The comparison of CDD and DaliLite alignments for an all- β protein pair from the superfamily cd00096. The structure-based sequence alignment produced by CDD (A) and DailLite (B) for two immunoglobulin proteins. The conserved cysteine pairs are colored in white. Otherwise, the same as in Figure 4. For this pair, all methods but VAST agreed with DaliLite, while VAST agreed with CDD. DaliLite achieved 0.0, 1.0 and 1.0 for fcar(0), fcar(4) and fcar(8), respectively.