 403:335-338" call /kinetics/LacI/lac_mRNA1/notes LOAD \ "The m-RNA transcribed by the lac operator" \ "" \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LacI/lac_mRNA1/lac_translation/notes LOAD \ "Translation of the lac mRNA." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al (2000)" \ "Nature 403: 335-338" call /kinetics/Lambda-cl/notes LOAD \ "This is a group of reactions resulting in the production" \ "of Lambda cl" call /kinetics/Lambda-cl/Lambda-cl-1/notes LOAD \ "Lambda-cl translated from lcl m-RNA" \ "Derived from Figure 1(c) stochastic version" \ "" \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/Lambda-cl/Degraded_lambda-cl_mRNA/notes LOAD \ "Degradation product of lambda cl m-RNA" call /kinetics/Lambda-cl/Lambda-cl_operator/notes LOAD \ "The lambda cl operator under normal conditions" \ "drives transcription of lambda cl" \ "" \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/Lambda-cl/Lambda-cl_operator/Lambda-cl_basal_transcription/notes LOAD \ "Basal transcription of the Lambda cl gene." \ "" \ "Rates from Fig 2" \ "Garcia and Elowitz et al. (2004)" \ "PNAS 101:10955-60" call /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction/notes LOAD \ "It signifies the first binding of the repressor" \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 224 /sec" \ "" \ "Box 1 " \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/Lambda-cl/Lambda-cl_operator_inhibition_reaction[1]/notes LOAD \ "It signifies the second binding of the repressor" \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 9 /sec" \ "" \ "Box 1 " \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/notes LOAD \ "This represents the promoter " \ "with one of its sites bound by the inhibitor." \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/Lambda-cl/Lambda-cl_operator_1st_bound/Lambda-cl_transcription/notes LOAD \ "Transcription of the Lambda cl gene " \ "with only one of its promoter sites activated." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/Lambda-cl/Degraded_Lambda-cl/notes LOAD \ "Degradation product of Lambda-cl protein" call /kinetics/Lambda-cl/lambda-cl_mRNA_degradation/notes LOAD \ "This reaction denotes the degradation of the lambda cl m-RNA," \ "the half life of which is two minutes." \ "" \ "t1/2 = 0.693/k where k denotes kf" \ "Elowitz M et al (2000)" \ "Nature 403 : 335-338" \ "" call /kinetics/Lambda-cl/Lambda-cl_degradation/notes LOAD \ "This reaction denotes the degradation of Lambda cl, " \ "" \ "kf is chosen from a random gaussian distribution. " \ "Ref: Fig 2" \ "Garcia & Elowitz et al. (2004) " \ "PNAS 101(30) 10955 - 60" call /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/notes LOAD \ "This represents the promoter " \ "with both of its sites bound by the inhibitor." \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/Lambda-cl/Lambda-cl_operator_2nd_bound/Lambda-cl_transcription1/notes LOAD \ "Transcription of the Lambda cl gene" \ "with both its promoter sites activated." \ "" \ "Rates from Box 1" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/Lambda-cl/lambda-cl_mRNA1/notes LOAD \ "The m-RNA transcribed by the Lcl operator" \ "" \ "Elowitz etal Nature 2000 Vol 403:335-338" call /kinetics/Lambda-cl/lambda-cl_mRNA1/lambda-cl_translation/notes LOAD \ "Translation the lambda cl mRNA." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al (2000)" \ "Nature 403:335-338" call /kinetics/LacI_2nd_copy/notes LOAD \ "This is a group of reactions resulting in the production" \ "of Lac." \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" \ "" \ "A second copy of the Lac gene " \ "has been introduced coupled to Lux I gene" \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" call /kinetics/LacI_2nd_copy/lac_mRNA/notes LOAD \ "The m-RNA transcribed by the lac operator" \ "" \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LacI_2nd_copy/lac_mRNA/lac_translation/notes LOAD \ "Translation of the lac mRNA." