EFI - Taxonomy 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.

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 EFI Tools were upgraded on 10/26/26. While the updated site is functionally identical to the old site, jobs run prior to 10/24/26 will only be available through the results link in the finalization email (not the Previous Jobs tab). User accounts created on the old site will no longer be available, and users are encouraged to create new accounts.

If you encounter issues, please report it to us via the Feedback page and our team will address your specific problem.

As the UniProt database increases in size, users may encounter difficulties in opening and visualizing SSNs with Cytoscape (too many nodes/edges for the RAM available on the user’s computer). As a result, low resolution SSNs (UniRef50 clusters and/or representative node SSNs) may be necessary to survey sequence-function space in large protein families. A solution for generating higher resolution SSNs is to restrict the input sequences to specific taxonomy categories (within the Superkingdom, Kingdom, Phylum, Class, Order, Family, Genus, or Species), thereby reducing the number of nodes/edges and/or allowing the use of UniRef90 clusters or UniProt members to generate the SSN.

This Taxonomy Tool provides a preview of the taxonomy distribution of the UniProt IDs in datasets with three input options: Families, list of families; FASTA, FASTA-formatted sequences; Accession IDs, UniProt, UniRef90 cluster, or UniRef50 cluster IDs. These are analogous to the Families option (Option B), FASTA option (Option C) and Accession IDs option (Option D) of EFI-EST.

The taxonomy distribution of the UniProt IDs in the input dataset is displayed as a "sunburst" in which the ranks of classification (Superkingdom, Kingdom, Phylum, Class, Order, Family, Genus, Species) are displayed radially, with Superkingdom at the center and Species in the outer ring. The sunburst is interactive, providing the ability to zoom to a selected taxonomy category. The numbers of UniProt IDs, UniRef90 cluster IDs, and UniRef50 cluster IDs in the selected category are displayed.

UniRef90 clusters contain sequences that share ≥90% sequence identity so usually are taxonomically homogeneous. UniRef50 clusters contain sequences that share ≥50% sequence identity, so often are taxonomically heterogeneous. When possible (determined by the RAM available to Cytoscape), users should generate taxonomy-specific SSNs with UniProt IDs or UniRef90 cluster IDs.

The UniProt, UniRef90, or UniRef50 cluster IDs can be transferred to the "Accession IDs" option (Option D) of EFI-EST to generate the SSN.

The Sequence BLAST, Families, FASTA, and Accession IDs options of EFI-EST also include Filter by Taxonomy in both the Generate and Database Completed/Analysis steps so that the user can select specific taxonomy categories when generating SSNs.

Information on Pfam families and clans and InterPro family sizes is available on the Family Information page.

Previous Jobs

Create a user account or login to see job history.

Retrieve taxonomy for families.

The UniProt IDs for family members are identified in UniProtKB with a list of Pfam families, InterPro families, and/or Pfam clans.

Pfam and/or InterPro Families and/or Pfam clans:

The input format is a single family or comma/space separated list of families. Families should be specified as PFxxxxx (five digits), IPRxxxxxx (six digits) or CLxxxx (four digits) for Pfam clans.

(Type at least 3 characters)

Fraction: Reduce the number of sequences used to a fraction of the full family size (≥ 1; default: 1)

Selects every Nth sequence in the family; the sequences are assumed to be added randomly to UniProtKB, so the selected sequences are assumed to be a representative sampling of the family. This allows reduction of the size of the SSN. Sequences in the family with SwissProt annotations will always be included; this may result in the size of the resulting data set being slightly larger than the fraction specified.

Filter by Taxonomy can be used to remove UniProt IDs that do not match the specified taxonomy categories.

The remaining UniProt IDs are used to generate the sunburst.

UniRef90 and UniRef50 clusters that contain the UniProt IDs are retrieved from the UniRef90 andUniRef50 databases using the lookup table provided by UniProt/UniRef. Clusters for which the cluster ID (representative sequence) matches the list of families are retained.

The numbers of UniProt IDs and both UniRef90 cluster and UniRef50 cluster IDs are displayed on the sunburst; the UniProt IDs and both UniRef90 cluster and UniRef50 cluster IDs are available for download and/or transfer to the Accession ID option (Option D) of EFI-EST to generate SSNs.

If the lists of UniRef90 or UniRef50 cluster IDs are used to generate SSNs with the Accession IDs option (Option D) of EFI-EST, the lists should (must!) be filtered with the same list of families (Filter by Family) and any specified taxonomy categories (Filter by Taxonomy) used to generate the lists.

This filtering removes the UniRef90 and UniRef50 clusters with cluster IDs ("representative sequences") or internal UniProt IDs that are not members of the specified families or have the selected taxonomy categories.

Fragment Option

UniProt designates a Sequence Status for each member: Complete if the encoding DNA sequence has both start and stop codons; Fragment if the start and/or stop codon is missing. Approximately 10% of the entries in UniProt are fragments.

Exclude Fragments:

Check to exclude UniProt-defined fragments in the results. [default: off]

For the UniRef90 and UniRef50 databases, clusters are excluded if the cluster ID ("representative sequence") is a fragment.

