EFI - Training Resources: From The Bench

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.

Reorganization of UniProtKB

With the current 2026_02 release, the UniProtKB database is reorganized to include an expanded number of Reference Proteomes to better capture biodiversity. This includes the removal of proteins from taxonomically unclassified organisms, i.e., those without a binomial species name (genus and species). The total number of accessions in UniProtKB has been reduced from 253,635,358 in the “legacy” 2025_03 release to 149,810,139 in the current 2026_02 release.

We are providing the option to select either the “legacy” 2025_03 database or the current UniProtKB database (now 2026_02) when generating SSNs. You can select the database in the “Database” accordion on the pages for the EFI-EST options, the EFI-GNT tool, and the Taxonomy Tool. We suggest that you compare the SSNs, GNNs, and GNDs generated from both databases as you explore the information you are seeking.

Because the “legacy” 2025_03 release contains UniProt IDs that are no longer active on the UniProt web site, we provide the Metadata Tool that provides access to the node attribute metadata for the UniProt IDs in the “legacy” 2025_03 release.

EFI Genomic Enzymology Tools

EFI-EST

EFI-GNT

EFI-CGFP

A "From The Bench" article was published in Biochemistry in 2019 describing the use of the EFI web tools with an analysis of the glycyl radical enzyme superfamily (GRE; IPR004184). PDF files of the article and the Supplementary Information that includes a detailed description of the tools are available for download.

Please use the following to cite 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

Download the paper in PDF format.

Download the supplementary methods (201 pages).

Download the supplementary figures and tables (25 pages).

We also provide access to the EFI-EST, EFI-GNT and EFI-CGFP jobs that were generated in the analysis of the GRE superfamily.

EST Jobs

ID	Job Name	Date Completed
29535	IPR004184_IP74_UniProt Families; IPR004184; Fragments: yes	6/20 09:20 PM
	IPR004184_IP74_UniProt_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 10:25 PM
	IPR004184_IP74_UniProt_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 10:25 PM
29535	IPR004184_IP74_UniProt Families; IPR004184; Fragments: yes	6/20 09:20 PM
	IPR004184_IP74_UniProt_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 10:25 PM
	IPR004184_IP74_UniProt_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 10:25 PM
29536	IPR004184_IP74_UniRef90 Families; IPR004184; UniRef90; Fragments: yes	6/20 04:10 PM
	IPR004184_IP74_UniRef90_Minlen650_AS120 SSN Threshold=120 Min=650	6/20 09:55 PM
	IPR004184_IP74_UniRef90_Minlen650_AS120 SSN Threshold=120 Min=650	6/20 09:55 PM
	IPR004184_IP74_UniRef90_Minlen650_AS185 SSN Threshold=185 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef90_Minlen650_AS185 SSN Threshold=185 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef90_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef90_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef90_Minlen650_AS320 SSN Threshold=320 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef90_Minlen650_AS320 SSN Threshold=320 Min=650	6/20 09:50 PM
29536	IPR004184_IP74_UniRef90 Families; IPR004184; UniRef90; Fragments: yes	6/20 04:10 PM
	IPR004184_IP74_UniRef90_Minlen650_AS120 SSN Threshold=120 Min=650	6/20 09:55 PM
	IPR004184_IP74_UniRef90_Minlen650_AS120 SSN Threshold=120 Min=650	6/20 09:55 PM
	IPR004184_IP74_UniRef90_Minlen650_AS185 SSN Threshold=185 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef90_Minlen650_AS185 SSN Threshold=185 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef90_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef90_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef90_Minlen650_AS320 SSN Threshold=320 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef90_Minlen650_AS320 SSN Threshold=320 Min=650	6/20 09:50 PM
29537	IPR004184_IP74_UniRef50 Families; IPR004184; UniRef50; Fragments: yes	6/20 03:25 PM
	IPR004184_IP74_UniRef50_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef50_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 09:50 PM
29537	IPR004184_IP74_UniRef50 Families; IPR004184; UniRef50; Fragments: yes	6/20 03:25 PM
	IPR004184_IP74_UniRef50_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 09:50 PM
	IPR004184_IP74_UniRef50_Minlen650_AS240 SSN Threshold=240 Min=650	6/20 09:50 PM

GNT Job

ID	Filename	Date Completed
10442	29536_IPR004184_IP74_UniRef90_Minlen650_AS240_full_ssn.xgmml Neighborhood Size=10 Co-occurrence=10	6/21 02:10 AM
10442	29536_IPR004184_IP74_UniRef90_Minlen650_AS240_full_ssn.xgmml Neighborhood Size=10 Co-occurrence=10	6/21 02:10 AM

CGFP Job

ID	Filename	Date Completed
2206	29546_29536_IPR004184_IP74_UniRef90_Minlen650_AS240_full_ssn_coloredssn.xgmml	6/21 12:07 AM
	PR004184_IP74_UniRef90_Minlen650_AS240_HMP [Quantify 2172]	6/22 06:47 PM

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