EFI - Training Resources: From The Bench

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
6/20 09:20 PM
IPR004184_IP74_UniProt_Minlen650_AS240
6/20 10:25 PM
29535 IPR004184 IP74 UniProt Minlen650 AS240 full ssn.xgmml
6/21 01:30 AM
29536 IPR004184_IP74_UniRef90
6/20 04:10 PM
IPR004184_IP74_UniRef90_Minlen650_AS120
6/20 09:55 PM
29536 IPR004184 IP74 UniRef90 Minlen650 AS120 full ssn.xgmml
6/20 10:55 PM
IPR004184_IP74_UniRef90_Minlen650_AS185
6/20 09:50 PM
29536 IPR004184 IP74 UniRef90 Minlen650 AS185 full ssn.xgmml
6/20 10:55 PM
IPR004184_IP74_UniRef90_Minlen650_AS240
6/20 09:50 PM
29536 IPR004184 IP74 UniRef90 Minlen650 AS240 full ssn.xgmml
6/20 10:55 PM
IPR004184_IP74_UniRef90_Minlen650_AS320
6/20 09:50 PM
29536 IPR004184 IP74 UniRef90 Minlen650 AS320 full ssn.xgmml
6/20 10:55 PM
29537 IPR004184_IP74_UniRef50
6/20 03:25 PM
IPR004184_IP74_UniRef50_Minlen650_AS240
6/20 09:50 PM
29537 IPR004184 IP74 UniRef50 Minlen650 AS240 full ssn.xgmml
6/20 10:55 PM

GNT Job

ID Filename Date Completed
10442 29536_IPR004184_IP74_UniRef90_Minlen650_AS240_full_ssn.xgmml
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
6/22 06:47 PM

If you use the EFI web tools, please cite us.

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