Gene ID "Gene Name (for reffence only, string)" Regulation Activity Delay (hours) Comments 1 Comments 2 (orrigional regulation format) Comments 3 Comments 4 b0002 not ( THR[media] > 0 or ILE[media] > 0 ) 0.25 more comments b0003 not ( THR[media] > 0 or ILE[media] > 0 ) 0.25 b0004 not ( THR[media] > 0 or ILE[media] > 0 ) 0.25 b0019 NhaR or RpoS 0.25 b0020 NA[media] > 0 0.25 b0031 not ( LYS[media] > 0 ) 0.25 b0032 not ( ArgR ) 0.25 "come back to this with ""excess pyrimidines""" b0033 not ( ArgR ) and OxyR 0.25 CHANGED b0034 ( (Fnr and ArcA ) or Crp ) and not ( NarL ) 0.25 CHANGED b0036 Crp and CaiF 0.25 b0038 Crp and CaiF 0.25 b0040 Crp and CaiF 0.25 b0052 RpoE 0.25 b0061 AraC or ( AraC and Crp ) 0.25 b0062 AraC or ( AraC and Crp ) 0.25 b0063 AraC or ( AraC and Crp ) 0.25 b0064 ARAB[media] > 0 0.25 b0071 not ( LEU[media] > 0 ) or Lrp 0.25 b0072 not ( LEU[media] > 0 ) or Lrp 0.25 b0073 not ( LEU[media] > 0 ) or Lrp 0.25 b0074 not ( LEU[media] > 0 ) or Lrp 0.25 b0077 Lrp and not ( LEU[media] > 0 ) 0.25 b0078 Lrp and not ( LEU[media] > 0 ) 0.25 b0080 not ( Surplus_FDP ) 0.25 "AND NOT (O2xt > 0), " b0104 not ( GLN[media] > 0 or GN[media] > 0 ) 0.25 These cause trouble in presence of GN b0112 not ( TyrR and ( PHE[media] > 0 or TYR[media] > 0 or TRP[media] > 0 ) ) 0.25 b0113 not ( Surplus_PYR ) or not ( ArcA or not ( Fnr ) ) 0.25 b0114 ( not ( PdhR ) or Fis ) and not ( ArcA and Fnr ) 0.25 b0115 ( not ( PdhR ) or Fis ) and not ( ArcA and Fnr ) 0.25 b0116 not ( ArcA and Fnr ) 0.25 b0118 not ( ArcA ) 0.25 The aconitases depend on many things but appear to have a basal level b0124 not ( Crp ) 0.25 b0125 Crp 0.25 b0162 GLRT[media] > 0 or GALRT[media] > 0 0.25 need to add GLYRT as an activator b0167 Lrp 0.25 b0180 not ( Stringent[stim] ) or CpxR or RpoE or FadR2 0.25 b0197 not ( MetJ ) 0.25 b0198 not ( MetJ ) 0.25 b0199 not ( MetJ ) 0.25 b0221 not ( FadR2 ) or not ( ArcA ) 0.25 b0273 not ( ArgR ) 0.25 b0312 not ( ArcA or BetI ) 0.25 b0313 not ( ArcA ) or CHOL[media] > 0 0.25 b0314 not ( BetI ) 0.25 b0331 PPNT[media] > 0 0.25 b0333 PPNT[media] > 0 0.25 b0334 PPNT[media] > 0 0.25 b0335 PPNT[media] > 0 0.25 b0336 not ( PurR or NRI_hi ) and OxyR 0.25 CHANGED b0337 not ( PurR ) or NRI_hi 0.25 b0338 CNO[media] > 0 0.25 b0340 CynR 0.25 b0341 CNO[media] > 0 0.25 b0343 CRP_noGLC and not ( LacI ) 0.25 b0344 CRP_noGLC and not ( LacI ) 0.25 b0345 not ( LCTS[media] > 0 ) 0.25 b0346 HPPPNT[media] > 0 0.25 b0347 MhpR 0.25 b0348 MhpR 0.25 b0349 MhpR 0.25 b0350 MhpR 0.25 b0351 MhpR 0.25 b0352 MhpR 0.25 b0365 Cbl and CysB 0.25 b0366 Cbl and CysB 0.25 b0367 Cbl and CysB 0.25 b0368 Cbl and CysB 0.25 b0388 not ( (TyrR and TYR[media] > 0 ) or ( TyrR and TYR[media] > 0 and TrpR ) ) 0.25 b0399 PhoR 0.25 b0400 PI[media] < 0.004 0.25 should be less than 4E-6 M b0403 MalT 0.25 b0428 not ( ArcA or Fnr ) 0.25 b0429 not ( ArcA or Fnr ) 0.25 b0430 not ( ArcA or Fnr ) 0.25 b0431 not ( ArcA or Fnr ) 0.25 b0432 not ( ArcA or Fnr ) 0.25 b0504 not ( O2[media] > 0 ) and not ( AllR ) and not ( NH3[media] > 0 ) 0.25 b0505 not ( AllR ) 0.25 b0506 OFF 0.25 "need to figure out how to represent, glyoxalate is the inactivator)" b0507 not ( AllR ) 0.25 b0509 not ( AllR ) 0.25 b0512 not ( AllR ) 0.25 b0514 not ( AllR ) 0.25 b0516 AllS 0.25 b0522 not ( PurR ) 0.25 b0523 not ( PurR ) 0.25 b0564 not ( CitB ) and not ( O2[media] > 0 ) 0.25 changed b0583 not ( Fur ) 0.25 b0593 not ( Fur ) 0.25 b0594 not ( Fur ) 0.25 b0595 not ( Fur ) 0.25 b0596 not ( Fur ) 0.25 b0612 CitB and not ( O2[media] > 0 ) 0.25 b0615 CitB 0.25 b0616 CitB 0.25 b0617 CitB 0.25 b0619 CIT[media] > 0 0.25 b0620 CitA 0.25 b0621 ON 0.25 OLD: (Fnr OR ArcA) b0652 not ( GLC[media] > 0 ) 0.25 b0653 not ( GLC[media] > 0 ) or not ( ArcA and Fnr ) 0.25 b0654 not ( GLC[media] > 0 ) 0.25 b0655 not ( GLC[media] > 0 ) 0.25 b0676 not ( NAG[media] > 0 or NAGA[c] > 0 ) 0.25 b0677 not ( NagC ) 0.25 b0678 not ( NagC ) or GLCA[media] > 0 0.25 b0679 not ( NagC ) 0.25 b0683 FE2[media] > 0 or not ( Fnr or ArcA ) 0.25 b0694 KdpD 0.25 b0695 not ( K[media] > 1 ) 0.25 OR high osmolarity b0696 KdpE 0.25 b0697 KdpE 0.25 b0698 KdpE 0.25 b0721 not ( ArcA and Fnr ) and ( Crp or Fis ) 0.25 b0722 not ( ArcA and Fnr ) and ( Crp or Fis ) 0.25 b0723 not ( ArcA and Fnr ) and ( Crp or Fis ) 0.25 b0724 not ( ArcA or Fnr ) or Crp or Fis 0.25 b0733 not ( O2[media] > 0 ) 0.25 CHANGED b0734 not ( O2[media] > 0 ) 0.25 CHANGED b0754 not ( (PHE[media] > 0 or TRP[media] > 0 ) and TyrR ) 0.25 b0757 not ( GLC[media] > 0 ) and not ( GalR or GalS ) or not ( Rob ) 0.25 b0758 not ( GLC[media] > 0 ) and not ( GalR or GalS ) or not ( Rob ) 0.25 b0759 not ( GLC[media] > 0 ) and not ( GalR or GalS ) or not ( Rob ) 0.25 b0774 not ( BirA ) 0.25 b0775 not ( BirA ) 0.25 b0776 not ( BirA ) and O2[media] > 0 0.25 CHANGED b0778 not ( BirA ) and O2[media] > 0 0.25 CHANGED b0840 ON 0.25 b0871 not ( Growth > 0 ) and RpoS 0.25 b0889 not ( LEU[media] > 0 ) 0.25 "AND NOT ""rich medium"" but how to define?, " b0894 Fnr and not ( NarL ) 0.25 b0895 Fnr and not ( NarL ) 0.25 b0896 not ( NarL ) 0.25 OLD: (Fnr AND NOT NarL) b0902 not ( O2[media] > 0 ) and ( Crp or not ( NarL ) ) 0.25 b0903 not ( O2[media] > 0 ) and ( Crp or not ( NarL ) ) 0.25 b0904 not ( O2[media] > 0 ) and ( Crp or not ( NarL ) ) 0.25 b0907 Lrp or not ( Crp ) 0.25 b0931 not ( NadR ) 0.25 b0954 not ( Stringent[stim] ) or CpxR or RpoE or FadR2 0.25 b0972 ( ArcA or Fnr ) and ( AppY ) 0.25 b0973 ( ArcA or Fnr ) and ( AppY ) 0.25 b0974 not ( O2[media] > 0 ) 0.25 b0993 TMAO[media] > 0 or not ( O2[media] > 0 ) 0.25 CHANGED b0995 ON 0.25 b0996 TorR or not ( NarL ) 0.25 b0997 TorR or not ( NarL ) 0.25 b1014 PRO[media] > 0 or Crp or Nac 0.25 b1015 PRO[media] > 0 or Crp or Nac 0.25 b1091 not ( Stringent[stim] ) 0.25 b1092 not ( Stringent[stim] ) 0.25 b1093 not ( Stringent[stim] ) or CpxR or RpoE or FadR2 0.25 b1095 not ( Stringent[stim] ) or CpxR or RpoE or FadR2 0.25 b1101 not ( Mlc ) or not ( Cra ) 0.25 b1109 not ( Fnr ) 0.25 b1131 not ( PurR ) 0.25 b1187 GLC[media] > 0 or not ( AC[media] > 0 ) 0.25 b1189 ALA[media] > 0 and not ( Crp ) 0.25 b1197 RpoS 0.25 b1207 not ( PurR ) 0.25 "Purine repressor, add later" b1221 