Figure 2.

A partially expanded view of the homology evidence and protein naming hierarchy used in RefSeq and PGAP annotation. Four families of beta-lactamases are shown (A, metallo, C, and D), each of which is more similar to various hydrolases of other substrates, such as RNA, than to any members of the other beta-lactamase classes. For each class, a protein profile HMM identifies members and suggests a protein product name, but further expansion of the hierarchy can reveal multiple child families, each identified by a more specific HMM that receives a higher precedence during annotation. The hierarchy of evidence largely follows an implicit hierarchy of protein names, with exceptions necessary occasionally, as when unrelated proteins perform closely related functions.