FunTree

FunTree integrates sequence, structure, phylogenetic, chemical, and mechanistic data to analyze enzyme function evolution within structurally defined superfamilies.

Key Features:

• Integrated Data Resources: Integrates sequence, structural, phylogenetic, chemical, and mechanistic datasets linked to structurally defined superfamilies and CATH classifications.
• Phylogenetic Analysis: Constructs phylogenetic trees from structurally informed multiple sequence alignments using domain-specific structural alignments supplemented with sequences and whole-sequence alignments based on shared multi-domain architectures.
• Functional Annotations: Annotates phylogenetic trees with metabolite similarity assessments and enzyme mechanism details sourced from the Catalytic Site Atlas and MACiE.
• Coverage: Encompasses 276 superfamilies, approximately 1800 enzyme reactions, and about 70% of sequence-assigned enzyme activities.

Scientific Applications:

• Evolutionary Studies: Investigate how novel enzymatic activities have emerged within structurally conserved superfamilies.
• Functional Analysis: Compare trends of enzyme functions and catalytic roles across multiple superfamilies.
• Mechanistic Insights: Relate catalytic mechanisms and active-site annotations to structural and evolutionary contexts using Catalytic Site Atlas and MACiE-derived information.

Methodology:

Constructs structurally informed multiple sequence alignments and phylogenetic trees from domain-specific structural alignments supplemented with sequences and whole-sequence alignments based on shared multi-domain architectures, and annotates trees with metabolite similarity metrics and mechanistic annotations from the Catalytic Site Atlas and MACiE.