metaid_0000039
initial amount: NaN
boundary condition: false
initial concentration: 0.01
in compartment: metaid_0000035
constant: false
type: Species
is: CHEBI:15746
has only substance units: false
is: C00750
name: Spermine

442757
stoichiometry: 1.0
species: metaid_0000038
type: SpeciesReference

metaid_0000030
constant: true
units: metaid_0000079
value: 0.02
name: KsANTZ
type: Parameter

metaid_0000071
kinetic law: 443311
product: 443299
reactant: 443287
is version of: GO:0046356
fast: false
reversible: false
name: VCOA
type: Reaction

443323
stoichiometry: 1.0
species: metaid_0000046
type: SpeciesReference

442577
units: metaid_0000077
value: 1.5
type: LocalParameter

metaid_0000019
constant: false
units: metaid_0000054
value: 0.677298510125025
name: Vmaxssat
type: Parameter

442277
exponent: -1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

443070
units: metaid_0000077
value: 100.0
type: LocalParameter

442217
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

443178
units: metaid_0000077
value: 0.06
type: LocalParameter

442409
stoichiometry: 1.0
species: metaid_0000037
type: SpeciesReference

metaid_0000062
is version of: http://identifiers.org/ec-code/4.1.1.17
is version of: R00670
kinetic law: 442361
type: Reaction
reactant: 442337
product: 442349
reversible: false
fast: false
name: Ornithine decarboxylase
is version of: REACT 1211.3

metaid_0000072
kinetic law: 443347
product: 443335
reactant: 443323
is version of: GO:0006085
fast: false
reversible: false
name: VACCOA
type: Reaction

