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.
The new Taxonomy Tool and Filter by Taxonomy feature facilitate higher resolution analyses of focused regions of sequence-function space using UniProt IDs instead of UniRef90 clusters or UniRef90 clusters instead of UniRef50 clusters. The J Mol Biol article describing these is available on the JMB Resources training page.
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
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
Each node in the submitted SSN has been colored by NC, and a Neighborhood Connectivity attribute
has been added with the NC factor.