Table S1: Location and directions of transposon insertions.

gene[a] / strain number[b] / 9 bp direct repeat[c] / last nucleotide transcribed
acrA / B15 / ATACCAAAG / 527
B40 / CACCAGGGC / 185
B52 / GCATTCGAC / 318
B133* / AACTGAACC / 146
B177 / CACCAGTGC / 185
acrB / B33 / GTTTAACGG / 820
B39 / ATGTTGACC / 2142
B50 / GTACGAGAG / 2681
B65 / GTGTAATGG / 3025
B141 / GTTGTTCGG / 536
B152 / ATCTCCGAC / 468
B155* / GGCCTTGGT / 2073
B168 / ACCCTGACC / 279
B171 / GCGCTGCAT / 2260
B176 / GGCTATGAC / 2574
B179 / GTACGGGGC / 1618[d]
B180 / GTACGGGGC / 1618d
B203 / GCCTACCGG / 2561
B209 / AGGTAGGCC / 2790
B222 / GGTTGCGGC / 647
arpB / B160 / AATCTCCTT / 13
cvpA / B193 / TTACTACAC / 137
dam / B23 / GCGTCGAAC / 747
B120 / GTACTGATG / 214
B127* / GGGCGGTAC / 328
damX / B34* / GTACTGAAC / 871
B165 / CCATTACAC / 1046
B183 / GACCTGAAC / 606
B230 / GCTGAGCAG / 1061
dcd / B167 / GATGAAGGC / 45
dnaQ / B119 / ACAGTAAAC / 475
B132* / CCATAACGC / 299
dsbB / B212 / GCGCTGATT / 180
envC / B5* / GGTTTGCAA / 58
B46 / GCCTTCACT / 1223
folA / B201 / GGTTTACGC / -43[e]
folK / B118 / TTCCTGATG / 421
B144* / GAGTTGGTG / 411
ftsE / B188* / GTCTACGAT / 294d
B190 / GTCTACGAT / 294d
ftsK / B13 / TCCTCAGGT / 1753
B24 / GTATTAAGC / 1840
B30 / AGGTTACCC / 1142
B61 / GTGCAGGAC / 3700
B64 / CTGTTGATG / 1051
B107 / CAGTATGTT / 2798
B115 / GATGATGAC / 3385
B117* / GGTCTGGAG / 2812[f]
B121 / GGTACTGGT / 4332
B140 / GGTCTGGAG / 2812f
B166 / ACTCTGGGC / 3625
B174 / ACCTGGTAC / -54d,[g]
B191 / ACCTGGTAC / -54d,g
B226 / GCCGTATTA / 1262
B229 / GGGTAAAGA / 2912
ftsX / B12 / GTTATATGG / 280f
B35* / GTTATATGG / 280f
B49 / GTTATATGG / 280f
htrA / B56 / ACCTGGAAC / 1138
lexA / B2 / GCCGACGCG / 83
B123* / GCGAAAGGG / 107
ompA / B16 / GTTGTTCTG / 774
polA / B215 / GTTACAGGC / 2606
purA / B158 / GCTTTCTAG / 544
purE / B219 / TTTCTGCTC / 133
purF / B195 / GCATTACGC / 295
B200* / TCGTAAGTC / 1037
purL / B216 / CCGCTGAAC / 391
recG / B47 / GATCTACTC / 111
B54 / CTCTTACAC / 117
B57 / GGAAGCGCA / 1505
B199* / GGCGTAAAG / 477
recN / B210 / GTCCGGCGT / 797
rep / B4* / ATTACGACC / 1038
B112 / GCCTATGTC / 1794
B138 / TCTCAAAAC / 443
B170 / CCCAGGTGG / 1591
B187 / GTGTAGGGC / 205
B196 / CCTGAAAGC / 530
B220 / GTGAAGAAG / 1642
rluD/ecfD / B218 / ATTGTAGCT / -73[h]
rpoZ / B6 / GTTCAGGAC / 25
ruvA / B59 / GACTCAGAG / 19
B103* / ACTGGGGGC / 326
B142 / ACGCAGGAG / -7[i]
ruvB / B110* / CGATGGCAC / 722
B131 / ACCTGTAGG / 845
ruvC / B109 / CTATCACCC / 448
B113* / CCCAGAGCG / 253
spoT / B134* / GGTTATGCC / 1260
B135 / CCGTAAGCT / 1499
B198 / CCGTTTAGG / 521
B207 / GCGCAGGAG / 1872
B213 / CTATATCGC / 887
B214 / CGTCCGGGC / 867
surA / B19* / GCATTAAGC / 744
B169 / GAGCTGAAC / 525d
B182 / GAGCTGAAC / 525d
tdcE / B154* / GCCGATCTC / 624
B192 / CTGTACGCC / 39
thyA / B66 / GCCGCGAAC / 670
tolC / B43 / GTACAACGC / 1217d
B55 / GTACAACGC / 1217d
B148 / GTCCATTAC / 188
B185 / CGCTTGAGC / 759
B189 / CCTCAACAC / 398
B194 / CAGTACGAT / 558
B202* / CCGACAAAC / 688
B208 / CTACTATCC / 644
B221 / AATTAGATC / 487
B228 / GCCTGAGCC / 43
tynA / B114 / CACCAGTAC / 1775
uvrD / B197* / ACTCCGGCC / 1468
B205 / CACCATATG / 309
xerD / B18 / CTACTGGGC / 807
B37 / CCACTGGAG / 396f
B53 / CCACTGGAG / 396f
B124 / GACCTTCTG / 668
B125 / GTGCAGATG / 798
B128 / GGTATAAAG / 205
B130* / CACTGGAGC / 397
B146 / GCATCACCC / 887
xerC / B42 / GGTCTGCGT / 444
B58 / AATCTATAC / 827
B104* / TCGCAACGC / 554
B105 / CGATAACCC / 76
B111 / AATCTATAC / 827
B122 / GTGCAGGAG / 786
B186 / AATCTATAC / 827
yebC / B129 / TTGCTGAAG / 337
yehB / B20 / GTCTATGAC / 1416
yejM / B156 / GAGCAAGGT / 711
yfgL / B157 / CGTCAGCGC / 653
yfgM / B48 / TCTGAGAGG / 625
yhcB / B62 / ATGACCTGT / 1330
yncD/yddW(1)j / B147 / CATTTACTT / +36k
yncD/yddW(2)j / B147 / AGCCGGGCC / 252l

