We used the HMMER 2.2 package (Eddy, 1998), to generate profiles for the lTP. A window of 42 residues (-35 +6) around the cleavage site of the lTP, and aligned it using ClustalW.
We created 3 profiles one for each of the Sec pathway sequences and the TAT pathway sequences, and one with the whole dataset.
The profiles were generated using raising the architecture prior from 0.85 to 0.95 (Zhang et al.,2003)
The profiles were generated using raising the architecture prior from 0.85 to 0.95 (Zhang et al.,2003)