Similar sequences in the sequence databases Distinctive patterns for different types of protein function Functionally important residues. Secondary and tertiary structure which provides more insights than the primary sequence. Database similarity searches are about five times more sensitive. For protein based entities you are closer to the actual biological function. The 3-D structure of similar proteins may be known.
Evolutionary relationships are more visible.
Annotation of protein sequence and related databases is often comprehensive. Overview of what can be done using bioinformatics. Similarity searches, multiple sequence analysis, motif searches and phylogeny. We are going to go through these exercises without questioning program details too much, due to time constraints. In real life, you should check out every option of a program and read about what the program is really doing and what the output means.