Tian et al. BMC Genomics 2010, 11:187 http://www.biomedcentral.com/1471-2164/11/187 Page 14 of 19 Figure 11 Exon duplication of nasonins. Peptides are indicated in boxes with color in gray for signal peptide (SP) and in other colors for NLDs. Lines mean the phase 1 introns between exons. Corresponding model structures of each domain are displayed in ribbon with different colors. Table 2 Maximum likelihood estimates of parameters and sites inferred to be under positive selection in the amino-terminal abaecin unit. Model l LRT Parameters Positive selected sites 4Y, 6P*, 8R, 11Q, 12K 4Y, 6P*, 8R, 11Q, 12K M0 M1a M2a M7 M8 -312.78 ω = 0.15 -306.30 p0 = 0.80, ω0 = 0.046 p1 = 0.20, ω1 = 1.00 -304.95 2.7 p0 = 0.80, ω0 = 0.05 p1 = 0.00, ω1 = 0.05315 p2 = 0.20, ω2 = 5.91067 -306.58 p = 0.48, q = 1.62 -304.00 5.16 p0 = 0.80, p = 1.06, q = 14.00 (p1 = 0.20), ω = 6.69 Note: l is the log likelihood; LRT is a likelihood ratio test, which is twice the log likelihood difference (2Δl) between models (M1a and M7) and their alternative models (M2a and M8): M1a/M2a = 2.7 (c2 significant value: P < 0.3); M7/M8 = 5.16 (0.05 < P < 0.1). Positively selected sites identified by the BEB method under M2a and M8 with posterior probabilities (p) > 0.6 are shown, in which those with p > 0.95 are indicated by bold and *. BLASTP and TBLASTN programs were used to charac- terize orthologues of known AMPs from A. mellifera against the database of N. vitripennis [93]. When search- ing for hymenoptaecin in flies, BLAST was carried out in Flybase [94]. The program WinGene [95] was employed to predict and translate a complete open read- ing frame from a selected nucleotide sequence. The N. vitripennis protein sequences downloaded from Gen- Bank [96] and the FTP site [97] were applied to perform ScanProsite on the ExPaSy sever [98]. Characteristics identification All sequences we identified as AMP-like peptides were submitted to SignalP 3.0 server [99] for signal pep- tide prediction. Peptide characteristics identified here were further analyzed on the ExPaSy server [100] for estimation of molecular weights and calculation of net charges at Protein Calculator [101]. Secondary structure prediction was done on the ExPaSy server [100]. To pre- dict amphiphilic structure of peptides, helical wheels models were calculated on the server [102]. Sequence alignment and structural analysis Amino acid sequences were aligned using Clustal X [103] with fine adjustment by hands and phylogenetic trees were constructed by MEGA 4.0 [104]. Structures were modeled from ab initio by I-TASSER on-line [105-107] or on the Structural Bioinformatics server by comparative modeling method [108]. Structure evalua- tion was carried out by Verify 3D [109,110]. The Multi- Prot server was used to do structural superimposition and calculation of root mean square deviation (RMSD) [111]. All model structures predicted here have been