Figure 7.
Multiple sequence alignment of m04ED with the predicted extracellular domains of other m02-m06 family members. The approximate positions of conserved secondary structure elements are highlighted on the top of each alignment block (β1-β9: β-strands, red ovals: α-helices). The position of the two disulfide bonds on the m04ED structure is indicated with capital C letters and connecting dashed lines, while high-confidence predicted glycosylation sites on the m04ED sequence are indicated with stars. Protein sequences for m02 (UniProt ID: YP_214010) m03 (YP_214011) m05 (YP_214013), and m06 (YP_214014) were all taken from the Smith MCMV genome: NC_004065. The sequence of m03.5 (ABM74010), not present in the Smith strain was taken from strain G1F.
To identify the ER-lumenal domains of these proteins from the full-length protein sequence, we first identified the end of the signal peptide using the SignalP (www.cbs.dtu.dk/services/SignalP/) and Phobius (http://phobius.sbc.su.se/) servers, then identified the start of transmembrane domains using TMpred (www.ch.embnet.org/software/TMPRED_form.html). Sequence alignments were constructed using ClustalW2 (www.ebi.ac.uk/Tools/msa/clustalw2/) and colored by sequence similarity using BoxShade (www.ch.embnet.org/software/BOX_form.html).