not ( Fnr ) and not ( ArcA ) 0.25 CHANGED b1223 Fnr or NarL 0.25 b1224 Fnr and NarL 0.25 b1225 Fnr and NarL 0.25 b1226 Fnr and NarL 0.25 b1227 Fnr and NarL 0.25 b1241 not ( O2[media] > 0 ) and not ( O2[media] > 0 and Cra ) and ( Fis or not ( NarL ) or RpoS ) 0.25 CHANGED b1260 not ( TrpR ) 0.25 b1262 not ( TrpR ) 0.25 b1263 not ( TrpR ) 0.25 b1264 not ( TrpR ) 0.25 b1275 not ( CYS[media] > 0 ) 0.25 "or Cystine or sulfide, but when to add?, " b1288 not ( Stringent[stim] ) or CpxR or RpoE or FadR2 0.25 b1323 ( TRP[media] > 0 or TYR[media] > 0 or PHE[media] > 0 ) or not ( O2[media] > 0 ) 0.25 b1334 ON 0.25 b1384 Crp 0.25 b1385 FeaR 0.25 b1386 FeaB 0.25 b1474 NarL 0.25 OLD: (Fnr OR NarL) b1475 Fnr or NarL 0.25 b1476 NarL 0.25 OLD: (Fnr OR NarL) b1493 not ( Growth > 0 ) or pH[stim] < 4 0.25 b1519 not ( Growth > 0 ) 0.25 b1521 not ( ExuR ) 0.25 b1524 not ( GLC[media] > 0 or ( NH3[media] > 0 and not ( Crp ) ) ) 0.25 b1531 not ( ArcA or not ( Fnr ) ) or OxyR or Salicylate[stim] 0.25 b1594 not ( GLC[media] > 0 ) 0.25 b1611 MarA or Rob or SoxS and not ( ArcA ) 0.25 b1612 not ( ArcA or Fnr ) 0.25 b1620 not ( MLT[media] > 0 ) 0.25 b1621 ( MalT and Crp ) or MalT 0.25 b1622 not ( MalI ) 0.25 b1623 AD[media] > 0 or HYXN[media] > 0 0.25 b1646 not ( Growth > 0 ) and not ( Fnr ) 0.25 b1658 HYXN[media] > 0 or GN[media] > 0 0.25 b1676 not ( Cra ) or not ( O2[media] > 0 ) 0.25 b1702 Cra and O2[media] > 0 0.25 CHANGED b1704 on 0.25 not ( TrpR ) *EWB regulation removed to allow growth on rich mdeia (6 fold acording to coli bible) b1732 not ( Growth > 0 ) 0.25 b1744 ( not ( Growth > 0 ) and RpoS ) or ( NRI_hi and RpoN ) 0.25 new rule JLR 8-21-03 b1745 ( not ( Growth > 0 ) and RpoS ) or ( NRI_hi and RpoN ) 0.25 new rule JLR 8-21-03 b1746 ( not ( Growth > 0 ) and RpoS ) or ( NRI_hi and RpoN ) 0.25 new rule JLR 8-21-03 b1747 ( not ( Growth > 0 ) and RpoS ) or ( NRI_hi and RpoN ) 0.25 new rule JLR 8-21-03 b1748 ( not ( Growth > 0 ) and RpoS ) or ( NRI_hi and RpoN ) 0.25 new rule JLR 8-21-03 b1805 not ( FadR2 ) 0.25 OLD: (NOT (FadR2) OR NOT (ArcA)) b1814 ( GLY[media] > 0 or LEU[media] > 0 or not ( O2[media] > 0 ) ) and ( not ( Lrp ) or ( Lrp and LEU[media] > 0 ) ) 0.25 b1817 CRP_noLAC or not ( Mlc ) 0.25 b1818 CRP_noLAC or not ( Mlc ) 0.25 b1819 CRP_noLAC or not ( Mlc ) 0.25 b1827 ArcA and Fnr and ( not ( KDG[media] > 0 ) and not ( UXUA[c] > 0 ) and not ( UXAA[c] > 0 ) ) 0.25 need to check b1849 not ( PurR ) 0.25 b1850 ON 0.25 *EWB see orggigional b1851 not ( GntR ) 0.25 b1896 RpoS 0.25 b1897 RpoS 0.25 b1898 AraC or ( AraC and Crp ) 0.25 b1899 AraC or ( AraC and Crp ) 0.25 b1900 AraC or ( AraC and Crp ) 0.25 b1901 AraC or ( AraC and Crp ) 0.25 b1907 not ( TyrR and TYR[media] > 0 ) 0.25 b1987 not ( SLF[media] > 0 or CYS[media] > 0 ) and CysB 0.25 b1988 NRI_low and RpoN 0.25 b1991 CBI[media] > 0 or Fnr 0.25 b1992 CBI[media] > 0 0.25 b1993 CBI[media] > 0 or Fnr 0.25 b2066 not ( THY[media] > 0 or CYTS[media] > 0 or URA[media] > 0 ) 0.25 b2087 not ( GLTL[media] > 0 ) 0.25 b2090 not ( GLTL[media] > 0 ) 0.25 b2091 not ( GatR ) 0.25 b2092 