from pandas import DataFrame
from trnlib.omeORM import *
from IPython.core.display import HTML
ome = Session()
catabolism = {}
anabolism = {}
chemiosmosis = {}
unclassified = {}
global_regs = {}
double_regs = {}
tRNA_prophage = {}
def flatten_to_genes(category):
genes = []
for x in category:
for y in category[x]:
try:
for z in category[x][y]: genes.append(z)
except:
genes.append(y)
return genes
tfs = catabolism.keys()+anabolism.keys()+chemiosmosis.keys()
index = []
data = [[],[],[]]
for tf in set(tfs):
try: cat_genes = len(flatten_to_genes(catabolism[tf]))
except: cat_genes = 0
try: ana_genes = len(flatten_to_genes(anabolism[tf]))
except: ana_genes = 0
try: chem_genes = len(flatten_to_genes(chemiosmosis[tf]))
except: chem_genes = 0
index.append(tf)
data[0].append(cat_genes)
data[1].append(ana_genes)
data[2].append(chem_genes)
df = DataFrame(index=index, data=array(data).T, columns=['Catabolic','Anabolic','Chemiosmotic'])
HTML(df.sort('Catabolic').to_html())
Catabolic | Anabolic | Chemiosmotic | |
---|---|---|---|
appY | 0 | 0 | 9 |
asnC | 0 | 3 | 0 |
fabR | 0 | 2 | 0 |
fhlA | 0 | 0 | 29 |
lysR | 0 | 1 | 0 |
argP | 0 | 6 | 1 |
birA | 0 | 5 | 0 |
metR | 0 | 5 | 1 |
narP | 0 | 0 | 47 |
putA | 1 | 0 | 0 |
nemR | 1 | 0 | 0 |
lldR | 1 | 0 | 1 |
dnaA | 1 | 8 | 0 |
betI | 1 | 2 | 0 |
trpR | 1 | 13 | 0 |
melR | 1 | 0 | 0 |
iscR | 1 | 0 | 24 |
dsdC | 2 | 0 | 0 |
kdgR | 2 | 0 | 0 |
murR | 2 | 0 | 0 |
mtlR | 2 | 0 | 0 |
dpiA | 2 | 8 | 1 |
xapR | 2 | 0 | 0 |
treR | 2 | 0 | 0 |
iclR | 3 | 0 | 0 |
tyrR | 3 | 7 | 0 |
metJ | 3 | 9 | 0 |
dhaR | 3 | 0 | 0 |
allS | 3 | 0 | 0 |
cynR | 3 | 0 | 0 |
dcuR | 3 | 0 | 4 |
rhaS | 4 | 0 | 0 |
prpR | 4 | 0 | 0 |
hcaR | 5 | 0 | 0 |
glpR | 5 | 0 | 4 |
gcvA | 5 | 0 | 0 |
rbsR | 5 | 0 | 0 |
uxuR | 5 | 0 | 0 |
xylR | 5 | 0 | 0 |
mhpR | 6 | 0 | 0 |
glcC | 6 | 0 | 0 |
idnR | 6 | 0 | 0 |
ulaR | 6 | 0 | 0 |
deoR | 6 | 0 | 0 |
nanR | 6 | 0 | 0 |
caiF | 7 | 0 | 4 |
nac | 7 | 7 | 0 |
narL | 8 | 2 | 101 |
allR | 8 | 0 | 0 |
cdaR | 9 | 0 | 0 |
araC | 9 | 0 | 0 |
cytR | 9 | 2 | 0 |
galR | 9 | 0 | 0 |
rutR | 9 | 4 | 2 |
galS | 9 | 0 | 0 |
fadR | 10 | 1 | 0 |
malT | 10 | 0 | 0 |
paaX | 11 | 0 | 0 |
gntR | 12 | 0 | 0 |
modE | 12 | 0 | 34 |
pdhR | 16 | 21 | 8 |
nagC | 20 | 2 | 3 |
purR | 20 | 25 | 1 |
cysB | 23 | 0 | 0 |
cra | 29 | 8 | 12 |
nsrR | 29 | 11 | 19 |
ntrC | 32 | 1 | 0 |
fnr | 33 | 39 | 81 |
argR | 41 | 55 | 11 |
lrp | 44 | 40 | 4 |
fur | 51 | 10 | 32 |
arcA | 98 | 55 | 67 |
crp | 253 | 69 | 42 |
catabolism['arcA'] = {
"transport": {
"carbohydrate": ['ptsG','mglA','mglB','mglC','kgtP','ugpB','ugpA','ugpE','ugpC','lldP','dcuA','dcuB'],
"amino_acid": ['potF','potG','potH','putP','oppA','oppB','oppC','oppD','oppF','hisJ','hisQ','hisM',
'hisP','argT','gabP','sstT','dppA','dppB','dppC','dppD','dppF','cycA'],
"nucleotides": ['nupC'],
"lipids": [],
"cofactors": ['feoB']
},
"recycling": {
"carbohydrate": ['mhpC','mhpD','mhpE','mhpF','fsaA','paaK','manA','yeiG','suhB','uxaC','ugpQ','pldA'],
"amino_acid": ['caiA','clpA','clpS','putA','pepN','puuA','puuD','astC','astD','astE','ygjG','pepQ'],
"lipids": ['fadE','fadD','fadI','fadJ','fadH','fadA','fadB'],
"nucleotides": ['xseA']
},
"glycolysis": ['lpd','gapA'],
"TCA": ['acnB','gltA','sdhC','sdhA','sdhD','sdhB','sucA','sucB','sucC','sucD','icd',
'aldA','fumA','glcB','glcD','glcE','glcF','glcG','mdh','fumB'],
"accessory": [],
"regulators": {
"carbohydrate": ['mhpR','ypdA','ypdB','glcC','aer'],
"amino_acid": ['puuR','gcvA','gcvB']
}
}
anabolism['arcA'] = {
"macromolecular_synthesis": ['rpsT','xthA','rplY','ndk','ygjD','rpsU','dnaG','pnp','rpsO','rbfA','infB',
'nusA','rpmA','rplU','nudE','mutM','rpmG','rpmB','recF','rpmH','rnpA'],
"biosynthesis": {
"carbohydrate": ['folE'],
"nucleotides": ['pncB','pntA','pntB','sthA'],
"amino_acids": ['thrA','thrB','thrC','carA','carB','leuD','gabD','gabT'],
"lipids": ['fabD','fabG','fabF',],
"cofactors": ['ribF','ispH','moaB','moaC','thiC','thiE','thiF','thiG','thiH','thiS']
},
"accessory": [],
"regulators": ['thrL','leuL','betI','bssR','infA','rcsB','cspA','rho']
}
chemiosmosis['arcA'] = {
"ETC": {
"dehydrogenases": ['nuoA','nuoB','nuoC','nuoE','nuoF','nuoG','nuoH','nuoI','nuoJ','nuoK',
'nuoL','nuoM','nuoN','hybA','hybB','hybC','hybD','hybE','hybF','hybG',
'hybO','glpD','lldD','fdoG','fdoH','fdoI'],
"oxidoreductases": ['cyoA','cyoB','cyoC','cyoD','cyoE','cydA','cydB','dsbB','msrB','mqo',
'lhgO','nrfA','nrfB','nrfC','nrfD','nrfF'],
"accessory": ['secG','glpE','glpG']
},
"fermentation": ['acs'],
"ion_pumps": ['kdpC','gsiB','gsiD','macA','cydD','cydC','cirA','ompC','mntH',
'hemG','osmY'],
"motility": ['flhC','flhD'],
"accessory": ['tpx','yncE','yqcA'],
"regulators": ['glpR','gadX','gadW','micF','feoC']
}
double_regs['arcA'] = ['rutR','argR','lldR']
unclassified['arcA'] = ['ybfA','ybhK','ybiU','mcbA','ybjX','phoH','yceD','ynaJ','yncD','ydgC','rstA','rstB','yejG',
'yfbM','ypdC','yfiF','csiD','yhgE','yhhJ','yhjE','yiaG','yieE','yigI','yigZ','yijD','yjcH',
'yjiR','psrD','csrB']
catabolism['fnr'] = {
"transport": {
"carbohydrate": ['ptsG','exuT'],
"amino_acid": ['aroP','metN','metI','metQ','potA','potB','potC','potD','tyrP'],
"nucleotides": ['uraA'],
"lipids": ['fadL']
},
