380669
constant: true
value: 1.0
type: Parameter

380580
kinetic law: 167227
product: 167215
product: 167203
reactant: 167191
fast: false
reversible: false
name: prod7
type: Reaction

380594
kinetic law: 167759
product: 167747
product: 167735
reactant: 167723
fast: false
reversible: false
name: Prod_FimE
type: Reaction

167118
stoichiometry: 1.0
species: 380517
type: SpeciesReference

380568
type: Reaction
reactant: 166661
reactant: 166637
fast: false
kinetic law: 166697
reversible: true
reactant: 166649
name: r7
reactant: 166673
product: 166685

166126
stoichiometry: 1.0
species: 380517
type: SpeciesReference

167735
stoichiometry: 1.0
species: 380517
type: SpeciesReference

380553
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s18
type: Species

167456
stoichiometry: 1.0
species: 380526
type: SpeciesReference

166913
stoichiometry: 1.0
species: 380520
type: SpeciesReference

166150
stoichiometry: 1.0
species: 380531
type: SpeciesReference

380658
constant: true
value: 0.00847626
type: Parameter

380648
constant: true
value: 1.01547
type: Parameter

167480
stoichiometry: 1.0
species: 380543
type: SpeciesReference

380593
kinetic law: 167711
product: 167699
reactant: 167687
reactant: 167675
fast: false
reversible: true
name: r_PfimB_RNAP
type: Reaction

166454
stoichiometry: 1.0
species: 380550
type: SpeciesReference

380628
constant: true
value: 0.666666667
type: Parameter

167021
stoichiometry: 1.0
species: 380551
type: SpeciesReference

380569
kinetic law: 166745
product: 166733
reactant: 166721
reactant: 166709
fast: false
reversible: true
name: r23
type: Reaction

380540
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s8
type: Species

166211
stoichiometry: 1.0
species: 380531
type: SpeciesReference

380554
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s24
type: Species

380638
constant: true
value: 0.001625
type: Parameter

380659
constant: true
value: 3.59662E-4
type: Parameter

380530
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: PfimE_HNS
type: Species

380645
constant: true
value: 3.7E-6
type: Parameter

166757
stoichiometry: 1.0
species: 380528
type: SpeciesReference

166478
stoichiometry: 1.0
species: 380517
type: SpeciesReference

167468
stoichiometry: 1.0
species: 380522
type: SpeciesReference

167723
stoichiometry: 1.0
species: 380541
type: SpeciesReference

380541
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: PfimE_RNAP
type: Species

380625
constant: true
value: 0.014705882
type: Parameter

380639
constant: true
value: 1.0
type: Parameter

167070
stoichiometry: 1.0
species: 380540
type: SpeciesReference

166138
stoichiometry: 2.0
species: 380519
type: SpeciesReference

167143
stoichiometry: 1.0
species: 380520
type: SpeciesReference

166551
stoichiometry: 1.0
species: 380549
type: SpeciesReference

380551
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s3
type: Species

167203
stoichiometry: 1.0
species: 380546
type: SpeciesReference

167408
stoichiometry: 1.0
species: 380533
type: SpeciesReference

167396
stoichiometry: 1.0
species: 380531
type: SpeciesReference

380581
kinetic law: 167287
product: 167275
reactant: 167263
reactant: 167251
reactant: 167239
fast: false
reversible: true
name: r21
type: Reaction

380591
kinetic law: 167663
reactant: 167651
fast: false
reversible: false
name: Deg_FimE
type: Reaction

380646
constant: true
value: 7.5E-7
type: Parameter

166162
stoichiometry: 1.0
species: 380539
type: SpeciesReference

166223
stoichiometry: 1.0
species: 380518
type: SpeciesReference

380626
constant: true
value: 10.0
type: Parameter

167130
stoichiometry: 2.0
species: 380519
type: SpeciesReference

167033
stoichiometry: 1.0
species: 380524
type: SpeciesReference

166308
stoichiometry: 3.0
species: 380519
type: SpeciesReference

167299
stoichiometry: 1.0
species: 380517
type: SpeciesReference

167082
stoichiometry: 1.0
species: 380540
type: SpeciesReference

380544
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s17
type: Species

166502
stoichiometry: 1.0
species: 380544
type: SpeciesReference

166865
stoichiometry: 1.0
species: 380520
type: SpeciesReference

380563
kinetic law: 166466
product: 166454
reactant: 166442
reactant: 166430
reactant: 166418
fast: false
reversible: true
name: r26
type: Reaction

