EFI - Enzyme Similarity 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

Download Colored SSN Files

Uploaded Filename: 27106_IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS240_full_ssn.xgmml.zip

Six node attributes were added to the input SSN: Cluster Sequence Count, Sequence Count Cluster Number, Cluster Node Count, Node Count Cluster Number, node.fillColor (according to Cluster Sequence Count, hexadecimal), and Node Count Fill Color (according to Cluster Node Count, hexadecimal).

The Data File Download tab provides the Color SSN with the nodes colored according to Cluster Sequence Count (node.fillColor).

To change the node colors in Cytoscape to Node Count Fill Color: 1) select all nodes; 2) on the Style Panel, click on the "?" in the Fill Color Property; 3) select "Remove Bypass"; 4) deselect the nodes (now default node color); and 5) open the Fill Color Property and select "Node Count Fill Color" as the Column and "Passthrough Mapping" as the Mapping Type. The nodes will be colored with the Node Count Fill Color.

The Data File Download tab also provides files for 1) the UniProt ID-Color-Cluster Number mapping table, 2) ID Lists and FASTA Files for each cluster, 3) cluster sizes, and 4) SwissProt annotations for clusters and singletons.

Submission Summary
Data File Download

Submission Summary Table

Job Number	27114
Input Option	Color SSN
Uploaded Filename	27106_IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS240_full_ssn.xgmml.zip
Database Version	UniProt: 2022-04 / InterPro: 91
Number of SSN clusters	271
Number of SSN singletons	220
SSN sequence source	UniRef90
Number of SSN (meta)nodes	5,801
Number of accession IDs in SSN	20,000

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 SSN

Each cluster in the submitted SSN has been identified and assigned a unique number and color.

Supplementary Files

Mapping Tables
	UniProt ID-Color-Cluster number mapping table
ID Lists and FASTA Files per Cluster
	UniProt ID lists per cluster
	UniRef90 ID lists per cluster
	FASTA files per UniProt cluster
	FASTA files per UniRef90 cluster
Miscellaneous Files
	Cluster sizes
	Cluster-based convergence ratio for UniProt IDs
	SwissProt annotations by cluster

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