not ( GatR ) 0.25 b2093 not ( GatR ) 0.25 b2094 not ( GatR ) 0.25 b2095 not ( GatR ) 0.25 b2096 not ( GatR ) 0.25 b2097 PYR[media] > 0 or LAC[media] > 0 and not ( GLC[media] > 0 ) 0.25 b2143 Crp and not ( CytR ) 0.25 b2148 Crp and not ( GalS ) 0.25 b2149 Crp and not ( GalS ) 0.25 b2150 Crp and not ( GalS ) 0.25 b2151 not ( LCTS[media] > 0 ) or not ( GLAC[media] > 0 ) 0.25 b2167 not ( Cra ) 0.25 b2168 not ( Cra ) 0.25 b2169 not ( Cra ) 0.25 b2210 not ( ArcA ) 0.25 b2219 ACTOAC[media] > 0 0.25 b2220 AtoS 0.25 b2221 AtoC 0.25 b2222 AtoC 0.25 b2223 AtoC 0.25 b2224 AtoC 0.25 b2232 O2[media] > 0 and Crp 0.25 b2234 not ( Fnr ) 0.25 b2235 not ( Fnr ) 0.25 b2239 not ( GlpR or Fnr ) and Crp 0.25 b2240 not ( GlpR ) and Crp 0.25 b2241 CRP_noRIB and ( Fnr or ArcA ) and not ( GlpR ) 0.25 b2242 CRP_noRIB and ( Fnr or ArcA ) and not ( GlpR ) 0.25 b2243 CRP_noRIB and ( Fnr or ArcA ) and not ( GlpR ) 0.25 b2306 not ( LYS[media] > 0 ) 0.25 b2307 not ( LYS[media] > 0 ) 0.25 b2308 not ( LYS[media] > 0 ) and not ( ArcA and Fnr ) 0.25 b2309 not ( ArcA or not ( Fnr ) ) or OxyR and not ( LYS[media] > 0 ) 0.25 b2310 not ( LYS[media] > 0 ) 0.25 b2311 not ( PurR ) 0.25 b2312 not ( PurR ) 0.25 b2344 not ( Crp or FadR or OmpR ) or not ( ArcA ) 0.25 CHANGED b2364 DSER[media] > 0 0.25 b2366 ( Crp and DsdC ) or DsdC 0.25 b2393 Crp or not ( CytR ) 0.25 b2405 XTSN[media] > 0 0.25 b2406 XapR 0.25 b2407 XapR 0.25 b2413 CysB 0.25 b2414 CysB 0.25 b2415 ON 0.25 b2416 ON 0.25 b2417 ON 0.25 b2421 CysB 0.25 b2422 CysB 0.25 b2424 CysB 0.25 b2479 not ( GLY[media] > 0 ) 0.25 b2492 ArcA or Fnr and ( Crp or not ( NarL ) ) 0.25 b2499 not ( PurR ) 0.25 b2500 not ( PurR ) 0.25 b2507 not ( PurR and Crp ) 0.25 b2508 not ( PurR and Crp ) 0.25 b2537 PPPNT[media] > 0 0.25 b2538 HcaR and not ( LBMedia[stim] ) 0.25 b2539 HcaR and not ( LBMedia[stim] ) 0.25 b2540 HcaR and not ( LBMedia[stim] ) 0.25 b2541 HcaR and not ( LBMedia[stim] ) 0.25 b2542 HcaR and not ( LBMedia[stim] ) 0.25 b2551 not ( GLY[media] > 0 ) or MetR or not ( PurR ) 0.25 b2553 Lrp 0.25 b2557 not ( PurR ) 0.25 b2564 RpoE 0.25 b2573 not ( OxyR ) 0.25 b2574 not ( NadR ) 0.25 b2599 not ( PHE[media] > 0 ) 0.25 b2600 not ( (PHE[media] > 10 or TYR[media] > 0 ) and TyrR ) 0.25 b2601 not ( (PHE[media] > 10 or TYR[media] > 0 ) and TyrR ) 0.25 b2702 not ( GutR ) and CRP_noGL 0.25 b2703 not ( GutR ) and CRP_noGL 0.25 b2704 not ( GutR ) and CRP_noGL 0.25 b2705 GutM and not ( GutR ) and CRP_noGL 0.25 b2706 ON 0.25 b2707 Fnr and not ( GLT[media] > 0 ) 0.25 b2719 FhlA and RpoN and not ( O2[media] > 0 ) 0.25 b2720 FhlA and RpoN and not ( O2[media] > 0 ) 0.25 b2721 FhlA and RpoN and not ( O2[media] > 0 ) 0.25 b2722 FhlA and RpoN and not ( O2[media] > 0 ) 0.25 b2723 FhlA and RpoN or not ( O2[media] > 0 ) 0.25 Tentative b2724 FhlA and RpoN and not ( O2[media] > 0 ) 0.25 b2731 not ( NO3[media] > 1 ) and not ( NO2[media] > 1 ) and not ( TMAO[media] > 1 ) and not ( DMSO[media] > 1 ) and For[media] > 1 0.25 b2741 not ( Growth > 0 ) 0.25 b2750 CysB 0.25 b2751 CysB 0.25 b2752 CysB 0.25 b2762 CysB 0.25 b2763 CysB 0.25 