Comparison of bound DNA sequences of homologous proteins. The alignments of the bound DNA sequences of homologous proteins by using the homeotic ubx/exd/DNA ternary complex (PDB entry 1B8I-A) as the query. (A) The z-score values and the bound DNA sequences of the complex 1B8I (PDB entry 1B8I-C and 1B8I-D), 1PUF (PDB entry 1PUF-D and 1PUF-E), and 1O4X (PDB entry 1O4X-C and 1O4X-D). All sequences are from 5' to 3'. (B) Alignments of bound DNA sequences of the complexes 1B8I and 1PUF. A colon denotes an identical pair and an asterisk denotes a contact nucleotide (asterisks are marked above/below alphabets on the upper/lower sequence of the alignment, respectively). (C) Alignments of bound DNA sequences of the complexes 1B8I and 1O4X.