BIOMD0000000253
type: SBMLModel
parameter: 892596
is described by: http://identifiers.org/pubmed/9612078
units def: 048453
reaction: 892547
area units: metaid_0000005
length unit: length
modified:
  W3 CDTF: Thu Dec 02 22:45:30 GMT 2010
species: metaid HMP
parameter: 892614
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
species: metaid Fru16P2
units def: 048489
reaction: 892548
volume units: metaid_0000003
rule: 892593
parameter: 892599
curated: true
rule: 892584
compartment: metaid cell
rule: 892587
parameter: 892632
species: metaid Glc
reaction: 892546
parameter: 892605
parameter: 892602
rule: 892590
is version of: GO:0006096
units def: 048429
parameter: 892623
species: metaid Tre6P
parameter: 892629
parameter: 892626
is homolog to: REACT 1383
is: MODEL1007200002
occurs in: http://identifiers.org/taxonomy/4932
rule: 892578
parameter: 892608
rule: 892581
created:
  W3 CDTF: Tue Jul 20 01:00:00 BST 2010
species: metaid ADP
parameter: 892620
rule: 892572
parameter: 892611
species: metaid ATP
rule: 892575
name: Teusink1998_Glycolysis_TurboDesign
parameter: 892595
parameter: 892617
units def: 048404
parameter: 892635
notes: This is the model described in the article: The danger of metabolic pathways with turbo design Teusink B, Walsh MC, van Dam K, Westerhoff HV Trends Biochem. Sci. 1998 May; Volume: 23 (Issue: 5 ): 162-9 9612078 , Abstract: Many catabolic pathways begin with an ATP-requiring activation step, after which further metabolism yields a surplus of ATP. Such a 'turbo' principle is useful but also contains an inherent risk. This is illustrated by a detailed kinetic analysis of a paradoxical Saccharomyces cerevisiae mutant; the mutant fails to grow on glucose because of overactive initial enzymes of glycolysis, but is defective only in an enzyme (trehalose 6-phosphate synthase) that appears to have little relevance to glycolysis. The ubiquity of pathways that possess an initial activation step, suggests that there might be many more genes that, when deleted, cause rather paradoxical regulation phenotypes (i.e. growth defects caused by enhanced utilization of growth substrate). The model represents the wild-type cell: 'guarded' glycolysis, which is the inhibition of the HK module by hexose monophosphate. The model reproduces figures 3c and 3d of the reference publication. To reproduce unguarded glycolysis, set parameter wild_type to '0'. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team. For more information see the terms of use . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
reaction: 892549
substance units: 048404
is version of: sce00010
time units: 048429

892596
type: Parameter
constant: false
value: NaN

048453
type: SBMLUnitsDef
unit: 048477
unit: 048465
name: mM

048477
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

048465
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

892547
type: Reaction
reactant: 048597
is version of: R00756
name: phosphofructokinase
product: 048621
is version of: http://identifiers.org/ec-code/2.7.1.11
kinetic law: 048633
is version of: GO:0008662
reversible: false
reactant: 048609
fast: false
is: SBO:0000176
is homolog to: REACT 1840

048597
type: SpeciesReference
stoichiometry: 1.0
species: metaid HMP

metaid HMP
type: Species
is: SBO:0000247
has only substance units: false
initial amount: NaN
in compartment: metaid cell
name: hexose monophosphate
constant: false
has part: CHEBI:17665
has part: CHEBI:16084
initial concentration: 0.1
boundary condition: false

metaid cell
type: Compartment
is: GO:0005622
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell

048621
type: SpeciesReference
stoichiometry: 1.0
species: metaid Fru16P2

metaid Fru16P2
type: Species
initial concentration: 1.0
is: SBO:0000247
constant: false
has only substance units: false
initial amount: NaN
in compartment: metaid cell
is: CHEBI:16905
name: fructose 1,6-bisphosphate
boundary condition: false

892559
type: LocalParameter
is: SBO:0000324
units: 048489
value: 30.0

048489
type: SBMLUnitsDef
unit: 048525
unit: 048513
unit: 048501
name: mM per min

048525
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND

048513
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

048501
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

048609
type: SpeciesReference
stoichiometry: 1.0
species: metaid ATP

metaid ATP
type: Species
name: ATP
initial amount: NaN
initial concentration: 4.0
has only substance units: false
constant: false
is: CHEBI:15422
is: SBO:0000247
in compartment: metaid cell
boundary condition: false

