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2.27 (Altschul et al., 1990) and giant viral protein sequences as queries against the NCBI GenBank non-redundant protein sequence database selleck kinase inhibitor (nr) to collect homologous sequences from the members of the three cellular domains of life (Bacteria, Archaea, and Eukarya). The number of target sequences was limited to 20,000 per query. Sequence Selection Criteria for Cellular Domains Conserved genes might possess multiple homologs in sequence databases, and random selection among these genes for phylogeny reconstruction might result in the selection of strongly biased non-representative sequence sets. Hence, we selected homologous sequences from various species corresponding to representatives from different phyla of Bacteria, Archaea, and Eukarya using TimeTree, as previously described (Sharma et al., 2014). TimeTree is a public knowledge-base of divergence times among organisms estimated from molecular data in published studies (Hedges et al., 2006). This resource facilitated here the selection of sequences from species that diverged approximately 500 million years ago, which allowed obtaining an appropriate set of members from the three cellular domains of life through a good Non-specific serine/threonine protein kinase equilibrium between comprehensiveness and representativeness. In addition, the genomes of most of these cellular organisms are available and have been annotated. The Taxon filter program was subsequently used to filter out taxon and gi identification numbers from the results of the BLAST analysis, which facilitated the downloading of selected protein sequences directly from the NCBI GenBank non-redundant database. Partial or identical sequences were removed through clustering using the CD-HIT suite program (Huang et al., 2010). Multiple Sequence Alignments and Phylogeny Reconstructions The obtained sequences were aligned using ROCK inhibitor the Muscle program (Edgar, 2004). Alignment quality was manually analyzed, and phylogenetic reconstructions were performed using ML inference, including the WAG model, and confidence values were calculated using the Shimodaira-Hasegawa (SH) test through the FastTree program (Price et al., 2010). Phylogenetic trees were constructed using the FigTree software program3. Phyletic Pattern Analysis with Clusters of Orthologous Groups of Protein Clusters of orthologous groups of proteins corresponding only to the selected functional COG categories [J, A, K, L, B, and F], encoding proteins involved in information storage and processing and nucleotide transport and metabolism, were used for the analysis. BLASTp searches for the selected COG categories, with e-values