Table 1. High-confidence CRP binding sites on the ETEC H10407 chromosome identified by ChIP-seq.
| Peak Centrea | Binding Site(s)b | Gene(s)c | K-12 Homologuesd |
| 45284 | TGTGATTGGTATCACA | ETEC_0040 | caiT |
| 92014 | AGTGATGGATGTCACG | (ETEC_0078) | (cra) |
| 176905 | AGCGTTCCACGTCACA | (ETEC_0150) | (hemL) |
| 408885 | TGTGATCTCTCTCGCA | ETEC_0385/ETEC_0386 | yahN/yahO |
| 461874 | TGTGCGCAAGATCACA | ETEC_0434 | ddlA |
| 463095 | TTTGCGCGAGGTCACA | (ETEC_0436) | (phoA) |
| 468009 | AGGGATCTGCGTCACA | ETEC_0443 | aroM |
| 492973 | ATCGATTGCGTTCACG | ETEC_0464 | tsx |
| 540805 | TGTGATCTTTATCACA | ETEC_0511 | maa |
| 574230 | GATGACGACGATCACA | (ETEC_0538) | (ybaT) |
| 683187 | AGTGATCGAGTTAACA | ETEC_0628 | cstA |
| 697540 | AGTGATTTGCGTCACA | ETEC_0639 | rnk |
| 739223 | CGTTACCCTTGTCGCA | ETEC_0680 | rihA |
| 941002 | TGTGATGAGTATCACG | ETEC_0869 | ybiJ |
| 958866 | TGTGTACGAAATCACA | ETEC_0886/ETEC_0887 | ybiS/ybiT |
| 1128472 | n.d. | (ETEC_1030) | (yccS) |
| 1205350 | AGTGATGTAGATCACA | ETEC_1101 | ycgZ |
| TGAGATCGAGCACACA | |||
| 1263558 | TTTGACGGCTATCACG | ETEC_1166 | ptsG |
| 1274886 | TGTGATCTGGATCACA | ETEC_1176/ETEC_1177 | ycfQ/bhsA |
| 1301786 | GATGATCCGCATCACA | (ETEC_1206)/ETEC_1207 | ETEC-specific/ETEC-specific |
| 1348166 | ATTGAACAGGATCACA | (ETEC_1259)/ETEC_1260 | (rluE)/icd |
| 1376374 | GGTGAGCTGGCTCACA | ETEC_1292/ETEC_1293 | ycgB/dadA |
| 1388620 | AGTGAGCCAGTTAACA | (ETEC_1303) | (dhal) |
| 1541732 | CGTGAACCGGGTCACA | ETEC_1443/ETEC_1444 | ycjZ/mppA |
| 1567885 | GTTAAGTAAAATCACA | ETEC_1462/ETEC_1463 | paaZ/paaA |
| 1701402 | TGTGATGGATGTCACT | ETEC_1568 | ydeN |
| 1767726 | TGTGATTAACAGCACA | ETEC_1628 | mlc |
| 1777143 | TGTGATCTAGCGCCAA | ETEC_1637 | pntA |
| 1811426 | CGTGATCAAGATCACG | (ETEC_1668A) | (ETEC specific) |
| 1859265 | ATTGAGCGGGATCACA | (ETEC_1713) | (sufS) |
| 1887513 | AGTGATGCGCATCACG | ETEC_1737 | aroH |
| TGCGAGGTGTGTCACA | |||
| 2126754 | TGTGGCGTGCATCACA | n.a. | n.a. |
| 2201816 | GGTGACGCGCGTCACA | ETEC_2057 | yedP |
| 2210222 | CGTGATCTCGCGCACA | ETEC_2065/ETEC_2066 | yedR/ETEC-specific |
| 2458348 | TGTGATCTGAATCTCA | ETEC_2278 | cdd |
| TGCGATGCGTCGCGCA | |||
| 2492757 | ATTGATCGCCCTCACA | ETEC_2309 | yeiQ |
| 2555083 | CGTGACCAAAGTCTCA | (ETEC_2360) | (yfaQ) |
| 2729713 | TTTGAAGCTTGTCACA | ETEC_2510/ETEC_2511 | mntH/nupC |
| 2735124 | AGTTATTCATGTCACG | ETEC_2514 | yfeC |
