Table 3.
Comparison of cumulative contact and readout position weight matrices for 4 prokaryotic (top) and 4 eukaryotic (bottom) transcription factors
|
SCOP v1.73 superfamily |
TF [PDB id] | Resolution (Å) | Robs | E-valuecontacts | E-valuereadout |
| Winged helix | CRP [1cgp] | 3 | 0.24 | 7.93E-03 | 3.76E-05 |
| C-terminal domain of the bipartite response regulators | NarL [1je8] | 2.12 | 0.23 | 3.58E-05 | 7.01E-07 |
| lambda repressor-like DNA-binding domains | PurR [2pua] | 2.9 | 0.16 | 4.33E-15 | 5.51E-01 (7.58E-04) |
| ribbon-helix-helix | MetJ [1cma] | 2.8 | 0.22 | 1.22E-01 | 3.30E-01 |
| Zn2/Cys6 DNA-binding domain | LEU3 [2er8] | 2.85 | 0.23 | 4.97E-06 | 5.52E-05 |
| HLH, helix-loop-helix DNA-binding domain | PHO4 [1a0a] | 2.8 | 0.23 | 3.57E-07 | 3.97E-07 |
| Homeodomain-like | RAP1 [1ign] | 2.25 | 0.21 | 5.52E-03 | 1.89E-02 (6.40E-04) |
| C2H2 and C2HC zinc fingers | ZIF268 [1aay] | 1.6 | 0.19 | 7.93E-14 | 1.99E-14 |
In the first column we include the name of the structural superfamily of each TF according to SCOP [37]. In the second column the name of each TF is followed by the PDB identifier of the structure used enclosed in brackets. The following two columns contain the resolution and the R-value of the crystals respectively. The last two columns report the E-values resulting from STAMP [38] local alignments between the structure-based PWMs obtained with the method of Morozov and Siggia [32] (E-valuecontacts) or our approach (E-valuereadout) and the corresponding cognate PWMs, extracted from the literature [43,49,53]. Parenthesized E-values were calculated after sampling interface rotamers with DNAPROT.