380558
product: 166235
reactant: 166198
reactant: 166211
type: Reaction
name: r8
reactant: 166186
reactant: 166223
fast: false
reversible: true
kinetic law: 166247

380584
reactant: 167384
fast: false
kinetic law: 167420
reversible: true
product: 167408
name: r6
type: Reaction
reactant: 167372
reactant: 167360
reactant: 167396

166769
stoichiometry: 1.0
species: 380528
type: SpeciesReference

380633
constant: true
value: 0.333333333
type: Parameter

380578
kinetic law: 167106
product: 167094
product: 167082
reactant: 167070
fast: false
reversible: false
name: prod8
type: Reaction

380533
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s6
type: Species

380683
constant: true
value: 1.0
type: Parameter

380523
constant: false
boundary condition: false
has only substance units: false
initial concentration: 30.0
initial amount: NaN
in compartment: 380515
name: RNAP
type: Species

380623
constant: true
value: 0.333333333
type: Parameter

380543
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: PfimB_HNS
type: Species

380545
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s20
type: Species

166490
stoichiometry: 1.0
species: 380531
type: SpeciesReference

380564
kinetic law: 166514
product: 166502
reactant: 166490
reactant: 166478
fast: false
reversible: true
name: r17
type: Reaction

380559
kinetic law: 166296
product: 166283
product: 166271
reactant: 166259
fast: false
reversible: false
name: prod6
type: Reaction

166235
stoichiometry: 1.0
species: 380540
type: SpeciesReference

380531
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: 380515
name: Prom
type: Species

380583
kinetic law: 167348
product: 167335
reactant: 167323
reactant: 167311
reactant: 167299
fast: false
reversible: true
name: r20
type: Reaction

166430
stoichiometry: 3.0
species: 380519
type: SpeciesReference

380634
constant: true
value: 10.0
type: Parameter

MODEL1004010002
volume units: 950046
species: 380523
parameter: 380678
reaction: 380584
reaction: 380581
reaction: 380570
reaction: 380569
species: 380544
parameter: 380628
parameter: 380669
parameter: 380648
species: 380535
parameter: 380646
parameter: 380644
reaction: 380559
species: 380528
reaction: 380556
parameter: 380636
reaction: 380588
parameter: 380633
parameter: 380634
parameter: 380664
compartment: 380515
species: 380554
species: 380538
parameter: 380684
species: 380530
parameter: 380685
parameter: 380683
parameter: 380680
species: 380536
parameter: 380681
species: 380551
reaction: 380576
parameter: 380631
parameter: 380651
reaction: 380564
reaction: 380563
species: 380526
parameter: 380689
parameter: 380668
reaction: 380561
species: 380524
parameter: 380639
reaction: 380593
parameter: 380659
parameter: 380655
parameter: 380656
curated: false
reaction: 380568
type: SBMLModel
length unit: 335510
parameter: 380645
parameter: 380643
parameter: 380688
species: 380517
species: 380545
parameter: 380676
species: 380529
parameter: 380626
reaction: 380580
parameter: 380624
species: 380533
is described by: http://identifiers.org/pubmed/20361050
notes: This the detailed model for 42°C from the article: Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli : Quantitative Analysis via Automated Model Abstraction. Hiroyuki Kuwahara, Chris J. Myers and Michael S. Samoilov PLoS Comput Biol. 2010 6(3): e1000723. doi: 10.1371/journal.pcbi.1000723 , Abstract: Uropathogenic Escherichia coli (UPEC) represent the predominant cause of urinary tract infections (UTIs). A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element—the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role i…
parameter: 380663
parameter: 380660
reaction: 380575
species: 380540
parameter: 380630
parameter: 380675
parameter: 380650
species: 380539
parameter: 380671
species: 380543
species: 380519
reaction: 380590
parameter: 380679
reaction: 380586
reaction: 380574

