EFI - Genome Neighborhood Tool

This web resource is supported by a Research Resource from the National Institute of General Medical Sciences (R24GM141196-01).

The tools are available without charge or license to both academic and commercial users.

RadicalSAM.org, our resource for investigating sequence-function space in the radical SAM superfamily, has been updated with sequences from the UniProt Release 2024_01 and InterPro Release 98 databases (January 24, 2024) !!

https://radicalsam.org

Results

Submitted Network Name: 26123_IP91_IPR004184_UniRef90_NoFragments_Bacteroidetes_Minlen650_AS240_PB_full_ssn

Submission Summary
Networks and GND
Other Files

The parameters for computing the GNN and associated files are summarized in the table.

Uploaded Filename	26123_IP91_IPR004184_UniRef90_NoFragments_Bacteroidetes_Minlen650_AS240_PB_full_ssn.xgmml.zip
Neighborhood Size	10
Input % Co-Occurrence	20

Please cite your use of the EFI tools:

Rémi Zallot, Nils Oberg, and John A. Gerlt, The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways. Biochemistry 2019 58 (41), 4169-4182. https://doi.org/10.1021/acs.biochem.9b00735

Nils Oberg, Rémi Zallot, and John A. Gerlt, EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. J Mol Biol 2023. https://doi.org/10.1016/j.jmb.2023.168018

Colored Sequence Similarity Network (SSN)

Each cluster in the submitted SSN has been identified and assigned a unique number and color. Node attributes for "Neighbor Pfam Families" and "Neighbor InterPro Families" have been added.

	# Nodes	# Edges	File Size (Zipped MB)
	333	13,658	<1

Genome Neighborhood Networks (GNNs)

GNNs provide a representation of the neighboring Pfam families for each SSN cluster identified in the colored SSN. To be displayed, neighboring Pfams families must be detected in the specified window and at a co-occurrence frequency higher than the specified minimum.

SSN Cluster Hub-Nodes: Genome Neighborhood Network (GNN)

Each hub-node in the network represents a SSN cluster. The spoke nodes represent Pfam families that have been identified as neighbors of the sequences from the center hub.

	File Size (Zipped MB)
	<1

Pfam Family Hub-Nodes Genome Neighborhood Network (GNN)

Each hub-node in the network represents a Pfam family identified as a neighbor. The spokes nodes represent SSN clusters that identified the Pfam family from the center hub.

	File Size (Zipped MB)
	<1

Mapping Tables, FASTA Files, ID Lists, and Supplementary Files

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