Computational protocol: Functional characterization of LotP from Liberibacter asiaticus

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Protocol publication

[…] Homologues of CLIBASIA_03135 were obtained using two iterations of a PSI‐BLAST search against a non‐redundant sequence database at the NCBI (www.blast.ncbi.nlm.nih.gov/). Redundant sequences were eliminated and alignments were made using the ClustalW (Thompson et al., ). The evolutionary history of LotP was inferred by using the maximum‐likelihood method based on the JTT matrix‐based model. The phylogenetic tree with the highest log likelihood (−15397.4801) was constructed. The initial data for the heuristic search was obtained automatically by applying neighbor‐joining and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model. The topology with superior log‐likelihood value was selected. The branch lengths were measured based on the number of substitutions per site. The analysis involved 96 amino acid sequences. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA7 (Kumar et al., ). Further, the phylogenetic tree was constructed using the online tool Itol: Interactive Tree of Life (Letunic and Bork, ). The main LotP protein scaffold was modelled in silico using the automated mode of the SWISS‐MODEL and PHYRE2 server (Arnold et al., ; Kelley and Sternberg, ). The crystal structure of C3M65A from the N‐terminal domain of Bacillus subtilis Lon Protease was retrieved as the best template. […]

Pipeline specifications

Software tools BLASTP, Clustal W, MEGA, iTOL, SWISS-MODEL, Phyre
Applications Phylogenetics, Protein structure analysis
Organisms Candidatus Liberibacter asiaticus, Diaphorina citri, Bacteria, Escherichia coli, Liberibacter crescens
Diseases Infection