Typical Output of an HMMerThread run. (A) Results from the HMMer-search against the PFAM conserved domain database. The input query was Dip13α/APPL1 [GenBank:NP_036228]. HMMer identified next to the PH- and PTB-domain 5 potential conserved domains in the N-terminus of the protein sequence. Of these five predicted domains, the BAR domain has the lowest E-value of 0.8 and was selected for further processing. (B) Results from the threading run identified the BAR domain from residues 4–224. By clicking on the orange bar, the user gets to the detailed results from the threading run (see C). The BAR domain can also be sent to the Annotation Engine and Threading Engine (link 'Send to ProFAT'). (C) Results from the threading run with the predicted N-terminal BAR domain of APPL1. Threader identified the two structures of Amphiphysin ([PDB:1URU]) and Arfaptin2 ([PDB:1I49]), which are both members of the BAR domain family with nearly 90% confidence.