"recycling": {
"carbohydrate": ['fsaA','arnA','mltA','envC'],
"amino_acid": ['pepT','yhbU','yhbV','ybiS','rnpA'],
"lipids": [],
"nucleotides": ['xseA']
},
"glycolysis": ['aceE','aceF','lpd','dhaK','dhaL','gapA','pykA','eno','gpmM'],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['caiF']
}
}
anabolism['fnr'] = {
"macromolecular_synthesis": ['ddlA','pnp','truB','rbfA','recF','rpmH','nrdA','nrdB',
'nrdD','upp','rplY','rpsU','nusA','infB','ung','nrdG',
'groL'],
"biosynthesis": {
"carbohydrate": ['ybiS'],
"nucleotides": ['pyrD','guaA','guaB','purM','purN','purA','ravA','katG',
'viaA'],
"amino_acids": ['thrB','thrC','argG','gltB','gltF','speA'],
"lipids": [],
"cofactors": []
},
"accessory": [],
"regulators": ['iraP','bssR','uspA','uspB','uspF','yfbV']
}
chemiosmosis['fnr'] = {
"ETC": {
"dehydrogenases": ['nuoA','nuoB','nuoC','nuoE','nuoF','nuoG','nuoH','nuoI','nuoJ','nuoK',
'nuoL','nuoM','nuoN','hybA','hybB','hybC','hybD','hybE','hybF','hybG',
'hybO','fdnH','fdnI'],
"oxidoreductases": ['cydA','cydB','hcr','dmsA','dmsB','dmsC','narG','narH','narI','narJ',
'frdA','frdB','frdC','frdD','nrfA','nrfB','nrfC','nrfD','nrfF','nirB',
'nirD','nirC','ynfE','ynfF','ynfG','ynfH'],
"accessory": ['hcp','nikA','nikB','nikC','nikD','nikE','fhuF','dmsD',
'ydhW','ydhY','secG','moaA','moaB','moaC','moaD','moaE']
},
"fermentation": ['pflB','focA','adhE','pta','ackA','yfiD'],
"ion_pumps": ['cydD','cydC','narK','pitA'],
"motility": [],
"accessory": ['msrB','ynjE','cysG'],
"regulators": ['narL','narX','nikR']
}
double_regs['fnr'] = []
global_regs['fnr'] = ['pdhR','arcA']
unclassified['fnr'] = ['uspF','ydcX','ydfZ','ynfK','ydjX','ydjY','ydjZ','ynjC','ynjD','ynjA','ynjB',
'yhbT','yhbS','yfcZ','yeaD','yedE','yecH','yfcC','yggC','yghA','yghB','yqhA',
'yqgC','yjeT','hsdS','hsdM','hsdR','yibN','csrB']
tRNA_prophage['fnr'] = ['yffL','metZ','metW','metV','yffS']
catabolism['fur'] = {
"transport": {
"carbohydrate": ['garP'],
"amino_acid": ['oppA','oppB','oppC','oppD','oppF'],
"nucleotides": [],
"lipids": [],
"cofactors": ['tonB','entS','fecA','fecB','fecC','fecD','fecE','fepA','fepC','fepD',
'fepE','fepG','fepF','fepB','exbB','exbD','feoA','feoB','fhuA','fhuB',
'fhuC','fhuD','fhuE','fhuF','fiu','mntH']
},
"recycling": {
"carbohydrate": ['garL','garR','garK'],
"amino_acid": ['gspO'],
"lipids": [],
"nucleotides": ['rnpB'],
"cofactors": ['fes']
},
"glycolysis": ['gpmA'],
"TCA": ['sdhA','sdhB','sdhC','sdhD','sucA','sucB','sucC','sucD','fumB'],
"accessory": [],
"regulators": {
"carbohydrate": [],
"amino_acid": [],
"cofactors": ['fecI','fecR','feoC',]
}
}
anabolism['fur'] = {
"macromolecular_synthesis": ['ybdZ'],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": ['nrdE','nrdF','nrdH','nrdI','pyrC','purF'],
"amino_acids": ['metH'],
"lipids": [],
"cofactors": []
},
"accessory": [],
"regulators": ['metJ','rpoS']
}
chemiosmosis['fur'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": ['cyoA','cyoB','cyoC','cyoD','cyoE','yqjH'],
"accessory": []
},
"fermentation": [],
"ion_pumps": ['cirA','rcnA'],
"motility": ['flhC','flhD'],
"accessory": ['entA','entB','entC','entD','entH','entE','entF',
'sufA','sufB','sufC','sufD', 'sufE','sufS','ftnA','hmp',
'katE','katG','sodA','sodB','zinT'],
"regulators": ['rcnR','ryhB']
}
double_regs['fur'] = ['purR']
unclassified['fur'] = ['nohA','ydfN','ygaC','yhhY','yjjZ','ompF','tfaQ']
a = flatten_to_genes(catabolism['fur'])+flatten_to_genes(anabolism['fur'])+flatten_to_genes(chemiosmosis['fur'])+unclassified['fur']+double_regs['fur']
ome = Session()
ome.query(RegulatoryNetwork).filter_by(reg_gene='fur').filter(not_(RegulatoryNetwork.regd_gene.in_(a))).all()
[RegulonDB fur --| fur]
catabolism['ntrC'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['argT','hisJ','hisQ','hisM','hisP','potF','potG','potH','potI',
'ddpA','ddpB','ddpC','ddpD','ddpF','glnP','glnQ','glnH'],
"nucleotides": ['rutG'],
"lipids": [],
"ions": ['amtB'],
"cofactors": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": ['astA','astB','astC','astD','astE','ddpX'],
"lipids": [],
"nucleotides": ['rutA','rutB','rutC','rutD','rutE','rutF'],
"cofactors": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": [],
"amino_acid": [],
"cofactors": ['cbl']
}
}
anabolism['ntrC'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": ['glnA'],
"lipids": [],
"cofactors": []
},
"accessory": [],
"regulators": []
}
chemiosmosis['ntrC'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": [],
"accessory": []
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"accessory": [],
"regulators": []
}
double_regs['ntrC'] = ['glnK','glnL','nac']
unclassified['ntrC'] = ['yeaG','yeaH','ygjG','yhdW','yhdX','yhdY','yhdZ']
a = flatten_to_genes(catabolism['ntrC'])+flatten_to_genes(anabolism['ntrC'])+flatten_to_genes(chemiosmosis['ntrC'])+unclassified['ntrC']+double_regs['ntrC']
ome.query(RegulatoryNetwork).filter_by(reg_gene='glnG').filter(not_(RegulatoryNetwork.regd_gene.in_(a))).all()
[RegulonDB glnG --? glnG]
catabolism['nac'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['gabP'],
"lipids": [],
"nucleotides": ['codB','nupC'],
"cofactors": []
},
"recycling": {
"carbohydrate": ['gabD'],
"amino_acid": ['gabT'],
