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.
Important Notice
The UniProtKB database used by the EFI tools is undergoing major reorganization
starting with the just-released version 2025_04
(https://www.uniprot.org/help/refprot_only_changes).
When the reorganization is
fully implemented (2026_02 release, Spring 2026), the number of proteins in
UniProtKB will decrease from ~253M accessions in the previous 2025_03 release
to ~141M accessions in the 2026_02 release.
In response to these changes, we will provide the previous 2025_03 release
until the 2026_02 release is available.
The current 2025_04 release removed 82M UniProt IDs; the UniProt pages
providing functional annotation for these IDs are no longer active. A new
Metadata Tool
provides access to the node attribute metadata for all UniProt
IDs in the 2025_03 release that the tools continue to use during the UniProtKB
reorganization. The Tool is available using the tab at the top of each page.
More information about the reorganization is located here.
Two node attributes were added to the input SSN: 1) Neighborhood Connectivity
that quantitates the internode connections and 2) Neighborhood Connectivity Coloring
that assigns a color based on the value of the NC.
The Data File Download tab provides the SSN with the nodes colored according to
the value of the Neighborhood Connectivity Coloring.
The Neighborhood Connectivity Color Scale download provides the color scale in
the SSN.
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 node in the submitted SSN has been colored by NC, and a Neighborhood Connectivity attribute
has been added with the NC factor.
