We focused on the 670 Pfam cross-taxa families that contain viruses and metazoa. A careful examination reveals that these instances reflect either missed annotations or the remnants of sequence exchange by virus infection. To distinguish these possibilities, we constructed sequence alignment trees for all 670 Pfam families. From the properties of the trees, we focused on 335 families that most likely contain viruses that hijacked sequences from their host. We found that most of the viral proteins in the orthologous families are much shorter and composed of simpler domain architectures. In almost all cases, the number of domains and the sequence of the tails and the inter-domain linkers are considerably shorter in the viral proteins relative to their counterpart host proteins. We discuss the potential of such short viral proteins to interfere with critical cellular functions and thus are candidates for manipulation strategies in defeating viral infection.