Percentage of transmembrane segments in the HOMEP2 set that are correctly aligned by each method.

Transmembrane segment definitions are taken from the structures according to the PDB_TM database (see Methods); matching is defined as correct if 50% (f50) or 90% (f90) of the residues are aligned. Results are sorted according to the level of sequence similarity of the sequence pair. The number of pairwise alignments is shown in parentheses.