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_UniProt_NoFragments

Network Name: IP91_IPR004184_UniProt_NoFragments_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	27256
Network Name	IP91_IPR004184_UniProt_NoFragments_Minlen650_AS240
Alignment Score	240
Minimum Length	650
Maximum Length	50,000
Total Number of Sequences After Filtering	20,089

Dataset Summary

EST Job Number	26121 (Original Dataset)
Database Version	UniProt: 2022-04 / InterPro: 91
Input Option	Families (Option B)
Job Name	IP91_IPR004184_UniProt_NoFragments
E-Value for SSN Edge Calculation	5
Pfam / InterPro Family	IPR004184
Number of IDs in Pfam / InterPro Family	21,636
Fraction Option	off
Domain Option	off
Exclude Fragments	Yes
Total Number of Sequences in Dataset	21,636
Total Number of Edges	217,671,851
Number of Unique Sequences	17,505
Convergence Ratio?	0.930

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
	20,089	47,499,276

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	15,986	27,061,467
95	7,879	4,912,158
90	6,623	2,928,401
85	5,685	1,783,730
80	4,903	1,112,553
75	4,237	636,171
70	3,631	325,427
65	3,149	161,485
60	2,759	75,869
55	2,461	38,497
50	2,247	26,146
45	2,113	22,903
40	1,937	19,798

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

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