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 Actinobacteria UniRef90_NoFragments_IPR004184_Actinobacteria

Network Name: IP91_IPR004184_NoFragments_Actinobacteria_UniRef90_NoFragments_IPR004184_Actinobacteria_Minlen650_AS240

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

Analysis Summary

Analysis Job Number26614
Network NameIP91_IPR004184_NoFragments_Actinobacteria_UniRef90_NoFragments_IPR004184_Actinobacteria_Minlen650_AS240
Alignment Score240
Minimum Length650
Maximum Length50,000
Total Number of Sequences After Filtering488

Dataset Summary

EST Job Number26147 (Original Dataset)
Database VersionUniProt: 2022-04 / InterPro: 91
Input OptionAccession IDs (Option D)
Job NameIP91_IPR004184_NoFragments Actinobacteria UniRef90_NoFragments_IPR004184_Actinobacteria
Input Sequence SourceUniRef90
E-Value for SSN Edge Calculation5
No matches file
Number of IDs in Uploaded File525 (525 UniProt ID matches and 0 unmatched)
Taxonomy CategoriesPhylum: actinobacteria
Family FilterIPR004184
Exclude FragmentsYes
Total Number of Sequences in Dataset522
Total Number of Edges129,212
Number of Unique Sequences522
Convergence Ratio?0.950
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
488 64,199


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
100 488 64,199
95 483 62,561
90 475 60,153
85 394 38,539
80 293 19,248
75 236 10,206
70 179 4,041
65 163 2,975
60 153 2,525
55 145 2,141
50 142 2,046
45 141 1,981
40 141 1,981

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

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