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_RSS_NoFragments Firmicutes UniRef90_NoFragments_RSS_Firmicutes

Network Name: IP91_RSS_NoFragments_Firmicutes_UniRef90_NoFragments_RSS_Firmicutes_Minlen140_AS11

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

Analysis Summary

Analysis Job Number26644
Network NameIP91_RSS_NoFragments_Firmicutes_UniRef90_NoFragments_RSS_Firmicutes_Minlen140_AS11
Alignment Score11
Minimum Length140
Maximum Length50,000
Total Number of Sequences After Filtering52,421

Dataset Summary

EST Job Number26174 (Original Dataset)
Database VersionUniProt: 2022-04 / InterPro: 91
Input OptionAccession IDs (Option D)
Job NameIP91_RSS_NoFragments Firmicutes UniRef90_NoFragments_RSS_Firmicutes
Input Sequence SourceUniRef90
E-Value for SSN Edge Calculation5
No matches file
Number of IDs in Uploaded File53,288 (53,288 UniProt ID matches and 0 unmatched)
Taxonomy CategoriesPhylum: firmicutes
Family FilterIPR000385, IPR001989, IPR002684, IPR003698, IPR003739, IPR004383, IPR004558, IPR004559, IPR005839, IPR005840, IPR005909, IPR005911, IPR005980, IPR006463, IPR006466, IPR006467, IPR006638, IPR007197, IPR010505, IPR010722, IPR010723, IPR011101, IPR011843, IPR012726, IPR012837, IPR012838, IPR012839, IPR013483, IPR013704, IPR013848, IPR013917, IPR014191, IPR016431, IPR016771, IPR016779, IPR016863, IPR017200, IPR017672, IPR017742, IPR017833, IPR017834, IPR019939, IPR019940, IPR020050, IPR020612, IPR022431, IPR022432, IPR022447, IPR022459, IPR022462, IPR022881, IPR022946, IPR023404, IPR023805, IPR023807, IPR023819, IPR023820, IPR023821, IPR023822, IPR023858, IPR023862, IPR023863, IPR023867, IPR023868, IPR023874, IPR023880, IPR023885, IPR023886, IPR023891, IPR023897, IPR023904, IPR023912, IPR023913, IPR023930, IPR023969, IPR023979, IPR023980, IPR023984, IPR023992, IPR023993, IPR023995, IPR024001, IPR024007, IPR024016, IPR024017, IPR024018, IPR024021, IPR024023, IPR024025, IPR024032, IPR024177, IPR024521, IPR024560, IPR024924, IPR025895, IPR026322, IPR026332, IPR026335, IPR026344, IPR026346, IPR026351, IPR026357, IPR026401, IPR026404, IPR026407, IPR026412, IPR026423, IPR026426, IPR026429, IPR026447, IPR026482, IPR027492, IPR027526, IPR027527, IPR027559, IPR027564, IPR027570, IPR027583, IPR027586, IPR027596, IPR027604, IPR027608, IPR027609, IPR027621, IPR027622, IPR027626, IPR027633, IPR030801, IPR030837, IPR030894, IPR030896, IPR030905, IPR030915, IPR030933, IPR030950, IPR030969, IPR030977, IPR030989, IPR031003, IPR031004, IPR031010, IPR031012, IPR031014, IPR031015, IPR031019, IPR031691, IPR032432, IPR033971, IPR033974, IPR033975, IPR033976, IPR034165, IPR034386, IPR034391, IPR034405, IPR034422, IPR034428, IPR034436, IPR034438, IPR034457, IPR034462, IPR034465, IPR034466, IPR034471, IPR034474, IPR034479, IPR034480, IPR034485, IPR034491, IPR034497, IPR034498, IPR034505, IPR034508, IPR034514, IPR034515, IPR034519, IPR034529, IPR034530, IPR034531, IPR034532, IPR034534, IPR034547, IPR034556, IPR034557, IPR034559, IPR034560, IPR034687, IPR038135, IPR039661, IPR040063, IPR040072, IPR040074, IPR040081, IPR040082, IPR040085, IPR040086, IPR040087, IPR040088, IPR041582, IPR045375, IPR045567, IPR045784, PF04055, PF06969, PF08497, PF12345, PF13186, PF16199, PF16881, PF19238, PF19288, PF19864
Exclude FragmentsYes
Total Number of Sequences in Dataset53,019
Total Number of Edges72,620,043
Number of Unique Sequences53,019
Convergence Ratio?0.052
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
52,421 61,254,499

 

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 52,421 61,254,499
95 52,322 61,027,367
90 51,997 60,368,121
85 48,584 52,799,557
80 45,111 45,651,800
75 41,706 39,267,401
70 38,328 33,390,845
65 34,653 27,302,625
60 30,844 21,660,254
55 26,767 16,317,931
50 22,534 11,346,902
45 18,744 7,451,574
40 15,448 4,619,845

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

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