TABLE 1.

Oligonucleotides used in this study

Name	Sequence (5′ to 3′)a	Restriction recognition site	Strand	Used to map transcription start upstream of:	Nucleotide positionb
gyrN	CCAATAACCACCATCCAAG		−	orf698	751122–751104
flaB	GCATGAGAAGTTAAAGCGGC		+	flaB	124446–124465
flgE	GACACCAGACCATAAAGACC		+	flgE	922547–922566
flgE2	GGATTAATGGGAGATGGCATG		−	orf906	956504–956484
flgB	AAGACCGATAATCCAACGCC		+	flgB	1641322–1641341
flgK	GATGTCTCTTATATCGCGCTCGG		+	orf1120	1186790–1186812
flaA	CGCATTGATATTTGTATTGACCTG		+	flaA	637268–637291
cagN	GTCAATGGTTTCGTTAGTC		−	cagA	579941–579923
ureA	CATAGTGGAGCATCAAC		+	ureA	77911–77927
ntrY	GAATGAAAAGAAACGCATCACTC		−	orf702	755012–754990
gyrA	CTGAATTATCTTGCATGTGTC		−	gyrA	752527–752507
ntrN	ATCATCTTCTACAATGGCG		−	flgR	755491–755473
ntr1	aatcgtgaattcTAGAGTGATGGGCGAAG	EcoRI	+		755102–755130
ntr2	aaaaaaggatccAGGCTTTTACGCATG	BamHI	−		755523–755497
ntr8	tgtccgggatccCAGAGCATCTATTAGAAAAGCGAG	BamHI	+		756042–756076
ntr9	tatgcactgcagCCCAAATGATACGCATCGCACAC	PstI	−		756437–756403
flgE3	attataggatccGCTATTCAAAGCGTTTGCGTTGG	BamHI	−		956559–956525
flgE4	attattgaattcTGTTCTCATTAAGCGCGAATAACG	EcoRI	+		956298–956333
flgE5	GCGATTTGGTGGGCTTggatccATTGACACCAGAC	BamHI	+		922521–922556
flgE6	CTAAAGCGAGTTgaattcTTAAGCTTGAGCGATAAC	EcoRI	−		922784–922749
flgB1	AAAGGGggatccACATTAGCGATGTTAGAAG	BamHI	+		1641273–1641303
flgB2	AATGGCTCTgaattcGCTTATCGCTCAAGC	EcoRI	−		1641514–1641485
flgK1	attattgaatcAAAAGCTTGAATCGCTAGCTG	EcoRI	+		1186713–1186745
flgK2	attattggatccCAAGCGGGGAATGCGATGAGC	BamHI	−		1187086–1187054
fla1	attataggatccGCATGAGAAGTTAAAGCGGCG	BamHI	+		124434–122466
fla2	attatagaattcCCTAACATGCCCTTTAGAGGC	EcoRI	−		124771–124739
gyr1	tatttaggatccCCAATAACCACCATCCAAGACATG	BamHI	−		751134–751099
gyr2	attattgaattccGATTGGCTAGGCATACAGCCCCCAG	EcoRI	+		750711–750746

^aCapital letters, H. pylori-derived sequences; lowercase letters, sequences added for cloning purposes; underlined letters, restriction recognition sites. 

^bAccording to the genome sequence published by Tomb et al. (33).