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.

Reorganization of UniProtKB

With the current 2026_02 release, the UniProtKB database is reorganized to include an expanded number of Reference Proteomes to better capture biodiversity. This includes the removal of proteins from taxonomically unclassified organisms, i.e., those without a binomial species name (genus and species). The total number of accessions in UniProtKB has been reduced from 253,635,358 in the “legacy” 2025_03 release to 149,810,139 in the current 2026_02 release.

We are providing the option to select either the “legacy” 2025_03 database or the current UniProtKB database (now 2026_02) when generating SSNs. You can select the database in the “Database” accordion on the pages for the EFI-EST options, the EFI-GNT tool, and the Taxonomy Tool. We suggest that you compare the SSNs, GNNs, and GNDs generated from both databases as you explore the information you are seeking.

Because the “legacy” 2025_03 release contains UniProt IDs that are no longer active on the UniProt web site, we provide the Metadata Tool that provides access to the node attribute metadata for the UniProt IDs in the “legacy” 2025_03 release.

Download Network Files

Submission Name: IPR004184_IP74_UniRef90

Network Name: IPR004184_IP74_UniRef90_Minlen650_AS240

SSN Overview
Network Files

The parameters used for the initial submission and the finalization are summarized in the table below.

Analysis Summary

Analysis Job Number	35892
Network Name	IPR004184_IP74_UniRef90_Minlen650_AS240
Alignment Score	240
Minimum Length	650
Maximum Length	50,000
Total Number of Sequences After Filtering	4,178

Dataset Summary

EST Job Number	29536 (Original Dataset)
Database Version	UniProt: 2019-04 / InterPro: 74
Input Option	Families (Option B)
Job Name	IPR004184_IP74_UniRef90
E-Value for SSN Edge Calculation	5
Pfam / InterPro Family	IPR004184
Number of IDs in Pfam / InterPro Family	20,232
Domain Option	off
UniRef Version	90
Number of Cluster IDs in UniRef90 Family	6,020
Exclude Fragments	No
Total Number of Sequences in Dataset	6,020
Total Number of Edges	13,553,197
Convergence Ratio?	0.748

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

The panels below provide files for full and representative node SSNs for download with the indicated numbers of nodes and edges. As an approximate guide, SSNs with ~2M edges can be opened with 16 GB RAM, ~5M edges can be opened with 32 GB RAM, ~10M edges can be opened with 64 GB RAM, ~20M edges can be opened with 128 GB RAM, ~40M edges can be opened with 256 GB RAM, and ~120M edges can be opened with 768 GB RAM.

Files may be transferred to the Genome Neighborhood Tool (GNT), the Color SSN utility, the Cluster Analysis utility, or the Neighborhood Connectivity utility.

Full Network ?

Each node in the network represents a single protein sequence.

	# Nodes	# Edges
	4,178	1,187,272

Representative Node Networks ?

In representative node (RepNode) networks, each node in the network represents a collection of proteins grouped according to percent identity. For example, for a 75% identity RepNode network, all connected sequences that share 75% or more identity are grouped into a single node (meta node). Sequences are collapsed together to reduce the overall number of nodes, making for less complicated networks easier to load in Cytoscape.

The cluster organization is not changed, and the clustering of sequences remains identical to the full network.

% ID	# Nodes	# Edges
100	4,178	1,187,272
95	4,158	1,168,872
90	4,104	1,115,997
85	3,592	723,325
80	3,114	450,040
75	2,720	266,863
70	2,382	150,891
65	2,090	79,301
60	1,826	35,250
55	1,648	19,635
50	1,513	13,805
45	1,447	12,492
40	1,361	11,841

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Portions of these data are derived from the Universal Protein Resource (UniProt) databases.

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