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)