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_UniRef50

Network Name: IPR004184_IP74_UniRef50_Minlen650_AS240

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	35895
Network Name	IPR004184_IP74_UniRef50_Minlen650_AS240
Alignment Score	240
Minimum Length	650
Maximum Length	50,000
Total Number of Sequences After Filtering	520

Dataset Summary

EST Job Number	29537 (Original Dataset)
Database Version	UniProt: 2019-04 / InterPro: 74
Input Option	Families (Option B)
Job Name	IPR004184_IP74_UniRef50
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	50
Number of Cluster IDs in UniRef50 Family	1,365
Exclude Fragments	No
Total Number of Sequences in Dataset	1,365
Total Number of Edges	449,488
Convergence Ratio?	0.483

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
	520	179

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	520	179
95	519	174
90	519	174
85	518	165
80	517	164
75	517	164
70	516	163
65	516	163
60	516	163
55	516	163
50	515	160
45	511	158
40	496	146

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

Click here to contact us for help, reporting issues, or suggestions.

% ID	# Nodes	# Edges
100	520	179
95	519	174
90	519	174
85	518	165
80	517	164
75	517	164
70	516	163
65	516	163
60	516	163
55	516	163
50	515	160
45	511	158
40	496	146

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% ID	# Nodes	# Edges
100	520	179
95	519	174
90	519	174
85	518	165
80	517	164
75	517	164
70	516	163
65	516	163
60	516	163
55	516	163
50	515	160
45	511	158
40	496	146

% ID	# Nodes	# Edges
100	520	179
95	519	174
90	519	174
85	518	165
80	517	164
75	517	164
70	516	163
65	516	163
60	516	163
55	516	163
50	515	160
45	511	158
40	496	146