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Because the “legacy” 2025_03 release contains UniProt IDs that are no longer active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.
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.