380579
reactant: 167155
product: 167167
reactant: 167118
type: Reaction
reactant: 167143
reversible: true
name: r5
kinetic law: 167179
reactant: 167130
fast: false

380522
constant: false
boundary condition: false
has only substance units: false
initial concentration: 20000.0
initial amount: NaN
in compartment: 380515
name: HNS
type: Species

167215
stoichiometry: 1.0
species: 380524
type: SpeciesReference

167384
stoichiometry: 1.0
species: 380520
type: SpeciesReference

380624
constant: true
value: 10.0
type: Parameter

167046
stoichiometry: 1.0
species: 380551
type: SpeciesReference

380520
constant: false
boundary condition: false
has only substance units: false
initial concentration: 10.0
initial amount: NaN
in compartment: 380515
name: IHF
type: Species

166393
stoichiometry: 1.0
species: 380524
type: SpeciesReference

380565
kinetic law: 166564
product: 166551
reactant: 166538
reactant: 166526
fast: false
reversible: true
name: r2
type: Reaction

167747
stoichiometry: 1.0
species: 380541
type: SpeciesReference

380546
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s7
type: Species

380649
constant: true
value: 0.00860736
type: Parameter

167094
stoichiometry: 1.0
species: 380524
type: SpeciesReference

380586
kinetic law: 167492
product: 167480
reactant: 167468
reactant: 167456
fast: false
reversible: true
name: r_PfimB_HNS
type: Reaction

166853
stoichiometry: 1.0
species: 380517
type: SpeciesReference

380556
kinetic law: 166174
product: 166162
reactant: 166150
reactant: 166138
reactant: 166126
fast: false
reversible: true
name: r19
type: Reaction

380575
kinetic law: 167009
product: 166997
reactant: 166985
reactant: 166973
fast: false
reversible: true
name: r18
type: Reaction

166601
stoichiometry: 1.0
species: 380518
type: SpeciesReference

380535
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s22
type: Species

380635
constant: true
value: 5.88235E-4
type: Parameter

380671
constant: true
value: 1.0
type: Parameter

380681
constant: true
value: 1.0
type: Parameter

380566
kinetic law: 166625
product: 166613
reactant: 166601
reactant: 166589
reactant: 166576
fast: false
reversible: true
name: r4
type: Reaction

167311
stoichiometry: 3.0
species: 380519
type: SpeciesReference

166442
stoichiometry: 1.0
species: 380531
type: SpeciesReference

380585
kinetic law: 167444
reactant: 167432
fast: false
reversible: false
name: Deg_FimB
type: Reaction

380576
kinetic law: 167058
product: 167046
product: 167033
reactant: 167021
fast: false
reversible: false
name: prod3
type: Reaction

380534
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s25
type: Species

380636
constant: true
value: 10.0
type: Parameter

166781
stoichiometry: 1.0
species: 380524
type: SpeciesReference

167372
stoichiometry: 3.0
species: 380519
type: SpeciesReference

380670
constant: true
value: 1.0
type: Parameter

166418
stoichiometry: 1.0
species: 380520
type: SpeciesReference

380622
constant: true
value: 1.0
type: Parameter

380680
constant: true
value: 1.0
type: Parameter

380651
constant: true
value: 3.65224E-4
type: Parameter

380524
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: switch
type: Species

380589
kinetic law: 167588
product: 167576
reactant: 167564
reactant: 167552
fast: false
reversible: true
name: r_PfimE_HNS
type: Reaction

166332
stoichiometry: 1.0
species: 380518
type: SpeciesReference

380661
constant: true
value: 3.59662E-4
type: Parameter

166685
stoichiometry: 1.0
species: 380546
type: SpeciesReference

380673
constant: true
value: 1.0
type: Parameter

380641
constant: true
value: 6.5E-7
type: Parameter

380573
kinetic law: 166901
product: 166889
reactant: 166877
reactant: 166865
reactant: 166853
fast: false
reversible: true
name: r3
type: Reaction

