EFI - Taxonomy 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.

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

Update of EFI Tools

The EFI Tools are being upgraded on 10/26/26. The site will not be available from 10/23-10/26 for maintenance.

While the updated site is functionally identical to the old site, jobs run prior to that date will only be available through the results link in the finalization email (not the Previous Jobs tab). User accounts created on the old site will no longer be available, and users are encouraged to create new accounts when the upgraded site becomes available.

As the UniProt database increases in size, users may encounter difficulties in opening and visualizing SSNs with Cytoscape (too many nodes/edges for the RAM available on the user’s computer). As a result, low resolution SSNs (UniRef50 clusters and/or representative node SSNs) may be necessary to survey sequence-function space in large protein families. A solution for generating higher resolution SSNs is to restrict the input sequences to specific taxonomy categories (within the Superkingdom, Kingdom, Phylum, Class, Order, Family, Genus, or Species), thereby reducing the number of nodes/edges and/or allowing the use of UniRef90 clusters or UniProt members to generate the SSN.

This Taxonomy Tool provides a preview of the taxonomy distribution of the UniProt IDs in datasets with three input options: Families, list of families; FASTA, FASTA-formatted sequences; Accession IDs, UniProt, UniRef90 cluster, or UniRef50 cluster IDs. These are analogous to the Families option (Option B), FASTA option (Option C) and Accession IDs option (Option D) of EFI-EST.

The taxonomy distribution of the UniProt IDs in the input dataset is displayed as a "sunburst" in which the ranks of classification (Superkingdom, Kingdom, Phylum, Class, Order, Family, Genus, Species) are displayed radially, with Superkingdom at the center and Species in the outer ring. The sunburst is interactive, providing the ability to zoom to a selected taxonomy category. The numbers of UniProt IDs, UniRef90 cluster IDs, and UniRef50 cluster IDs in the selected category are displayed.

UniRef90 clusters contain sequences that share ≥90% sequence identity so usually are taxonomically homogeneous. UniRef50 clusters contain sequences that share ≥50% sequence identity, so often are taxonomically heterogeneous. When possible (determined by the RAM available to Cytoscape), users should generate taxonomy-specific SSNs with UniProt IDs or UniRef90 cluster IDs.

Files with the UniProt, UniRef90 cluster, and UniRef50 cluster IDs and FASTA-formatted sequences at the selected taxonomy category can be downloaded.

The UniProt, UniRef90, or UniRef50 cluster IDs can be transferred to the "Accession IDs" option (Option D) of EFI-EST to generate the SSN.

The Sequence BLAST, Families, FASTA, and Accession IDs options of EFI-EST also include Filter by Taxonomy in both the Generate and Database Completed/Analysis steps so that the user can select specific taxonomy categories when generating SSNs.

Information on Pfam families and clans and InterPro family sizes is available on the Family Information page.

Submission is currently disabled due to site maintenance.

UniProt Version: 2026_02
InterPro Version: 109

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