Knowledge-based Identification of Pathway Enzymes

Knowledge-based Identification of Pathway Enzymes (KIPEs) identifies and characterizes enzymes involved in metabolic pathways, with emphasis on flavonoid biosynthesis, by combining sequence similarity analysis with inspection of functionally relevant amino acid residues and domains in peptide sequences.

Key Features:

• Sequence Similarity Analysis: Comprehensive sequence similarity assessments map candidate peptide sequences from transcriptome assemblies or genomic data to known pathway enzymes.
• Functional Amino Acid Inspection: Examination of functionally relevant amino acid residues and domains refines predictions of enzyme functionality and specificity.
• Knowledge Integration: Compilation and use of datasets of known flavonoid biosynthesis enzymes and associated functional residues provide a reference framework for annotation.

Scientific Applications:

• Flavonoid Biosynthesis Studies: Identification and characterization of enzymes involved in plant flavonoid biosynthetic pathways.
• Enzyme Discovery and Annotation: Annotation of pathway enzymes and discovery of novel enzymatic candidates from transcriptome and genome data.
• Applied Case Study: Analysis of Croton tiglium transcriptome to recover enzyme candidates for all steps of the flavonoid biosynthetic network and compare with reported metabolites.

Methodology:

Compile comprehensive datasets of known flavonoid biosynthesis enzymes including functionally relevant amino acids; perform sequence similarity analysis of candidate sequences from transcriptome assemblies or genomic data against the dataset; validate identified candidates by inspecting specific amino acid residues and domains critical to enzyme activity.