Analyses protein sequence, predicts function and searches sequence. Uniclust databases cluster UniProtKB sequences at the level of 90%, 50% and 30% pairwise sequence identity. The sequences in the database are annotated with matches to Pfam, SCOP domains, and proteins in the protein data bank (PDB), using our HHblits homology detection tool. The database contains 17% more Pfam domain annotations than UniProt. The Uniclust server facilitates profiting from the Uniclust databases and deep HHblits domain annotations.