Computational protocol: Vibrio Type III Effector VPA1380 Is Related to the Cysteine Protease Domain of Large Bacterial Toxins

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Protocol publication

[…] VPA1380-related sequences were collected using default settings of BLAST against the NR database with the sequence query (GI|28901235|). To identify the closest related structures, we queried the PDB70 database (April 10, 2014) with the same sequence using the HHPRED server . VPA1380-related sequences were aligned to the top identified structure sequences (3fzy A, 3pa8A, and 3ho6A) using PROMALS3D , with manual adjustments guided by secondary structure predictions for VPA1380 (JPRED server ), HHPRED alignments, and conserved hydrophobicity patterns. The resulting alignment extended the initial HHPRED alignment to include the VPA1380 C-terminus, but is lacking a portion of the N-terminus (starts at residue 116). […]

Pipeline specifications

Software tools HHPred, PROMALS3D, JPred
Applications Protein structure analysis, Amino acid sequence alignment
Organisms Vibrio parahaemolyticus, Saccharomyces cerevisiae
Diseases Foodborne Diseases, Drug-Related Side Effects and Adverse Reactions
Chemicals Cysteine, Phytic Acid