We used the HMMER 2.2 package (Eddy, 1998), to generate profiles for the cTP and mTP. We tried several alignments, and the ones we found performed best were:
For the cTP, the 15 N-terminal residues are aligned to the left, the next 8 residues in the middle and the rest to the right
0-15--------16-23-----24-cleavage site+9
For the mTP, the 10 N-terminal residues are aligned to the left and the rest to the right
0-10--------11-cleavage site+9
The profiles were generated using raising the architecture prior from 0.85 to 0.95 (Zhang et al., 2003)
For the cTP, the 15 N-terminal residues are aligned to the left, the next 8 residues in the middle and the rest to the right
0-15--------16-23-----24-cleavage site+9
For the mTP, the 10 N-terminal residues are aligned to the left and the rest to the right
0-10--------11-cleavage site+9
The profiles were generated using raising the architecture prior from 0.85 to 0.95 (Zhang et al., 2003)