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Table 1 Putative SO2426 gene targets containing the predicted SO2426-binding site

From: SO2426 is a positive regulator of siderophore expression in Shewanella oneidensisMR-1

ORF Functional Category/Gene Product Motif Strand Distancea E-valueb
  Cellular processes     
SO2280    bicyclomycin resistance protein AACGCTCAGGCAAA - -241 2.06E-04
  Central intermediary metabolism     
     5-methylthioadenosine nucleosidase/S-     
SO3705    adenosylhomocysteine nucleosidase, putative GTCAGCCAGCAAAA + +21 4.73E-05
  Energy metabolism     
SO2743    acetyl-coenzyme A synthetase (acs) AAAAAAGAGCAAAA - -160 1.46E-05
  Hypothetical proteins     
SO1188    conserved hypothetical protein AAAACTCAGCAGAA - -113 2.08E-06
SO1190    conserved hypothetical protein CTAAGGCAACAAAA - +12 2.38E-05
SO1770    glycerate kinase, putative ACAACCCAGAAGAA - -177 2.61E-05
SO3025    conserved hypothetical protein GCAAAACATCAAAA + -234 1.13E-04
SO3062    hypothetical protein ATAAATCAGGAGAA + -5 7.64E-06
SO4499    hypothetical protein CTGCAACAGGAGAA + -5 1.19E-05
SO4504    conserved hypothetical protein ATGTCCCAGACAAA + -169 1.06E-04
SO4719    conserved hypothetical protein ATGAACCACAAGAA + -199 9.88E-05
  Transport and binding proteins     
SO0139    ferritin (ftn) CAAAAGCAACAAAA - -63 2.08E-06
SO1580    TonB-dependent heme receptor AAAAAGCAGAAAAA - -112 3.68E-06
SO1771    permease, GntP family CTACAACAGCCAAA + -41 2.81E-06
SO2045    cation efflux family protein CACCCTCAACAGAA + +11 5.98E-05
SO3030    siderophore biosynthesis protein (alcA) CTGTAACAGCAAAT + -133 2.86E-05
SO3032    siderophore biosynthesis protein, putative CCGGATCAGCAAAA + -284 1.46E-05
SO3033    ferric alcaligin siderophore receptor ATCAAACAGCCAAA + -112 3.20E-06
SO3063    sodium:alanine symporter family protein CAAAAACAACAGAA + -18 1.09E-06
SO4150    transporter, putative AAAAAACTGCAGAA + +16 7.64E-06
SO4516    ferric vibriobactin receptor (viuA) CAGTAGCAGAAGAA + -249 1.62E-05
SO4743    TonB-dependent receptor, putative CAAAAACAACAAAT - -168 2.38E-05
  Signal transduction     
SO2426    DNA-binding response regulator CAATACCTGCCAAA + -88 5.12E-05
  1. aDistance in base pairs of the start of the potential SO2426 binding site from the first nucleotide of the predicted translation start codon of the corresponding gene listed in the first column. bThe E-value of the motif is an estimate of the number of motifs with the same width and number of occurrences that would have equal or higher log likelihood ratio if the training set sequences had been generated randomly according to the background model [30].