The alignment of protein sequences is the most powerful computational tool available to the molecular biologist. Where one sequence is of unknown structure and function, its alignment with another sequence that is well characterized in both structure and function immediately reveals the structure and function of the first sequence. This ideal transfer of information is, unfortunately, not always attained and can fail either because the two sequences are equally uncharacterized (although they might align quite well) or because the alignment is too poor to be trusted. Both these situations can be helped if the analysis is extended to incorporate more sequences. In the former case, the addition of further sequences can reveal portions of the protein that are important in structure and function (even if that structure or function is unknown), whereas in the latter, the revelation of conserved patterns can help add confidence in the alignment.