443262
units: metaid_0000077
value: 41.0
type: LocalParameter

443287
stoichiometry: 1.0
species: metaid_0000045
type: SpeciesReference

442697
units: metaid_0000077
value: 1.5
type: LocalParameter

442745
stoichiometry: 1.0
species: metaid_0000042
type: SpeciesReference

BIOMD0000000190
parameter: metaid_0000019
species: metaid_0000038
is: MODEL6812345601
rule: metaid_0000055
creator:
  ORG:
    orgname: University of M?laga. CIBERER (Enfermedades Raras)
  n:
    given: Armando
    family: Reyes-Palomares
rule: metaid_0000061
species: metaid_0000044
units def: metaid_0000076
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
parameter: metaid_0000025
creator:
  ORG:
    orgname: University of Barcelona
  n:
    given: Marta
    family: Cascante
parameter: metaid_0000034
parameter: metaid_0000021
species: metaid_0000036
parameter: metaid_0000022
units def: metaid_0000056
curated: true
is version of: GO:0006595
species: metaid_0000040
units def: metaid_0000077
species: metaid_0000039
is described by: http://identifiers.org/pubmed/16709566
reaction: metaid_0000065
reaction: metaid_0000074
notes: SBML creators: Armando Reyes-Palomares * , Carlos Rodríguez-Caso +, Raul Montañez * , Marta Cascante $, Francisca Sánchez-Jiménez * , Miguel A. Medina * * ProCel Group, Department of Molecular Biology and Biochemistry, Faculty of Sciences, Campus de Teatinos, University of Malaga and CIBER de Enfermedades Raras (CIBER-ER). + Complex Systems Lab (ICREA-UPF), Barcelona Biomedical Research Park (PRBB-GRIB). $ Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona. http://asp.uma.es Metabolic modeling of polyamine metabolism in mammals. Rodríguez-Caso,C et al.: J Biol Chem 2006 : 281:21799-812. The model reproduces the dynamical behavior of the polyamine metabolism in mammals. In this model there are some additions and corrections to the publication. All perturbations and analysis have produced results very close to the published experiments. The model was successfully tested on CoPaSi v.4.4 (build 26). Parameters not included in the publication: 1. Parameters for SSAT kinetic constants: KmAcCoA = 1.5 µM KmCoA = 40 µM 2. Parameters for equation MAT (table 1): Vmax_MAT = 0.45 µM/min Km_MAT = 41 µM Ki_MET_MAT = 50 µM 3. Erratum.: The corrected ODE for time-dependent variable Antz is: KsANTZ*(1-1/(1+Keq*0.01*([D]+[S])))-KdANTZ*[Antz] According to these modifications the new steady-state analysis results are: Metabolites: [P]= 104.681 µM [D]= 76.7492 µM [S]= 58.0135 µM [SAM]= 52.327 µM [A]= 0.0101962 µM [aS]= 0.0245375 µM [aD]= 0.832236 µM Time-dependent global parameters: [Antz] = 0.574038 µM Vmaxodc = 1.28315 µM/min Vmaxssat = 0.673814 µM/min Vmaxsamdc = 0.36829 µM/min 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. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedd…
parameter: metaid_0000029
reaction: metaid_0000066
reaction: metaid_0000062
parameter: metaid_0000030
time units: metaid_0000016
reaction: metaid_0000067
parameter: metaid_0000026
reaction: metaid_0000072
species: metaid_0000046
species: metaid_0000045
units def: metaid_0000075
parameter: metaid_0000032
compartment: metaid_0000035
parameter: metaid_0000024
creator:
  ORG:
    orgname: University of Malaga
  n:
    given: Miguel A.
    family: Medina
parameter: metaid_0000033
rule: metaid_0000057
species: metaid_0000043
parameter: metaid_0000020
rule: metaid_0000059
species: metaid_0000042
species: metaid_0000041
area units: metaid_0000005
units def: metaid_0000079
created:
  W3 CDTF: Mon Sep 08 16:27:37 BST 2008
length unit: length
reaction: metaid_0000064
reaction: metaid_0000073
reaction: metaid_0000069
parameter: metaid_0000028
units def: metaid_0000054
reaction: metaid_0000070
reaction: metaid_0000071
creator:
  ORG:
    orgname: University of Malaga
  n:
    given: Francisca
    family: Sánchez-Jiménez
rule: metaid_0000060
species: metaid_0000037
units def: metaid_0000016
units def: metaid_0000017
parameter: metaid_0000031
name: Rodriguez-Caso2006_Polyamine_Metabolism
parameter: metaid_0000023
rule: metaid_0000058
type: SBMLModel
occurs in: http://identifiers.org/taxonomy/40674
volume units: metaid_0000004
creator:
  ORG:
    orgname: Universitat Pompeu Fabra
  n:
    given: Carlos
    family: Rodríguez-Caso
occurs in: http://identifiers.org/taxonomy/9989
units def: metaid_0000078
creator:
  ORG:
    orgname: University of Malaga
  n:
    given: Raul
    family: Montañez
substance units: metaid_0000017
units def: metaid_0000053
reaction: metaid_0000063
parameter: metaid_0000018
reaction: metaid_0000068
parameter: metaid_0000027

metaid_0000073
kinetic law: 443371
reactant: 443359
is version of: GO:0009447
fast: false
reversible: false
name: Putrescine efflux
type: Reaction

442205
exponent: -2.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

443082
units: metaid_0000077
value: 40.0
type: LocalParameter

442997
stoichiometry: 1.0
species: metaid_0000037
type: SpeciesReference

442265
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

442589
units: metaid_0000077
value: 40.0
type: LocalParameter

443383
units: metaid_0000076
value: 0.01
type: LocalParameter

metaid_0000074
kinetic law: 443407
reactant: 443395
fast: false
reversible: false
name: aD efflux
type: Reaction

443299
stoichiometry: 1.0
species: metaid_0000046
type: SpeciesReference

443274
units: metaid_0000054
value: 0.45
type: LocalParameter

442097
exponent: -1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000075
unit: 442217
unit: 442205
unit: 442193
name: uM^(-1)min^(-2)
type: SBMLUnitsDef

