Pfam consist of parts A and B. Ion Reporter™ Software uses Pfam-A. "A is curated and contains well-characterized protein domain families with high quality alignments, which are maintained by using manually checked seed alignments and HMMs to find and align all members", according to this site:
See also the following link for information about Pfam:
The Pfam protein families database:: R.D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, J.E. Pollington, O.L. Gavin, P. Gunesekaran, G. Ceric, K. Forslund, L. Holm, E.L. Sonnhammer, S.R. Eddy, A. Bateman. Nucleic Acids Research (2010) Database Issue 38:D211-222
Note: Pfam annotations for all domains of the gene's protein are added for any variant.