b2764 CysB 0.25 b2787 SdaR 0.25 b3126 SdaR 0.25 b2796 Crp or not ( Lrp and LEU[media] > 0 and Crp ) 0.25 b2797 ON 0.25 (Crp) plays a role but is too constraining in this case b2799 ( ( ( FucR or RMN[media] > 0 ) and not ( O2[media] > 0 ) ) and Crp ) or ( (FucR or RMN[media] > 0 ) and not ( O2[media] > 0 ) ) 0.25 b2800 ( FucR and Crp ) or FucR 0.25 b2801 ( FucR and Crp ) or FucR 0.25 b2802 ( FucR and Crp ) or FucR 0.25 b2803 ( FucR and Crp ) or FucR 0.25 b2805 FUC[media] > 0 0.25 "OR (FUC6Pxt > 0) removed FUC6Pxt JLR check with MC, " b2808 not ( GcvR ) 0.25 b2818 not ( ArgR ) 0.25 b2837 not ( LCTS[media] > 0 ) or not ( GLAC[media] > 0 ) 0.25 b2838 LysR and not ( LYS[media] > 0 ) 0.25 have to add LysR here b2839 not ( LYS[media] > 0 ) 0.25 b2841 Crp 0.25 b2903 ( not ( GcvR ) and GcvA ) or Lrp or not ( PurR ) 0.25 b2904 not ( Fnr or ArcA ) and ( (not ( GcvR ) and GcvA ) or Lrp or not ( PurR ) ) 0.25 b2905 O2[media] > 0 and ( (not ( GcvR ) and GcvA ) or Lrp or not ( PurR ) ) 0.25 b2927 Crp 0.25 b2938 not ( PurR ) 0.25 b2943 not ( GalR ) or GalS and ( Crp or not ( Crp ) ) 0.25 b2957 Fnr and Crp 0.25 b2964 Crp or not ( CytR ) or not ( DeoR ) 0.25 b2965 not ( Crp ) 0.25 b2975 not ( ArcA ) and GlcC 0.25 b2976 not ( ArcA ) and GlcC 0.25 b2980 AC[media] > 0 or GLCLT[media] > 0 0.25 b2987 not ( PhoB ) 0.25 b2994 FhlA and RpoN and not ( O2[media] > 0 ) 0.25 b2997 FhlA and RpoN and not ( O2[media] > 0 ) 0.25 b3008 not ( MetJ ) 0.25 b3061 not ( O2[media] > 0 ) and TART[media] > 0 0.25 b3062 not ( O2[media] > 0 ) and TART[media] > 0 0.25 b3091 not ( ExuR ) 0.25 b3092 not ( ExuR ) 0.25 b3093 not ( ExuR ) 0.25 b3094 not ( UXAC1R[c] > 0 ) and not ( UXAC2R[c] > 0 ) and not ( UXUBR[c] > 0 ) and not ( UXABR[c] > 0 ) and not ( UXAC1R[c] < 0 ) and not ( UXAC2R[c] < 0 ) and not ( UXUBR[c] < 0 ) and not ( UXABR[c] < 0 ) 0.25 "need to check also, " b3111 Crp 0.25 OLD: OR NOT(O2xt>0) b3112 Crp or not ( O2[media] > 0 ) 0.25 b3114 Crp or Fnr or LysR or TdcA or not ( TdcR ) 0.25 b3115 Crp or Fnr or LysR or TdcA or not ( TdcR ) 0.25 b3116 Crp or Fnr or LysR or TdcA or not ( TdcR ) 0.25 b3117 Crp or Fnr or LysR or TdcA or not ( TdcR ) 0.25 b3118 THR[media] > 0 and SER[media] > 0 and VAL[media] > 0 and ILE[media] > 0 and not ( O2[media] > 0 ) 0.25 b3119 THR[media] > 0 and SER[media] > 0 and VAL[media] > 0 and ILE[media] > 0 and not ( O2[media] > 0 ) 0.25 b3124 SdaR 0.25 b3125 SdaR 0.25 b3128 SdaR 0.25 b3161 not ( TrpR ) or ( TyrR and ( PHE[media] > 0 or TYR[media] > 0 ) ) 0.25 b3202 ON 0.25 b3212 ( Lrp and not ( LEU[media] > 0 ) ) or not ( NRI_hi and ( GLU[media] > 0 or ARG[media] > 0 or ASP[media] > 0 or HIS[media] > 0 or PRO[media] > 0 ) ) 0.25 b3213 ( Lrp and not ( LEU[media] > 0 ) ) or not ( NRI_hi and ( GLU[media] > 0 or ARG[media] > 0 or ASP[media] > 0 or HIS[media] > 0 or PRO[media] > 0 ) ) 0.25 b3236 not ( ArcA ) 0.25 b3237 ARG[media] > 0 0.25 b3261 Growth > 0 0.25 b3357 CRP_noGLC 0.25 b3359 not ( ArgR ) 0.25 b3365 Fnr and NarL 0.25 b3366 Fnr and NarL 0.25 b3367 Fnr and NarL 0.25 b3368 AppY or SoxS or NarL 0.25 changed b3405 