I have run hmmsearch (using HMMER 3.2v) and got output in pfam tabular format. For domain position I got two co-ordinates (start and end) i.e envelope co-ordinates and alignment co-ordinates. I have used highly conserved sequence to build my hmm profile to search against a proteome. I will used these co-ordinates to construct phylogenetic tree and modelled the structure. Which co-ordinates correctly defines my domain hits? And according to which co-ordinates I should trimmed/extract my sequence to select my domain position. I am confused to choose between these two (envelope and alignment) co-ordinates.