Fig. 3
Oyster IAPs possess conserved and novel BIR domains with potentially altered secondary structure. A Alignment (MAFFT) of representative Type I and Type II BIR-defining amino acid sequences (highlighted with black boxes) of selected vertebrate and invertebrate model organisms (Drosophila melanogaster, Homo sapiens, Mus musculus, Danio rerio) with oyster IAP sequences revealed oysters possess both conserved and novel Type I and Type II domains. Three novel types of BIR domains (Type X, Type Y, and Type NZBIR) were identified in oysters. “Total Genes” indicate the number of oyster IAP genes with each identified BIR domain type, with the most represented highlighted in red. * = Conserved aa positions across all C. gigas (Ostreida) and C. virginica (Ostreida) BIR sequences. Zn2+ = positions in model organisms involved in Zinc atom stabilization. V = variable aa position used in BIR domain classification. B Predicted protein secondary structure analysis by RaptorX. Secondary structure predictions were made at the three class (SS3, red bar, H = alpha helix, E = beta sheet, C = coil) and eight class levels (SS8, blue bar, H = alpha helix, G = five-turn helix, I = extended strand in beta ladder, E = isolated beta bridge, T = hydrogen bonded turn, S = bend, L = loop) for representative BIR type amino acid sequence examples (SEQ, grey bar). Characteristic regions used in classification are outlined in black. Type X and Type BIRs may have shortened alpha helix structures while Type NZBIR does not have altered secondary structure but loss of Cysteine may prevent Zinc coordination