CyanoLyase

CyanoLyase curates sequences and amino-acid motifs of phycobilin lyases and related proteins to identify and classify enzymes that catalyze covalent attachment of phycobilins to phycobiliproteins and to support prediction of chromophorylation patterns in PBPs from cyanobacteria and red algae.

Key Features:

• Sequence aggregation: Aggregates phycobilin lyase and related protein sequences from available genomes using similarity searches seeded with biochemically characterized enzyme sequences.
• Classification: Organizes curated sequences into three clans and 32 families.
• Amino-acid motif computation: Computes family-specific amino-acid motifs using the Protomata learner.
• BLAST: Enables sequence similarity searches against the curated lyase sequence set.
• Protomatch: Implements a pattern-matching approach to rapidly identify and annotate lyases in new genomes.
• Phylogenetic analyses: Performs phylogenetic analyses to resolve evolutionary relationships among phycobilin lyase families.
• Functional descriptions and phyletic profiles: Provides functional annotations and presence/absence profiles across genomes to inform family function and distribution.
• Chromophorylation prediction: Predicts chromophorylation patterns of phycobiliproteins for different strains based on lyase annotations and motifs.
• Bibliography: Curates an extensive bibliography on phycobilin lyases and the genomes included in the database.

Scientific Applications:

• Genome annotation: Identification and annotation of phycobilin lyases in cyanobacterial and red algal genomes.
• Comparative genomics: Analysis of phyletic profiles to compare lyase family distribution across strains and species.
• Evolutionary studies: Reconstruction of evolutionary relationships among phycobilin lyase families using phylogenetic analyses.
• Chromophorylation prediction: Prediction of chromophore attachment sites and chromophorylation patterns in phycobiliproteins.
• Protein engineering and biotechnology: Informing design and selection of natural or synthetic PBPs for applications such as fluorescent markers.

Methodology:

Sequences are collected by similarity searches seeded with biochemically characterized enzymes, classified into three clans and 32 families, motifs are computed with the Protomata learner, and annotation/identification uses BLAST, Protomatch pattern matching, and phylogenetic analyses.