"lipids": [],
"nucleotides": ['codA'],
"cofactors": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['asnC'],
"amino_acid": [],
"cofactors": []
}
}
anabolism['nac'] = {
"macromolecular_synthesis": ['mnmG'],
"biosynthesis": {
"carbohydrate": ['mioC'],
"nucleotides": [],
"amino_acids": ['serA','gdhA','gltB','gltD','gltF'],
"lipids": [],
"cofactors": []
},
"accessory": [],
"regulators": []
}
chemiosmosis['nac'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": [],
"accessory": []
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"accessory": [],
"regulators": []
}
double_regs['nac'] = []
unclassified['nac'] = []
a = flatten_to_genes(catabolism['nac'])+flatten_to_genes(anabolism['nac'])+flatten_to_genes(chemiosmosis['nac'])+unclassified['nac']+double_regs['nac']
ome.query(RegulatoryNetwork).filter_by(reg_gene='nac').filter(not_(RegulatoryNetwork.regd_gene.in_(a))).all()
[RegulonDB nac --| nac]
catabolism['modE'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['oppA','oppB','oppC','oppD','oppF'],
"lipids": [],
"nucleotides": [],
"cofactors": ['modA','modB','modC']
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": ['deoA','deoB','deoC','deoD'],
"cofactors": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": [],
"amino_acid": [],
"cofactors": []
}
}
anabolism['modE'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": [],
"lipids": [],
"cofactors": []
},
"accessory": [],
"regulators": []
}
chemiosmosis['modE'] = {
"ETC": {
"dehydrogenases": ['hycB','hycC','hycD','hycE','hycF','hycG'],
"oxidoreductases": ['napA','napB','napC','napD','napF','napG','napH','dmsA','dmsB',
'dmsC'],
"accessory": ['ccmA','ccmB','ccmC','ccmD','ccmE','ccmF','ccmG','ccmH',
'moaA','moaB','moaC','moaD','moaE','hycH','hycI']
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"accessory": [],
"regulators": ['hycA','narL','narX']
}
double_regs['modE'] = []
unclassified['modE'] = []
a = flatten_to_genes(catabolism['modE'])+flatten_to_genes(anabolism['modE'])+flatten_to_genes(chemiosmosis['modE'])+unclassified['modE']+double_regs['modE']
ome.query(RegulatoryNetwork).filter_by(reg_gene='modE').filter(not_(RegulatoryNetwork.regd_gene.in_(a))).all()
[]
catabolism['iscR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": [],
"cofactors": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": ['rnlA'],
"cofactors": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": [],
"amino_acid": [],
"cofactors": []
}
}
anabolism['iscR'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": [],
"lipids": [],
"cofactors": []
},
"accessory": [],
"regulators": []
}
chemiosmosis['iscR'] = {
"ETC": {
"dehydrogenases": ['hyaA','hyaB','hyaC','hyaD','hyaE','hyaF'],
"oxidoreductases": ['napA','napB','napC','napD','napF','napG','napH'],
"accessory": ['erpA']
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"accessory": ['sufA','sufB','sufC','sufD', 'sufE','sufS','nfuA',
'iscA','iscS','iscU'],
"regulators": []
}
double_regs['iscR'] = []
unclassified['iscR'] = ['ydiU']
a = flatten_to_genes(catabolism['iscR'])+flatten_to_genes(anabolism['iscR'])+flatten_to_genes(chemiosmosis['iscR'])+unclassified['iscR']+double_regs['iscR']
ome.query(RegulatoryNetwork).filter_by(reg_gene='iscR').filter(not_(RegulatoryNetwork.regd_gene.in_(a))).all()
[RegulonDB iscR --| iscR]
catabolism['lrp'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['brnQ','potF','potG','potH','artM','artQ','artI','artP','oppC','leuE','ygaW','sdaC',
'yqeG','sstT','livF','livG','livM','livH','livK','dtpB','dppA','dppB','dppC','dppD','dppF',
'gltP'
],
"nucleotides": [],
"lipids": ['fadL']
},
"recycling": {
"carbohydrate": ['yqeF'],
"amino_acid": ['pepD','ompT','sdaA','sdaB','gcvP','gcvH','gcvT','tdhA','kbl'],
"lipids": [],
"nucleotides": ['upp']
},
"glycolysis": ['dhaK','dhaL','dhaM'],
"TCA": ['aceK'],
"accessory": ['eco'],
"regulators": {
"carbohydrate": ['araC']
}
}
anabolism['lrp'] = {
"macromolecular_synthesis": ['lplA'],
"biosynthesis": {
"carbohydrate": ['folM','yhhK'],
"nucleotides": ['galU','purM','purN',],
"amino_acids": ['thrA','thrB','thrC','leuD','leuC','leuB','leuA','leuL','ilvI','ilvH','aroG',
'dadX','yfbQ','serA','ansB','gltB','gltD','gltF','avtA','ilvL','ilvM','ilvE',
'ilvA','lysU'],
"lipids": []
},
"regulators": ['ftsQ','ftsA','ftsZ','topA','uspE','lexA','yciT','stpA','fimA','fimC']
}
chemiosmosis['lrp'] = {
"ETC": {
"dehydrogenases": ['dadA'],
"oxidoreductases": ['napC'],
"accessory": ['ccmE']
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": ['gadY']
}
unclassified['lrp'] = ['ybgS','ybhP','ybhQ','ybiJ','ycgB','yciN','yfcC','yfcZ','yffR','csiE','yhjE','yjbJ','yjbQ','yjbR','ytfJ']
catabolism['crp'] = {
"transport": {
"carbohydrate": ['agaV','agp','araE','araF','araG','araH','ascF','bglG','chbA','chbB','chbC','dctA',
'dcuA','dcuB','exuT','fucP','galP','gatA','gatB','gatC','gntU','idnT','lacY','lamB',
'malK','malF','malG','malE','manX','manZ','manY','mglA','mglB','mglC','mtlA','murP',
'nagE','nanT','nanC','ptsG','ptsH','ptsI','rbsA','rbsB','rbsC','rhaT','srlA','srlB',
'srlE','treB','ugpA','ugpB','ugpC','ugpE','uhpT','uidB','ulaA','ulaB','ulaC','xylF',
'xylG','xylH','yiaM','yiaN','yiaO','crr'],
