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_NoFragments Firmicutes UniRef90_NoFragments_IPR004184_Firmicutes

Network Name: IP91_IPR004184_NoFragments_Firmicutes_UniRef90_NoFragments_IPR004184_Firmicutes_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	26615
Network Name	IP91_IPR004184_NoFragments_Firmicutes_UniRef90_NoFragments_IPR004184_Firmicutes_Minlen650_AS240
Alignment Score	240
Minimum Length	650
Maximum Length	50,000
Total Number of Sequences After Filtering	2,467

Dataset Summary

EST Job Number	26149 (Original Dataset)
Database Version	UniProt: 2022-04 / InterPro: 91
Input Option	Accession IDs (Option D)
Job Name	IP91_IPR004184_NoFragments Firmicutes UniRef90_NoFragments_IPR004184_Firmicutes
Input Sequence Source	UniRef90
E-Value for SSN Edge Calculation	5
No matches file
Number of IDs in Uploaded File	2,679 (2,679 UniProt ID matches and 0 unmatched)
Taxonomy Categories	Phylum: firmicutes
Family Filter	IPR004184
Exclude Fragments	Yes
Total Number of Sequences in Dataset	2,673
Total Number of Edges	3,410,048
Number of Unique Sequences	2,673
Convergence Ratio?	0.955

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
	2,467	515,667

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	2,467	515,667
95	2,459	509,182
90	2,424	489,330
85	2,088	314,700
80	1,755	183,870
75	1,462	93,107
70	1,233	46,875
65	1,063	25,267
60	903	11,339
55	825	7,846
50	779	6,735
45	745	6,316
40	699	5,883

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

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