MODEL1004010002
type: SBMLModel
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
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

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

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

380678
type: Parameter
constant: true
value: 1.0

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

167384
type: SpeciesReference
stoichiometry: 1.0
species: 380520

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

167408
type: SpeciesReference
stoichiometry: 1.0
species: 380533

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

167372
type: SpeciesReference
stoichiometry: 3.0
species: 380519

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

167360
type: SpeciesReference
stoichiometry: 1.0
species: 380517

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

167396
type: SpeciesReference
stoichiometry: 1.0
species: 380531

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

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

167275
type: SpeciesReference
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species: 380536

380536
type: Species
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initial concentration: 0.0
initial amount: NaN
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name: s21

167263
type: SpeciesReference
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species: 380518

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

167251
type: SpeciesReference
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species: 380531

167239
type: SpeciesReference
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species: 380519

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

166781
type: SpeciesReference
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species: 380524

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

166769
type: SpeciesReference
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species: 380528

380528
type: Species
constant: false
boundary condition: false
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initial amount: NaN
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name: s4

166757
type: SpeciesReference
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species: 380528

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

166733
type: SpeciesReference
stoichiometry: 1.0
species: 380538

380538
type: Species
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initial amount: NaN
in compartment: 380515
name: s23

166721
type: SpeciesReference
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species: 380531

166709
type: SpeciesReference
stoichiometry: 2.0
species: 380519

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

380628
type: Parameter
constant: true
value: 0.666666667

380669
type: Parameter
constant: true
value: 1.0

380648
type: Parameter
constant: true
value: 1.01547

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

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

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

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

166283
type: SpeciesReference
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species: 380533

166271
type: SpeciesReference
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species: 380524

166259
type: SpeciesReference
stoichiometry: 1.0
species: 380533

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

166162
type: SpeciesReference
stoichiometry: 1.0
species: 380539

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

166150
type: SpeciesReference
stoichiometry: 1.0
species: 380531

166138
type: SpeciesReference
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species: 380519

166126
type: SpeciesReference
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species: 380517

380636
type: Parameter
constant: true
value: 10.0

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

167528
type: SpeciesReference
stoichiometry: 1.0
species: 380529

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

167516
type: SpeciesReference
stoichiometry: 1.0
species: 380518

167504
type: SpeciesReference
stoichiometry: 1.0
species: 380529

380633
type: Parameter
constant: true
value: 0.333333333

380634
type: Parameter
constant: true
value: 10.0

380664
type: Parameter
constant: true
value: 0.0424317

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

380684
type: Parameter
constant: true
value: 1.0

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

380685
type: Parameter
constant: true
value: 1.0

380683
type: Parameter
constant: true
value: 1.0

380680
type: Parameter
constant: true
value: 1.0

380681
type: Parameter
constant: true
value: 1.0

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

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

167046
type: SpeciesReference
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species: 380551

167033
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species: 380524

167021
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species: 380551

380631
type: Parameter
constant: true
value: 0.666666667

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

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

166502
type: SpeciesReference
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species: 380544

166490
type: SpeciesReference
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species: 380531

166478
type: SpeciesReference
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species: 380517

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

166454
type: SpeciesReference
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species: 380550

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

166442
type: SpeciesReference
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species: 380531

166430
type: SpeciesReference
stoichiometry: 3.0
species: 380519

166418
type: SpeciesReference
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species: 380520

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

380689
type: Parameter
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value: 1.0

380668
type: Parameter
constant: true
value: 0.0143234

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

166393
type: SpeciesReference
stoichiometry: 1.0
species: 380524

166380
type: SpeciesReference
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species: 380548

380548
type: Species
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initial concentration: 0.0
initial amount: NaN
in compartment: 380515
name: s5

166368
type: SpeciesReference
stoichiometry: 1.0
species: 380548

380639
type: Parameter
constant: true
value: 1.0

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

167699
type: SpeciesReference
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species: 380529

167687
type: SpeciesReference
stoichiometry: 1.0
species: 380526

167675
type: SpeciesReference
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species: 380523