"amino_acid": ['cirA','dsdX','gabP','lsrA','lsrB','lsrC','lsrD','melB','proP','sohB','tdcC','tnaB'],
"nucleotides": ['nupC','nupG','tsx'],
"lipids": ['fadL'],
"cofactors": ['modA','modB','modC']
},
"recycling": {
"carbohydrate": ['araB','araA','araD','ascB','bglB','bglF','caiA','caiB','caiC','caiD','caiD','caiE',
'chbF','chbG','chbA','chbR','fucA','fucO','fucK','fucI','galE','galT','galK','galM','gatD',
'gatZ','gatY','gutQ','hofM','hofN','hofO','hofP','idnD','idnK','paaA','idnO','kbaZ','lacA',
'lacZ','lsrF','lsrG','lyxK','malS','melA','metK','mtlD','murQ','nagA','nagB','nanA','nanE',
'nanK','nanM','paaB','paaC','paaD','paaF','paaG','paaH','paaI','paaJ','paaK','maoC','prpB',
'prpC','prpD','prpE','rbsD','rbsK','rhaA','rhaB','sgbE','sgbh','sgbU','srlD','tam','treC',
'ugpQ','uidA','uidC','ulaD','ulaE','ulaF','uxaA','uxaB','uxaC','uxuA','uxuB','xylA','xylB',
'yiaK','yiaL'],
"amino_acid": ['cdd','dsdA','mhpC','mhpF','putP','speC','tdcB','tdcC','tdcD','tdcE','tdcF','tdcG','tnaA'],
"lipids": ['mpl'],
"nucleotides": ['cyaR','deoA','deoB','deoC','deoD','hpt','udp','xseA']
},
"glycolysis": ['aceE','aceF','fbaA','gapA','pgk'],
"TCA": ['aceB','aceA','aceK','acnA','acnB','aspA','fumA','fumB','mdh','sdhA','sdhB','sdhC','sdhD',
'sucA','sucB','sucC','sucD'],
"accessory": ['aldA','aldB',],
"regulators": {
"carbohydrate": ['aer','araC','caiT','cstA','cyaA','dcuR','dgsA','feaR','galS','glcC','gutM',
'idnR','malT','melR','mtlR','nagC','pdhR','prpR','rbsR','rhaR','rhaS','sfsA','srlR','uxuR',
'xylR','yiaJ','caiF'],
"nucleotides": ['cytR'],
"amino_acid": ['tdcA','tnaC']
}
}
anabolism['crp'] = {
"macromolecular_synthesis": ['cpdB','dusB','metY','nrdA','nrdB','ppiA','rimP','rpoH','rpoS','rpsO','truB','pnp'],
"biosynthesis": {
"carbohydrate": ['glgA','glgC','glgP'],
"nucleotides": ['epd','guaA','guaB','nagD','pncB','yeiA','yeiT','ubiG'],
"amino_acids": ['gdhA','ansB','argG','aroA','dadX','gabD','gabT','glnA','ilvB','ilvN','mhpD','mhpE',
'serA','serC'],
"lipids": ['fadD','fadH']
},
"accessory": ['entA','entB','entC','entD','entE','entH','fecA','fecB','fecC','fecD','fecE',
'fepA','nfuA','zraR','zraS'],
"regulators": ['csgF','fur','glgS','glnG','glnL','grpE','gyrA','hupA','hupB','infB','ivbL','lsrR',
'nusA','rbfA','spf']
}
chemiosmosis['crp'] = {
"ETC": {
"dehydrogenases": ['gcd','dadA'],
"oxidoreductases": ['cyoA','cyoB','cyoC','cyoD','cyoE','fixA','fixB','fixC','fixX','lhgO','nirB',
'nirD','nirC'],
"accessory": ['cysG','trxA']
},
"fermentation": ['acs','actP','focA','focB','hyfA','hyfB','hyfC','hyfD','hyfE','hyfG','hyfH'
'hyfI','hyfJ','hyfR','pflB','yjcH'],
"ion_pumps": ['osmY'],
"motility": ['flhC','flhD'],
"regulators": ['gadX'],
"pH": ['gadA','gadB','gadC','gadE','sodA','sodB'],
}
unclassified['crp'] = ['azuC','chpA','chpR','cdgD','csgE','csgG','csiD','csiE','dksA','envZ','fis','ybiL','hlyE','hofB','hofC',
'marA','marB','marR','mdtE','mdtF','ompA','ompF','ompR','oxyR','ppdD','psiE','relA','sbmC','trg',
'ychH','yhfA','ykgR','ynfK']
catabolism['purR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['sdaC','gltS','gltP'],
"nucleotides": ['codB','tsx','uraA','xanP','yieG'],
"lipids": []
},
"recycling": {
"carbohydrate": ['glpQ','glpT'],
"amino_acid": ['sdaB','gcvP','gcvH','gcvT'],
"lipids": ['mltF'],
"nucleotides": ['upp','xseA','yieH','codA']
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['malT']
}
}
anabolism['purR'] = {
"macromolecular_synthesis": ['mnmC','ppiA','sirA'],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": ['purC','purE','purF','purK','purL','purM','purN','purT','ubiX','guaB',
'glyA','purD','purH','pyrI','pyrB','pyrL'],
"amino_acids": ['carA','carB'],
"lipids": ['fabB',]
},
"accessory": ['fhuC','fhuD','fhuB'],
"regulators": []
}
chemiosmosis['purR'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": [],
"accessory": []
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": ['gadX']
}
unclassified['purR'] = ['ydiJ','yebG','yohH','cvpA','yfgO','yfgC','yfgD','ssnA','ygfT','yhhQ','ryjA']
catabolism['argR'] = {
"transport": {
"carbohydrate": ['hcaT'],
"amino_acid": ['aroP','dtpD','potF','potG','potH','potI','artJ','artM','artQ','artI','artP','ybjE',
'ydgI','hisJ','hisQ','hisM','hisP'],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['hchA','eutM','eutD','eutT','eutQ','eutP','eutS','glmM','gph','phnO','phnB','phnS'],
"amino_acid": ['puuB','puuE','astE','astB','astD','astA','astC'],
"lipids": ['dapE'],
"nucleotides": []
},
"glycolysis": ['pfkB','rpe',],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['galS']
}
}
anabolism['argR'] = {
"macromolecular_synthesis": ['asnT','trpS'],
"biosynthesis": {
"carbohydrate": ['folM','mreD','mreC','mreB'],
"nucleotides": ['yeaJ','ubiX','purF','pyrI','pyrL','pyrB'],
"amino_acids": ['carA','carB','argF','hisG','hisD','hisC','hisB','hisA','hisF','hisI','argA',
'argG','gltB','gltD','gltF','argD','aroB','aroK','argE','argC','argB','argH',
],
"lipids": ['plsC','waaK','rfaZ','waaY','waaJ','waaI','waaB','rfaS','waaP','waaG','waaQ']
},
"accessory": [],
"regulators": ['crl','ftsZ','dps','mukE','mukB','ycbW','hisL','stpA','dam','damX',]
}
chemiosmosis['argR'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": [],
"accessory": ['trxB']
