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.
RadicalSAM.org, our resource for investigating sequence-function space in the radical SAM superfamily, has been updated with sequences from the UniProt Release 2024_01 and InterPro Release 98 databases (January 24, 2024) !!

https://radicalsam.org

Download Network Files

Submission Name: IP91_IPR004184_UniRef90_NoFragments_Archaea

Network Name: IP91_IPR004184_UniRef90_NoFragments_Archaea_Minlen650_AS240

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

Analysis Summary

Analysis Job Number26602
Network NameIP91_IPR004184_UniRef90_NoFragments_Archaea_Minlen650_AS240
Alignment Score240
Minimum Length650
Maximum Length50,000
Total Number of Sequences After Filtering263

Dataset Summary

EST Job Number26135 (Original Dataset)
Database VersionUniProt: 2022-04 / InterPro: 91
Input OptionFamilies (Option B)
Job NameIP91_IPR004184_UniRef90_NoFragments_Archaea
E-Value for SSN Edge Calculation5
Pfam / InterPro FamilyIPR004184
Number of IDs in Pfam / InterPro Family25,513
Domain Optionoff
UniRef Version90
Number of Cluster IDs in UniRef90 Family340
Taxonomy Categories:Archaea
Exclude FragmentsYes
Total Number of Sequences in Dataset340
Total Number of Edges52,654
Number of Unique Sequences340
Convergence Ratio?0.914
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
263 2,074

 

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
100 263 2,074
95 263 2,074
90 261 2,041
85 242 1,651
80 229 1,456
75 213 1,146
70 197 857
65 179 580
60 171 522
55 167 452
50 164 421
45 163 414
40 161 405

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

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