metagRoot

metagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize enriched protein families associated with plant root microbiomes and provide comprehensive annotations with ecological and structural context.

Key Features:

• Protein Family Characterization: Characterizes 71,091 enriched protein families, each containing at least 100 sequences.
• Multiple Sequence Alignments: Provides multiple sequence alignments for each protein family.
• CRISPR Element Annotation: Annotates protein families with CRISPR elements.
• Hidden Markov Models: Includes Hidden Markov Models for protein family representation.
• Taxonomic and Functional Classifications: Assigns taxonomic and functional classifications to protein families.
• Ecosystem and Geolocation Metadata: Enriches protein families with ecosystem and geolocation metadata.
• Predicted 3D Structures: Provides predicted 3D structures using AlphaFold2.

Scientific Applications:

• Root Microbiome Molecular Landscape: Decodes the molecular landscape of root-associated microbial communities.
• Microbiome-Informed Agriculture: Advances microbiome-informed agricultural practices by integrating ecological and structural context.

Methodology:

Protein families are predicted using AlphaFold2 for 3D structure prediction and annotated with multiple sequence alignments, CRISPR elements, Hidden Markov Models, taxonomic and functional classifications, and ecosystem and geolocation metadata.