},
"ATP synthase": ['atpC','atpD','atpG','atpA','atpH','atpF','atpE','atpB','atpI'],
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": ['narL']
}
unclassified['argR'] = ['yaaU','ykgA','yahA','dacC','ycbU','ycbF','ycbV','ycfD','isrA','ydeN','yoaI','yeaL',
'yoeI','yfcC','cvpA','yffL','yffB','ypfN','yqaE','yraQ']
catabolism['cra'] = {
"transport": {
"carbohydrate": ['manY','fruA','fruB','ptsH'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['fruK','mtlD','envC'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": ['dhaM','dhaL','dhaK','dhaK','pykF','ppsA','ppsR','gapA','glk','eno','fbaA','pgk',
'gpmM','pfkA','tpiA','fbp'],
"TCA": ['sucB','icd','aceB','aceK'],
"accessory": [],
"regulators": {
"carbohydrate": ['dhaR','crr']
}
}
anabolism['cra'] = {
"macromolecular_synthesis": ['rpoS',],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": ['pntA','epd'],
"amino_acids": ['carA','leuD','leuC','leuB','leuA'],
"lipids": []
},
"accessory": [],
"regulators": []
}
chemiosmosis['cra'] = {
"ETC": {
"dehydrogenases": ['nuoA','nuoB','nuoC','nuoE','nuoF','nuoK'],
"oxidoreductases": ['cyoD','cyoC','cyoE','nirD'],
"accessory": ['msrB']
},
"fermentation": ['adhE'],
"ion_pumps": [],
"motility": [],
"regulators": []
}
global_regs['cra'] = ['pdhR','crp']
unclassified['cra'] = ['ydgH','yeaC','yeaD']
catabolism['pdhR'] = {
"transport": {
"carbohydrate": ['ygaH','glcA','ynfM'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['ybiV','prpC','prpB'],
"amino_acid": [],
"lipids": [],
"nucleotides": ['hpt','envC']
},
"glycolysis": ['aceE','aceF','lpd','yfiD'],
"TCA": ['glcD','glcB','glcG','glcF'],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
anabolism['pdhR'] = {
"macromolecular_synthesis": ['tig'],
"biosynthesis": {
"carbohydrate": ['murC','murD','murE','murG','mraY'],
"nucleotides": [],
"amino_acids": ['aroF','tyrA','metB'],
"accessory": ['fecA','fecB','fecC','fecD','fecE'],
"lipids": ['lipA']
},
"accessory": [],
"regulators": ['ftsW','ftsI','ftsL','dnaB','mraW','metR']
}
chemiosmosis['pdhR'] = {
"ETC": {
"dehydrogenases": ['ndh','glpD'],
"oxidoreductases": ['cyoA','cyoB','cyoC','cyoD','cyoE'],
"accessory": ['hemL']
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": []
}
global_regs['pdhR'] = ['pdhR']
unclassified['pdhR'] = ['hha','tomB','yfgH','yhjX']
catabolism['narL'] = {
"transport": {
"carbohydrate": ['dcuA','dcuB'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": ['pflB'],
"TCA": ['aspA','fumB'],
"accessory": [],
"regulators": {
"carbohydrate": ['caiF','dcuR','dcuS']
}
}
anabolism['narL'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": ['ubiA','ubiC'],
"amino_acids": [],
"lipids": []
},
"accessory": [],
"regulators": []
}
chemiosmosis['narL'] = {
"ETC": {
"dehydrogenases": ['fdhF','fdnG','fdnH','fdnI','hyaA','hyaB','hyaC','hyaD','hyaE','hyaF',
'hybA','hybB','hybC','hybD','hybE','hybF','hybG','hybO','nuoA','nuoB',
'nuoC','nuoD','nuoE','nuoF','nuoG','nuoH','nuoI','nuoJ','nuoK','nuoL',
'nuoM','nuoN','torA','torC','torD','ydhT','ydhU','ydhV','ydhW','ydhX',
'ydhY'],
"oxidoreductases": ['napB','dmsA','dmsB','dmsC','dmsD','frdA','frdB','frdC','frdD','hcr',
'napA','napC','napD','napF','napG','napH','narG','narH','narI','nirB',
'nirC','nirD','nrfA','nrfB','nrfC','nrfD','nrfE','nrfF','nrfG',],
"accessory": ['ccmA','ccmB','ccmC','ccmD','ccmE','ccmF','ccmG','ccmH','cysG','hcp',
'moeA','moeB','nikA','nikB','nikC','nikD','nikE','norV','norW','ynfE',
'ynfF','ynfG','ynfH','ytfE']
},
"fermentation": ['adhE','focA'],
"ion_pumps": ['cydD','cydC','narJ','narK'],
"motility": [],
"regulators": ['nikR']
}
unclassified['narL'] = ['ogt','yeaR','yoaG']
catabolism['trpR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['mtr'],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
anabolism['trpR'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": ['aroL','aroM','trpE','trpD','trpC','trpB','trpA','aroH'],
"lipids": []
},
"accessory": ['fhuC','fhuD','fhuB'],
"regulators": ['trpL','trpR']
}
unclassified['trpR'] = ['yaiA','ftnB','mdtL']
chemiosmosis['appY'] = {
"ETC": {
"dehydrogenases": ['hyaA','hyaB','hyaC','hyaD','hyaE','hyaF'],
"oxidoreductases": ['appB','appC'],
"accessory": []
},
"fermentation": [],
"pH": ['appA'],
"ion_pumps": [],
"motility": [],
"regulators": []
}
unclassified['appY'] = ['yccB']
catabolism['rutR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": ['rutG'],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": ['nemA'],
"lipids": [],
"nucleotides": ['rutA','rutB','rutC','rutD','rutE','rutF']
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['nemR']
}
}
anabolism['rutR'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": ['carA','carB'],
"lipids": []
},
"accessory": ['fepB'],
"regulators": ['gmr']
}
chemiosmosis['rutR'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": [],
"accessory": []
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": ['gadW','gadX']
}
unclassified['rutR'] = []
catabolism['cytR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": ['nupC','nupG','tsx'],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": ['cdd'],
"lipids": [],
"nucleotides": ['deoA','deoB','deoC','deoD','udp']
