I have downloaded the SMART hmm profiles and created a HMM DB using, then I have queried some sequences using this db and hmmpfam (from hmmer2). I was expecting that if I query the same sequence on SMART web service the results will be similar, but they are very different. Any hints on what I might be doing wrong?
I'm querying the U5WTH2_MYCKA for example. The sequence itself. The web interface gives me one transmembrane domain from position 20 to 42 and three low complexity regions (two of them overlapping). It also shows an EccE from Pfam.
I'm querying the same sequence locally and the lowest E-value is for RES_2 from positions 328 to 441 and this does not even overlap with any of the regions given by web interface. There are multiple other domains in this local query result as well which I understand some of them shouldn't be present in web result because of the threshold, but at least the highest ranking ones I expect to be the same.