| 2795423 | TGTGAGCCATGACACA | (ETEC_2572)/ETEC_2573 | (aegA)/narQ |
| 2810983 | CGTGATCAAGATCACA | ETEC_2586 | hyfA |
| 2887131 | TTTGATCTCGCTCACA | (ETEC_2666)/ETEC_2665 | (xseA)/guaB |
| 3012645 | TGTGATCCCCACAACA | (ETEC_2793) | (ung) |
| 3048307 | TTTGACGAGCATCACC | (ETEC_2822) | (emrB) |
| 3132920 | GGTGACCGGTTTCACA | ETEC_2905/ETEC_2906 | ascG /ascF |
| 3161660 | TGTGACCGTGGTCGCA | (ETEC_2933) | (nlpD) |
| 3184337 | CGTGATGCGTGTAACA | (ETEC_2956)/ETEC_2955 | (cysI)/cysH |
| 3196088 | TGTGATTACGATCACA | ETEC_2966/ETEC_2967 | ygcW/yqcE |
| 3223792 | AGTGATCTTGATCTCA | ETEC_2986 | sdaC |
| AGTTATGTATCTATCA | |||
| 3234980 | TGCGATCGTTATCACA | (ETEC_2994)/ETEC_2995 | (fucU)/fucR |
| 3265047 | TGTGACCTGGGTCACG | ETEC_3017 | rppH |
| 3324543 | TGTGGGCTACGTAACA | (ETEC_3075) | (ydhD) |
| 3361162 | n.d. | ETEC_3105 | serA |
| 3368992 | TTTGATGCACCGCACA | (ETEC_3113) | (ygfI) |
| 3382158 | TGTGATCTACAACACG | ETEC_3126 | cmtB |
| 3390811 | TGTGATTTGCTTCACA | ETEC_3133 | galP |
| 3408173 | TGTGATGTGGATAACA | ETEC_3154 | nupG |
| 3442697 | TGTGATGATTGTCGCA | ETEC_3186 | ETEC-specific |
| 3558573 | AGTGATTTGGCTCACA | ETEC_3291 | ygiS |
| 3580767 | AGTGACTTGCATCACA | (ETEC_3318) | (yqiH) |
| 3635301 | ATTGATCTAACTCACG | ETEC_3362 | uxaC |
| 3642302 | CTTGAAGTGGGTCACA | (ETEC_3372) | (yqjG) |
| 3665634 | TGTGATCAATGTCAAT | ETEC_3393/ETEC_3394 | garP/garD |
| TGTGCTTTAGCGCGCA | |||
| 3721308 | GGTGATTGATGTCACC | (ETEC_3446) | (greA) |
| 3785700 | CGTGGGTCGCATCACA | (ETEC_3510) | (mreC) |
| 3878729 | GGTGATTTTGATCACG | ETEC_3614/ETEC_3615 | ppiA /tsgA |
| 3908574 | GGTGATCGCGCTCACA | (ETEC_3645) | (hofM) |
| 3918861 | TGTGAGTGGAATCGCA | ETEC_3652/ETEC_3653 | yhgE/pck |
| 3986400 | CGTGATTTTATCCACA | ETEC_3707 | rpoH |
| 4105040 | AGTAAGGCAAGTCCCT | n.a. | n.a. |
| 4111116 | TGTGACGGGGCTAACA | (ETEC_3806) | (wecH) |
| 4153055 | TGTGATCTGAATCACA | ETEC_3840 | yibI |
| TGTGATCTACAGCATG | |||
| 4153191 | TGTGATTGATATCACA | ETEC_3841 | mtlA |
| TGTGATGAACGTCACG | |||
| 4158433 | n.d. | ETEC_3846 | lldP |
| 4196869 | TGCAATCGATATCACA | ETEC_3886 | dinD |
| 4251326 | CTTACTCCTGCTCACA | ETEC_3938 | ETEC specific |
| 4266125 | GGTGATGGCATCCGCG | (ETEC_3956) | (nepI) |
| 4290730 | GGTGAGCAAAACCACG | (ETEC_3979) | (yidR) |
| 4322430 | ATTGACCTGAGTCACA | (ETEC_4010) | (yieL) |
| 4340544 | CTTGACCACGGTCAGA | (ETEC_4025)/ETEC_4024 | (atpA)/atpG |