high_osmolarity[stim] 0.25 b3415 not ( GntR ) and CRP_GLCN 0.25 b3416 MalT 0.25 b3417 MalT 0.25 b3418 MLT[media] > 0 or MLTTR[media] > 0 or MLTTT[media] > 0 or MLTHX[media] > 0 or MLTPT[media] > 0 0.25 b3423 not ( GL[media] > 0 ) and O2[media] > 0 0.25 b3425 Crp 0.25 b3426 CRP_noMAL and not ( ArcA or GlpR ) 0.25 b3428 Crp 0.25 b3437 not ( GntR ) and CRP_GLCN 0.25 b3438 not ( GLCN[media] > 0 ) 0.25 b3450 Crp or PhoB 0.25 b3451 Crp or PhoB 0.25 b3452 Crp or PhoB 0.25 b3453 Crp or PhoB or not ( Fnr or ArcA ) 0.25 b3454 not ( LEU[media] > 0 ) or Lrp 0.25 b3455 not ( LEU[media] > 0 ) or Lrp 0.25 b3456 not ( LEU[media] > 0 ) or Lrp 0.25 b3457 not ( LEU[media] > 0 ) or Lrp 0.25 b3458 not ( LEU[media] > 0 ) or Lrp 0.25 b3460 not ( LEU[media] > 0 ) or Lrp 0.25 b3500 OxyR and RpoS 0.25 b3517 not ( Growth > 0 and not ( Crp ) ) or pH[stim] < 4 0.25 b3519 RpoS 0.25 OR osmotic shock b3526 not ( KdgR ) 0.25 b3528 CRP_noMAN and not ( ArcA ) and DcuR and RpoN 0.25 b3564 ( XylR and Crp ) or XylR 0.25 b3565 ( XylR and Crp ) or XylR 0.25 b3566 ( XylR and Crp ) or XylR 0.25 b3567 ( XylR and Crp ) or XylR 0.25 b3568 ( XylR and Crp ) or XylR 0.25 b3569 XYL[media] > 0 0.25 "Probably also Catabolite Repression, " b3572 not ( ALA[media] > 0 or LEU[media] > 0 ) 0.25 b3574 not ( FUC[media] > 0 ) 0.25 AND NOT ascorbate b3575 not ( YiaJ ) and Crp 0.25 b3579 Crp or YiaJ 0.25 b3581 not ( YiaJ ) 0.25 b3583 not ( YiaJ ) 0.25 b3588 RpoS and Crp 0.25 b3599 not ( MtlR ) 0.25 b3600 not ( MtlR ) 0.25 b3601 not ( MNT[media] > 0 ) 0.25 b3603 not ( ArcA ) 0.25 b3605 LLAC[media] > 0 and O2[media] > 0 0.25 b3607 CysB 0.25 b3616 not ( Lrp ) and LEU[media] > 0 0.25 b3617 not ( Lrp ) and LEU[media] > 0 0.25 b3642 not ( URA[media] > 0 or GN[media] > 0 ) 0.25 b3653 ASP[media] > 0 0.25 b3666 Crp or UhpA 0.25 b3668 G6P[media] > 0 0.25 b3669 UhpB 0.25 b3670 not ( LEU[media] > 0 or VAL[media] > 0 ) and Crp 0.25 b3671 not ( LEU[media] > 0 or VAL[media] > 0 ) and Crp 0.25 b3691 GALNT[media] > 0 0.25 b3692 GALNT[media] > 0 0.25 b3693 GALNT[media] > 0 0.25 b3708 Crp and ( TRP[media] > 0 or CYS[media] > 0 ) 0.25 b3709 Crp and TRP[media] > 0 0.25 b3725 PhoB 0.25 b3726 PhoB 0.25 b3727 PhoB 0.25 b3728 PhoB 0.25 b3730 NagC 0.25 b3743 not ( ASN[media] > 0 ) and NRI_hi 0.25 "AsnC will have to be updated for NR-I effects, " b3744 not ( ASN[media] > 0 ) and AsnC 0.25 Keep in mind as a troublemaker b3748 CRP_noXYL and not ( RbsR ) 0.25 b3749 CRP_noXYL and not ( RbsR ) 0.25 b3750 CRP_noXYL and not ( RbsR ) 0.25 b3751 CRP_noXYL and not ( RbsR ) 0.25 b3752 CRP_noXYL and not ( RbsR ) 0.25 b3753 not ( RIB[media] > 0 ) 0.25 b3767 ( not ( LEU[media] > 0 or ILE[media] > 0 or VAL[media] > 0 ) and Lrp ) and not ( OxyR ) 0.25 CHANGED b3768 not ( LEU[media] > 0 or ILE[media] > 0 or VAL[media] > 0 ) and Lrp 0.25 b3769 ( not ( LEU[media] > 0 or ILE[media] > 0 or VAL[media] > 0 ) and Lrp ) and Fnr 0.25 b3773 not ( VAL[media] > 0 ) 0.25 b3774 IlvY 0.25 b3806 not ( Crp ) and Fnr 0.25 b3828 not ( MET[media] > 0 ) 0.25 b3829 not ( MetJ ) and MetR 0.25 b3831 not ( CytR ) or Crp 0.25 b3845 not ( FadR2 ) or not ( ArcA ) 0.25 b3846 not ( FadR2 ) or not ( ArcA ) 0.25 b3868 NH3[media] <=2 0.25 b3869 ON 0.25 b3870 Crp and RpoN 0.25 could make growth on glucose and GLN difficult b3892 NO3[media] > 0 0.25 OLD: ((O2xt > 0) OR ((NOT (O2xt > 0) AND (NO3xt > 0)))) b3893 not ( ArcA or SoxS ) or ( ArcA and NO3[media] > 0 ) 0.25 b3894 not ( ArcA or not ( Fnr ) ) or ( ArcA and Fnr and NO3[media] > 0 ) 0.25 b3902 RhaS or ( RhaS and Crp ) 0.25 b3903 RhaS or ( RhaS and Crp ) 0.25 b3904 RhaS or ( RhaS and Crp ) 0.25 b3905 RhaR 0.25 b3906 RMN[media] > 0 0.25 b3907 RhaS or ( RhaS and Crp ) 0.25 b3908 not ( ArcA or Fur ) or MarA or Rob or SoxS 0.25 b3909 not ( KdgR ) 0.25 b3912 Stress[stim] 0.25 b3917 CysB and O2[media] > 0 0.25 CHANGED b3926 CRP_noMAL and not ( GlpR ) 0.25 b3934 CYTD[media] > 0 0.25 b3938 MET[media] > 0 0.25 b3939 not ( MetJ ) 0.25 b3940 not ( MetJ ) 0.25 b3942 Growth > 0 and OxyR and RpoS 0.25 b3951 ArcA or Fnr 0.25 b3952 ON 0.25 OLD: (ArcA OR Fnr) b3958 not ( ArgR ) 0.25 b3959 not ( ArgR ) 0.25 b3960 not ( ArgR ) 0.25 b3961 ON 0.25 b3973 BT[media] > 0 0.25 b4005 not ( PurR ) 0.25 b4013 not ( MetJ ) or MetR 0.25 b4014 not ( IclR or not ( Cra ) ) or not ( ArcA ) 0.25 b4015 not ( IclR or not ( Cra ) ) or not ( ArcA ) 0.25 b4018 FadR 0.25 b4019 MetR 0.25 b4024 on 0.25 not ( LYS[media] > 0 ) "* EWB removed regulation to allow growth on rich media, according to E. coli bible, only 50% inhib at 0.2mM Lys" b4031 XylR 0.25 b4032 ( MalT and Crp ) or MalT 0.25 b4033 ( MalT and Crp ) or MalT 0.25 b4034 ( MalT and Crp ) or MalT 0.25 b4035 ( MalT and Crp ) or MalT 0.25 b4036 ( MalT and Crp ) or MalT 0.25 b4039 not ( Fnr ) and Crp 0.25 b4040 not ( Fnr ) and Crp 0.25 b1190 ( ALA[media] > 0 or DALA[media] > 0 ) and Crp 0.25 b4054 not ( (PHE[media] > 0 or TYR[media] > 0 ) and TyrR ) 0.25 PHExt represses to a weaker extent b4062 SoxR 0.25 b4063 H2O2[media] > 0 or Oxidative_Stress[stim] 0.25 b4069 RpoS or Fnr or ( not ( IclR ) and CRP_noSUCC ) 0.25 b4079 FhlA and RpoN and not ( O2[media] > 0 ) 0.25 b4089 not ( RIB[media] > 0 ) 0.25 b4090 not ( RpiR ) 0.25 b4111 not ( Crp ) and Fis and RpoS 0.25 b4116 pH[stim] < 7 and not ( O2[media] > 0 ) and not ( Rich_Medium[stim] ) 0.25 b4117 AdiY 0.25 b4118 MELI[media] > 0 or ( MELI[media] > 0 and Crp ) 0.25 b4119 MelR or ( MelR and Crp ) 0.25 b4120 MelR or ( MelR and Crp ) 0.25 b4122 Fnr or not ( Crp ) or DcuR or not ( NarL ) 0.25 b4123 CRP_noMAN and Fnr and DcuR and not ( NarL ) 0.25 b4124 DcuS 0.25 b4125 SUCC[media] > 1 or ASP[media] > 1 or FUM[media] > 1 or MAL[media] > 1 0.25 b4131 ArcA or CadC 0.25 b4132 ArcA or CadC 0.25 b4133 LYS[media] > 0 0.25 b4139 ( Crp and not ( Fnr ) ) or Fnr 0.25 b4151 not ( O2[media] > 0 ) and ( DcuR or not ( NarL ) ) 0.25 CHANGED b4152 not ( O2[media] > 0 ) and ( DcuR or not ( NarL ) ) 0.25 CHANGED b4153 not ( O2[media] > 0 ) and ( DcuR or not ( NarL ) ) 0.25 CHANGED b4154 not ( O2[media] > 0 ) and ( DcuR or not ( NarL ) ) 0.25 CHANGED b4177 not ( PurR ) or RpoE 0.25 #NAME? b4238 not ( O2[media] > 0 ) 0.25 b4239 ( not ( TreR ) and Crp ) or not ( TreR ) 0.25 b4240 ( not ( TreR ) and Crp ) or not ( TreR ) 0.25 b4241 not ( TRE[media] > 0 ) 0.25 b4244 not ( URA[media] > 0 or GN[media] > 0 ) 0.25 b4245 not ( URA[media] > 0 or GN[media] > 0 ) 0.25 b4254 not ( ArgR ) 0.25 b4264 IDN[media] > 0 or 5KG[media] > 0 0.25 b4265 IdnR 0.25 b4266 IdnR 0.25 b4267 IdnR 0.25 b4321 Crp and not ( GLCN[media] > 0 ) 0.25 b4322 not ( ExuR and not ( UxuR ) ) or O2[media] > 0 0.25 CHANGED b4323 not ( ExuR ) and not ( UxuR ) 0.25 b4324 not ( UXUBR[c] > 0 ) and not ( UXAC1R[c] > 0 ) and not ( UXUBR[c] < 0 ) and not ( UXAC1R[c] < 0 ) 0.25 "need to check, " b4381 not ( DeoR ) or ( not ( DeoR ) and Crp and not ( CytR ) ) 0.25 b4382 not ( DeoR or CytR ) and Crp 0.25 b4383 not ( DeoR ) or ( not ( DeoR ) and Crp and not ( CytR ) ) or ( INS[media] > 0 or GN[media] > 0 ) 0.25 b4384 not ( DeoR ) or ( not ( DeoR ) and not ( CytR ) ) or INS[media] > 0 or GN[media] > 0 0.25 b4390 high_NAD[stim] 0.25 b4393 TRP[media] > 0 0.25 b4396 dipyridyl[stim] 0.25 b4401 Fnr and not ( OxyR ) 0.25 b0068 O2[media] > 0 0.25 b0133 ON 0.25 b0401 not ( O2[media] > 0 ) 0.25 b0864 not ( O2[media] > 0 ) 0.25 b0963 ON 0.25 b1210 ON 0.25 b1656 not ( O2[media] > 0 ) 0.25 b1779 not ( O2[media] > 0 ) 0.25 b2021 ON 0.25 b2040 O2[media] > 0 0.25 b2463 O2[media] > 0 0.25 b2530 O2[media] > 0 0.25 b2676 O2[media] > 0 0.25 b2747 O2[media] > 0 0.25 b2779 ON 0.25 b2925 not ( O2[media] > 0 ) 0.25 b3041 ON 0.25 b3089 not ( O2[media] > 0 ) 0.25 b3612 not ( O2[media] > 0 ) 0.25 b3771 ON 0.25 b3805 not ( O2[media] > 0 ) 0.25 b3916 not ( O2[media] > 0 ) 0.25 b3919 ON 0.25 b3956 ON 0.25 b3990 O2[media] > 0 0.25 b4232 O2[media] > 0 0.25 b0720 ON 0.25 b0726 not ( ArcA ) 0.25 b0727 not ( ArcA ) 0.25 b0729 ON 0.25 b1136 ON 0.25 b1415 ON 0.25 b2587 not ( ArcA ) 0.25 b3962 not ( ArcA ) 0.25 b2297 ON 0.25 b0207 ON 0.25 b0828 ON 0.25 b0888 ON 0.25 b1033 not ( Fnr or ArcA ) 0.25 b1297 ON 0.25 b2296 Fnr and ArcA 0.25 b2677 not ( Fnr or ArcA ) 0.25 b3770 ON 0.25 b3993 not ( Fnr or ArcA ) 0.25 b3994 not ( Fnr or ArcA ) 0.25 b4160 ON 0.25 b0755 not ( ArcA and Fnr ) 0.25 b0854 not ( ArcA and Fnr ) 0.25 b2129 not ( ArcA and Fnr ) 0.25 b2153 ON 0.25 b0066 ON 0.25 b0067 ON 0.25 b0860 ON 0.25 b0861 ON 0.25 b0862 ON 0.25 b0423 ON 0.25 b3991 ON 0.25 b3992 ON 0.25 b4407 ON 0.25 b2675 ON 0.25 b0728 ON 0.25 b2678 ON 0.25 b2679 ON 0.25 b2128 ON 0.25 b2130 ON 0.25 b2131 ON 0.25 b0855 ON 0.25 b0856 ON 0.25 b0857 ON 0.25 b1261 not ( TrpR ) 0.25 b1276 ON 0.25 Tentative b3957 not ( ArgR ) 0.25 b0945 not ( CYTS[media] > 0 ) or GN[media] > 0 or not ( PurR ) 0.25 b1062 not ( CYTS[media] > 0 ) or GN[media] > 0 or not ( PurR ) 0.25 b2323 not ( Stringent[stim] ) or CpxR or RpoE or FadR2 0.25 CHANGED b2423 CysB 0.25 b2476 not ( PurR ) 0.25 b2926 ON 0.25 b2276 ON 0.25 b2277 ON 0.25 b2278 ON 0.25 b2279 ON 0.25 b2280 ON 0.25 b2281 ON 0.25 b2282 ON 0.25 b2283 ON 0.25 b2284 ON 0.25 b2285 ON 0.25 b2286 ON 0.25 b2287 ON 0.25 b2288 ON 0.25 b1613 ON 0.25 b0242 ON 0.25 Tentative b1761 not ( Nac or GLU[media] > 0 ) 0.25 CHANGED b2425 CysB 0.25 b0886 CysB 0.25 b0887 CysB 0.25