Computational protocol: An aspartyl cathepsin, CTH3, is essential for proprotein processing during secretory granule maturation in Tetrahymena thermophila

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Protocol publication

[…] Using protein BLAST (blastp), the T. thermophila CTH1, CTH2, and CTH3 genes were used to identify potential homologues in ciliates, apicomplexans, Arabidopsis, and H. sapiens, listed in Supplemental Table S3. Similarly, the T. thermophila CAR1 sequence was used to identify homologues in ciliates, listed in Supplemental Table S4. For tree building, the top hits were selected from each lineage, assembled, and aligned with ClustalX (1.8), and maximum-likelihood trees were constructed with MEGA5 (Molecular Evolutionary Genetics Analysis: www.megasoftware.net/). Gapped regions were excluded in a complete manner, and percentage bootstrap values from 1000 replicates were derived. [...] The coding sequence of the aspartic proteases, cysteine proteases, and zinc carboxypeptidase were analyzed for conserved active site residues by the National Center for Biotechnology Information Conserved Domain Database and protein BLAST () and for signal peptides by SignalP (). Alignment of protein sequences was performed using ClustalX (1.8) with default parameters. […]

Pipeline specifications

Software tools DELTA-BLAST, BLASTP, Clustal W, MEGA, SignalP
Applications Phylogenetics, Amino acid sequence alignment
Organisms Tetrahymena thermophila