Table 9.
Consensus/Patser prediction in regions without binding sites reported in RegulonDB
| Regulatory protein and genes thought to be regulated by it | Above threshold | Site coordinates and score | Site sequence |
| ArcA (8) | |||
| aceB | + | i:-164;f:-144;sc:9.48 | TTCATATTGTTATCAACAAG |
| fadB | - | - | - |
| fumA | - | - | - |
| fumC | + | i:-74;f:-54;sc:10.82 | AATAATAAGTGAGCTAAAAG |
| glpA | - | i:-184;f:-164;sc:6.11 | AAGAAAACATTCATAAATTA |
| hyaA | - | - | - |
| lpdA | + | i:-228;f:-208;sc:8.43 | TAAAAATTGTTAACAATTTT |
| sucA | - | - | - |
| ArgR (13) | |||
| argD | - | i:-70;f:-50;sc:11.12 | TAGTGATTTTTTATGCATAT |
| CRP (6) | |||
| cirA | + | i:-51;f:-31;sc:6.39 | ATGTGAGCGATAACCCATTT |
| dsdA | - | - | - |
| ebgA | + | i:-91;f:-71;sc:7.53 | TCGTGATCCAGTTAAAGTAA |
| flhD | + | i:-269;f:-249;sc:10.86 | GTGTGATCTGCATCACGCAT |
| fucA | + | i:-399;f:-379;sc:10.18 | ATATGACGGCGGTCACACTT |
| fucP | + | i:-205;f:-185;sc:9.74 | AAGTGATGGTAGTCACATAA |
| glgC | - | i:-166;f:-146;sc:3.60 | TCGCAATTAACGCCACGCTT |
| gntK | + | i:-169;f:-149;sc:11.49 | ATTTGAAGTAGCTCACACTT |
| lpdA | - | i:-335;f:-315;sc:3.73 | TGGTGATGTAAGTAAAAGAG |
| melA | - | i:-228;f:-208;sc:3.79 | CTGCGAGTGGGAGCACGGTT |
| speC | - | i:-16;f:4;sc:5.55 | GTTTGACCCATATCTCATGG |
| srlA | + | i:-91;f:-71;sc:8.89 | TTGCGATCAAAATAACACTT |
| ubiG | - | i:-234;f:-214;sc:5.93 | CAATGACCGACATCGCATAA |
| CysB (4) | |||
| cysP | + | i:-237;f:-217;sc:7.04 | TTTATTTGTCATTTTGGCCC |
| CytR (1) | |||
| nupC | - | - | - |
| FNR (7) | |||
| aspA | - | i:-367;f:-347;sc:3.88 | CATGGGCAACCTGAATAAAG |
| cyoA | - | i:-182;f:-162;sc:4.31 | TTTGTTATAACGCCCTTTTG |
| icdA | - | i:-105;f:-85;sc:6.30 | AATCATTAACAAAAAATTGC |
| sdhC | - | i:-4;f:16;sc:3.89 | ATTCATGATAAGAAATGTGA |
| FruR (5) | |||
| aceB | + | i:-253;f:-233;sc:11.44 | GATCGTTAAGCGATTCAGCA |
| fruB | + | i:-38;f:-18;sc:13.85 | GAGGCTGAATCGTTTCAATT |
| ppsA | + | i:-105;f:-85;sc:6.29 | TTTGCTTGAACGATTCACCG |
| IHF (7) | |||
| caiT | + | i:-83;f:-63;sc:8.41 | AATAATAATTATATTAAATG |
| ecpD | + | i:-39;f:-19;sc:8.96 | ATTATTCCCTGTTTTAATTA |
| himA | - | - | - |
| himD | - | i:-136;f:-116;sc:6.43 | ATTCCGAAGTTTGTTGAGTT |
| hycA | - | i:-73;f:-53;sc:6.57 | TAATAACAATAAATTAAAAG |
| hypA | - | i:-155;f:-135;sc:6.75 | TTAATTTATTGTTATTAAAG |
| narK | - | i:-106;f:-86;sc:6.66 | AAATATCAATGATAGATAAA |
| ompR | - | i:-135;f:-115;sc:6.39 | TATACTTAAGCTGCTGTTTA |
| sucA | - | - | - |
| LexA (9) | |||
| umuD | + | i:-40;f:-20;sc:10.80 | CTACTGTATATAAAAACAGT |
| Lrp (8) | |||
| livK | + | i:-235;f:-215;sc:8.35 | TGCCGTTATTTTATGCTGAC |
| sdaA | - | i:-317;f:-297;sc:4.95 | ATCACCCTTTAGATATCTAC |
| serA | - | i:-79;f:-59;sc:6.62 | TGCCGCAATATTATTTTTTG |
| NarL (7) | |||
| adhE | - | i:-160;f:-140;sc:6.11 | ATAACTCTAATGTTTAAACT |
| caiF | - | i:-163;f:-143;sc:5.62 | CAAATAATAGCGTGTCATGG |
| torC | - | i:-20;f:0;sc:4.98 | ATAATTCTACAGGGGTTATT |
| PurR (11) | |||
| codB | + | i:-84;f:-64;sc:13.10 | CCACGAAAACGATTGCTTTT |
| prsA | + | i:-360;f:-340;sc:12.33 | GCAAGAAAACGTTTTCGCGA |
| speA | - | i:-136;f:-116;sc:7.05 | AAAAGAAACCGGTTGCGCAG |
Data and analysis as described in Table 8. sc, Score as obtained from Patser. The number of families used was the same for any method, but we only show families where the methods provided significant results.