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
anabolism['cytR'] = {
"macromolecular_synthesis": ['ppiA','rpoH'],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": [],
"lipids": []
},
"accessory": [],
"regulators": []
}
catabolism['allR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": ['ybbW','ybbY'],
"lipids": []
},
"recycling": {
"carbohydrate": ['allA','allB','gcl','glxK','hyi'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['allS']
}
}
catabolism['allS'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['allC','allD','allE'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['araC'] = {
"transport": {
"carbohydrate": ['araE','araF','araG','araH'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['araB','araA','araD','xylA','xylB'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
unclassified['araC'] = ['araJ']
anabolism['argP'] = {
"macromolecular_synthesis": ['dnaN','recF'],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": ['nrdA','nrdB'],
"amino_acids": ['dapB'],
"lipids": []
},
"accessory": [],
"regulators": ['dnaA',]
}
chemiosmosis['argP'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": [],
"accessory": []
},
"fermentation": [],
"ion_pumps": ['argO'],
"motility": [],
"regulators": []
}
anabolism['asnC'] = {
"macromolecular_synthesis": ['mnmG'],
"biosynthesis": {
"carbohydrate": ['mioC'],
"nucleotides": [],
"amino_acids": ['asnA'],
"lipids": []
},
"accessory": [],
"regulators": []
}
catabolism['betI'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['betT'],
"nucleotides": [],
"lipids": []
}
}
anabolism['betI'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": ['betA','betB'],
"lipids": []
},
"accessory": [],
"regulators": []
}
anabolism['birA'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": ['bioA','bioB','bioC','bioD','bioE'],
"nucleotides": [],
"amino_acids": [],
"lipids": []
},
"accessory": [],
"regulators": []
}
catabolism['caiF'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['caiA','caiB','caiC','caiD','caiD','caiE'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['caiT']
}
}
chemiosmosis['caiF'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": ['fixA','fixB','fixC','fixX'],
"accessory": []
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": []
}
catabolism['cdaR'] = {
"transport": {
"carbohydrate": ['garP','gudP'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['garD','garL','garR','garK','gudD','gudX'],
"amino_acid": [],
"lipids": [],
"nucleotides": ['rnpA']
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['cynR'] = {
"transport": {
"carbohydrate": ['cynX'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['cynS','cynT'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['cysB'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['tauA','tauB','tauC'],
"nucleotides": [],
"lipids": [],
"cofactors": ['cysA','cysW','cysU','cysP','cysD','cysN','cysC','ssuA','ssuB','ssuC']
},
"recycling": {
"carbohydrate": ['ssuD','ssuE'],
"amino_acid": ['cysA','cysJ','cysI','cysH','cysK','cysM','tauD'],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": [],
"cofactors": ['cbl']
}
}
unclassified['cysB'] = ['hslJ']
catabolism['dcuR'] = {
"transport": {
"carbohydrate": ['dctA','dcuB'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": ['fumB'],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
chemiosmosis['dcuR'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": ['frdA','frdB','frdC','frdD'],
"accessory": []
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": []
}
catabolism['deoR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": ['nupG','tsx'],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": ['deoA','deoB','deoC','deoD',]
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['dhaR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": ['dhaK','dhaL','dhaM'],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['dnaA'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": ['aldA'],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
anabolism['dnaA'] = {
"macromolecular_synthesis": ['dnaN','nrdA','nrdB','polA','recF','rpoH'],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": ['guaA','guaB'],
"amino_acids": [],
"lipids": []
},
"accessory": [],
"regulators": []
}
unclassified['dnaA'] = ['yjeV']
catabolism['dpiA'] = {
"transport": {
"carbohydrate": ['exuT'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": ['mdh'],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
anabolism['dpiA'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": ['citC','citD','citE','citF','citG','citX'],
"nucleotides": [],
"amino_acids": [],
"lipids": []
},
"accessory": [],
"regulators": ['dpiA','dpiB']
}
chemiosmosis['dpiA'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": [],
"accessory": []
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": ['appY']
}
catabolism['dsdC'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['dsdX'],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": ['dsdA'],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
anabolism['fabR'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": [],
"lipids": ['fabA','fabB']
