BIOMD0000000062
type: SBMLModel
units def: metaid_0000017
units def: metaid_0000022
parameter: metaid_0000003
reaction: metaid_0000013
reaction: metaid_0000015
compartment: metaid_0000007
rule: metaid_0000033
reaction: metaid_0000020
creator:
  ORG:
    orgname: California Institute of Technology
  n:
    given: Harish
    family: Dharuri
parameter: metaid_0000026
name: Bhartiya2003_Tryptophan_operon
is described by: http://identifiers.org/pubmed/12787031
units def: metaid_0000023
created:
  W3 CDTF: Thu Feb 04 17:43:13 GMT 2010
substance units: metaid_0000017
units def: metaid_0000021
curated: true
rule: metaid_0000018
time units: metaid_0000021
is version of: GO:0000162
rule: metaid_0000031
occurs in: http://identifiers.org/taxonomy/562
reaction: metaid_0000014
species: metaid_0000009
parameter: metaid_0000028
area units: area
parameter: metaid_0000004
parameter: metaid_0000027
creator:
  ORG:
    orgname: Stellenbosh University
  n:
    given: Jacky L
    family: Snoep
species: metaid_0000010
reaction: metaid_0000019
notes: SBML level 2 code originaly generated for the JWS Online project by Jacky Snoep using PySCeS Run this model online at http://jjj.biochem.sun.ac.za To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online , Bioinformatics, 20:2143-2144 BioModels Curation : The model reproduces Fig 3 of the publication. By substituting a value of 1.4 for Tex it is possible to reproduce Fig 3C and 3D(iii), Fig 3A and 3D(i), are obtained by setting Tex=0. Also, note that the tryptophan concentrations have been normalized by 82 micromolar in the figures; the normalized concetrations can be obtained via the parameters To/s/t_norm. The model was successfully tested on MathSBML and Copasi. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team. For more information see the terms of use . To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
rule: metaid_0000030
length unit: length
rule: metaid_0000034
modified:
  W3 CDTF: Wed May 16 11:21:54 BST 2012
volume units: metaid_0000323
is: MODEL6624111460
parameter: metaid_0000029
units def: metaid_0000024
species: metaid_0000025
rule: metaid_0000032
species: metaid_0000008
parameter: metaid_0000005
parameter: metaid_0000006

metaid_0000017
type: SBMLUnitsDef
unit: 743005
name: micromole

743005
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

metaid_0000022
type: SBMLUnitsDef
unit: 743041
unit: 743029
name: microM

743041
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

743029
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

metaid_0000003
type: Parameter
constant: true
units: metaid_0000022
value: 100.0

metaid_0000013
type: Reaction
kinetic law: 743125
modifier: 743113
product: 743101
is version of: GO:0006417
fast: false
reversible: true
name: Anthranilate synthase synthesis

674491
type: LocalParameter
units: metaid_0000022
value: 0.0033

674490
type: LocalParameter
units: dimensionless
value: 1.92

674489
type: LocalParameter
units: metaid_0000022
value: 3.53

674488
type: LocalParameter
units: metaid_0000024
value: 65.0

metaid_0000024
type: SBMLUnitsDef
unit: 743089
name: per_min

743089
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND

metaid_0000010
type: Species
name: Total tryptophan
has only substance units: false
is: CHEBI:27897
boundary condition: false
is: C00806
initial amount: NaN
constant: false
initial concentration: 0.0
in compartment: metaid_0000007

metaid_0000007
type: Compartment
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell

743101
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

metaid_0000008
type: Species
is: P00895
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000007
name: Anthranilate synthase

metaid_0000015
type: Reaction
kinetic law: 743197
modifier: 743185
modifier: 743173
product: 743161
is version of: GO:0000162
fast: false
reversible: true
name: Tryptophan synthesis

674496
type: LocalParameter
units: metaid_0000022
value: 810.0

674494
type: LocalParameter
units: metaid_0000024
value: 25.0

743161
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000009
type: Species
has only substance units: false
initial amount: NaN
constant: false
in compartment: metaid_0000007
boundary condition: false
initial concentration: 0.0
is: CHEBI:27897
is: C00806
name: Synthesized tryptophan

metaid_0000020
type: Reaction
kinetic law: 743246
reactant: 743234
fast: false
reversible: true
name: Tryptophan dilution due to cell growth

674502
type: LocalParameter
units: metaid_0000024
value: 0.01

743234
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000026
type: Parameter
constant: false
units: dimensionless
value: NaN
name: Ts_norm

metaid_0000023
type: SBMLUnitsDef
unit: 743077
unit: 743065
unit: 743053
name: microM_per_min

743077
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND

743065
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

743053
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

metaid_0000021
type: SBMLUnitsDef
unit: 743017
name: minutes

743017
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

metaid_0000014
type: Reaction
kinetic law: 743149
reactant: 743137
fast: false
reversible: true
name: Enzyme dilution due to cell growth

674492
type: LocalParameter
units: metaid_0000024
value: 0.01

743137
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

metaid_0000028
type: Parameter
constant: false
units: dimensionless
value: NaN
name: Tt_norm

metaid_0000004
type: Parameter
constant: true
units: metaid_0000022
value: 0.14

metaid_0000027
type: Parameter
constant: false
units: dimensionless
value: NaN
name: To_norm

metaid_0000019
type: Reaction
kinetic law: 743222
reactant: 743210
is version of: GO:0006412
fast: false
reversible: true
name: Tryptophan consumption for protein synthesis

674500
type: LocalParameter
units: metaid_0000022
value: 0.2

674498
type: LocalParameter
units: metaid_0000023
value: 25.0

743210
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000029
type: Parameter
constant: false
units: dimensionless
value: NaN
name: Enz_norm

metaid_0000025
type: Species
constant: false
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: NaN
in compartment: metaid_0000007
name: exog. Trp

metaid_0000005
type: Parameter
constant: true
units: metaid_0000022
value: 0.9

metaid_0000006
type: Parameter
constant: true
units: metaid_0000022
value: 380.0