892614
type: Parameter
constant: true
value: 10.0

892548
type: Reaction
has version: http://identifiers.org/ec-code/4.2.1.11
has version: R01512
has version: http://identifiers.org/ec-code/4.1.2.13
has version: R00200
has version: http://identifiers.org/ec-code/2.7.2.3
reversible: false
has version: R00658
is: SBO:0000176
has version: http://identifiers.org/ec-code/5.4.2.1
has version: R01061
name: lower
has version: http://identifiers.org/ec-code/1.2.1.12
has version: R01070
fast: false
kinetic law: 048682
reactant: 048645
has version: http://identifiers.org/ec-code/5.3.1.1
reactant: 048658
has version: http://identifiers.org/ec-code/2.7.1.40
has version: R01015
product: 048670
has version: R01518

892567
type: LocalParameter
is: SBO:0000322
units: 048453
value: 0.1

892564
type: LocalParameter
is: SBO:0000322
units: 048453
value: 1.0

892561
type: LocalParameter
is: SBO:0000324
units: 048489
value: 20.0

048645
type: SpeciesReference
stoichiometry: 1.0
species: metaid Fru16P2

048658
type: SpeciesReference
stoichiometry: 4.0
species: metaid ADP

metaid ADP
type: Species
initial amount: NaN
in compartment: metaid cell
is: SBO:0000247
boundary condition: true
has only substance units: false
name: ADP
constant: false
initial concentration: NaN
is: CHEBI:16761

048670
type: SpeciesReference
stoichiometry: 4.0
species: metaid ATP

892599
type: Parameter
constant: false
value: NaN

892632
type: Parameter
is: SBO:0000261
constant: true
units: 048453
value: 10.0

metaid Glc
type: Species
in compartment: metaid cell
constant: false
initial concentration: 10.0
boundary condition: true
has only substance units: false
initial amount: NaN
is: SBO:0000247
name: glucose
is: CHEBI:17925

892546
type: Reaction
is version of: http://identifiers.org/ec-code/2.7.1.1
modifier: 048573
is: SBO:0000176
reversible: false
kinetic law: 048585
is version of: GO:0004396
fast: false
reactant: 048537
is version of: R02848
is homolog to: REACT 1318
reactant: 048549
name: hexokinase
product: 048561

metaid Tre6P
type: Species
is: SBO:0000247
boundary condition: true
has only substance units: false
is: CHEBI:18283
name: trehalose 6-phosphate
constant: false
initial concentration: NaN
initial amount: NaN
in compartment: metaid cell

892558
type: LocalParameter
units: dimensionless
value: 1.0

892555
type: LocalParameter
is: SBO:0000261
units: 048453
value: 4.422

892552
type: LocalParameter
is: SBO:0000322
units: 048453
value: 1.0

892551
type: LocalParameter
is: SBO:0000322
units: 048453
value: 0.15

892550
type: LocalParameter
is: SBO:0000324
units: 048489
value: 68.0

048537
type: SpeciesReference
stoichiometry: 1.0
species: metaid Glc

048549
type: SpeciesReference
stoichiometry: 1.0
species: metaid ATP

048561
type: SpeciesReference
stoichiometry: 1.0
species: metaid HMP

892605
type: Parameter
constant: false
value: NaN

892602
type: Parameter
constant: false
value: NaN

048429
type: SBMLUnitsDef
unit: 048441
name: min

048441
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

892623
type: Parameter
is: SBO:0000194
constant: true
units: 048453
value: 0.06

892629
type: Parameter
constant: true
value: 1.0

892626
type: Parameter
constant: true
value: 1.0

892608
type: Parameter
constant: false
value: NaN

892620
type: Parameter
constant: true
value: 1000.0

892611
type: Parameter
is: SBO:0000194
constant: true
units: 048453
value: 1.0

892595
type: Parameter
constant: false
value: NaN

892617
type: Parameter
constant: true
value: 5.0E-4

048404
type: SBMLUnitsDef
unit: 048417
name: mmol

048417
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

892635
type: Parameter
constant: true
value: 10.0

892549
type: Reaction
is: SBO:0000176
name: ATPase
is version of: http://identifiers.org/ec-code/3.6.1.3
is version of: GO:0016887
product: 048706
reversible: false
kinetic law: 048718
reactant: 048694
fast: false

048706
type: SpeciesReference
stoichiometry: 1.0
species: metaid ADP

892569
type: LocalParameter
is: SBO:0000322
units: 048453
value: 3.0

892568
type: LocalParameter
is: SBO:0000324
units: 048489
value: 68.0

048694
type: SpeciesReference
stoichiometry: 1.0
species: metaid ATP