442985
units: metaid_0000054
value: 10.35
type: LocalParameter

443094
units: metaid_0000054
value: 10.95
type: LocalParameter

metaid_0000065
reactant: 442637
fast: false
modifier: 442673
product: 442661
reversible: false
is version of: R03910
type: Reaction
reactant: 442625
kinetic law: 442685
is version of: http://identifiers.org/ec-code/2.3.1.57
name: Spermidine/spermine N1-acetyltransferase for D
product: 442649

metaid_0000040
initial concentration: 0.01
initial amount: NaN
has only substance units: false
boundary condition: false
name: Spermidine
is: CHEBI:16610
is: C00315
in compartment: metaid_0000035
constant: false
type: Species

442889
stoichiometry: 1.0
species: metaid_0000040
type: SpeciesReference

metaid_0000054
unit: 442145
unit: 442133
unit: 442121
name: uMpermin
type: SBMLUnitsDef

443009
stoichiometry: 1.0
species: metaid_0000038
type: SpeciesReference

metaid_0000029
constant: true
units: metaid_0000076
value: 0.02
name: KdANTZ
type: Parameter

442517
stoichiometry: 1.0
species: metaid_0000045
type: SpeciesReference

442829
units: metaid_0000077
value: 0.6
type: LocalParameter

metaid_0000076
unit: 442229
name: permin
type: SBMLUnitsDef

442601
units: metaid_0000077
value: 130.0
type: LocalParameter

metaid_0000016
unit: 442073
name: minute
type: SBMLUnitsDef

443395
stoichiometry: 1.0
species: metaid_0000042
type: SpeciesReference

442385
units: metaid_0000077
value: 60.0
type: LocalParameter

metaid_0000066
modifier: 442781
name: Polyamine oxidase for aD
is version of: REACT 1548.3
product: 442757
modifier: 442793
fast: false
kinetic law: 442805
is version of: http://identifiers.org/ec-code/1.5.3.11
is version of: R03899
type: Reaction
reactant: 442745
reversible: false
modifier: 442769

443154
units: metaid_0000077
value: 0.1
type: LocalParameter

442709
units: metaid_0000077
value: 40.0
type: LocalParameter

metaid_0000053
unit: 442109
unit: 442097
name: peruM
type: SBMLUnitsDef

442109
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

442289
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

442973
units: metaid_0000077
value: 15.0
type: LocalParameter

442121
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

443130
stoichiometry: 1.0
species: metaid_0000039
type: SpeciesReference

443190
units: metaid_0000077
value: 25.0
type: LocalParameter

metaid_0000063
modifier: 442433
type: Reaction
fast: false
is version of: R00178
product: 442409
name: S-adenosylmethionine decarboxylase
modifier: 442421
reversible: false
reactant: 442397
kinetic law: 442445
is version of: http://identifiers.org/ec-code/4.1.1.50

442085
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000042
initial concentration: 0.01
name: N1-Acetylspermidine
boundary condition: false
has only substance units: false
is: C00612
constant: false
type: Species
in compartment: metaid_0000035
initial amount: NaN
is: CHEBI:22204

metaid_0000017
unit: 442085
name: µmole
type: SBMLUnitsDef

metaid_0000077
unit: 442253
unit: 442241
name: microM
type: SBMLUnitsDef

metaid_0000027
constant: true
units: metaid_0000076
value: 0.02
name: KdSAMDC
type: Parameter

442301
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

443250
units: metaid_0000077
value: 50.0
type: LocalParameter

442661
stoichiometry: 1.0
species: metaid_0000046
type: SpeciesReference

metaid_0000064
name: Spermidine/Spermine N1-acetyltransferase for S
is version of: http://identifiers.org/ec-code/2.3.1.57
kinetic law: 442565
product: 442541
type: Reaction
reversible: false
is version of: R03910
modifier: 442553
reactant: 442505
fast: false
product: 442529
reactant: 442517

