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.

Download Colored SSN Files

Uploaded Filename: 29537_IPR004184_IP74_UniRef50_Minlen650_AS240_full_ssn.xgmml

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	29548
Input Option	Color SSN
Uploaded Filename	29537_IPR004184_IP74_UniRef50_Minlen650_AS240_full_ssn.xgmml
Database Version	UniProt: 2019-04 / InterPro: 74
Number of SSN clusters	234
Number of SSN singletons	174
SSN sequence source	UniRef50
Number of SSN (meta)nodes	520
Number of accession IDs in SSN	16,292

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
	UniRef50 ID lists per cluster
	FASTA files per cluster
Miscellaneous Files
	Cluster sizes
	SwissProt annotations by cluster

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