},
"accessory": [],
"regulators": []
}
catabolism['fadR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": ['fadD','fadL']
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": ['fadA','fadB','fadC','fadE','fadH','fadI','fadJ'],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['iclR']
}
}
anabolism['fadR'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": [],
"lipids": []
},
"accessory": [],
"regulators": ['uspA']
}
chemiosmosis['fhlA'] = {
"ETC": {
"dehydrogenases": ['fdhF','hycB','hycC','hycD','hycE','hycF','hycG','hydN',
'hyfA','hyfB','hyfG','hyfI','hyfC','hyfD','hyfE','hyfF',
'hyfH','hypA','hypB'],
"oxidoreductases": [],
"accessory": ['hycH','hycI','hyfJ','hypC','hypD','hypE','hypF']
},
"fermentation": ['focB'],
"ion_pumps": [],
"motility": [],
"regulators": ['hycA','hyfR']
}
catabolism['galR'] = {
"transport": {
"carbohydrate": ['mglA','mglB','mglC','galP'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['galE','galT','galK','galM'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['galS']
}
}
catabolism['galS'] = {
"transport": {
"carbohydrate": ['mglA','mglB','mglC','galP'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['galE','galT','galK','galM'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['galR']
}
}
catabolism['gcvA'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": ['gcvP','gcvH','gcvT','gcvA','gcvB'],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['glcC'] = {
"transport": {
"carbohydrate": ['glcA'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": ['glcD','glcE','gclF','glcB','glcG'],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['glpR'] = {
"transport": {
"carbohydrate": ['glpF'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['glpQ','glpT','glpX','glpK'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
chemiosmosis['glpR'] = {
"ETC": {
"dehydrogenases": ['glpA','glpB','glpC','glpD'],
"oxidoreductases": [],
"accessory": []
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": []
}
catabolism['gntR'] = {
"transport": {
"carbohydrate": ['gntT','gntU','gntX','idnT'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['gntK','idnD','idnK','idnO'],
"amino_acid": [],
"lipids": [],
"nucleotides": ['nfuA']
},
"glycolysis": ['eda','edd'],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['idnR']
}
}
catabolism['hcaR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['hcaB','hcaC','hcaD','hcaE','hcaF'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['iclR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": ['aceB','aceA','aceK'],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['idnR'] = {
"transport": {
"carbohydrate": ['gntU','idnT'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['gntK','idnD','idnK','idnO'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['kdgR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": ['edd','eda'],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['lldR'] = {
"transport": {
"carbohydrate": ['lldP'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
chemiosmosis['lldR'] = {
"ETC": {
"dehydrogenases": ['lldD'],
"oxidoreductases": [],
"accessory": []
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": []
}
anabolism['lysR'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": ['lysA'],
"lipids": []
},
"accessory": [],
"regulators": []
}
catabolism['malT'] = {
"transport": {
"carbohydrate": ['malK','malF','malG','malE','lamB','malM'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['malP','malQ','malS','malZ'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['melR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['melA'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['metJ'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['metQ','metI','metN'],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
anabolism['metJ'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": ['folE'],
"nucleotides": [],
"amino_acids": ['metA','metB','metC','metE','metF','metK','metL'],
"lipids": []
},
"accessory": [],
"regulators": ['metR']
}
unclassified['metJ'] = ['ahpC','ahpF','yeiB']
anabolism['metR'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": ['glyA'],
"amino_acids": ['metA','metE','metH'],
"lipids": []
},
"accessory": [],
"regulators": ['metR']
}
chemiosmosis['metR'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": [],
"accessory": []
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": [],
"accessory": ['hmp']
}
catabolism['mhpR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['mhpA','mhpB','mhpC','mhpD','mhpE','mhpF'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['mtlR'] = {
"transport": {
"carbohydrate": ['mtlA'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['mtlD'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['murR'] = {
"transport": {
"carbohydrate": ['murP'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['murQ'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['nagC'] = {
"transport": {
"carbohydrate": ['chbA','chbB','chbC','chiP','crr','galP','manX','manZ','manY'
'nagE','nanC','ptsH','ptsI'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['chbF','chbG','chbA','chbR','nagA','nagB','nanM'],
