The comparison of CDD and DaliLite alignments for an all- α protein pair from the superfamily cd00299. The structure-based sequence alignment produced by CDD (A) and DaliLite (B) for two α-helical proteins. The color in the sequence name is used for the corresponding structure in the structure superpositions below. The aligned residues are indicated by the upper case letters. The residues aligned in the reference alignment are shaded blue. These sequence alignments were used to generate structural superpositions, by CDD in the left and middle panels (C and D) and by DaliLite in the right panel (E). The orientation of the red structure (d1neu_) is the same in all three panels. Aligned residue pairs are connected by cyan lines, in the left panel according to the CDD and in the middle and right panels according to the DaliLite alignments. Short fragments at the C-termini were cut off and the regions where CDD and DaliLite agree are shown in ribbon, for better visibility of the equivalences. DaliLite achieved 0.453, 0.953 and 0.953 for fcar(0), fcar(4) and fcar(8), respectively. The pictures were prepared using CHIMERA (UCSF, Computer Graphics Lab).