Sequence analysis of Flavivirus Envelope proteins. (A) Outline of WNV structural proteins C, PrM and E. (B) Presence of conserved 461PS/AAP464 and 349YCYL352 motifs in the Flavivirus envelope protein. Selected Flavivirus proteins were downloaded from NCBI , aligned with MAFFT  and the respective motif regions visualized in Jalview  using ClustalX-like coloring based on physicochemical properties and conservation. Virus names are shown left with NCBI GI number. (C) Frequency of YCYL and PAAP motif variants in WNV envelope. Significant protein hits (E<0.001) were first identified with Delta-BLAST  starting with the sequence of the envelope glycoprotein structure (PDB:2hg0) against NCBI’s non-redundant protein database restricting to West Nile virus sequences only. All hits were next aligned with MAFFT after discarding those without sequence information for the YCYL or PAAP region and removing 100% identical sequences using Jalview. The resulting set of 286 WNV sequences was analyzed for the respective motif occurrences.
Garg et al. BMC Microbiology 2013 13:197 doi:10.1186/1471-2180-13-197