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.

Cluster Analyses and Downloads

Uploaded Filename: 26131_IP91_IPR004184_UniRef90_NoFragments_Bacteroidetes_Minlen650_AS240_full_ssn.xgmml

The Data File Download tab provides the Color SSN with the nodes colored according to node.fillColor (Cluster Sequence Count).

Six node attributes were added to the input SSN: Cluster Sequence Count, Sequence Count Cluster Number, Cluster Node Count, Node Count Cluster Number, node.fillColor (according to Cluster Sequence Count, hexadecimal), and Node Count Fill Color (according to Cluster Node Count, hexadecimal).

To change the node colors in Cytoscape to Node Count Fill Color: 1) select all nodes; 2) on the Style Panel, click on the "?" in the Fill Color Property; 3) select "Remove Bypass"; 4) deselect the nodes (default node color); and 5) open the Fill Color Property and select "Node Count Fill Color" as the Column and "Passthrough Mapping" as the Mapping Type. The nodes will be recolored.

The Data File Download tab also provides files for 1) UniProt ID-Color-Cluster Number mapping table, 2) ID Lists and FASTA Files for each cluster, 3) cluster sizes, and 4) SwissProt annotations for clusters and singletons. The number of UniRef/UniProt IDs for each cluster is displayed in the WebLogos, HMMs, and Length Histograms tabs.

The WebLogos tab provides the WebLogo (generated using http://weblogo.threeplusone.com/) and MSA (generated using MUSCLE) for the node IDs in each SSN cluster containing at least the specified "Minimum Node Count". The MSA can be viewed with Jalview (https://www.jalview.org/). This tab also provides the percent identity matrix for the multiple sequence alignment, as computed by Clustal-Omega.

The Consensus Residues tab provides a tab-delimited text file with the number of the conserved residues and their MSA positions for each specified residue in each SSN cluster (numbered by Cluster Sequence Count) containing at least the specified "Minimum Node Count".

The HMMs tab provides the HMM for each SSN cluster containing at least the specified "Minimum Node Count". The Skylign download provides the image of the HMM generated from the MSA (https://skylign.org/). The HMM text file can be viewed interactively by uploading to https://skylign.org/ and selecting "Information Content – Above Background"; the probability of each amino acid residue and probability and length of an insert at each position is provided. The p

The Length Histograms tab provides length histograms for each cluster containing at least the specified "Minimum Node Count".

Submission Summary
Data File Download
WebLogos
Consensus Residues
HMMs
Length Histograms

Submission Summary Table

Job Number	26229
Input Option	Cluster Analysis
Uploaded Filename	26131_IP91_IPR004184_UniRef90_NoFragments_Bacteroidetes_Minlen650_AS240_full_ssn.xgmml
Database Version	UniProt: 2022-04 / InterPro: 91
Analysis Options	Weblogo, HMM, Consensus Residue, Length Histogram (AAs=C; Thresholds=0.9,0.8,0.7,0.6,0.5,0.4,0.3,0.2,0.1; )
Number of SSN clusters	24
Number of SSN singletons	13
SSN sequence source	UniRef90
Number of SSN (meta)nodes	333
Number of accession IDs in SSN	1,122

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

Colored SSN

Each cluster in the submitted SSN has been identified and assigned a unique number and color.

Supplementary Files

Mapping Tables
	UniProt ID-Color-Cluster number mapping table
ID Lists and FASTA Files per Cluster
	UniProt ID lists per cluster
	UniRef90 ID lists per cluster
	FASTA files per UniProt cluster
	FASTA files per UniRef90 cluster
Miscellaneous Files
	Cluster sizes
	SwissProt annotations by cluster

WebLogos

If the WebLogo is missing for Node Cluster 1 (and additional clusters with large numbers of nodes), repeat the job with a "Maximum Node Count" in the Sequence Filter input window. MUSCLE can fail with a "large" number of sequences (variable, anywhere from >750 to >1500).

WebLogos for FASTA UniProt cluster (full length sequences)

2 MB

Percent Identity Matrix for FASTA UniProt cluster (full length sequences)

<1 MB

Sequence Cluster 1 / Node Cluster 1

Full Sequences

Number of IDs: UniProt: 675, UniRef90: 136

MSA PNG

Sequence Cluster 2 / Node Cluster 2

Full Sequences

Number of IDs: UniProt: 271, UniRef90: 121

MSA PNG

Sequence Cluster 5 / Node Cluster 3

Full Sequences

Number of IDs: UniProt: 14, UniRef90: 9

MSA PNG

Sequence Cluster 8 / Node Cluster 4

Full Sequences

Number of IDs: UniProt: 8, UniRef90: 8

MSA PNG

Sequence Cluster 6 / Node Cluster 5

Full Sequences

Number of IDs: UniProt: 12, UniRef90: 8

MSA PNG

Sequence Cluster 7 / Node Cluster 6

Full Sequences

Number of IDs: UniProt: 11, UniRef90: 6

MSA PNG

Consensus Residues

C
	Consensus residue position summary table (full)	<1 MB

HMMs

If the HMM is missing for Node Cluster 1 (and additional clusters with large numbers of nodes), repeat the job with a "Maximum Node Count" in the Sequence Filter input window. MUSCLE can fail with a "large" number of sequences (variable, anywhere from >750 to >1500).

HMMs for FASTA UniProt cluster (full length sequences)

4 MB