BIOMD0000000380
type: SBMLModel
species: metaid ppi
parameter: metaid trh 0
rule: 259078
parameter: 345302
occurs in: http://identifiers.org/taxonomy/4932
species: metaid pho
parameter: 345290
reaction: metaid tps
parameter: metaid udg 0
parameter: 345297
species: metaid g1p
volume units: 498095
species: metaid glx
parameter: 345287
rule: 259080
reaction: metaid tpp
reaction: metaid nth
parameter: 345284
created:
  W3 CDTF: Mon Jul 12 01:00:00 BST 2010
substance units: 949014
units def: 949038
reaction: metaid ugp
species: metaid trh
units def: 949123
rule: 259073
species: metaid g6p
name: Smallbone2011_TrehaloseBiosynthesis
is: MODEL1010010000
species: metaid utp
species: metaid t6p
species: metaid glc
species: metaid f6p
parameter: 345299
time units: 949038
species: metaid atp
reaction: metaid pgm
reaction: 345185
compartment: metaid medium
parameter: metaid g6p 0
reaction: metaid pgi
species: metaid h2o
rule: 259074
modified:
  W3 CDTF: Wed May 16 15:48:51 BST 2012
parameter: metaid t6p 0
compartment: metaid cell
species: metaid udg
units def: 949014
parameter: metaid g1p 0
parameter: metaid glc 0
species: metaid udp
units def: 949062
rule: 259077
area units: 498119
species: metaid h
length unit: length
reaction: metaid hxk
notes: This model is from the article: Building a Kinetic Model of Trehalose Biosynthesis in Saccharomyces cerevisiae. Smallbone K, Malys N, Messiha HL, Wishart JA, Simeonidis E. Methods Enzymol. 2011;500:355-70. 21943906 , Abstract: In this chapter, we describe the steps needed to create a kinetic model of a metabolic pathway based on kinetic data from experimental measurements and literature review. Our methodology is presented by utilizing the example of trehalose metabolism in yeast. The biology of the trehalose cycle is briefly reviewed and discussed. This SBML model is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org ). This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 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.
rule: 259083
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
is version of: GO:0005992
curated: true
parameter: 345294
is described by: http://identifiers.org/pubmed/21943906
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
units def: 949099
initial assignment: BIOMD0000000380#
species: metaid adp

metaid ppi
type: Species
constant: false
boundary condition: true
initial amount: NaN
name: diphosphate
in compartment: metaid cell
initial concentration: NaN
is: SBO:0000247
is: CHEBI:18361
has only substance units: false

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

metaid trh 0
type: Parameter
constant: true
units: 949062
value: 0.05

949062
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unit: 949075
name: mM

949087
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exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

949075
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

345302
type: Parameter
constant: false
units: dimensionless
value: NaN
name: log10 change in UDP glucose

metaid pho
type: Species
initial amount: NaN
constant: false
in compartment: metaid cell
has only substance units: false
boundary condition: true
is: CHEBI:43474
initial concentration: NaN
is: SBO:0000247
name: phosphate

345290
type: Parameter
constant: false
units: dimensionless
value: NaN
name: log10 change in glucose 1-phosphate

metaid tps
type: Reaction
product: 949521
reactant: 949472
name: T6P synthase
product: 949496
is version of: http://identifiers.org/ec-code/2.4.1.15
product: 949508
reactant: 949484
fast: false
is: SBO:0000176
kinetic law: 949533
reversible: false

949521
type: SpeciesReference
stoichiometry: 1.0
species: metaid h

metaid h
type: Species
constant: false
initial concentration: NaN
name: H+
initial amount: NaN
is: CHEBI:24636
in compartment: metaid cell
boundary condition: true
has only substance units: false
is: SBO:0000247

949472
type: SpeciesReference
stoichiometry: 1.0
species: metaid g6p

metaid g6p
type: Species
is: SBO:0000247
in compartment: metaid cell
constant: false
has only substance units: false
boundary condition: false
is: CHEBI:17665
name: glucose 6-phosphate
initial amount: NaN
initial concentration: 2.675

949496
type: SpeciesReference
stoichiometry: 1.0
species: metaid t6p

metaid t6p
type: Species
constant: false
initial concentration: 0.02
is: SBO:0000247
initial amount: NaN
is: CHEBI:18283
has only substance units: false
in compartment: metaid cell
name: trehalose 6-phosphate
boundary condition: false

949508
type: SpeciesReference
stoichiometry: 1.0
species: metaid udp

metaid udp
type: Species
constant: false
name: UDP
in compartment: metaid cell
boundary condition: true
is: SBO:0000247
initial concentration: 0.2815
initial amount: NaN
has only substance units: false
is: CHEBI:17659

949484
type: SpeciesReference
stoichiometry: 1.0
species: metaid udg

metaid udg
type: Species
name: UDP glucose
in compartment: metaid cell
constant: false
is: SBO:0000247
is: CHEBI:18066
has only substance units: false
initial concentration: 0.7
boundary condition: false
initial amount: NaN

