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) !!
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 Sequence Similarity Network (SSN)
Each cluster in the submitted SSN has been identified and assigned a unique number and color.
Node attributes for "Neighbor Pfam Families" and "Neighbor InterPro Families" have been added.
# Nodes
# Edges
File Size (Zipped MB)
5,419
2,021,943
48
Genome Neighborhood Networks (GNNs)
GNNs provide a representation of the neighboring Pfam families for each SSN
cluster identified in the colored SSN. To be displayed, neighboring Pfams
families must be detected in the specified window and at a co-occurrence
frequency higher than the specified minimum.
Each hub-node in the network represents a SSN cluster. The spoke nodes
represent Pfam families that have been identified as neighbors of the sequences
from the center hub.
File Size (Zipped MB)
3
Pfam Family Hub-Nodes Genome Neighborhood Network (GNN)
Each hub-node in the network represents a Pfam family identified as a neighbor.
The spokes nodes represent SSN clusters that identified the Pfam family from
the center hub.
File Size (Zipped MB)
5
Genome Neighborhood Diagrams (GNDs)
Diagrams representing genomic regions around the genes encoded for the
sequences from the submitted SSN are generated. All genes present in the
specified window can be visualized
(no minimal co-occurrence frequency filter or neighborhood size threshold is applied).
Diagram data can be downloaded in .sqlite file format for later review in the View Saved Diagrams tab.
Action
File Size (Zipped MB)
Opens GND explorer in a new tab.
Diagram data for later review
157
Mapping Tables, FASTA Files, ID Lists, and Supplementary Files
Mapping Tables
Neighbor Pfam domain fusions at specified minimal co-occurrence frequency
3 MB
Neighbor Pfam domains at specified minimal co-occurrence frequency
4 MB
Neighbor Pfam domain fusions at 0% minimal co-occurrence frequency
11 MB
Neighbor Pfam domains at 0% minimal co-occurrence frequency
12 MB
Neighbors without Pfam assigned
<1 MB
Miscellaneous Files
No matches/no neighbors file
<1 MB
Pfam family/cluster co-occurrence table file
3 MB
GNN hub cluster sequence count file
<1 MB
Cluster size file
<1 MB
SwissProt annotations per SSN cluster
<1 MB
SwissProt annotations by singleton
<1 MB
Please change parameters or select a new file to upload before refiltering.