Figure 2

The predicted structure of a transcription factor in SoyDB. The electrostatic polarization (a) (blue, positive; red, negative), sphere (b) and ribbon (c) visualizations of MULTICOM predicted structure for GM00002. (d) a segment of the pair-wise alignment between 1WID (PDB template of GM00002) and GM00002, and, below, the DNA-binding site predictions from three independent tools: DNABindR [70], BindN [71], and DP-Bind [72] ("+" indicates predicted DNA-binding positions, "-" indicates gap or no prediction). The green regions in the sequence of 1WID are the DNA-binding regions identified by experimental methods [73]. The green regions in GM00002 sequence are the two DNA-binding regions derived from the alignment with 1WID. The predicted DNA-binding regions in GM00002 are illustrated in green in (b) and (c). (c) the side chains of the predicted binding regions. (a), (d), and (c) are in the same orientation. The electrostatic polarization (a) was computed and mapped to protein surface by Swiss-PDB viewer (deep view) [74], and the structures in sphere (b) and ribbon styles (c) were made with PyMol [75].