345262
type: LocalParameter
units: dimensionless
value: 1.0

metaid shock tps
type: LocalParameter
units: dimensionless
value: 12.0

345260
type: LocalParameter
units: 949062
value: 0.886

345258
type: LocalParameter
units: 949062
value: 3.8

345257
type: LocalParameter
units: 949123
value: 1.371

949123
type: SBMLUnitsDef
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unit: 949147
unit: 949135
name: mM per min

949159
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multipler: 60.0
kind: SECOND

949147
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kind: LITRE

949135
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

metaid udg 0
type: Parameter
constant: true
units: 949062
value: 0.7

345297
type: Parameter
constant: false
units: dimensionless
value: NaN
name: log10 change in trehalose

metaid g1p
type: Species
is: CHEBI:16077
name: glucose 1-phosphate
has only substance units: false
initial concentration: 0.1
initial amount: NaN
in compartment: metaid cell
constant: false
is: SBO:0000247
boundary condition: false

metaid glx
type: Species
initial concentration: 100.0
has only substance units: false
initial amount: NaN
in compartment: metaid medium
constant: false
is: CHEBI:17925
name: glucose
boundary condition: true
is: SBO:0000247

metaid medium
type: Compartment
is: GO:0005576
constant: true
size: 1.0
spatial dimensions: 3.0
name: medium

345287
type: Parameter
constant: false
units: dimensionless
value: NaN
name: log10 change in glucose

metaid tpp
type: Reaction
reactant: 949424
product: 949436
kinetic law: 949460
name: T6P phosphatase
reversible: false
fast: false
is: SBO:0000176
is version of: http://identifiers.org/ec-code/3.1.3.12
product: 949448
reactant: 949412

949424
type: SpeciesReference
stoichiometry: 1.0
species: metaid h2o

metaid h2o
type: Species
constant: false
is: CHEBI:15377
initial amount: NaN
has only substance units: false
boundary condition: true
initial concentration: NaN
in compartment: metaid cell
is: SBO:0000247
name: water

949436
type: SpeciesReference
stoichiometry: 1.0
species: metaid trh

metaid trh
type: Species
initial concentration: 0.05
initial amount: NaN
has only substance units: false
boundary condition: false
is: SBO:0000247
constant: false
name: trehalose
in compartment: metaid cell
is: CHEBI:16551

metaid shock tpp
type: LocalParameter
units: dimensionless
value: 18.0

metaid Kt6p tpp
type: LocalParameter
units: 949062
value: 0.5

345253
type: LocalParameter
units: 949123
value: 6.5

949448
type: SpeciesReference
stoichiometry: 1.0
species: metaid pho

949412
type: SpeciesReference
stoichiometry: 1.0
species: metaid t6p

metaid nth
type: Reaction
product: 949569
reactant: 949545
is: SBO:0000176
fast: false
name: trehalase
is version of: http://identifiers.org/ec-code/3.2.1.28
reactant: 949557
reversible: false
kinetic law: metaid kineticLaw nth

949569
type: SpeciesReference
stoichiometry: 2.0
species: metaid glc

metaid glc
type: Species
initial amount: NaN
in compartment: metaid cell
name: glucose
boundary condition: false
has only substance units: false
is: SBO:0000247
is: CHEBI:17925
constant: false
initial concentration: 0.09675

949545
type: SpeciesReference
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species: metaid trh

949557
type: SpeciesReference
stoichiometry: 1.0
species: metaid h2o

metaid shock nth
type: LocalParameter
units: dimensionless
value: 6.0

345265
type: LocalParameter
units: 949062
value: 2.99

345263
type: LocalParameter
units: 949123
value: 15.2

345284
type: Parameter
constant: true
units: dimensionless
value: 0.0
name: heat

949014
type: SBMLUnitsDef
unit: 949026
name: mmol

949026
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

949038
type: SBMLUnitsDef
unit: 949050
name: min

949050
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

metaid ugp
type: Reaction
is version of: http://identifiers.org/ec-code/2.7.7.9
reactant: 949581
kinetic law: metaid kineticLaw ugp
name: UDP glucose phosphorylase
product: 949629
fast: false
reactant: 949593
reactant: 949605
is: SBO:0000176
product: 949617
reversible: false

949581
type: SpeciesReference
stoichiometry: 1.0
species: metaid g1p

metaid shock ugp
type: LocalParameter
units: dimensionless
value: 16.0

metaid Kiudg ugp
type: LocalParameter
units: 949062
value: 0.0035

metaid Kg1p ugp
type: LocalParameter
units: 949062
value: 0.32

metaid Kiutp ugp
type: LocalParameter
units: 949062
value: 0.11

metaid Kutp ugp
type: LocalParameter
units: 949062
value: 0.11

345267
type: LocalParameter
units: 949123
value: 36.82

949629
type: SpeciesReference
stoichiometry: 1.0
species: metaid ppi

949593
type: SpeciesReference
stoichiometry: 1.0
species: metaid utp

metaid utp
type: Species
initial concentration: 0.6491
is: SBO:0000247
constant: false
name: UTP
has only substance units: false
boundary condition: true
is: CHEBI:46398
in compartment: metaid cell
initial amount: NaN

