Fig. 2: Discovery of glycoproteins across the Flaviviridae.

a, RdRp phylogeny rooted on the tombusviruses (removed for visualization), with each genus or subclade colour-coded as in Fig. 1a. b, Foldseek structure-based homology e-value heat maps for the stated references, colour-coded as shown in the key. In the case of E1, E2, E, prM and MTase the values represent summary e values after comparison with a range of relevant reference structures (Methods). c, Host species tropism for each virus. ‘Vectored’ refers to those assigned as ‘Yes’ or ‘Potentially’ in Supplementary Table 3. Vertical lines within the heat map demark divisions between major clades. d–g, Representative reference structures and Foldseek hits for E1 (d), E2 (e), E (f) and prM (g). For each hit only the Foldseek-aligned residues are shown for any given structure, metrics provide e value, sequence identity, structural alignment score (local distance difference test (LDDT), ranging from 0 to 1) and protein structure prediction method. Predicted structures are colour-coded by pLDDT confidence scores, as shown in the key. In d,e, the reference structures are previously published ColabFold models³⁶, In f,g, experimental structures are used (PDB: 7QRF and 6ZQI, respectively). CSFV, classical swine fever virus; HCV, hepatitis C virus.