from CellScribe import *
from model.compartments import e
from model.metabolites import *
from model.genes import SP_2169, SP_2170, SP_2171, SP_1648, SP_1649, SP_1650, SP_1858, SP_1857, SP_1552
from model.operons import psaBCA
zinc = Metabolite("zinc", kegg="C00038")
zinc_rxn = Reaction(name="zinc_rxn",
reactants=e(zinc) + h2o + atp,
products=zinc + adp + phosphate,
pairs=[(e(zinc), zinc)])
GeneAssociation(zinc_rxn, SP_2169 & SP_2170 & SP_2171)
manganese = Metabolite("manganese", kegg="C00034")
manganese_rxn = Reaction(name="manganese_rxn",
reactants=e(manganese) + atp,
products=manganese + adp + phosphate,
pairs=[(e(manganese), manganese)])
SczA = Gene("SP_1858")
czcD = Gene("SP_1857")
If(SczA, ~czcD)
If(zinc, ~SczA)
GeneAssociation(manganese_rxn, SP_1648 & SP_1649 & SP_1650)
PsaR = Gene("SP_1638")
If(PsaR & (zinc | manganese), ~psaBCA)
from CellScribe import *
from model.compartments import e
from model.metabolites import *
from model.genes import SP_1386, SP_1387, SP_1388, SP_1389, SP_1386, SP_1387, SP_1388, SP_1389, SP_1580
spermidine = Metabolite("spermidine", kegg="C00315")
putrescine = Metabolite("putrescine", kegg="C00134")
spermidine_rxn = Reaction(name="spermidine_rxn",
reactants=e(spermidine) + h2o + atp,
products=spermidine + adp + phosphate,
pairs=[(spermidine, putrescine), (atp, adp)],
minors=[atp, adp])
GeneAssociation(spermidine_rxn, SP_1386 & SP_1387 & SP_1388 & SP_1389)
putrescine_rxn = Reaction(name="putrescine_rxn",
reactants=e(putrescine) + h2o + atp,
products=putrescine + adp + phosphate)
GeneAssociation(putrescine_rxn, SP_1386 & SP_1387 & SP_1388 & SP_1389)
cellobiose = Metabolite("cellobiose", kegg="C00185")
cellobiose_rxn = Reaction(name="cellobiose_rxn",
reactants=e(cellobiose) + h2o + atp,
products=cellobiose + adp + phosphate)
chitobiose = Metabolite("chitobiose", kegg="C01674")
chitobiose_rxn = Reaction(name="chitobiose_rxn",
reactants=e(chitobiose) + h2o + adp,
products=chitobiose + adp + phosphate)
#majors
bDGlu = Metabolite("beta-D-Glucose", kegg="C00221")
bDGlu6P = Metabolite("beta-D-Glucose 6-phosphate", kegg="C01172")
Dfru6P = Metabolite("D-fructose 6-phosphate", kegg="C00085")
Dfru16bisP = Metabolite("D-fructose 1,6-bisphosphate", kegg="C00354")
Dglycerald3P = Metabolite("D-glyceraldehyde 3-phosphate", kegg="C00118")
glyceroneP = Metabolite("glycerone phosphate", kegg="C00111")
BisPDglycerate13 = Metabolite("1,3-Bisphospho-D-glycerate", kegg="C00236")
PDglycerate3 = Metabolite("3-phospho-D-glycerate", kegg="C00197")
PDglycerate2 = Metabolite("2-phospho-D-glycerate", kegg="C00631")
phosphoenolpyruvate = Metabolite("phosphoenolpyruvate", kegg="C00074")
pyruvate = Metabolite("pyruvate", kegg="C00022")
glucokinase = Reaction(name="glucokinase",
reactants=e(bDGlu) + atp,
products=bDGlu6P + adp + H,
pairs=[(bDGlu, bDGlu6P), (atp, adp)],
minors=[atp, adp, H]
)
SP_0668 = Gene("SP_0668")
GeneAssociation(glucokinase, SP_0668)
