Figure 3.

Iterative growth of a homologous over-extension. (A) The raw PSI-BLAST output of a search querying a PF00668 embedded domain against the standard curated Pfam library at iteration 5. The portion of the alignment that contains the PF00668 homologous domain is shown in blue, while the over-extension onto the structurally unrelated PF00550 domain is shown in red. (B) A diagram that tracks the progression of the alignments shown in (A) from iterations 2 through 5. The alignment on the partial PF00668 domain begins as the first FP in the search at iteration 3, and continues to overextend further onto the unrelated PF00550 domain (in red) in subsequent iterations. By iteration 5, the entire unrelated PF00550 domain is covered by the overextended alignment.