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_NoFragments Firmicutes UniRef90_NoFragments_IPR004184_Firmicutes

Network Name: IP91_IPR004184_NoFragments_Firmicutes_UniRef90_NoFragments_IPR004184_Firmicutes_Minlen650_AS240

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

Analysis Summary

Analysis Job Number26615
Network NameIP91_IPR004184_NoFragments_Firmicutes_UniRef90_NoFragments_IPR004184_Firmicutes_Minlen650_AS240
Alignment Score240
Minimum Length650
Maximum Length50,000
Total Number of Sequences After Filtering2,467

Dataset Summary

EST Job Number26149 (Original Dataset)
Database VersionUniProt: 2022-04 / InterPro: 91
Input OptionAccession IDs (Option D)
Job NameIP91_IPR004184_NoFragments Firmicutes UniRef90_NoFragments_IPR004184_Firmicutes
Input Sequence SourceUniRef90
E-Value for SSN Edge Calculation5
No matches file
Number of IDs in Uploaded File2,679 (2,679 UniProt ID matches and 0 unmatched)
Taxonomy CategoriesPhylum: firmicutes
Family FilterIPR004184
Exclude FragmentsYes
Total Number of Sequences in Dataset2,673
Total Number of Edges3,410,048
Number of Unique Sequences2,673
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

New to Cytoscape?

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

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