ProtScreen

ProtScreen analyzes proteomes from lactic acid bacteria species, including Lactobacilli, Enterococci, Lactococci, Carnobacteria, and Leuconostocs, using sequences from UniProt and NCBI to identify Sortase A Dependent Proteins (SDPs) and characterize LPXTG motifs.

Key Features:

• Proteome scope: Analyzes proteomes from lactic acid bacteria (Lactobacilli, Enterococci, Lactococci, Carnobacteria, Leuconostocs).
• Data sources: Processes genomic and proteomic sequences obtained from UniProt and NCBI.
• SDP identification: Identifies Sortase A Dependent Proteins (SDPs) from input sequences.
• Motif recognition: Recognizes the LPXTG motif critical for sortase A recognition and cleavage and analyzes the X-position variability.
• Frequency analysis: Computes frequency and abundance of amino acids at the X position within the LPXTG motif across LAB strains.
• Docking simulations: Performs docking simulations to assess interaction dynamics between sortase A and SDPs.

Scientific Applications:

• Understanding Probiotic Persistence: Elucidates mechanisms of bacterial attachment to the host intestine via sortase A and SDPs, enhancing understanding of probiotic persistence in the gut.

Methodology:

Extracts data from established databases, performs motif recognition using built-in algorithms, conducts frequency analysis of amino acids in the LPXTG motif, and performs docking simulations to assess interaction dynamics between sortase A and SDPs.