EFI - Enzyme Similarity Tool

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".