442817
units: metaid_0000077
value: 14.0
type: LocalParameter

442505
stoichiometry: 1.0
species: metaid_0000039
type: SpeciesReference

443106
stoichiometry: 1.0
species: metaid_0000037
type: SpeciesReference

442073
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

metaid_0000041
initial concentration: 0.01
boundary condition: false
is: C02567
constant: false
in compartment: metaid_0000035
type: Species
name: N1-Acetylspermine
initial amount: NaN
has only substance units: false
is: CHEBI:17312

metaid_0000018
constant: false
units: metaid_0000054
value: 1.27905671844446
name: Vmaxodc
type: Parameter

metaid_0000078
unit: 442289
unit: 442277
unit: 442265
name: minperuM
type: SBMLUnitsDef

metaid_0000028
constant: true
units: metaid_0000079
value: 1.0
name: KsSAMDC
type: Parameter

443166
units: metaid_0000077
value: 60.0
type: LocalParameter

442373
units: metaid_0000077
value: 1300.0
type: LocalParameter

metaid_0000068
fast: false
is version of: R01920
reversible: false
name: Spermidine synthase
reactant: 442997
product: 443021
is version of: http://identifiers.org/ec-code/2.5.1.16
reactant: 443009
kinetic law: 443033
type: Reaction

metaid_0000025
constant: true
units: metaid_0000076
value: 0.2
name: KdSSAT
type: Parameter

442349
stoichiometry: 1.0
species: metaid_0000038
type: SpeciesReference

443359
stoichiometry: 1.0
species: metaid_0000038
type: SpeciesReference

442937
units: metaid_0000077
value: 14.0
type: LocalParameter

metaid_0000031
constant: true
units: metaid_0000076
value: 0.004
name: R
type: Parameter

442397
stoichiometry: 1.0
species: metaid_0000036
type: SpeciesReference

442493
units: metaid_0000077
value: 50.0
type: LocalParameter

443118
stoichiometry: 1.0
species: metaid_0000040
type: SpeciesReference

442613
units: metaid_0000077
value: 35.0
type: LocalParameter

metaid_0000045
initial amount: NaN
is: CHEBI:15351
boundary condition: true
type: Species
is: C00024
name: Acetyl-CoA
constant: true
in compartment: metaid_0000035
initial concentration: 39.5
has only substance units: false

442877
stoichiometry: 1.0
species: metaid_0000041
type: SpeciesReference

metaid_0000067
is version of: http://identifiers.org/ec-code/1.5.3.11
kinetic law: 442925
reversible: false
is version of: R03899
fast: false
modifier: 442913
name: Polyamine oxidase for aS
type: Reaction
is version of: REACT 2231.4
modifier: 442901
product: 442889
reactant: 442877

443202
units: metaid_0000054
value: 3.23
type: LocalParameter

metaid_0000026
constant: true
units: metaid_0000079
value: 0.001
name: KsSSAT
type: Parameter

metaid_0000032
constant: true
units: dimensionless
value: 4.44
name: C
type: Parameter

443045
units: metaid_0000077
value: 0.3
type: LocalParameter

442145
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000046
in compartment: metaid_0000035
has only substance units: false
is: C00010
initial amount: NaN
type: Species
is: CHEBI:15346
constant: true
boundary condition: true
initial concentration: 160.0
name: CoA

442961
units: metaid_0000077
value: 50.0
type: LocalParameter

metaid_0000043
initial amount: NaN
has only substance units: false
in compartment: metaid_0000035
constant: true
is: C00073
is: CHEBI:16643
boundary condition: true
type: Species
name: Methionine
initial concentration: 50.0

443058
units: metaid_0000077
value: 0.8
type: LocalParameter

metaid_0000023
constant: true
units: metaid_0000053
value: 0.05
name: KdODC
type: Parameter

442481
units: metaid_0000077
value: 500.0
type: LocalParameter

442337
stoichiometry: 1.0
species: metaid_0000044
type: SpeciesReference

metaid_0000056
unit: 442181
unit: 442169
unit: 442157
name: peruMpermin
type: SBMLUnitsDef

metaid_0000033
constant: false
units: metaid_0000076
value: 0.004
name: Kaccoa
type: Parameter

