Table 3.
Phylogenetic Footprinting Results for Selected Species Combinationsa
| Speciesb | Number of orthologous data sets | Motif predictions with all species included | Correspondence with known sitesc |
|---|---|---|---|
| EC-ST | 161 | 98.8% (159/161) | 55.3% (88/159) |
| EC-YP | 138 | 94.2% (130/138) | 66.9% (87/130) |
| EC-VC | 112 | 83.0% (93/112) | 62.4% (58/93) |
| EC-HI | 72 | 81.9% (59/72) | 62.7% (37/59) |
| EC-SO | 91 | 69.2% (63/91) | 55.6% (35/63) |
| EC-PA | 92 | 48.9% (45/92) | 37.8% (17/45) |
| EC-BU | 27 | 85.2% (23/27) | 39.1% (9/23) |
| EC-AF | 46 | 58.7% (27/46) | 48.1% (13/27) |
| EC-XF | 50 | 54.0% (27/50) | 33.3% (9/27) |
| EC-VC-HI | 65 | 50.8% (33/65) | 75.8% (25/33) |
| EC-YP-SO | 86 | 36.0% (31/86) | 67.7% (21/31) |
| EC-YP-PA | 86 | 19.8% (17/86) | 70.6% (12/17) |
| EC-ST-YP-VC | 103 | 42.7% (44/103) | 86.4% (38/44) |
a
Results for all species combinations are in the Supplementary Data.
b
Species abbreviations are as follows: EC, Escherichia coli; ST, Salmonella typhi; YP, Yersinia pestis; VC, Vibrio cholerae; HI, Haemophilus influenzae; SO, Shewanella oneidensis; PA, Pseudomonas aeruginosa; BU, Buchnera sp.; AF, Acidithiobacillus ferrooxidans; and XF, Xylella fastidiosa.
c
Correspondence with known E. coli transcription factor binding sites was calculated only for those motif predictions that contained sites from all the species included in the data set.