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.
Option C now uses the sequences supplied in the FASTA file to calculate edge values and the IDs in the headers to retrieve node attribute information from UniProt. Like Option D, the user can specify that the input sequences are UniProt, UniRef90, or UniRef50 for retrieval of node attribute information.

Download Network Files

Submission Name: IP91_IPR004184_UniRef90_NoFragments

Network Name: IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS90

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

Analysis Summary

Analysis Job Number26583
Network NameIP91_IPR004184_UniRef90_NoFragments_Minlen650_AS90
Alignment Score90
Minimum Length650
Maximum Length50,000
Total Number of Sequences After Filtering5,801

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
5,801 5,336,053

 

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 5,801 5,336,053
95 5,772 5,271,892
90 5,681 5,076,383
85 4,964 3,713,147
80 4,264 2,618,535
75 3,708 1,910,970
70 3,184 1,329,162
65 2,762 949,780
60 2,400 692,978
55 2,162 563,158
50 1,983 453,503
45 1,879 391,357
40 1,728 305,683

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

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