"amino_acid": [],
"lipids": [],
"nucleotides": ['nagD']
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
anabolism['nagC'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": ['glmS','glmU'],
"nucleotides": [],
"amino_acids": [],
"lipids": []
},
"accessory": [],
"regulators": []
}
chemiosmosis['nagC'] = {
"ETC": {
"dehydrogenases": [],
"oxidoreductases": [],
"accessory": []
},
"fermentation": [],
"ion_pumps": ['feoA','feoB','feoC'],
"motility": [],
"regulators": []
}
unclassified['nagC'] = ['creA','creB','creC','creD','dinI','fimB','ybfN','ydeP']
catabolism['nanR'] = {
"transport": {
"carbohydrate": ['nanT'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['nanA','nanE','nanK','nanC','nanM'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
unclassified['nanR'] = ['fimB','yhcH']
chemiosmosis['narP'] = {
"ETC": {
"dehydrogenases": ['fdhF','fdnG','fdnH','fdnI','hyaA','hyaB','hyaC','hyaD','hyaE','hyaF',
],
"oxidoreductases": ['hcr','napA','napB','napC','napG','napH','napD','napF','nirB','nirD',
'nirC','nrfA','nrfB','nrfC','nrfD','nrfE','nrfF','nrfG','ydhT','ydhU',
'ydhX','ydhW','ydhV','ydhY'],
"accessory": ['ytfE','ccmA','ccmB','ccmC','ccmD','ccmE','ccmF','ccmG','ccmH','cysG',
'hcp','norV','norW']
},
"fermentation": [],
"ion_pumps": [],
"motility": [],
"regulators": []
}
unclassified['narP'] = ['yeaR','yoaG']
catabolism['nemR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": ['nemA'],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['nsrR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['putP','ptrA','xasA'],
"nucleotides": [],
"lipids": [],
"cofactors": ['feoA','feoB','tehA','sufA']
},
"recycling": {
"carbohydrate": ['ydhO','feaB','mhpE','mhpT','yibD','ydbD','yafB','yfcE'],
"amino_acid": ['hflB','tynA','maoC','putA','caiA','caiT','yccA','ydhO'],
"lipids": [],
"nucleotides": ['yieH','cdd','ygiF']
},
"glycolysis": ['aceE'],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": ['feaR'],
"amino_acid": ['dsdC']
}
}
anabolism['nsrR'] = {
"macromolecular_synthesis": ['rluB','ftsJ','thrS','clpB','yccK','rpsE','rplR'],
"biosynthesis": {
"carbohydrate": ['folB'],
"nucleotides": ['nrdA','nrdB'],
"amino_acids": [],
"lipids": []
},
"accessory": [],
"regulators": ['yfhB']
}
chemiosmosis['nsrR'] = {
"ETC": {
"dehydrogenases": ['hycA','hypA','ndh'],
"oxidoreductases": ['hcr'],
"accessory": ['grxD','ytfE','hcp','nrfA','dsbA','hcp','sodB','napF',
'yfcF']
},
"fermentation": [],
"ion_pumps": ['yggT'],
"motility": ['fliA','fliC','fliK','fliL'],
"regulators": ['torS']
}
global_regs['nsrR'] = ['pdhR','lrp']
unclassified['nsrR'] = ['ygiH','yciQ','mqsR','ygiV','ybeH','yneF','yneG','yihF','yccM','yncL','ydcX',
'intZ','yffL','htrG','yigI','yggS','ydfE','intQ','ymcA','ymcB','ydcM','yfhH',
'ygbA','mutS','recC','yeeO','smpA','recN','yddW','cbrB']
catabolism['paaX'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['paaA','paaB','paaC','paaE','paaF','paaG','paaH','paaI','paaJ',
'paaK','maoC'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['prpR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['prpB','prpC','prpD','prpE'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['putA'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['putP'],
"nucleotides": [],
"lipids": []
},
}
catabolism['rbsR'] = {
"transport": {
"carbohydrate": ['rbsA','rbsB','rbsC'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['rbsD','rbsK'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
}
catabolism['rhaS'] = {
"transport": {
"carbohydrate": ['rhaT'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['rhaA','rhaB','rhaD'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['treR'] = {
"transport": {
"carbohydrate": ['treB'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['treC'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['tyrR'] = {
"transport": {
"carbohydrate": [],
"amino_acid": ['aroP','mtr','tyrP'],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": [],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
anabolism['tyrR'] = {
"macromolecular_synthesis": [],
"biosynthesis": {
"carbohydrate": [],
"nucleotides": [],
"amino_acids": ['aroF','aroG','aroL','aroM','folA','tyrA','tyrB'],
"lipids": []
},
"accessory": [],
"regulators": []
}
unclassified['tyrR'] = ['yaiA']
catabolism['ulaR'] = {
"transport": {
"carbohydrate": ['ulaA','ulaB','ulaC'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['ulaD','ulaE','ulaF'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['uxuR'] = {
"transport": {
"carbohydrate": ['gntP','uidB','uidC'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['uxuA','uxuB'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['xapR'] = {
"transport": {
"carbohydrate": ['xapB'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['xapA'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}
catabolism['xylR'] = {
"transport": {
"carbohydrate": ['xylF','xylG','xylH'],
"amino_acid": [],
"nucleotides": [],
"lipids": []
},
"recycling": {
"carbohydrate": ['xylA','xylB'],
"amino_acid": [],
"lipids": [],
"nucleotides": []
},
"glycolysis": [],
"TCA": [],
"accessory": [],
"regulators": {
"carbohydrate": []
}
}