To check for anomalous or incorrect sites, as well as sequencing inconsistencies, we verified that all of the input sites from E. coli were also found as outputs in the genome search. 39 high-scoring input sites, based on footprinting experiments done in E. coli, were not found in the E. coli K12 genome. These sequencing inconsistencies are listed below (these are either sequencing inconsistencies or inconsistencies within the literature):
DNA-binding gene downstream protein of site in question reference ----------- ------------------- --------- ada ada J Biol Chem 270: 8285-8289 (1995) araC araE JMB 170:1049 (83), JBC 267:24848 (92) (compilation) crp uxuAB Mol Gen Genet 202:112-119 (86) crp cea1 Mol Gen Genet 215:537 (89) cea2 " " " crp mtl Wang, MX, Church GM. Nature 360:606-10 (92) fis rrnBI Mol Microbiol 6:3257 (92) rrnBII " " " lexA uvrA Nuc Acids Res 16:5089-105 (88) lexA-1 " " " hipB hipB-04 J Bac 176:4081 lrp sfa1 Mol Microbiol 11:605,94 sfa2 " " " sfa3 " " " daa-1 " " " nagC manX-2 EMBOJ 14:3958-65 (95), JMB 217:661 ompR flhDC-1 J. Bacteriol 177:4696-4702, 95. flhDC-2 " " " rpoD uxuAB Nuc Acids Res 21(7):1507-1516 (93) frd " " " clca " " " groE " " " livJ " " " livK " " " mtl " " " pac " " " secE " " " dnaT " " " hsd " " " sucAB " " " hsd " " " uvrB-P1 " " " dnaT " " " rpsA-P1 " " " rpsA-P2 " " " metJ-P1 " " " orf83-P1 " " " hisB " " " rpoH-P1 " " "