EFI - Enzyme Similarity Tool

Download Network Files

Submission Name: IPR004184_IP74_UniRef90

Network Name: IPR004184_IP74_UniRef90_Minlen650_AS320

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

Analysis Summary

Analysis Job Number35893
Network NameIPR004184_IP74_UniRef90_Minlen650_AS320
Alignment Score320
Minimum Length650
Maximum Length50,000
Total Number of Sequences After Length Filtering4,178

Dataset Summary

EST Job Number29536 (Original Dataset)
Database VersionUniProt: 2019-04 / InterPro: 74
Input OptionFamilies (Option B)
Job NameIPR004184_IP74_UniRef90
Pfam / InterPro FamilyIPR004184
Number of IDs in Pfam / InterPro Family20,232
Domain Optionoff
UniRef Version90
Number of Cluster IDs in UniRef90 Family6,020
Exclude FragmentsNo
Total Number of Sequences in Dataset6,020
Total Number of Edges13,553,197
Convergence Ratio?0.748

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
4,178 104,102

 

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 4,178 104,102
95 4,158 102,056
90 4,104 96,665
85 3,592 59,103
80 3,114 33,614
75 2,720 18,968
70 2,382 10,211
65 2,090 6,800
60 1,826 4,761
55 1,648 3,818
50 1,513 3,171
45 1,447 2,967
40 1,361 2,777

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

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