EFI - Genome Neighborhood Tool

The Nugget

EFI-GNT is a web tool that analyzes genome neighborhoods in bacteria and fungi to provide insights into the metabolic function and activity of uncharacterized enzymes, increasing the confidence of predictions through a combination of sequence homology and genomic context information.

Key quotes

"Analysis of the genome neighborhood for an uncharacterized enzyme may provide genomic context, providing insights into its activity and metabolic function."
"The GNNs generated by EFI-GNT identify the protein families encoded by genes proximal to the input sequences, offering valuable information about the types of reactions catalyzed by the genome neighbors."
"The large-scale collection and organization of genome context enabled by EFI-GNT may allow the identification of enzymes in metabolic pathways that are not co-localized in the user’s 'target' organism."

Genes encoding metabolic pathways in bacteria and fungi are often co-localized in the genome.
Analysis of the genome neighborhood can offer insights into the activity and metabolic function of uncharacterized enzymes.
The combination of sequence homology and genome context information enhances the confidence of predictions.

Using SSN for Queries:
- GNN organizes proteins encoded by the genome neighborhood for each query sequence based on Pfam family.
- The GNNs identify protein families near the query sequences, providing information on the types of reactions catalyzed by these neighbors.
Two GNN Formats:
- SSN Cluster Hub-Nodes Format:
  - SSN clusters with query genes are central hubs in GNN, with neighboring Pfam families depicted as spoke-nodes.
  - Enables the identification of potential pathway members linked to query sequences and inference of reactions.
- Pfam Family Hub-Nodes Format:
  - Each neighborhood Pfam family is central in a GNN cluster, with SSN clusters finding these families as neighbors depicted around them.
  - Helps assess if clusters in the query SSN are isofunctional and identifies members with different functions.

💡 Use EFI-GNT to analyze genome neighborhoods in bacteria and fungi for valuable insights into enzyme functions and metabolic pathways.
🧬 GNNs generated by EFI-GNT organize proteins based on Pfam family, aiding in the identification of potential pathway members and types of reactions catalyzed.
🌐 EFI-GNT allows for high-throughput acquisition and organization of genome context, increasing the confidence of enzyme function predictions.
🔬 Understand the advantages of utilizing genome context information alongside sequence homology in predicting metabolic pathways and enzyme functions.

This summary contains AI-generated information and may have important inaccuracies or omissions.