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al (2000)" \ "Nature 403: 335-338" call /kinetics/LacI_2nd_copy/lac_mRNA_degradation/notes LOAD \ "This reaction denotes the degradation of the lac m-RNA," \ "the half life of which is two minutes." \ "t1/2 = 0.693/k where k denotes kf" \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LacI_2nd_copy/Degraded_lac_mRNA/notes LOAD \ "Degradation product of lac m-RNA" call /kinetics/LacI_2nd_copy/Lac_operator/notes LOAD \ "The Lac operator under normal conditions" \ "drives transcription of Lac" \ "" \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LacI_2nd_copy/Lac_operator/Lac_basal_transcription/notes LOAD \ "Basal transcription of the Lac gene." \ "" \ "Rates from Fig 2" \ "Garcia and Elowitz et al.(2004)" \ "PNAS 101: 10955-60" call /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/notes LOAD \ "This represents the promoter " \ "with one of its sites bound by the inhibitor." \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LacI_2nd_copy/Lac_operator_1st_bound/Lac_transcription/notes LOAD \ "Transcription of the Lac gene " \ "with only one of its promoter sites activated." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al. (2000) N" \ "Nature 403: 335-338" call /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/notes LOAD \ "This represents the promoter " \ "with both of its sites bound by the inhibitor." \ "" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LacI_2nd_copy/Lac_operator_2nd_bound/Lac_transcription1/notes LOAD \ "Transcription of the Lac gene " \ "with both its promoter sites activated." \ "" \ "Rates from Box 1 " \ "Elowitz, M. et al. (2000) " \ "Nature 403: 335-338" call /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction/notes LOAD \ "It signifies the first binding of the repressor" \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 224 /sec" \ "" \ "Box 1 " \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LacI_2nd_copy/Lac_operator_inhibition_reaction[1]/notes LOAD \ "It signifies the second binding of the repressor" \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 9 /sec" \ "" \ "Box 1 " \ "Elowitz, M. et al (2000)" \ "Nature 403:335-338" call /kinetics/LacI_2nd_copy/Lac_operator_activation_reaction/notes LOAD \ "It signifies the binding of the activator" \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 224 /sec" \ "" \ "Used first binding rates for repressor from Box 1 " \ "Elowitz, M. et al (2000)" \ "Nature 403:335-338" call /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/notes LOAD \ "This represents the promoter bound to the activator." call /kinetics/LacI_2nd_copy/Lac_operator_activator_bound/Lac_active_transcription/notes LOAD \ "Lac transcription from the activator bound Lac gene." \ " " \ "" \ "kcat is taken from Garcia & Elowitz et al. (2004) " \ "PNAS 101: 10955-60" call /kinetics/LuxI/notes LOAD \ "This is a group of reactions resulting in the production" \ "of autoinducer protein. This has been introduced into" \ "the repressilator as a quorum sensing mechanism." \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" call /kinetics/LuxI/luxI_mRNA/notes LOAD \ "The m-RNA transcribed by the luxI operator" \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" \ "" \ "As described for components of the Repressilator" \ "by Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LuxI/luxI_mRNA/luxI_translation/notes LOAD \ "Rates from" \ "Box 1 Elowitz et al (2003)" \ "Nature 403:335-338" call /kinetics/LuxI/luxI_mRNA_degradation/notes LOAD \ "This reaction denotes the degradation of the luxI m-RNA," \ "the half life of which is two minutes." \ "t1/2 = 0.693/k where k denotes kf" \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" \ "" \ "As described for components of the Repressilator" \ "by Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LuxI/AI_degradation/notes LOAD \ "Degradation of autoinducer." \ "kf = 0.2, McMillen et al (2002) PNAS 99(2): 679-84" \ "" call /kinetics/LuxI/LuxR/notes LOAD \ "Lux R assumed to be constitutively produced." \ "" call /kinetics/LuxI/LuxR_binding_autoinducer/notes LOAD \ "Binding of Lux R to the autoinducer protein" \ "Kf = 5e+06 /M = 5 /uM" \ "" \ "McMillen, M. et al. (2002)" \ "PNAS USA 99(2): 679-84" \ "" \ "" call /kinetics/LuxI/LuxR-AI/notes LOAD \ "Lux R complexed with AI" \ "" call /kinetics/LuxI/AI-1/notes LOAD \ "AI translated from luxI m-RNA" \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" \ "" \ "As described for components of the Repressilator" \ "by Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LuxI/AI_diffusion/notes LOAD \ "Diffusion of the autoinducer from inside the cell to the" \ "outside and vice versa." \ "" \ "Garcia-Ojalvo, J et al. (2004)" \ "PNAS USA 101(30):10955-10960" call /kinetics/LuxI/Degraded_luxI_mRNA/notes LOAD \ "Degradation product of lux I m-RNA" call /kinetics/LuxI/LuxR-AI_complex_dimerization/notes LOAD \ "Dimerization of the complex between" \ "Lux R and the autoinducer protein" \ "Kf = 1.8e+18 /sec/M = 1.8 /sec/uM" \ "" \ "McMillen, M. et al. (2002)" \ "PNAS USA 99(2):679-684" \ "" call /kinetics/LuxI/LuxI_operator_1st_bound/notes LOAD \ "This represents the promoter " \ "with one of its sites bound by the inhibitor." \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" \ "" \ "As described for components of the Repressilator" \ "by Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LuxI/LuxI_operator_1st_bound/LuxI_transcription/notes LOAD \ "Transcription of the LuxI gene" \ "with only one of its promoter sites activated." \ "" \ "Garcia-Ojalvo, J. et al (2004)" \ "PNAS USA 101(30):10955-10960" \ "" \ "As described for components of the Repressilator in Box 1 " \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LuxI/LuxI_operator_2nd_bound/notes LOAD \ "This represents the promoter" \ "with both of its sites bound by the inhibitor." \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" \ "" \ "As described for components of the Repressilator" \ "by Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LuxI/LuxI_operator/notes LOAD \ "The LuxI operator under normal conditions" \ "drives transcription of LuxI" \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" \ "" \ "As described for components of the Repressilator" \ "by Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LuxI/LuxI_operator/LuxI_basal_transcription/notes LOAD \ "Basal transcription of the Lux I gene." \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" \ "" \ "As described for components of the Repressilator in Box 1" \ "Elowitz, M. et al. (2000)" \ "Nature 403:335-338" call /kinetics/LuxI/LuxR-AI_degradation/notes LOAD \ "Degradation of autoinducer complexed to LuxR, " \ "kf = 0.2, " \ "McMillen et al (2002)" \ "PNAS 99(2) 679 - 84" \ "" call /kinetics/LuxI/Degraded_AI/notes LOAD \ "Degradation product of autoinducer." call /kinetics/LuxI/Degraded_LuxR-AI/notes LOAD \ "Degradation product of the complex of Lux R with AI" call /kinetics/LuxI/LuxI_operator_inhibitor_reaction[1]/notes LOAD \ "This signifies the second binding of the repressor" \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 9 /sec" \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" \ "" \ "As described for components of the Repressilator in Box 1" \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LuxI/LuxI_operator_inhibitor_reaction/notes LOAD \ "This signifies the second binding of the repressor" \ "with the operator" \ "" \ "Kf = 1 /nM/sec" \ "Kb = 224 /sec" \ "" \ "Garcia-Ojalvo, J. et al. (2004)" \ "PNAS USA 101(30):10955-10960" \ "" \ "As described for components of the Repressilator in Box 1" \ "Elowitz, M. et al. (2000) " \ "Nature 403:335-338" call /kinetics/LuxI/LuxI_degradation/notes LOAD \ "This reaction denotes degradation of LuxI, kf = 25, " \ "" \ "McMillen et al (2002)" \ "PNAS 99(2): 679-84" \ "" call /kinetics/LuxI/AI_form/notes LOAD \ "Formation of Autoinducer" \ "The forward rate has taken from " \ "PNAS 101: 10955-60" \ " by Garcia & Elowitz et al (2004)" call /kinetics/LuxI/2_LuxR-AI/notes LOAD \ "Dimer of Lux R - AI complex" \ "" call /kinetics/LuxI/Degraded_2_LuxR-AI/notes LOAD \ "Degradation product of the dimer " \ "of the complex of Lux R with AI" call /kinetics/LuxI/2_LuxR-AI_degradation/notes LOAD \ "Degradation of the dimer of the complex between" \ "Lux R and autoinducer. " \ "kf = 0.2, " \ "McMillen et al (2002)" \ "PNAS 99(2) 679-84" \ "" complete_loading