Sequencing Inconsistencies

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			"	"	"

Abigail Manson McGuire
Genetics Department
Harvard Medical School/BCMP
200 Longwood Ave.
Boston, MA. 02115.
E-mail: amcguire@arep.med.harvard.edu
Telephone: (617) 432-4136