[a]Alternate gene names: arpB (b1720/b1721), ecfD (b2595), envC (yibP), rluD (sfhB), yfgL (b2512), yfgM (b2513), yncD (b1451), yddW (b1491).

[b]Strains numbered up to B67 were isolated in the screen involving transfer to plates with nalidixic acid and X-gal, and all others were isolated in the screen where colonies were plated directly on X-gal plates (without nalidixic acid) (see Materials and Methods). For strains where multiple insertions were isolated, an asterisk (*) denotes the strain used in the quantitative assays.

[c]The 9 bp repeat of the insertion was determined using the forward primer from the EZ::TNTM <KAN-2> Tnp TransposomeTM Kit (5′-ACCTACAACAAAGCTCTCATCAACC-3′). The last base of the inferred repeat shows the last intact nucleotide of the gene, reading in the 5′ to 3′ direction with respect to transcription.

[d] For each strain, these insertions were isolated from a single electroporation event and therefore may be clones.

[e]This insertion is located 43 nucleotides upstream of the start codon of the folA gene.

[f] For each strain, these insertions, while identical, were isolated independently and are therefore not clones.

[g]These insertions are located 54 nucleotides upstream of the start codon of the ftsK gene.

[h]The transposon insertion is located between these two genes. However, it interrupts a predicted promoter for the ecfD gene and is located 73 nucleotides upstream of the start codon of ecfD.

[i] This insertion is located 7 nucleotides upstream of the start codon of the ruvA gene.

j This insertion mutant has two transposon; see text.

k This insertion is located 35 nucleotides downstream of the stop codon of the yncD gene.

l For only this insertion, the 9 bp repeat was determined using the reverse primer from the EZ::TNTM <KAN-2> Tnp TransposomeTM Kit (5′-GCAATGTAACATCAGAGATTTTGAG-3′). The last base of the inferred repeat shows the last intact nucleotide of the yddWgene, reading in the 5′ to 3′ direction with respect to transcription.