949605
type: SpeciesReference
stoichiometry: 1.0
species: metaid h

949617
type: SpeciesReference
stoichiometry: 1.0
species: metaid udg

metaid f6p
type: Species
is: CHEBI:16084
is: SBO:0000247
initial concentration: 0.625
initial amount: NaN
boundary condition: true
constant: false
name: fructose 6-phosphate
in compartment: metaid cell
has only substance units: false

345299
type: Parameter
constant: false
units: dimensionless
value: NaN
name: log10 change in trehalose 6-phosphate

metaid atp
type: Species
boundary condition: true
is: SBO:0000247
has only substance units: false
name: ATP
in compartment: metaid cell
is: CHEBI:15422
initial amount: NaN
initial concentration: 2.525
constant: false

metaid pgm
type: Reaction
kinetic law: 949400
product: 949388
reactant: 949376
is version of: http://identifiers.org/ec-code/5.4.2.2
is: SBO:0000176
fast: false
reversible: true
name: phosphoglucomutase

metaid shock pgm
type: LocalParameter
units: dimensionless
value: 16.0

metaid Keq pgm
type: LocalParameter
units: dimensionless
value: 0.1667

metaid Kg1p pgm
type: LocalParameter
units: 949062
value: 0.023

metaid Kg6p pgm
type: LocalParameter
units: 949062
value: 0.05

345243
type: LocalParameter
units: 949123
value: 0.3545

949388
type: SpeciesReference
stoichiometry: 1.0
species: metaid g1p

949376
type: SpeciesReference
stoichiometry: 1.0
species: metaid g6p

345185
type: Reaction
kinetic law: metaid kineticLaw hxt
product: 949279
reactant: 949267
is: SBO:0000185
fast: false
reversible: true
name: glucose transport

metaid shock hxt
type: LocalParameter
units: dimensionless
value: 8.0

metaid Ki hxt
type: LocalParameter
units: dimensionless
value: 0.91

metaid Kglc hxt
type: LocalParameter
units: 949062
value: 1.1918

345210
type: LocalParameter
units: 949123
value: 97.24

949279
type: SpeciesReference
stoichiometry: 1.0
species: metaid glc

949267
type: SpeciesReference
stoichiometry: 1.0
species: metaid glx

metaid g6p 0
type: Parameter
constant: true
units: 949062
value: 2.675

metaid pgi
type: Reaction
kinetic law: metaid kineticLaw pgi
product: 949255
reactant: 949243
is version of: http://identifiers.org/ec-code/5.3.1.9
is: SBO:0000176
fast: false
reversible: true
name: G6P isomerase

345209
type: LocalParameter
units: dimensionless
value: 1.0

metaid Keq pgi
type: LocalParameter
units: dimensionless
value: 0.3

metaid Kf6p pgi
type: LocalParameter
units: 949062
value: 0.29

metaid Kg6p pgi
type: LocalParameter
units: 949062
value: 1.4

345202
type: LocalParameter
units: 949123
value: 1071.0

949255
type: SpeciesReference
stoichiometry: 1.0
species: metaid f6p

949243
type: SpeciesReference
stoichiometry: 1.0
species: metaid g6p

metaid t6p 0
type: Parameter
constant: true
units: 949062
value: 0.02

metaid g1p 0
type: Parameter
constant: true
units: 949062
value: 0.1

metaid glc 0
type: Parameter
constant: true
units: 949062
value: 0.09765

metaid hxk
type: Reaction
modifier: 949352
product: 949316
reversible: false
kinetic law: 949364
name: hexokinase
is version of: http://identifiers.org/ec-code/2.7.1.1
reactant: 949304
reactant: 949292
fast: false
product: 949340
product: 949328
is: SBO:0000176

949316
type: SpeciesReference
stoichiometry: 1.0
species: metaid g6p

metaid shock hxk
type: LocalParameter
units: dimensionless
value: 8.0

metaid Kitrh hxk
type: LocalParameter
units: 949062
value: 0.04

metaid Keq hxk
type: LocalParameter
units: dimensionless
value: 2000.0

metaid Kadp hxk
type: LocalParameter
units: 949062
value: 0.23

metaid Kg6p hxk
type: LocalParameter
units: 949062
value: 30.0

metaid Katp hxk
type: LocalParameter
units: 949062
value: 0.15

metaid Kglc hxk
type: LocalParameter
units: 949062
value: 0.08

345220
type: LocalParameter
units: 949123
value: 289.6

949304
type: SpeciesReference
stoichiometry: 1.0
species: metaid atp

949292
type: SpeciesReference
stoichiometry: 1.0
species: metaid glc

949340
type: SpeciesReference
stoichiometry: 1.0
species: metaid h

949328
type: SpeciesReference
stoichiometry: 1.0
species: metaid adp

metaid adp
type: Species
in compartment: metaid cell
is: CHEBI:16761
initial concentration: 1.282
name: ADP
initial amount: NaN
constant: false
boundary condition: true
is: SBO:0000247
has only substance units: false

345294
type: Parameter
constant: false
units: dimensionless
value: NaN
name: log10 change in glucose 6-phosphate

949099
type: SBMLUnitsDef
unit: 949111
name: per min

949111
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND