Computational protocol: Molecular Characterization and Comparative Sequence Analysis of Defense-Related Gene, Oryza rufipogon Receptor-Like Protein Kinase 1

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Protocol publication

[…] OrufRPK1 amino acid sequence was used for homology searches against the Rice Kinase Database [,,], Rice Genome Annotation Project database [,] and Gramene Database [,]. A total of 15 orthologous OrufRPK1 gene sequences were selected for phylogenetic analysis (). A maximum likelihood phylogenetic tree was constructed using MrBayes 3.2.0 program []. [...] Homology modeling of OrufRPK1, OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1 used a similarity based approach for modeling three dimensional proteins with Modeler Version 9v8 [,]. The LRR domain of polygalacturonase-inhibiting protein (1ogqA) [] and kinase domain of interleukin-1 receptor-associated kinase 4 (2nruB) [] templates were used for comparative modeling of the four predicted protein structures. These domains were defined using ROBETTA web server [] which provides both ab initio and comparative models of protein domains []. Ginzu algorithm searches for homologs in various protein structures through PSI-BLAST searches were used to define domain boundaries for the given input sequence []. […]

Pipeline specifications

Software tools MrBayes, Robetta, BLASTP
Databases Gramene RKD RGAP
Applications Phylogenetics, Protein structure analysis
Organisms Oryza rufipogon, Oryza sativa Indica Group, Oryza sativa