Truncated domains in the fusion proteins.

Nontrivial cases of fusion proteins are shown where breakpoint falls into a Pfam domain. The abbreviated column identifiers are as follows: Pfid, Pfam identifier; fplen, fusion protein length; bp, breakpoint; Dlen, domain length, Dbeg, Dend, domain match beginning and end, respectively; N/C, the retained half of the truncated domain; Dfract, the retained fraction of the truncated domain; IUleft, IUright, the predicted disorder for the truncated domain and its “mirror” (same number of amino acids as in the truncated domain) on the opposite side of the breakpoint. In the IUleft/IUright columns the value for the truncated domain is italicized whereas the disorder value for its “mirror” is shown in bold. In the last column possible strategies are shown for the truncated domains to follow to avoid elimination by the proteasomal degradation system [49]. “No PDB” indicates the lack of any PDB structures associated with the protein family in question, which together with high predicted disorder values raises the suspicion of the domain being intrinsically disordered. When a PDB code is shown with a list of numbers (shown in bold italic) they indicate positions in the actual domains that are presumably indifferent to truncation based on the exposed hydrophobic surface of the truncated domain (as shown in detail in Figure 4).