Identification of a TPR-ASH domain structure in TRAPPII complex subunits. (A) Domain architecture of known and putative TRAPPII subunits, represented by human TRAPPC8, -9, -10, -11, and -13. Reciprocal HHpred searches identified the regions containing ASH domains, as shown. TRAPPC8 (region 912-1032; local probability 96.98, E = 0.0038), TRAPPC9 (region 725-795; local probability 97.20, E = 0.002), TRAPPC11 (region 748-1133; local probability 96.69, E = 0.012), TRAPPC13 (region 71-150; probability = 97.21, E = 0.0013). The TRAPPC10 C-terminus is more distantly related to the ASH domain. Three iterative HMM-HMM searches of TRAPPC10 region 1072-1158 (local search mode) produced a match to PapD with probability 91.01 and E = 0.85. TPR repeat regions were identified by HHpred and TPRpred (see main text). A minimum of two TPR repeats was used as an exclusion criterium. Human TRAPPC10 was only shown to contain TPR repeats in HHpred. (B) Multiple sequence alignment of ASH domains identified previously  and here. Sequences were aligned using MAFFT (http://myhits.isb-sib.ch/cgi-bin/mafft) here only representing the partial ASH regions surrounding the conserved asparagine (N). The secondary structure, predicted by HHpred, is shown above the alignment (arrows indicating β-sheets) and the derived consensus amino acids of the alignment are shown below. Consensus abbreviations were obtained in Jalview (http://www.jalview.org/): hydrophobic (h, blue), polar (light green), acidic (violet), glycine (brown), proline (brown green), and asparagine (dark green). For simplicity, only representative proteins found in the first iterative HHpred search with Trs120 against human PFAM profiles are aligned. The representative sequences include: Schizosaccharomyces pombe (Sp) Trs120, human (Hs) TRAPPC8, -9, -11, and -13, as well as human DLEC1, Hydin, CCDC108, Cxorf22, RW1, and the PFAM entry of bacterial PapD (as displayed by HHpred). For a graphical output showing results of the initial HHpred search with human DLEC1 (residues 769-980) as search query, see Additional file 1: Figure S1.