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()) 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() 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() 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() 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() 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": [] } }