EFI - Enzyme Similarity Tool

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The tools are available without charge or license to both academic and commercial users.

Download Network Files

Submission Name: IP91_RSS_NoFragments Betaproteobacteria UniRef90_NoFragments_RSS_Betaproteobacteria

Network Name: IP91_RSS_NoFragments_Betaproteobacteria_UniRef90_NoFragments_RSS_Betaproteobacteria_Minlen140_AS11

SSN Overview
Network Files

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

Analysis Summary

Analysis Job Number	26652
Network Name	IP91_RSS_NoFragments_Betaproteobacteria_UniRef90_NoFragments_RSS_Betaproteobacteria_Minlen140_AS11
Alignment Score	11
Minimum Length	140
Maximum Length	50,000
Total Number of Sequences After Filtering	11,936

Dataset Summary

EST Job Number	26192 (Original Dataset)
Database Version	UniProt: 2022-04 / InterPro: 91
Input Option	Accession IDs (Option D)
Job Name	IP91_RSS_NoFragments Betaproteobacteria UniRef90_NoFragments_RSS_Betaproteobacteria
Input Sequence Source	UniRef90
E-Value for SSN Edge Calculation	5
No matches file
Number of IDs in Uploaded File	12,168 (12,168 UniProt ID matches and 0 unmatched)
Taxonomy Categories	Class: betaproteobacteria
Family Filter	IPR000385, 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 Fragments	Yes
Total Number of Sequences in Dataset	12,029
Total Number of Edges	4,773,476
Number of Unique Sequences	12,029
Convergence Ratio?	0.066

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
	11,936	4,364,852

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	11,936	4,364,852
95	11,864	4,308,967
90	11,721	4,196,025
85	10,600	3,347,493
80	9,523	2,655,497
75	8,395	2,015,699
70	7,234	1,451,825
65	6,077	967,691
60	5,118	641,733
55	4,447	422,055
50	3,954	293,725
45	3,646	229,675
40	3,471	202,159

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

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