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: 29536_IPR004184_IP74_UniRef90_Minlen650_AS240_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	29536_IPR004184_IP74_UniRef90_Minlen650_AS240_full_ssn.xgmml
Neighborhood Size	10
Input % Co-Occurrence	10
Number of SSN clusters	200
Number of SSN singletons	196
SSN sequence source	UniRef90
Number of SSN (meta)nodes	4,178
Number of accession IDs in SSN	16,274

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)
	4,178	1,187,272	29

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)
	3

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)
	6

Genome Neighborhood Diagrams (GNDs)

Diagrams representing genomic regions around the genes encoded for the sequences from the submitted SSN are generated. All genes present in the specified window can be visualized (no minimal co-occurrence frequency filter or neighborhood size threshold is applied). Diagram data can be downloaded in .sqlite file format for later review in the View Saved Diagrams tab.

Action		File Size (Zipped MB)
	Opens GND explorer in a new tab.
	Diagram data for later review	149

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

Mapping Tables
	Neighbor Pfam domain fusions at specified minimal co-occurrence frequency	3 MB
	Neighbor Pfam domains at specified minimal co-occurrence frequency	4 MB
	Neighbor Pfam domain fusions at 0% minimal co-occurrence frequency	9 MB
	Neighbor Pfam domains at 0% minimal co-occurrence frequency	10 MB
Data Files per SSN Cluster
	UniProt ID lists per cluster	<1 MB
	UniRef90 ID lists per cluster	<1 MB
	FASTA files per cluster	6 MB
	Neighbors without Pfam assigned	<1 MB
Miscellaneous Files
	No matches/no neighbors file	<1 MB
	Pfam family/cluster co-occurrence table file	2 MB
	GNN hub cluster sequence count file	<1 MB
	Cluster size file	<1 MB
	SwissProt annotations per SSN cluster	<1 MB
	SwissProt annotations by singleton	<1 MB

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