167323
stoichiometry: 1.0
species: 380531
type: SpeciesReference

166259
stoichiometry: 1.0
species: 380533
type: SpeciesReference

380631
constant: true
value: 0.666666667
type: Parameter

380688
constant: true
value: 1.0
type: Parameter

380515
constant: true
size: 1.0
spatial dimensions: 3.0
type: Compartment

166344
stoichiometry: 1.0
species: 380535
type: SpeciesReference

380686
constant: true
value: 1.0
type: Parameter

380650
constant: true
value: 0.00860736
type: Parameter

166613
stoichiometry: 1.0
species: 380528
type: SpeciesReference

380588
kinetic law: 167540
product: 167528
product: 167516
reactant: 167504
fast: false
reversible: false
name: Prod_FimB
type: Reaction

167675
stoichiometry: 1.0
species: 380523
type: SpeciesReference

380525
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: 380515
name: PfimE
type: Species

380660
constant: true
value: 1.1956E-4
type: Parameter

166283
stoichiometry: 1.0
species: 380533
type: SpeciesReference

380640
constant: true
value: 6.53E-8
type: Parameter

380574
kinetic law: 166961
product: 166949
reactant: 166937
reactant: 166925
reactant: 166913
fast: false
reversible: true
name: r25
type: Reaction

167275
stoichiometry: 1.0
species: 380536
type: SpeciesReference

166889
stoichiometry: 1.0
species: 380551
type: SpeciesReference

380560
kinetic law: 166356
product: 166344
reactant: 166332
reactant: 166320
reactant: 166308
fast: false
reversible: true
name: r22
type: Reaction

166973
stoichiometry: 1.0
species: 380531
type: SpeciesReference

166538
stoichiometry: 1.0
species: 380531
type: SpeciesReference

380630
constant: true
value: 1.0
type: Parameter

380536
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s21
type: Species

167528
stoichiometry: 1.0
species: 380529
type: SpeciesReference

166320
stoichiometry: 1.0
species: 380531
type: SpeciesReference

166198
stoichiometry: 3.0
species: 380519
type: SpeciesReference

380685
constant: true
value: 1.0
type: Parameter

380675
constant: true
value: 1.0
type: Parameter

167576
stoichiometry: 1.0
species: 380530
type: SpeciesReference

380526
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: 380515
name: PfimB
type: Species

380644
constant: true
value: 8.0E-5
type: Parameter

166673
stoichiometry: 1.0
species: 380518
type: SpeciesReference

167360
stoichiometry: 1.0
species: 380517
type: SpeciesReference

380663
constant: true
value: 1.1956E-4
type: Parameter

167239
stoichiometry: 2.0
species: 380519
type: SpeciesReference

166949
stoichiometry: 1.0
species: 380534
type: SpeciesReference

380549
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s2
type: Species

380571
kinetic law: 166841
product: 166829
reactant: 166817
reactant: 166805
fast: false
reversible: true
name: r24
type: Reaction

380676
constant: true
value: 1.0
type: Parameter

167651
stoichiometry: 1.0
species: 380517
type: SpeciesReference

167335
stoichiometry: 1.0
species: 380545
type: SpeciesReference

166380
stoichiometry: 1.0
species: 380548
type: SpeciesReference

380539
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s19
type: Species

380561
kinetic law: 166406
product: 166393
product: 166380
reactant: 166368
fast: false
reversible: false
name: prod5
type: Reaction

166805
stoichiometry: 3.0
species: 380519
type: SpeciesReference

167687
stoichiometry: 1.0
species: 380526
type: SpeciesReference

380684
constant: true
value: 1.0
type: Parameter

380643
constant: true
value: 3.0E-4
type: Parameter

380674
constant: true
value: 1.0
type: Parameter

380548
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s5
type: Species

166526
stoichiometry: 1.0
species: 380520
type: SpeciesReference

380538
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s23
type: Species

167263
stoichiometry: 1.0
species: 380518
type: SpeciesReference

166877
stoichiometry: 1.0
species: 380531
type: SpeciesReference

167626
stoichiometry: 1.0
species: 380541
type: SpeciesReference

380528
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s4
type: Species

380518
constant: false
boundary condition: false
has only substance units: false
initial concentration: 127.0
initial amount: NaN
in compartment: 380515
name: FimB
type: Species

