EFI - Enzyme Similarity Tool

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) !!

https://radicalsam.org

Download Network Files

Submission Name: IP91_IPR004184_UniRef90_NoFragments

Network Name: IP91_IPR004184_UniRef90_NoFragments_Bacteroidetes_Minlen650_AS240

The parameters used for the initial submission and the finalization are summarized in the table below.

Analysis Summary

Analysis Job Number26591
Network NameIP91_IPR004184_UniRef90_NoFragments_Bacteroidetes_Minlen650_AS240
Alignment Score240
Taxonomy CategoriesPhylum: Bacteroidetes
Minimum Length650
Maximum Length50,000
Total Number of Sequences After Filtering333

Dataset Summary

EST Job Number26123 (Original Dataset)
Database VersionUniProt: 2022-04 / InterPro: 91
Input OptionFamilies (Option B)
Job NameIP91_IPR004184_UniRef90_NoFragments
E-Value for SSN Edge Calculation5
Pfam / InterPro FamilyIPR004184
Number of IDs in Pfam / InterPro Family25,513
Domain Optionoff
UniRef Version90
Number of Cluster IDs in UniRef90 Family6,937
Exclude FragmentsYes
Total Number of Sequences in Dataset6,937
Total Number of Edges20,962,994
Number of Unique Sequences6,937
Convergence Ratio?0.871
Please cite your use of the EFI tools:

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

The panels below provide files for full and representative node SSNs for download with the indicated numbers of nodes and edges. As an approximate guide, SSNs with ~2M edges can be opened with 16 GB RAM, ~5M edges can be opened with 32 GB RAM, ~10M edges can be opened with 64 GB RAM, ~20M edges can be opened with 128 GB RAM, ~40M edges can be opened with 256 GB RAM, and ~120M edges can be opened with 768 GB RAM.

Files may be transferred to the Genome Neighborhood Tool (GNT), the Color SSN utility, the Cluster Analysis utility, or the Neighborhood Connectivity utility.

Full Network ?

Each node in the network represents a single protein sequence.

# Nodes # Edges
333 13,658

 

Representative Node Networks ?

In representative node (RepNode) networks, each node in the network represents a collection of proteins grouped according to percent identity. For example, for a 75% identity RepNode network, all connected sequences that share 75% or more identity are grouped into a single node (meta node). Sequences are collapsed together to reduce the overall number of nodes, making for less complicated networks easier to load in Cytoscape.

The cluster organization is not changed, and the clustering of sequences remains identical to the full network.

% ID # Nodes # Edges
100 333 13,658
95 332 13,542
90 327 13,067
85 267 8,374
80 216 5,100
75 185 3,476
70 163 2,242
65 138 1,251
60 126 857
55 120 749
50 112 597
45 110 577
40 109 576

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Portions of these data are derived from the Universal Protein Resource (UniProt) databases.

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