Dealing with IDs of genes or the proteins they encode is often nontrivial. In the SEED database, we use IDs that specify proteinencoding genes in a rapidly growing set of genomes, and we support correspondences between these IDs and those used by other annotation efforts. The SEED has two notions of equivalence: (i) two IDs that represent either protein-encoding genes or protein sequences are said to be sequence equivalent if the protein sequences are identical and (ii) two IDs that represent either exactly the same protein-encoding gene or the precise protein encoded by the gene (that is, ''the protein sequence of gene X in genome Y'') are said to be precisely equivalent. Unfortunately, in the presence of multiple versions of thousands of genomes, perfect maintenance of the ''precisely equivalent'' correspondence is virtually impossible.