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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.