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

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Submission Name: IP91_RSS_NoFragments Epsilonproteobacteria UniRef90_NoFragments_RSS_Epsilonproteobacteria

Network Name: IP91_RSS_NoFragments_Epsilonproteobacteria_UniRef90_NoFragments_RSS_Epsilonproteobacteria_Minlen140_AS11

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

Analysis Summary

Analysis Job Number26647
Network NameIP91_RSS_NoFragments_Epsilonproteobacteria_UniRef90_NoFragments_RSS_Epsilonproteobacteria_Minlen140_AS11
Alignment Score11
Minimum Length140
Maximum Length50,000
Total Number of Sequences After Filtering3,830

Dataset Summary

EST Job Number26195 (Original Dataset)
Database VersionUniProt: 2022-04 / InterPro: 91
Input OptionAccession IDs (Option D)
Job NameIP91_RSS_NoFragments Epsilonproteobacteria UniRef90_NoFragments_RSS_Epsilonproteobacteria
Input Sequence SourceUniRef90
E-Value for SSN Edge Calculation5
No matches file
Number of IDs in Uploaded File3,884 (3,884 UniProt ID matches and 0 unmatched)
Taxonomy CategoriesClass: epsilonproteobacteria
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 Dataset3,870
Total Number of Edges566,074
Number of Unique Sequences3,870
Convergence Ratio?0.076
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
3,830 513,294

 

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 3,830 513,294
95 3,804 502,977
90 3,754 487,584
85 3,321 372,993
80 2,915 275,596
75 2,591 209,664
70 2,300 155,828
65 2,082 121,703
60 1,871 91,009
55 1,660 66,613
50 1,490 49,706
45 1,404 41,459
40 1,312 33,564

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

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