Computational protocol: Prediction of Extracellular Proteases of the Human Pathogen Helicobacter pylori Reveals Proteolytic Activity of the Hp1018/19 Protein HtrA

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Protocol publication

[…] Proteases were compiled for the reference data set by selecting all entries from the UniProtKB/SwissProt database (version 6.7) containing the keyword “protease”, but lacking the phrases “inhibitor*”, “probable*”, “fragment*”, “hypothetical*”, “putative*”, “possible*” or “predicted*” in the keyword and description fields, where the asterisk is a wildcard for any arbitrary suffix. The NCBI BLAST package was employed for pairwise sequence alignment . The Blastp program was used for protein-protein comparison. Tblastn was used to compare the whole DNA sequence of H. pylori strain 26695 with the protease sequence set. The substitution matrices PAM30, PAM70, PAM250, BLOSUM45, BLOSUM62 and BLOSUM80 were used with default parameter settings (e.g. scoring penalties, window size). […]

Pipeline specifications

Databases UniProtKB
Application Amino acid sequence alignment
Organisms Helicobacter pylori, Homo sapiens
Diseases Neoplasms, Stomach Neoplasms