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providing functional annotation for these IDs are no longer active.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.
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.
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.