380656
constant: true
value: 0.00847626
type: Parameter

166661
stoichiometry: 1.0
species: 380531
type: SpeciesReference

166937
stoichiometry: 1.0
species: 380531
type: SpeciesReference

380678
constant: true
value: 1.0
type: Parameter

166186
stoichiometry: 1.0
species: 380520
type: SpeciesReference

167564
stoichiometry: 1.0
species: 380522
type: SpeciesReference

380666
constant: true
value: 0.0430879
type: Parameter

380664
constant: true
value: 0.0424317
type: Parameter

380550
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s26
type: Species

167432
stoichiometry: 1.0
species: 380518
type: SpeciesReference

167251
stoichiometry: 1.0
species: 380531
type: SpeciesReference

167155
stoichiometry: 1.0
species: 380531
type: SpeciesReference

380519
constant: false
boundary condition: false
has only substance units: false
initial concentration: 20.0
initial amount: NaN
in compartment: 380515
name: Lrp
type: Species

380529
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: PfimB_RNAP
type: Species

167504
stoichiometry: 1.0
species: 380529
type: SpeciesReference

166997
stoichiometry: 1.0
species: 380553
type: SpeciesReference

380655
constant: true
value: 1.21409E-4
type: Parameter

166368
stoichiometry: 1.0
species: 380548
type: SpeciesReference

166721
stoichiometry: 1.0
species: 380531
type: SpeciesReference

167699
stoichiometry: 1.0
species: 380529
type: SpeciesReference

166637
stoichiometry: 2.0
species: 380519
type: SpeciesReference

166817
stoichiometry: 1.0
species: 380531
type: SpeciesReference

380665
constant: true
value: 0.0141053
type: Parameter

380570
kinetic law: 166793
product: 166781
product: 166769
reactant: 166757
fast: false
reversible: false
name: prod4
type: Reaction

380590
kinetic law: 167639
product: 167626
reactant: 167614
reactant: 167601
fast: false
reversible: true
name: r_PfimE_RNAP
type: Reaction

380629
constant: true
value: 0.001625
type: Parameter

166576
stoichiometry: 1.0
species: 380520
type: SpeciesReference

167614
stoichiometry: 1.0
species: 380525
type: SpeciesReference

380653
constant: true
value: 1.21409E-4
type: Parameter

166649
stoichiometry: 1.0
species: 380520
type: SpeciesReference

380654
constant: true
value: 3.65224E-4
type: Parameter

167552
stoichiometry: 1.0
species: 380525
type: SpeciesReference

380668
constant: true
value: 0.0143234
type: Parameter

166925
stoichiometry: 2.0
species: 380519
type: SpeciesReference

166985
stoichiometry: 1.0
species: 380518
type: SpeciesReference

167191
stoichiometry: 1.0
species: 380546
type: SpeciesReference

167516
stoichiometry: 1.0
species: 380518
type: SpeciesReference

167167
stoichiometry: 1.0
species: 380548
type: SpeciesReference

380517
constant: false
boundary condition: false
has only substance units: false
initial concentration: 13.0
initial amount: NaN
in compartment: 380515
name: FimE
type: Species

166709
stoichiometry: 2.0
species: 380519
type: SpeciesReference

380689
constant: true
value: 1.0
type: Parameter

166271
stoichiometry: 1.0
species: 380524
type: SpeciesReference

166829
stoichiometry: 1.0
species: 380554
type: SpeciesReference

166589
stoichiometry: 1.0
species: 380531
type: SpeciesReference

167601
stoichiometry: 1.0
species: 380523
type: SpeciesReference

166733
stoichiometry: 1.0
species: 380538
type: SpeciesReference

380679
constant: true
value: 1.0
type: Parameter