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: IP91_IPR004184_UniRef90_NoFragments

Network Name: IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS120

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	27280
Network Name	IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS120
Alignment Score	120
Minimum Length	650
Maximum Length	50,000
Total Number of Sequences After Filtering	5,801

Dataset Summary

EST Job Number	27106 (Original Dataset)
Database Version	UniProt: 2022-04 / InterPro: 91
Input Option	Families (Option B)
Job Name	IP91_IPR004184_UniRef90_NoFragments
E-Value for SSN Edge Calculation	5
Pfam / InterPro Family	IPR004184
Number of IDs in Pfam / InterPro Family	25,513
Domain Option	off
UniRef Version	90
Number of Cluster IDs in UniRef90 Family	6,937
Exclude Fragments	Yes
Total Number of Sequences in Dataset	6,937
Total Number of Edges	20,963,002
Number of Unique Sequences	6,937
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	3,744,673

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	3,744,673
95	5,772	3,692,502
90	5,681	3,529,963
85	4,964	2,452,601
80	4,264	1,607,807
75	3,708	1,084,571
70	3,184	688,226
65	2,762	448,791
60	2,400	294,464
55	2,162	224,139
50	1,983	172,932
45	1,879	145,105
40	1,728	106,903

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

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