Table 1.

Number of profiles detecting additional sequences

Profile type	Search method	Hierarchy	No. of profiles	No. of profiles detecting additional sequences	Percentage
Merged	HMMer	fold	1185	167	14.09
Merged	PSI-BLAST	fold	1185	154	13.41
Merged	HMMer	superfamily	748	308	41.17
Merged	PSI-BLAST	superfamily	748	407	54.41
Unmerged	HMMer	—	903	56	6.20
Unmerged	PSI-BLAST	—	903	44	4.87