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.
Option C now uses the sequences supplied in the FASTA file to calculate edge values and the IDs in the headers to retrieve node attribute information from UniProt. Like Option D, the user can specify that the input sequences are UniProt, UniRef90, or UniRef50 for retrieval of node attribute information.
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
IPR004184_IP74_UniProt_Minlen650_AS240
6/20 10:25 PM
29535 IPR004184_IP74_UniProt
6/20 09:20 PM
IPR004184_IP74_UniProt_Minlen650_AS240
6/20 10:25 PM
IPR004184_IP74_UniProt_Minlen650_AS240
6/20 10:25 PM
29536 IPR004184_IP74_UniRef90
6/20 04:10 PM
IPR004184_IP74_UniRef90_Minlen650_AS120
6/20 09:55 PM
IPR004184_IP74_UniRef90_Minlen650_AS120
6/20 09:55 PM
IPR004184_IP74_UniRef90_Minlen650_AS185
6/20 09:50 PM
IPR004184_IP74_UniRef90_Minlen650_AS185
6/20 09:50 PM
IPR004184_IP74_UniRef90_Minlen650_AS240
6/20 09:50 PM
IPR004184_IP74_UniRef90_Minlen650_AS240
6/20 09:50 PM
IPR004184_IP74_UniRef90_Minlen650_AS320
6/20 09:50 PM
IPR004184_IP74_UniRef90_Minlen650_AS320
6/20 09:50 PM
29536 IPR004184_IP74_UniRef90
6/20 04:10 PM
IPR004184_IP74_UniRef90_Minlen650_AS120
6/20 09:55 PM
IPR004184_IP74_UniRef90_Minlen650_AS120
6/20 09:55 PM
IPR004184_IP74_UniRef90_Minlen650_AS185
6/20 09:50 PM
IPR004184_IP74_UniRef90_Minlen650_AS185
6/20 09:50 PM
IPR004184_IP74_UniRef90_Minlen650_AS240
6/20 09:50 PM
IPR004184_IP74_UniRef90_Minlen650_AS240
6/20 09:50 PM
IPR004184_IP74_UniRef90_Minlen650_AS320
6/20 09:50 PM
IPR004184_IP74_UniRef90_Minlen650_AS320
6/20 09:50 PM
29537 IPR004184_IP74_UniRef50
6/20 03:25 PM
IPR004184_IP74_UniRef50_Minlen650_AS240
6/20 09:50 PM
IPR004184_IP74_UniRef50_Minlen650_AS240
6/20 09:50 PM
29537 IPR004184_IP74_UniRef50
6/20 03:25 PM
IPR004184_IP74_UniRef50_Minlen650_AS240
6/20 09:50 PM
IPR004184_IP74_UniRef50_Minlen650_AS240
6/20 09:50 PM

GNT Job

ID Filename Date Completed
10442 29536_IPR004184_IP74_UniRef90_Minlen650_AS240_full_ssn.xgmml
6/21 02:10 AM
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

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