2.4. Genomic characterization of PCV4
The putative ORFs of E115 strain (GenBank no. MT882344) and the other
three PCV4 genomes available from GenBank (MT015686, MK986820, MK948416)
were predicted using ORF Finder tool
(https://www.ncbi.nlm.nih.gov/orffinder/, last accessed on August 2020)
with the minimum length of 50 amino acids and the start codon was
strictly selected as ATG. The function of the putative proteins of PCV4
were analyzed by BLAST (Johnson et al., 2008) and InterPro (Mitchell et
al., 2019). Other motifs appeared in the putative encoding genes and
were identified using ScanProsite (de Castro et al., 2006), using the
PROSITE databases and other publication functional motifs, reviewed by
Sobhy (2016). The putative nuclear localization signal (NLS) was
predicted by cNLS Mapper (Kosugi, Hasebe, Tomita, & Yanagawa, 2009).
Sequence alignment was done by MAFFT using the L-INS-i method (Katoh &
Standley, 2013). Conserved regions from aligned sequences were further
analyzed and represented by MEME-suit programs (Bailey et al., 2009).
The conserved motifs were identified as short peptides with at least 4
residues in length which were mostly unchanged among input sequences or
substituted by ones with similar biochemical properties. The
protein-peptide interaction function of the conserved motifs was
anticipated by LMDIPred web server which predicts short linear peptides
that might bind to SH3, WW or PDZ modules (Sarkar, Jana, & Saha, 2018).