#reference paper: S Shen-Orr et al. Nature Genetics 2002 acrAB -| acrR ada_alkB -> ada_alkB ada_alkB -| ada_alkB aidB -> ada_alkB alkA -> ada_alkB adiA -> adiA_adiY slp -> alpA appCBA -> appY araBAD -> araC araBAD -| araC araC -| araC araE -> araC araE -| araC araFG_araH_1H_2 -> araC araFG_araH_1H_2 -| araC araJ -> araC aceBAK -| arcA appCBA -> arcA appY -> arcA betIBA -| arcA cydAB -> arcA cyoABCDE -| arcA dctA -| arcA fadBA -| arcA focA_pflB -> arcA fumA -| arcA fumC -| arcA glcDEFGB -| arcA glpACB -| arcA gltA -| arcA icdA -| arcA lctPRD -| arcA mdh -| arcA nuoABCEFGHIJKLMN -| arcA sodA -| arcA argCBH -| argR argD -| argR argE -| argR argF -| argR argI -| argR argR -| argR carAB -| argR arsEFG -| arsR asnA -> asnC asnC -| asnC atoDAB -> atoC atoDAE -> atoC betIBA -| betIBA betT -| betIBA bioA -| birA_murA bioBFCD -| birA_murA cadBA -> cadC caiTABCDE -> caiF fixABCX -> caiF ssuEADCB -> cbl tauABCD -> cbl cpxAR -> cpxAR cpxP -> cpxAR dsbA -> cpxAR ecfI -> cpxAR htrA -> cpxAR motABcheAW -| cpxAR rotA -> cpxAR skp_lpxDA_fabZ -> cpxAR tsr -| cpxAR xprB_dsbC_recJ -> cpxAR acs -> crp aldB -> crp ansB -> crp araBAD -> crp araC -> crp araE -> crp araFG_araH_1H_2 -> crp araJ -> crp caiF -> crp caiTABCDE -> crp cirA -> crp cpdB -> crp crp -> crp crp -| crp cyaA -| crp dadAX -> crp dctA -| crp dcuB_fumB -| crp deoCABD -> crp deoCABD -| crp dsdXA -> crp ebgAC -> crp epd_pgk -> crp fadL -| crp fixABCX -> crp flhDC -> crp focA_pflB -> crp fucAO -> crp fucPIKUR -> crp fur -> crp galETKM -> crp galETKM -| crp galS -> crp glgCAP -> crp glgS -> crp glnALG -> crp glpACB -> crp glpD -> crp glpFK -> crp glpTQ -> crp gltA -> crp gntKU -> crp gntT -> crp ivbL_ilvBN -> crp lacZYA -> crp malEFG -> crp malI -| crp malK_lamB_malM -> crp malS -> crp malT -> crp malXY -> crp malXY -| crp manXYZ -> crp melAB -> crp melR -> crp mglBAC -> crp nagBACD -> crp nagE -> crp nupG -> crp nupG -| crp ompA -| crp ppiA -> crp ppiA -| crp proP -> crp proP -| crp ptsHI_crr -> crp ptsHI_crr -| crp rhaBAD -> crp rhaBAD -| crp rhaT -> crp rpoH -> crp rpoH -| crp sdhCDAB_b0725_sucABCD -> crp speC -| crp srlAEBD_gutM_srlR_gutQ -> crp tdcABCDEFG -> crp tnaLAB -> crp tsx -> crp tsx -| crp ubiG -> crp udp -> crp uhpT -> crp yhfA -> crp yhfA -| crp yiaKLMNOPQRS -> crp csgBA -> csgDEFG csgDEFG -> csgDEFG gyrA -> cspA hns -> cspA cynR -| cynR cynTSX -> cynR cysB -| cysB cysDNC -> cysB cysJIH -> cysB cysK -> cysB cysPUWAM -> cysB tauABCD -> cysB deoCABD -| cytR nupC -| cytR nupG -| cytR ppiA -| cytR rpoH -| cytR tsx -> cytR tsx -| cytR udp -| cytR deoCABD -| deoR nupG -| deoR tsx -| deoR nrdAB -> dnaA rpoH -| dnaA dsdC -| dsdC dsdXA -> dsdC ebgAC -| ebgR emrRAB -| emrRAB ompC -> envY_ompT ompF -> envY_ompT ompC -> evgA exuR -| exuR exuT -| exuR uxaCA -| exuR uxuABR -| exuR fabA -> fadR fadBA -| fadR fadL -| fadR iclMR -| fadR uspA -| fadR fecABCDE -> fecIR fecIR -> fecIR fdhF -> fhlA hycABCDEFGH -> fhlA hypABCDE -> fhlA flgAMN -> flhDC flgBCDEFGHIJK -> flhDC flhBAE -> flhDC fliAZY -> flhDC fliE -> flhDC fliFGHIJK -> flhDC fliLMNOPQR -> flhDC flgBCDEFGHIJK -> fliAZY flgKL -> fliAZY flgMN -> fliAZY flhBAE -> fliAZY fliAZY -> fliAZY fliC -> fliAZY fliDST -> fliAZY fliE -> fliAZY fliFGHIJK -> fliAZY fliLMNOPQR -> fliAZY motABcheAW -> fliAZY tarTapcheRBYZ -> fliAZY tsr -> fliAZY acs -> fnr ansB -> fnr arcA -> fnr aspA -> fnr caiF -> fnr cydAB -| fnr cyoABCDE -| fnr dcuB_fumB -> fnr dmsABC -> fnr fdnGHI -> fnr fnr -| fnr focA_pflB -> fnr frdABCD -> fnr glpACB -> fnr hypABCDE -> fnr icdA -| fnr narGHJI -> fnr narK -> fnr ndh -| fnr nirBDC_cysG -> fnr nuoABCEFGHIJKLMN -| fnr sdhCDAB_b0725_sucABCD -| fnr tdcABCDEFG -> fnr aceBAK -| FruR adhE -| FruR fruBKA -| FruR icdA -> FruR ppsA -> FruR ptsHI_crr -> FruR ptsHI_crr -| FruR pykF -| FruR fucAO -> fucPIKUR fucPIKUR -> fucPIKUR cirA -| fur entCEBA -| fur fecIR -| fur fepA_entD -| fur fepB -| fur fepDGC -| fur fhuACDB -| fur fur -| fur sodA -| fur tonB -| fur galETKM -| GalR galS -| GalR galS -| galS mglBAC -| galS gatYZABCDR_2 -| gatR_1 gcvA -| gcvA gcvTHP -> gcvA gcvTHP -| gcvA gcvTHP -| gcvR glcDEFGB -> glcC glnALG -> glnALG glnALG -| glnALG glnHPQ -> glnALG glnHPQ -| glnALG nac -> glnALG glpACB -| glpR glpD -| glpR glpFK -| glpR glpTQ -| glpR edd_eda -| gntR gntKU -| gntR gntT -| gntR hcaA1A2CBD_yphA -> hcaR hcaR -| hcaR aceBAK -> himA caiTABCDE -| himA carAB -> himA carAB -| himA dps -> himA ecpD_htrE -> himA focA_pflB -> himA glcDEFGB -> himA glnHPQ -> himA glnHPQ -| himA himA -| himA himD -| himA hycABCDEFGH -> himA hypABCDE -> himA narGHJI -> himA narK -> himA nuoABCEFGHIJKLMN -| himA ompC -| himA ompF -> himA ompF -| himA ompR_envZ -| himA osmE -| himA pspABCDE -> himA sodA -| himA tdcABCDEFG -> himA hipBA -> hipBA caiF -| hns flhDC -> hns fliAZY -> hns hns -| hns nhaA -> hns osmC -> hns rcsAB -> hns stpA -| hns hycABCDEFGH -| hycA zraP -> hydHG aceBAK -| iclMR acs -| iclMR idnDOTR -> idnDOTR ilvC -> ilvY ilvY -| ilvY kdpABC -> kdpDE lacZYA -| lacI leuLABCD -> leuO lexA_dinF -| lexA_dinF polB -| lexA_dinF recA -| lexA_dinF recN -| lexA_dinF rpsU_dnaG_rpoD -| lexA_dinF ssb -| lexA_dinF sulA -| lexA_dinF umuDC -| lexA_dinF uvrA -| lexA_dinF uvrB -| lexA_dinF uvrC -| lexA_dinF uvrD -| lexA_dinF gcvTHP -> lrp gltBDF -> lrp ilvIH -> lrp kbl_tdh -> lrp kbl_tdh -| lrp livJ -| lrp livKHMGF -| lrp lrp -| lrp lysU -| lrp ompC -| lrp ompF -> lrp oppABCDF -| lrp osmC -> lrp sdaA -| lrp serA -> lrp stpA -> lrp lysA -> lysR lysR -| lysR tdcABCDEFG -> lysR malI -| malI malXY -| malI malEFG -> malT malK_lamB_malM -> malT malPQ -> malT malS -> malT malZ -> malT fpr -> marRAB fumC -> marRAB marRAB -| marRAB nfo -> marRAB sodA -> marRAB zwf -> marRAB melAB -> melR melR -| melR metA -| metJ metC -| metJ metF -| metJ metJ -| metJ metR -| metJ glyA -> metR metA -> metR metH -> metR metR -| metR mhpABCDFE -> mhpR malT -| mlc manXYZ -| mlc ptsG -| mlc ptsHI_crr -| mlc moaABCDE -> moaABCDE modABC -| modE mtlADR -| mtlADR gdhA -| nac nac -| nac putAP -> nac nadB -| nadR pncB -| nadR glmUS -> nagBACD glmUS -| nagBACD manXYZ -| nagBACD nagBACD -| nagBACD nagE -| nagBACD adhE -| narL caiF -| narL dcuB_fumB -| narL dmsABC -| narL fdnGHI -> narL focA_pflB -| narL frdABCD -| narL narGHJI -> narL narK -> narL nirBDC_cysG -> narL nrfABCDEFG -> narL nuoABCEFGHIJKLMN -> narL torCAD -| narL nhaA -> nhaR acs -> nlpD_rpoS adhE -> nlpD_rpoS aldB -> nlpD_rpoS alkA -> nlpD_rpoS appY -> nlpD_rpoS cpxAR -> nlpD_rpoS dps -> nlpD_rpoS ftsQAZ -> nlpD_rpoS katG -> nlpD_rpoS narZYWV -> nlpD_rpoS nhaA -> nlpD_rpoS osmC -> nlpD_rpoS osmY -> nlpD_rpoS proP -> nlpD_rpoS csgBA -> ompR_envZ csgDEFG -> ompR_envZ fadL -| ompR_envZ flhDC -| ompR_envZ ompC -> ompR_envZ ompF -> ompR_envZ ompF -| ompR_envZ ahpCF -> oxyR dps -> oxyR gorA -> oxyR katG -> oxyR oxyR -| oxyR pdhR_aceEF_lpdA -| pdhR_aceEF_lpdA phnCDE_f73_phnFGHIJKLMNOP -> phoBR phoA -> phoBR phoBR -> phoBR phoE -> phoBR pstSCAB_phoU -> phoBR pspABCDE -> pspF codBA -| purR cvpA_purF_ubiX -| purR gcvTHP -| purR