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
Families; IPR004184		 6/20 09:20 PM
IPR004184_IP74_UniProt_Minlen650_AS240
SSN Threshold=240 Min=650		 6/20 10:25 PM
29535 IPR004184 IP74 UniProt Minlen650 AS240 full ssn.xgmml
Color SSN		 6/21 01:30 AM
29536 IPR004184_IP74_UniRef90
Families; IPR004184; UniRef90		 6/20 04:10 PM
IPR004184_IP74_UniRef90_Minlen650_AS120
SSN Threshold=120 Min=650		 6/20 09:55 PM
29536 IPR004184 IP74 UniRef90 Minlen650 AS120 full ssn.xgmml
Color SSN		 6/20 10:55 PM
IPR004184_IP74_UniRef90_Minlen650_AS185
SSN Threshold=185 Min=650		 6/20 09:50 PM
29536 IPR004184 IP74 UniRef90 Minlen650 AS185 full ssn.xgmml
Color SSN		 6/20 10:55 PM
IPR004184_IP74_UniRef90_Minlen650_AS240
SSN Threshold=240 Min=650		 6/20 09:50 PM
29536 IPR004184 IP74 UniRef90 Minlen650 AS240 full ssn.xgmml
Color SSN		 6/20 10:55 PM
IPR004184_IP74_UniRef90_Minlen650_AS320
SSN Threshold=320 Min=650		 6/20 09:50 PM
29536 IPR004184 IP74 UniRef90 Minlen650 AS320 full ssn.xgmml
Color SSN		 6/20 10:55 PM
29537 IPR004184_IP74_UniRef50
Families; IPR004184; UniRef50		 6/20 03:25 PM
IPR004184_IP74_UniRef50_Minlen650_AS240
SSN Threshold=240 Min=650		 6/20 09:50 PM
29537 IPR004184 IP74 UniRef50 Minlen650 AS240 full ssn.xgmml
Color SSN		 6/20 10:55 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

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

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

Click here to contact us for help, reporting issues, or suggestions.

Carl R. Woese Institute for Genomic Biology
University of Illinois at Urbana-Champaign
1206 W. Gregory Drive Urbana, IL 61801
efi@enzymefunction.org