pgi = Reaction(name="pgi",
reactants=bDGlu6P,
products=Dfru6P,
pairs=[b - D - Glu, b - D - Glu6P],
reversible=True
)
SP_2070 = Gene("SP_2070")
pgi = GeneAssociation(pgi, SP_2070)
from CellScribe import *
from model.compartments import e
from model.metabolites import *
from model.genes import SP_1032, SP_1033, SP_1034, SP_1035, SP_1869, SP_1870, SP_1871, SP_1872, SP_0242, SP_0243
iron = Metabolite("iron", kegg="C14819")
iron_rxn = Reaction(name="iron_rxn",
reactants=e(iron) + h2o + atp,
products=iron + adp + phosphate,
pairs=[(e(iron), iron)])
GeneAssociation(iron_rxn, SP_1032 & SP_1033 & SP_1034 & SP_1035 or
SP_1869 & SP_1870 & SP_1871 & SP_1872)
#iron vs ferrichrome? reaction states that it transfers ferrichrome
#Pit 2 is first & Pit 1 is second (PiuB,PiuC,PiuD,PiuA)
#SP_0241 pseudogene
#ritR regulates pit1
#regulation
#sp_0240
from CellScribe import *
from model.compartments import e
from model.metabolites import *
from model.genes import SP_1032, SP_1033, SP_1034, SP_1035, SP_1869, SP_1870, SP_1871, SP_1872, SP_0242, SP_0243
iron = Metabolite("iron", kegg="C14819")
iron_rxn = Reaction(name="iron_rxn",
reactants=e(iron) + h2o + atp,
products=iron + adp + phosphate,
pairs=[(e(iron), iron)])
GeneAssociation(
iron_rxn, SP_1032 & SP_1033 & SP_1034 & SP_1035
or SP_1869 & SP_1870 & SP_1871 & SP_1872)
#iron vs ferrichrome? reaction states that it transfers ferrichrome
#Pit 2 is first & Pit 1 is second (PiuB,PiuC,PiuD,PiuA)
#SP_0241 pseudogene
#ritR regulates pit1
#regulation
#sp_0240
from CellScribe import *
from model.compartments import e
from model.metabolites import atp, adp, phosphate
from model.genes import SP_1860, SP_1861
choline_rxn = Reaction(name="choline_rxn",
reactants=e(choline) + atp,
products=choline + adp + phosphate)
GeneAssociation(choline_rxn, SP_1860 & SP_1861)
choline = Metabolite("choline", kegg="C00114")
choline_rxn = Reaction(name="choline",
reactants=e(choline) + atp,
products=choline + adp + phosphate,
pairs=[(e(choline), choline)])
GeneAssociation(choline_rxn, SP_1860 & SP_1861)
from CellScribe import *
from model.compartments import e
from model.metabolites import *
from model.genes import SP_2169, SP_2170, SP_2171, SP_1648, SP_1649, SP_1650, SP_1858, SP_1857, SP_1552
from model.operons import psaBCA
zinc = Metabolite("zinc", kegg="C00038")
zinc_rxn = Reaction(name="zinc_rxn",
reactants=e(zinc) + h2o + atp,
products=zinc + adp + phosphate,
pairs=[(e(zinc), zinc)])
GeneAssociation(zinc_rxn, SP_2169 & SP_2170 & SP_2171)
manganese = Metabolite("manganese", kegg="C00034")
manganese_rxn = Reaction(name="manganese_rxn",
reactants=e(manganese) + atp,
products=manganese + adp + phosphate,
pairs=[(e(manganese), manganese)])
SczA = Gene("SP_1858")
czcD = Gene("SP_1857")
If(SczA, ~czcD)
If(zinc, ~SczA)
GeneAssociation(manganese_rxn, SP_1648 & SP_1649 & SP_1650)
PsaR = Gene("SP_1638")
If(PsaR & (zinc | manganese), ~psaBCA)