UniProt IDs in UniRef90 and UniRef50 clusters with complete cluster IDs are removed from the clusters if they are fragments.

Filter by Taxonomy

From preselected conditions, the user can select "Bacteria, Archaea, Fungi", "Eukaryota, no Fungi", "Fungi", "Viruses", "Bacteria", "Eukaryota", or "Archaea" to restrict the retrieved sequences to these taxonomy groups, i.e., the taxonomy filter is applied after the specified number of sequences is retrieved.

"Bacteria, Archaea, Fungi", "Bacteria", "Archaea", and "Fungi" select organisms that may provide genome context (gene clusters/operons) useful for inferring functions.

The retrieved sequences also can be restricted to taxonomy categories within the Superkingdom, Kingdom, Phylum, Class, Order, Family, Genus, and Species ranks. Multiple conditions are combined to be a union of each other.

The sequences from the UniRef90 and UniRef50 databases are the UniRef90 and UniRef50 clusters for which the cluster ID ("representative sequence") matches the specified taxonomy categories. The UniProt members in these clusters that do not match the specified taxonomy categories are removed from the cluster.

The taxonomy database used for filtering is maintained by the UniProt group is based on the NCBI taxonomy database https://www.ncbi.nlm.nih.gov/taxonomy, and is supplemented with data specific to the UniProt Knowledgebase (UniProtKB).

Length Filter

Minimum Length:

Maximum Length:

Job name:

Database Version:

E-mail:

You will be notified by e-mail when your submission has been processed.

Retrieve taxonomy for FASTA files.

The input is a list of FASTA-formatted sequences in which the headers contain a UniProt ID. The UniProt ID is required because it is used to retrieve the taxonomy from the UniProt database (FASTA header "reading").

The UniProt IDs for the family members are retrieved; these are used to calculate the sunburst.

Input FASTA-formatted sequences with UniProt accession IDs in the header or upload a file.

Sequences:

FASTA File:

Select a FASTA file containing IDs and sequences to upload

Job name:

Database Version:

E-mail:

You will be notified by e-mail when your submission has been processed.

Retrieve taxonomy for accession IDs.

The input is a list of UniProt, UniRef90 cluster or UniRef50 cluster IDs. For the UniRef90 and UniRef50 clusters, the UniProt IDs in the clusters are retrieved using the lookup table provided by UniProt/UniRef.

Filter by Family and/or Filter by Taxonomy can be used to remove UniProt IDs that do not match a list of Pfam families, InterPro families, and/or Pfam clans and/or specified taxonomy categories. This may be desirable/necessary if the input list is obtained from 1) the Color SSN or Cluster Analysis utility for a Families option (Option B) EFI-EST SSN or, 2) the Families option of the Taxonomy Tool.

The remaining UniProt IDs are used to generate the sunburst.

Use UniProt IDs
Use UniRef50 or UniRef90 Cluster IDs

Input a list of UniProt, NCBI, or Genbank (protein) accession IDs, or upload a text file.

Sequences:

Accession IDs File:

Select a text file containing UniProt IDs to upload

Input a list of UniRef50 or UniRef90 cluster accession IDs, or upload a text file.

Sequences:

Accession IDs File:

Select a text file containing UniRef IDs to upload

Input accession IDs are:

Fragment Option

Exclude Fragments:

Check to exclude UniProt-defined fragments in the results. [default: off]

For the UniRef90 and UniRef50 databases, clusters are excluded if the cluster ID ("representative sequence") is a fragment.

UniProt IDs in UniRef90 and UniRef50 clusters with complete cluster IDs are removed from the clusters if they are fragments.

Filter by Taxonomy

"Bacteria, Archaea, Fungi", "Bacteria", "Archaea", and "Fungi" select organisms that may provide genome context (gene clusters/operons) useful for inferring functions.

Filter by Family

The input list of UniRef90 or UniRef50 cluster IDs should (must!) be filtered with the same list of Pfam families, InterPro families, and/or Pfam clans used to generate the IDs, if:

The input list of UniRef90 or UniRef50 IDs is obtained from 1) the Color SSN or Cluster Analysis utility for a Families option (Option B) EFI-EST SSN, 2) the Families option of the Taxonomy Tool, or 3) the Accession IDs option of the Taxonomy Tool.

Input a list of Pfam families, InterPro families, and/or Pfam clans to restrict the UniProt and/or UniRef IDs in the SSN to these families.

Family(s):

The input format is a single family or comma/space separated list of families. Families should be specified as PFxxxxx (five digits), IPRxxxxxx (six digits) or CLxxxx (four digits) for Pfam clans.

For input lists of UniRef90 and UniRef50 clusters, the cluster ID (representative sequence) is used to identify those that match the list of families and are included in the SSN. The UniProt members in these clusters that do not match the input families are removed from the cluster and are not included in the SSN node attributes.

Job name:

Database Version:

E-mail:

You will be notified by e-mail when your submission has been processed.