April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
Given a protein sequence, SitesBLAST finds homologs that have known functional residues and shows whether the functional residues are conserved. (example)
SitesBLAST's database includes (1) SwissProt entries with experimentally-supported functional features; and (2) protein structures with bound ligands, from the BioLip database.
Or try Sites on a Tree or PaperBLAST
Lawrence Berkeley National Laboratory