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.

Download Network Files

Submission Name: IPR004184_IP74_UniRef90

Network Name: IPR004184_IP74_UniRef90_Minlen650_AS320

SSN Overview
Network Files

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

Analysis Summary

Analysis Job Number	35893
Network Name	IPR004184_IP74_UniRef90_Minlen650_AS320
Alignment Score	320
Minimum Length	650
Maximum Length	50,000
Total Number of Sequences After Filtering	4,178

Dataset Summary

EST Job Number	29536 (Original Dataset)
Database Version	UniProt: 2019-04 / InterPro: 74
Input Option	Families (Option B)
Job Name	IPR004184_IP74_UniRef90
E-Value for SSN Edge Calculation	5
Pfam / InterPro Family	IPR004184
Number of IDs in Pfam / InterPro Family	20,232
Domain Option	off
UniRef Version	90
Number of Cluster IDs in UniRef90 Family	6,020
Exclude Fragments	No
Total Number of Sequences in Dataset	6,020
Total Number of Edges	13,553,197
Convergence Ratio?	0.748

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
	4,178	104,102

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	4,178	104,102
95	4,158	102,056
90	4,104	96,665
85	3,592	59,103
80	3,114	33,614
75	2,720	18,968
70	2,382	10,211
65	2,090	6,800
60	1,826	4,761
55	1,648	3,818
50	1,513	3,171
45	1,447	2,967
40	1,361	2,777

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

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