EFI - Enzyme Similarity Tool

This web resource is supported by a Research Resource from the National Institute of General Medical Sciences (R24GM141196-01).

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Download Network Files

Submission Name: IP91_RSS_UniRef90_NoFragments_Gammaproteobacteria

Network Name: IP91_RSS_UniRef90_NoFragments_Gammaproteobacteria_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	27245
Network Name	IP91_RSS_UniRef90_NoFragments_Gammaproteobacteria_Minlen140_AS11
Alignment Score	11
Minimum Length	140
Maximum Length	50,000
Total Number of Sequences After Filtering	28,530

Dataset Summary

EST Job Number	27093 (Original Dataset)
Database Version	UniProt: 2022-04 / InterPro: 91
Input Option	Families (Option B)
Job Name	IP91_RSS_UniRef90_NoFragments_Gammaproteobacteria
E-Value for SSN Edge Calculation	5
Pfam / InterPro Family	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
Number of IDs in Pfam / InterPro Family	773,531
Domain Option	off
UniRef Version	90
Number of Cluster IDs in UniRef90 Family	29,331
Taxonomy Categories:	Class: gammaproteobacteria
Exclude Fragments	Yes
Total Number of Sequences in Dataset	29,331
Total Number of Edges	26,332,210
Number of Unique Sequences	29,331
Convergence Ratio?	0.061

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
	28,530	24,151,832

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	28,530	24,151,832
95	28,315	23,842,312
90	27,845	22,988,054
85	24,604	17,356,289
80	21,952	13,359,385
75	19,768	10,533,338
70	17,580	8,119,620
65	15,206	5,979,383
60	12,739	4,128,662
55	10,665	2,782,069
50	8,870	1,619,248
45	7,760	1,035,574
40	7,114	788,891

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

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