I am trying to (and understand how to) extract the consensus of a protein alignment from its HMM profile (produced by HMMer2). I understand that from the "match emission line" I can get the corresponding amino acid (the one with the higher match emission score) when the most probable transition is 'm->m'. Am I right in assuming that a "dot" has to be inserted in the consensus when the most probable transition is 'm->d' or 'd->d'? what happens with 'd->', 'm->i', and 'i->i'? Any help would be appreciated.