HangOut flowchart. Starting from a query domain (blue-red, with inserted domain in yellow removed), a PSI-BLAST search of the NCBI non-redundant database (NR) is performed (Step 1) to produce alignments. Erroneously-extended regions (yellow) that cross the insertion boundary (vertical dotted line) are removed to produce a "cleaned" alignment (Step 2-1). Remaining contaminants not crossing the domain boundary are removed by PSI-BLAST profiles built from the long insertion (Step 2-2). The PSI-BLAST result is checked for convergence (Step 3), and possibly continued from Step 1.