Two examples of alignments on which all methods agree but which is different from that of CDD. The alignments on the left and right panels are from cd00531 and cd01984, respectively. The names of the protein domains aligned are given at the top of each panel. The method which generated the alignment is indicated at the left of the sequence by the first two letters of its name. Only a part of the sequence is shown in each case, which includes the region that is aligned differently by the methods and by the CDD. The aligned residues are indicated by uppercase letters. The residues aligned identically by all methods but differently by CDD are shaded.