HHpred hits and probability scores.

HHpred (http://toolkit.tuebingen.mpg.de/hhpred) is a tool for sequence database searching and structure prediction that looks for proteins of known structure that are homologous to the protein of interest. The table shows the top three HHpred hits for the four AP-5 subunits, as well as the associated protein SPG11. “Prob” refers to the probability for a homologous relationship. The probability is >95% for the four AP-5 subunits and corresponding subunits of AP-1, AP-2, and F-COPI complexes, and >80% for SPG11 and two structural coat proteins, clathrin heavy chain and β′-COP. The same clathrin heavy chain hit (1xi4_A) appears twice for SPG11 because of alignments of different regions of SPG11 with different regions of clathrin heavy chain (residues 1644–2268 with residues 337–766; and residues 1200–1806 with residues 567–1362).