| 4344649 | TGTGATCTGAAGCACG | ETEC_4030 | atpI |
| 4373517 | TGTAATGCTGGTAACA | (ETEC_4051) | (ilvG) |
| 4402013 | CGTGCTGCATATCACG | (ETEC_4077) | (rffM) |
| 4412999 | CGTGATCAATTTAACA | ETEC_4085/ETEC_4085 | hemC /cyaA |
| 4438352 | GGTGATGAGTATCACG | ETEC_4107/ETEC_4108 | ysgA /udp |
| TGTGATTTGAATCACT | |||
| 4508745 | TGTGATATTTGTCACA | (ETEC_4165)/ETEC_4164 | (fdhD)/fdoG |
| 4517442 | CGTGATCGCTGTCCCA | (ETEC_4173) | (rhaA) |
| 4564670 | TGCGATCCGCCTCATA | ETEC_4216/ETEC_4217 | ptsA/frwC |
| 4668870 | TGTAACAGAGATCACA | ETEC_4289/ETEC_4290 | malE/malK |
| 4725047 | TGTGCGGATGATCACA | n.a. | n.a. |
| 4731402 | TGTGATCTTGCGCATA | (ETEC_4365) | (aphA) |
| 4761367 | CGTGATGGCTGTCACG | ETEC_4389 | fdhF |
| 4846352 | n.d. | ETEC_4464 | ETEC-specific |
| 4848117 | CGTGAGTTCTGTCACA | n.a. | n.a. |
| 4863253 | TTTGATCAACATCGCA | (ETEC_4478) | (ETEC-specific) |
| 4873926 | GGTGATCTATTTCACA | ETEC_4486/ETEC_4487 | aspA/fxsA |
| 4930149 | TGTGATGAACTTCAAA | ETEC_4545/ETEC_4546 | yjfY/rpsF |
| 4940903 | TGTGATCACTATCGCA | ETEC_4557/ETEC_4558 | ETEC-specific/ytfA |
| 4993073 | TGTGACTGGTATCTCG | (ETEC_4604) | (valS) |
| 5002854 | TGTAACCTTTGTCACA | ETEC_4610/tRNA-Leu | yjgB/tRNA-Leu |
| 5030724 | TGCGATGAATGTCACA | ETEC_4633/ETEC_4634 | gntP /uxuA |
| 5129400 | CGTACCGTCGGTCACA | (ETEC_4736) | (yjjI) |
| 5129944 | TGTGATGTATATCGAA | ETEC_4736/ETEC_4737 | yjjI/deoC |
a
Chomosome coordinate of the ChIP-seq peak in H10407. Underlined text indicates that the ChIP-seq peak maps to sequence that is not conserved in E. coli K-12.
b
CRP binding site sequence predicted by MEME. “n.d.” indicates that MEME did not detect a putative binding site.
c
Genes in parentheses indicate that the ChIP-seq peak is located within that gene. Downstream genes are only listed if the annotated gene start is ≤300 bp downstream of the CRP ChIP-seq peak. “n.a.” indicates that no genes starts are ≤300 bp from the CRP ChIP-seq peak.
d
E. coli K-12 homologues are listed for the ETEC genes in the previous column. Genes in parentheses indicate that the ChIP-seq peak is located within that gene. “n.a.” indicates that no genes starts are ≤300 bp from the CRP ChIP-seq peak. “ETEC-specific” indicates that there is no K-12 homologue. Underlined genes have been identified as CRP targets in a previous ChIP-chip study [15]. Bold genes are listed as CRP targets in the Ecocyc database.