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.
RadicalSAM.org, our resource for investigating sequence-function space in the radical SAM superfamily, has been updated with sequences from the UniProt Release 2024_01 and InterPro Release 98 databases (January 24, 2024) !!
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.
