BIOMD0000000458
type: SBMLModel
species: meta ser
species: meta serA
reaction: meta PSA
species: meta p3g
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
modified:
  W3 CDTF: Mon Jun 10 14:56:22 BST 2013
length unit: length
area units: area
species: meta php
reaction: meta PSP
species: meta serB
is: MODEL1203210000
name: Smallbone2013 - Serine biosynthesis
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
curated: true
species: meta serC
notes: Smallbone2013 - Serine biosynthesis Kinetic modelling of metabolic pathways in application to Serine biosynthesis. This model is described in the article: Kinetic Modeling of Metabolic Pathways: Application to Serine Biosynthesis Kieran Smallbone, Natalie J. Stanford Methods in Molecular Biology. 2013; 985:113-121 Abstract: In this chapter, we describe the steps needed to create a kinetic model of a metabolic pathway using kinetic data from both experimental measurements and literature review. Our methodology is presented by using the example of serine biosynthesis in E. coli. As there are no plots to be reproduced as curation figure, table 6 and 7 that corresponds to steady state concentration of metabolite and steady state fluxes of reactions has been reproduced. This model is hosted on BioModels Database and identified by: BIOMD0000000458 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.
reaction: meta PDH
compartment: meta cell
created:
  W3 CDTF: Tue Mar 20 00:00:00 GMT 2012
is described by: http://identifiers.org/pubmed/23417802
species: meta pser

meta ser
type: Species
boundary condition: true
initial amount: NaN
name: serine
in compartment: meta cell
has only substance units: false
is: CHEBI:17115
is: SBO:0000247
constant: true
initial concentration: 4.9

meta cell
type: Compartment
is: GO:0005622
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell

meta serA
type: Species
name: serA
is: SBO:0000252
initial concentration: 1.15
initial amount: NaN
in compartment: meta cell
has only substance units: false
constant: true
boundary condition: true
is: P0A9T0

meta PSA
type: Reaction
fast: false
is: SBO:0000176
reversible: true
name: phosphoserine aminotransferase
is: http://identifiers.org/ec-code/2.6.1.52

meta serC
type: Species
boundary condition: true
has only substance units: false
initial concentration: 0.1
is: P23721
constant: true
in compartment: meta cell
is: SBO:0000252
name: serC
initial amount: NaN

http://identifiers.org/biomodels.db/BIOMD0000000458#_0a08c29f_2977_42cc_aa23_e756310e365c
type: LocalParameter
value: 0.0017

http://identifiers.org/biomodels.db/BIOMD0000000458#_35131fb7_6754_463d_a0e1_22c0642dc97d
type: SBMLUnitsDef
name: mM

http://identifiers.org/biomodels.db/BIOMD0000000458#fed4bdc0_0072_4db8_b74b_79539703befe
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

http://identifiers.org/biomodels.db/BIOMD0000000458#_0282a9cd_7b30_42c8_a429_c6d3cf90bd66
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

http://identifiers.org/biomodels.db/BIOMD0000000458#_898c16d9_1f28_4c45_aeef_118a487f65a2
type: LocalParameter
value: 0.0015

http://identifiers.org/biomodels.db/BIOMD0000000458#cc9dd4b2_b2f4_439a_882d_7a7aa6143557
type: LocalParameter
value: 1.75

http://identifiers.org/biomodels.db/BIOMD0000000458#_92ca75f4_7c78_4db9_91b8_c2e11ac6a77c
type: SBMLUnitsDef
name: per s

http://identifiers.org/biomodels.db/BIOMD0000000458#b83470a9_0fa2_4f0d_bfa9_83eeeccbf571
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

meta pser
type: Species
initial concentration: 0.09
initial amount: NaN
in compartment: meta cell
is: CHEBI:57524
boundary condition: false
has only substance units: false
constant: false
name: phosphoserine
is: SBO:0000247

meta php
type: Species
has only substance units: false
name: phosphohydroxypyruvate
is: CHEBI:18110
is: SBO:0000247
constant: false
initial concentration: 0.6
in compartment: meta cell
boundary condition: false
initial amount: NaN

http://identifiers.org/biomodels.db/BIOMD0000000458#_8d117dbd_51f7_4e1d_80c3_024b6d137f03
type: SpeciesReference
stoichiometry: 1.0
species: meta pser

http://identifiers.org/biomodels.db/BIOMD0000000458#d5385c25_870f_47a1_a2d5_b299926b076b
type: SpeciesReference
stoichiometry: 1.0
species: meta php

meta p3g
type: Species
is: SBO:0000247
constant: true
has only substance units: false
initial concentration: 2.36
boundary condition: true
is: CHEBI:58272
in compartment: meta cell
initial amount: NaN
name: 3-phosphoglycerate

http://identifiers.org/biomodels.db/BIOMD0000000458#_50e38b88_2a22_46a0_8377_2d0b603384b3
type: SBMLUnitsDef
name: mmol

http://identifiers.org/biomodels.db/BIOMD0000000458#_08015d00_837f_4f74_896f_7578cb4fa36a
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

meta PSP
type: Reaction
name: phosphoserine phosphatase
is: http://identifiers.org/ec-code/3.1.3.3
fast: false
reversible: true
is: SBO:0000176

meta serB
type: Species
name: serB
is: SBO:0000252
is: P0AGB0
constant: true
initial amount: NaN
in compartment: meta cell
boundary condition: true
has only substance units: false
initial concentration: 0.25

http://identifiers.org/biomodels.db/BIOMD0000000458#_40909b07_e64f_4f29_9f57_cd0fce8154a9
type: LocalParameter
value: 0.15

http://identifiers.org/biomodels.db/BIOMD0000000458#_03fcd319_9101_42da_b71f_52456c4ba3bc
type: LocalParameter
value: 0.0015

http://identifiers.org/biomodels.db/BIOMD0000000458#dc865abd_e044_44d5_8ce6_6fa2e32ebc21
type: LocalParameter
value: 1.43

http://identifiers.org/biomodels.db/BIOMD0000000458#_5669a643_fa2f_4bb3_a21f_a79492198c73
type: SpeciesReference
stoichiometry: 1.0
species: meta ser

http://identifiers.org/biomodels.db/BIOMD0000000458#_27dd1b2e_08d3_4e4d_ba73_f18bc60e1e48
type: SpeciesReference
stoichiometry: 1.0
species: meta pser

meta PDH
type: Reaction
name: phosphoglycerate dehydrogenase
is: http://identifiers.org/ec-code/1.1.1.95
is: SBO:0000176
fast: false
reversible: true

http://identifiers.org/biomodels.db/BIOMD0000000458#a7f59278_2428_41e9_9385_56b8fc06d66f
type: SpeciesReference
stoichiometry: 1.0
species: meta php

http://identifiers.org/biomodels.db/BIOMD0000000458#_18376e6d_ffb2_477a_b7fc_78a68e4d2785
type: LocalParameter
value: 0.0038

http://identifiers.org/biomodels.db/BIOMD0000000458#_2c105bba_adf8_4b56_a9bd_c8f972f95729
type: LocalParameter
value: 0.0032

http://identifiers.org/biomodels.db/BIOMD0000000458#_608b49c5_2783_4e46_a0b2_11ce11e6665f
type: LocalParameter
value: 1.2

http://identifiers.org/biomodels.db/BIOMD0000000458#fc9ace49_973f_4567_b1fc_64635e59e411
type: LocalParameter
value: 0.55

http://identifiers.org/biomodels.db/BIOMD0000000458#_8047280e_34af_42d0_a5d0_429a5caf6a44
type: SpeciesReference
stoichiometry: 1.0
species: meta p3g