An example of the refinement of the CE alignment. The structure-based sequence alignments by CE alone (A), CE followed by SE (B) and CE followed by RSE (C) are shown with the shaded blocks indicating CDD reference alignments. The disulfide-forming cysteine residue pairs are highlighted in yellow. The aligned and unaligned residues are indicated by uppercase and lowercase letters, respectively. The panels D and E show the superpositions by CE and after refinement by RSE, respectively. The aligned residue pairs are indicated by white lines. The cysteine residues are in yellow. The blue and red structures represent the SCOP domains d1a6aa1 and d1cdi_1, respectively.