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

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

380656
type: Parameter
constant: true
value: 0.00847626

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

166661
type: SpeciesReference
stoichiometry: 1.0
species: 380531

166637
type: SpeciesReference
stoichiometry: 2.0
species: 380519

166649
type: SpeciesReference
stoichiometry: 1.0
species: 380520

166673
type: SpeciesReference
stoichiometry: 1.0
species: 380518

166685
type: SpeciesReference
stoichiometry: 1.0
species: 380546

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

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

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

380688
type: Parameter
constant: true
value: 1.0

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

380676
type: Parameter
constant: true
value: 1.0

380626
type: Parameter
constant: true
value: 10.0

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

167215
type: SpeciesReference
stoichiometry: 1.0
species: 380524

167203
type: SpeciesReference
stoichiometry: 1.0
species: 380546

167191
type: SpeciesReference
stoichiometry: 1.0
species: 380546

380624
type: Parameter
constant: true
value: 10.0

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

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

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

166997
type: SpeciesReference
stoichiometry: 1.0
species: 380553

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

166985
type: SpeciesReference
stoichiometry: 1.0
species: 380518

166973
type: SpeciesReference
stoichiometry: 1.0
species: 380531

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

380630
type: Parameter
constant: true
value: 1.0

380675
type: Parameter
constant: true
value: 1.0

380650
type: Parameter
constant: true
value: 0.00860736

380671
type: Parameter
constant: true
value: 1.0

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

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

167626
type: SpeciesReference
stoichiometry: 1.0
species: 380541

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

167614
type: SpeciesReference
stoichiometry: 1.0
species: 380525

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

167601
type: SpeciesReference
stoichiometry: 1.0
species: 380523

380679
type: Parameter
constant: true
value: 1.0

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

167480
type: SpeciesReference
stoichiometry: 1.0
species: 380543

167468
type: SpeciesReference
stoichiometry: 1.0
species: 380522

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

167456
type: SpeciesReference
stoichiometry: 1.0
species: 380526

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

166949
type: SpeciesReference
stoichiometry: 1.0
species: 380534

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

166937
type: SpeciesReference
stoichiometry: 1.0
species: 380531

166925
type: SpeciesReference
stoichiometry: 2.0
species: 380519

166913
type: SpeciesReference
stoichiometry: 1.0
species: 380520

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

167432
type: SpeciesReference
stoichiometry: 1.0
species: 380518

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

167335
type: SpeciesReference
stoichiometry: 1.0
species: 380545

167323
type: SpeciesReference
stoichiometry: 1.0
species: 380531

167311
type: SpeciesReference
stoichiometry: 3.0
species: 380519

167299
type: SpeciesReference
stoichiometry: 1.0
species: 380517

380666
type: Parameter
constant: true
value: 0.0430879

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

167651
type: SpeciesReference
stoichiometry: 1.0
species: 380517

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

166344
type: SpeciesReference
stoichiometry: 1.0
species: 380535

166332
type: SpeciesReference
stoichiometry: 1.0
species: 380518

166320
type: SpeciesReference
stoichiometry: 1.0
species: 380531

166308
type: SpeciesReference
stoichiometry: 3.0
species: 380519

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

166235
type: SpeciesReference
stoichiometry: 1.0
species: 380540

166198
type: SpeciesReference
stoichiometry: 3.0
species: 380519

166211
type: SpeciesReference
stoichiometry: 1.0
species: 380531

166186
type: SpeciesReference
stoichiometry: 1.0
species: 380520

166223
type: SpeciesReference
stoichiometry: 1.0
species: 380518

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

167155
type: SpeciesReference
stoichiometry: 1.0
species: 380531

167167
type: SpeciesReference
stoichiometry: 1.0
species: 380548

167118
type: SpeciesReference
stoichiometry: 1.0
species: 380517

167143
type: SpeciesReference
stoichiometry: 1.0
species: 380520

167130
type: SpeciesReference
stoichiometry: 2.0
species: 380519

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

167094
type: SpeciesReference
stoichiometry: 1.0
species: 380524

167082
type: SpeciesReference
stoichiometry: 1.0
species: 380540

167070
type: SpeciesReference
stoichiometry: 1.0
species: 380540

380638
type: Parameter
constant: true
value: 0.001625

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

380658
type: Parameter
constant: true
value: 0.00847626

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

380629
type: Parameter
constant: true
value: 0.001625

380625
type: Parameter
constant: true
value: 0.014705882

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

166613
type: SpeciesReference
stoichiometry: 1.0
species: 380528

166601
type: SpeciesReference
stoichiometry: 1.0
species: 380518

166589
type: SpeciesReference
stoichiometry: 1.0
species: 380531

166576
type: SpeciesReference
stoichiometry: 1.0
species: 380520

380623
type: Parameter
constant: true
value: 0.333333333

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

167576
type: SpeciesReference
stoichiometry: 1.0
species: 380530

167564
type: SpeciesReference
stoichiometry: 1.0
species: 380522

167552
type: SpeciesReference
stoichiometry: 1.0
species: 380525

380686
type: Parameter
constant: true
value: 1.0

380622
type: Parameter
constant: true
value: 1.0

380674
type: Parameter
constant: true
value: 1.0

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

380670
type: Parameter
constant: true
value: 1.0

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

166551
type: SpeciesReference
stoichiometry: 1.0
species: 380549

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

166538
type: SpeciesReference
stoichiometry: 1.0
species: 380531

166526
type: SpeciesReference
stoichiometry: 1.0
species: 380520

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

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

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

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

166889
type: SpeciesReference
stoichiometry: 1.0
species: 380551

166877
type: SpeciesReference
stoichiometry: 1.0
species: 380531

166865
type: SpeciesReference
stoichiometry: 1.0
species: 380520

166853
type: SpeciesReference
stoichiometry: 1.0
species: 380517

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

166829
type: SpeciesReference
stoichiometry: 1.0
species: 380554

166817
type: SpeciesReference
stoichiometry: 1.0
species: 380531

166805
type: SpeciesReference
stoichiometry: 3.0
species: 380519

380673
type: Parameter
constant: true
value: 1.0

380649
type: Parameter
constant: true
value: 0.00860736

380665
type: Parameter
constant: true
value: 0.0141053

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

167747
type: SpeciesReference
stoichiometry: 1.0
species: 380541

167735
type: SpeciesReference
stoichiometry: 1.0
species: 380517

167723
type: SpeciesReference
stoichiometry: 1.0
species: 380541