Using HMMer to find P-Loop domain sequences.

Having seen what regular expressions are good and bad for, let's move on to using HMMs for sequence classification.

1. Find the Pfam website at Sanger and
   
2. Download The Pfam_fs model for the ``P-loop ATPase protein family''.
   
3. Search for matches to the domain among E. coli proteins using ehmmsearch. How many domains were matched in how many proteins? How many have an E-value less than 0.05? Do you see the motif that you worked with earlier?