TABLE 2.

Oligonucleotides used in this study

Designation	Sequencea
Red-mediated deletions
PhoP-Del-For	5′-AACGCTAGACTGTTCTTATTGTTAACACAAGGGAGAAGAGGTGTAGGCTGGAGCTGCTTC-3′
PhoP-Del-Rev	5′-GCGCAATTCAAAAAGATATCCTTGTCCGCGTACGGTGGTACATATGAATATCCTCCTTAG-3′
OmpR-Del-For	5′-TACAATTTGTTGCGAACCTTTGGGAGTACAGACAATGCAAGTGTAGGCTGGAGCTGCTTC-3′
EnvZ-Del-Rev2	5′-GAGAAGAAAGGGAGGGTAATACCTCCCTTTCTTATGCCTCCATATGAATATCCTCCTTAG-3′
SlyA-Del-For2	5′-AATCAGCATAATAACTTAGCAAGCTAATTATAAGGAGATGGTGTAGGCTGGAGCTGCTTC-3′
SlyA-Del-Rev2	5′-TGTGGTCACATGGCCACACGTATGCCCCTGCACCTCAATCCATATGAATATCCTCCTTAG-3′
luc reporter fusions
SseA-Red-Rep-For	5′-TTAGCACGTTAATTATCTATCGTGTATATGGAGGGGAATGatggaagacgccaaaaacataa-3′
SseA-Red-Rep-Rev	5′-CCCCATAAGATGTTTCCTGAAGACATTATGCTTTACCTTTTcgtgtaggctggagctgcttc-3′
SsaB-Red-Luc-For	5′-AATTTGATAGAAACTCCCATTTATGTCTGAGGAGGGATTCatggaagacgccaaaaacataa-3′
SsaB-Red-Rep-Rev	5′-TAGTAAAATTAAGATTAAACGTTTATTTACTACCATTTTAcgtgtaggctggagctgcttc-3′
SsaG-Red-Luc-For	5′-CCAGTATCCTTACGATGTATTTATTTTAAGGAAAAGCATTatggaagacgccaaaaacataa-3′
SsaG-Red-Rep-Rev	5′-TTCCAGCAGCAACCGTCGAACATCGTCGCTAATAACTTCAcgtgtaggctggagctgcttc-3′
SseG-Red-Luc-For	5′-CATTAATGGACAGTTCTGATCATACATCTCGGGGAGAACCatggaagacgccaaaaacataa-3′
SseG-Red-Rep-Rev	5′-AGAAAGCAATGAACATCCGGTATATACCTGAAAACGATTAcgtgtaggctggagctgcttc-3′
SseI-Red-Luc-For	5′-CGGACAGATACTATATGTAAATTTATAAAGGTTTTTTGTTatggaagacgccaaaaacataa-3′
SseI-Red-Rep-Rev	5′-ATTGACAGGGTTCTGACAGACGTCCTCCACGGTGCGCTTAcgtgtaggctggagctgcttc-3′
SseL-Red-FLuc-For	5′-CATATTCGCTACTTTCACTTACCAGGAAACAGAGCAAAatggaagacgccaaaaacataa-3′
SseL-Red-Rep-Rev	5′-CATTTCAGGATAAGAGCCTAATGGGATAGGCTCTAAGTACcgtgtaggctggagctgcttc-3′
SifA-Red-Luc-For	5′-ATTATGTAGTCATTTTTACTCCAGTATAAGTGAGATTAATatggaagacgccaaaaacataa-3′
SifA-Red-Luc-Rev	5′-ACCCTGAACGTGACGTCTGAGAAAGCGTCGTCTGATTTTAgtgtaggctggagctgcttc-3′
SifB-Red-Luc-For	5′-CCAGTAATGAAGTATCATATAATCACTTGTGGTCTACATTatggaagacgccaaaaacataa-3′
SifB-Red-Rep-Rev	5′-GCCAGGGGATTGTAAATCCATACTATTTATGGTGTGATCAcgtgtaggctggagctgcttc-3′
SseK1-Red-Luc-For	5′-TAAAATATGTAATGAAGTAAGTATGGAGCATTTAATTGTTatggaagacgccaaaaacataa-3′
SseK1-Red-Rep-Rev	5′-TTTTATGTATTCAATAGCATGATTATTGCCATTTCCGCTAcgtgtaggctggagctgcttc-3′
SseK2-Red-Luc-For	5′-AAATTAAGGTTAAAAACTGATAATTTAAGCGTGTAAAAATatggaagacgccaaaaacataa-3′
SseK2-Red-Rep-Rev	5′-GACGGTGGGAAGGGTGAGTAAAACAAGGCTATCATGATTAcgtgtaggctggagctgcttc-3′
SspH1-Red-Luc-For	5′-TTAATCTCTTTTCATTGTGCTGTAAATTAGGCAGTGGAATatggaagacgccaaaaacataa-3′
SspH1-Red-Rep-Rev	5′-ACCGCACCACATTCGCCTGGTGCGGTGAATATCGTGCTCAcgtgtaggctggagctgcttc-3′
SspH2-Red-Luc-For	5′-CGGACAGATACTATATGTAAATTTATAAAGGTTTTTTGTTatggaagacgccaaaaacataa-3′
SspH2-Red-Rep-Rev	5′-ATATCTTTGTCGCACCGCACCTCATTCACCTGGTGCATCAcgtgtaggctggagctgcttc-3′
PipB-Red-Luc-For	5′-CCTATAAGGAGTCGGCTCACTTCCATAAGAAGGAATCAAAatggaagacgccaaaaacataa-3′
PipB-Red-Rep-Rev	5′-CTGTTTGAATACTTCTTGTTTATAAAATCCCTTTATCTCGAcgtgtaggctggagctgcttc-3′
PipB2-Red-Luc-For2	5′-TTTTATCATGCACTGTGTTGCTGTCTCTGGGAGAAAATATatggaagacgccaaaaacataa-3′
PipB2-Red-Rep-Rev	5′-TTTCACTATAAAATTCGTTAAAGAGTGTTTGTGTGCTTGTcgtgtaggctggagctgcttc-3′
SlrP-Luc-For	5′-TCTGTTACTTTAGGTTACGTTCAGATCAGGTAGGGAAAATatggaagacgccaaaaacataa-3′
SlrP-Rep-Rev	5′-AACAGGCTCTCTCCCTCTTCTGATAAACTGCGTTCAGCTAcgtgtaggctggagctgcttc-3′
GogB-Red-Luc-For	5′-TTGCCTGAATGAAAATAAATGTAATAATGATAGCTTGGTAatggaagacgccaaaaacataa-3′
GogB-Red-Rep-Rev2	5′-CTATATATAAATATATTAATTGCATATTTTTTTAAAGTCAcgtgtaggctggagctgcttc-3′
SteC-Red-Luc-For	5′-GTGGTTACAGTAGTTACAAATCAGGTTTTTATATGTTTGCatggaagacgccaaaaacataa-3′
SteC-Red-Rep-Rev	5′-GCCCCCGGCGATTCGCAGAAAAGAACGGAACTAAATGCTAcgtgtaggctggagctgcttc-3′

^aLowercase letters indicate sequences complementary to the template plasmid.