443214
stoichiometry: 1.0
species: metaid_0000043
type: SpeciesReference

442529
stoichiometry: 1.0
species: metaid_0000041
type: SpeciesReference

442193
exponent: -1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

442625
stoichiometry: 1.0
species: metaid_0000040
type: SpeciesReference

metaid_0000024
constant: true
units: metaid_0000079
value: 5.0
name: KsODC
type: Parameter

metaid_0000069
kinetic law: 443142
reactant: 443118
is version of: http://identifiers.org/ec-code/2.5.1.22
fast: false
reversible: false
reactant: 443106
type: Reaction
product: 443130
is version of: R02869
name: Spermine synthase

442457
units: metaid_0000077
value: 0.5
type: LocalParameter

442865
units: metaid_0000054
value: 10.35
type: LocalParameter

metaid_0000034
constant: false
units: metaid_0000076
value: 0.012
name: Kcoa
type: Parameter

442133
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

metaid_0000044
is: CHEBI:15729
name: L-Ornithine
boundary condition: true
type: Species
constant: true
initial amount: NaN
initial concentration: 300.0
is: C00077
in compartment: metaid_0000035
has only substance units: false

442181
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

442541
stoichiometry: 1.0
species: metaid_0000046
type: SpeciesReference

442637
stoichiometry: 1.0
species: metaid_0000045
type: SpeciesReference

443226
stoichiometry: 1.0
species: metaid_0000036
type: SpeciesReference

442325
exponent: -2.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

443335
stoichiometry: 1.0
species: metaid_0000045
type: SpeciesReference

metaid_0000021
constant: false
units: metaid_0000054
value: 0.574589492832405
name: Antz
type: Parameter

442169
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

metaid_0000035
is: GO:0005829
constant: true
size: 1.0
spatial dimensions: 3.0
name: Cytosol
type: Compartment

442241
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000022
constant: true
units: metaid_0000053
value: 1.0
name: Keq
type: Parameter

442853
units: metaid_0000077
value: 15.0
type: LocalParameter

442469
units: metaid_0000077
value: 2.5
type: LocalParameter

442721
units: metaid_0000077
value: 130.0
type: LocalParameter

443021
stoichiometry: 1.0
species: metaid_0000040
type: SpeciesReference

metaid_0000036
is: C00019
in compartment: metaid_0000035
constant: false
has only substance units: false
initial amount: NaN
type: Species
name: S-adenosyl-L-methionine
boundary condition: false
initial concentration: 0.01
is: CHEBI:15414

442649
stoichiometry: 1.0
species: metaid_0000042
type: SpeciesReference

442949
units: metaid_0000077
value: 0.6
type: LocalParameter

442313
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000037
constant: false
boundary condition: false
type: Species
is: C01137
is: CHEBI:15625
in compartment: metaid_0000035
has only substance units: false
initial concentration: 0.01
initial amount: NaN
name: S-adenosylmethioninamine

442229
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

442253
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

442157
exponent: -1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000020
constant: false
units: metaid_0000054
value: 0.367465856805639
name: Vmaxsamdc
type: Parameter

metaid_0000070
kinetic law: 443238
product: 443226
reactant: 443214
is version of: R00177
is version of: http://identifiers.org/ec-code/2.5.1.6
fast: false
reversible: false
name: Methionine adenosyltransferase
type: Reaction

442733
units: metaid_0000077
value: 35.0
type: LocalParameter

metaid_0000079
unit: 442325
unit: 442313
unit: 442301
name: uM(min)^-2
type: SBMLUnitsDef

443419
units: metaid_0000076
value: 0.01
type: LocalParameter

metaid_0000038
type: Species
in compartment: metaid_0000035
has only substance units: false
initial amount: NaN
boundary condition: false
is: C00134
constant: false
name: Putrescine
initial concentration: 0.01
is: CHEBI:17148

442841
units: metaid_0000077
value: 50.0
type: LocalParameter

W3 CDTF: Thu Jul 05 15:37:34 BST 2012