TABLE 2.

Primers used in this study

Primer	Clone	Gene designationa	Fragment sizeb (bp)	Sequencec
Promoter fusions and EMSA
CD6.1-A1	CD-1	Zn-dependent alcohol dehydrogenase	244*	5′-GGCGTCGACGTTGGATCACTACCAGC-3′
CD6.1-A2				5′-GGCGGATCCGGGGAATTCAGTAGCAG-3′
CD6.2-A2	CD-2	secY	330*	5′-GGCGGATCCGCCATGAGTGGCAACTCC-3′
CD6.2-B1				5′-GGCGTCGACGCTAAAACCGTGGCTGG-3′
CD6.2-C1	CD-2	secY	526	5′-GGCGTCGACGCCATGAGTGGCAACTCC-3′
CD6.2-C2				5′-GGCGGATCCCCGCATCTCGGAATGCC-3′
CD6.3-A1	CD-3	Transcriptional regulator of ABC iron transport system	495	5′-GGCGTCGACTTCCTAGAAATAGCAGG-3′
CD6.3-A2				5′-GGCGGATCCCCTTCTTAGCGGGAGCC-3′
CD6.3-B1			243*	5′-GGCGTCGACCGCTATTGAAGAACTGTG-3′
CD6.4-A1	CD-4	recA	569	5′-GGCGTCGACGCAGATACTGTACTGCG-3′
CD6.4-A2				5′-GGCGGATCCGTTGGTTGCTGCGTCTTAC-3′
CD6.4-B1			342*	5′-GGCGTCGACCTGGTTTGATTTGTGCG-3′
CD7.4-A1	CD-7-4	ywjA	380*	5′-GGCGTCGACCGAACATATATGACCGACC-3′
CD7.4-A2				5′-GGCGGATCCGATCGCACAGTTGAGTCC-3′
CD7.20-A1	CD-20	piuB	150*	5′-GGCGTCGACCATAACGTTGAAATATAGAC-3′
CD7.20-A2				5′-GGCGGATCCCTGCTTCTCGGCGGACG-3′
CD7.40-A1	CD-40	chtA	211*	5′-GGCGTGGACGAGTTGTGGTCTAGGTGG-3′
CD7.40-A2				5′-GGCGGATCCCAAAGACGTAAGTGTTGC-3′
HtaA-1	CD-50	htaA	319*	5′-GGCGGATCCGCAGCAGCCATTAGTCC-3′
HtaA-2				5′-GGCGTCGACGGGGAGGCTGTGGGCAGG-3′
HtaC-1	CD-50	htaC	319	5′-GGCGGATCCGGGGAGGCTGTGGGCAGG-3′
HtaC-2				5′-GGCGTCGACGCAGCAGCCATTAGTCC-3′
FrgA-1	CD-frg	frgA	236*	5′-GGCGGATCCATGATTACAAGGAAAGTG-3′
FrgA-2				5′-GGCGTCGACCTTGAGCGTTAGTCGAGG-3′
FrgD-1	CD-frg	frgD	236	5′-GGCGTCGACATGATTACAAGGAAAGTG-3′
FrgD-2				5′-GGCGGATCCCTTGAGCGTTAGTCGAGG-3′
SidA-1	CD-sid	sidA	499*	5′-GGCGTCGACCGGGGCCGGTGGCGGCG-3′
SidA-2				5′-GGCGGATCCGGCGGTGAGAATTTCGG-3′
TprT-1	CD-sid	Transcriptional regulator	499	5′-GGCGGATCCCGGGGCCGGTGGCGGCG-3′
TprT-2				5′-GGCGTCGACGGCGGTGAGAATTTCGG-3′
Vector integration mutants
SidA-C1	CD-sid	C-terminal sidA mutant	711	5′-GGCGGATCCCGTCCACtACTGAGCAACGAT-3′
SidA-C2				5′-GGCGTCGACGGCGAATTCGCATaGTTCCAATTGCGTGCA-3′
SidA-2	CD-sid	N-terminal sidA mutant	819	5′-GGCGTCGACGGCGAATTCGCCATATAgGGCCCCGTCGACCC-3′
SidA-3				5′-GGCGGATCCGTCcTAAGTCATCTCGGCTAG-3′
SidB-1	CD-sid	sidB mutant	810	5′-GGCGTCGACGGCGAATTCGAATGCtGATTCCCAGGCATCC-3′
SidB-2				5′-GGCGGATCCCACCTaAGCATGTGCGTGCATCGA-3′
CdtP-2	CD-sid	cdtP mutant	630	5′-GGCGTCGACGGCGAATTCCGCTAgATCCACGGACGCTGGCCG-3′
CdtP-3				5′-GGCGGATCCGTCCTaACCCACGCGGTTGAACAC-3′

^aThe first gene in the operon is specified.

^bAsterisks indicate PCR product was used in EMSA.

^cBold letters identify restriction sites and lowercase letters identify base changes to insert in-frame stop codons.