Amino acid sequence comparison resulting from a BLAST search done with the DpAV4 ORF90 as a query, and the best hit corresponding to the protein encoded by the ORF1 of the ichnovirus segment GfV-C20 (Subject; Genbank Acc. N° YP_001029423) Figure 2 Amino acid sequence comparison resulting from a BLAST search done with the DpAV4 ORF90 as a query, and the best hit corresponding to the protein encoded by the ORF1 of the ichnovirus segment GfV-C20 (Subject; Genbank Acc. N° YP_001029423). analysis revealed that most conservation occurred at the level of hydrophobic residues, as expected for structural proteins (Additional file 3a and 3b). The size variability of the hinges between conserved domains and the conservation of hydrophobic residues might explain why BLAST searches using iridoviral and ascoviral MCP sequences have limited ability to detect MCP orthologs in phycodnavirus and asfarvirus genomes. We designed two syntactic models (see Materials and Methods), which together were able to specifically align all MCP sequences of the four virus families. Importantly, WAPAM aligned the CsIV ichnovirus P44 structural protein with both models. Complementary structural and HCA confirmed the presence of the seven conserved domains in this CsIV structural protein ( Fig. 3a and Additional file 3c).