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Table 5 Evolution of LexA binding motif: comparison between annotated and predicted motifs.

From: Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

Taxon Annotated motif Predicted motif Most significant dyads Genes Dyads
    pattern sig nb match coverage tested significant
Alpha proteobacteria GAAC nnnnnnnGAAC ttggAAC acatagagAAC aga AACn8AAC 18.64 26 24 92% 33800 125
Beta proteobacteria - cacTG TATAattATACAG tg ATACAG 11.12 14 9 64% 21649 14
Gammaproteobacteria CTGT nnnnnnnnACAG aCTGt atatatataCAG tt CTGn10CAG 38.67 54 44 81% 39229 142
Xanthomonadales TTAGTArwa wTACTAa gTTAGTAata cTACTA Ac TACTAA 7.5 7 5 71% 15535 76
Delta proteobacteria GGTTnnCnnnnGnnnACC CTRHAMRY BYGTTCAGS GTAAGT GTAAGT 3.98 6 3 50% 17622 3
Cyanobacteria RGTAC nnnDGTWC B aggtAC AtaTGTacc t ACAn2TGT 6.06 11 7 64% 13696 50
Firmicutes CGAACR nRYGTTY C tacgAACa tatGTTc gta AACn4GTT 38.79 40 39 98% 31695 140
Actinobacteria CGAACR nRYGTTY C aaTCGAACa catgtTC GAACat TCGAAC 30.95 17 17 100% 34155 139
  1. For each analysis at a given taxonomical level (column 1), the annotated motif (column 2) is compared with the predicted motif (column 3) with matching letters in bold. Capital letters in the predicted motif correspond to the most significant dyad (column 4, with significance score in column 5). The gene coverage is the fraction of genes whose upstream sequence contains at least one occurrence of the most significant dyad. The last columns indicate the number of tested dyads and the number of dyads detected as significant (sig > 0), respectively.