EFI - Training Resources: JMB Resources
https://radicalsam.org
As the UniProtKB database and the protein families identified by Pfam and InterPro continue to increase in size, analyses of sequence-function space in SSNs is increasingly difficult. We have developed the ability to generate SSNs from taxonomy categories, allowing higher resolution analyses of focused regions of sequence-function space using UniProt IDs instead of UniRef90 clusters or UniRef90 clusters instead of UniRef50 clusters.
An article has been published in the 2023 Computational Resources for Molecular Biology issue of Journal of Molecular Biology that describes the Taxonomy Tool and Filter by Taxonomy features that we have developed. The article includes examples of the use of both the Taxonomy Tool and Filter by Taxonomy with analyses of both the glycyl radical enzyme superfamily (GRE; IPR004184) and the radical SAM superfamily (RSS).
Please use the following to cite the EFI tools:
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
Download the paper in PDF format.
Download the supplementary figures.
Download the supplementary tutorials.
We also provide access to the EFI-EST, EFI-GNT and EFI-CGFP jobs that were generated in the analyses described in the article.
GRE
GRE: Taxonomy Tool
| ID | Job Name | Date Completed |
|---|---|---|
| 26116 | IP91_IPR004184_All Families; IPR004184; Fragments: yes |
11/6 06:55 PM |
| 26116 | IP91_IPR004184_All Families; IPR004184; Fragments: yes |
11/6 06:55 PM |
| 26117 | IP91_IPR004184_NoFragments Families; IPR004184; Fragments: no |
11/6 06:55 PM |
| 26117 | IP91_IPR004184_NoFragments Families; IPR004184; Fragments: no |
11/6 06:55 PM |
| 26118 | IP91_IPR004184_NoFragments_Minlen650 Families; IPR004184; Fragments: no |
11/6 06:55 PM |
| 26118 | IP91_IPR004184_NoFragments_Minlen650 Families; IPR004184; Fragments: no |
11/6 06:55 PM |
GRE: UniProt SSN
| ID | Job Name | Recent Activity |
|---|---|---|
| 26121 | IP91_IPR004184_UniProt_NoFragments Families; IPR004184; Fragments: no |
11/6 11:55 PM |
| IP91_IPR004184_UniProt_NoFragments_Minlen650_AS240 SSN Threshold=240 Min=650 |
1/27 05:30 AM | |
| 26121 | IP91_IPR004184_UniProt_NoFragments Families; IPR004184; Fragments: no |
11/6 11:55 PM |
| IP91_IPR004184_UniProt_NoFragments_Minlen650_AS240 SSN Threshold=240 Min=650 |
1/27 05:30 AM |
GRE: UniRef90 SSN
GRE: Families option of the Taxonomy Tool with transfer of UniRef90 cluster IDs to the Accession IDs option
GRE: GNT from Families option of the Taxonomy Tool with transfer of UniRef90 cluster IDs to the Accession IDs option
GRE: CGFP from Families option of the Taxonomy Tool with transfer of UniRef90 cluster IDs to Accession IDs option
GRE: Families option, Filter by Taxonomy in the Analysis Step
GRE: Families option, Filter by Taxonomy in the Generate Step
RSS
RSS: Taxonomy Tool
RSS: UniRef50 SSN
| ID | Job Name | Recent Activity |
|---|---|---|
| 26155 | IP91_RSS_UniRef50_NoFragments Families; IPR000385, IPR001989, ...; UniRef50; Fragments: no |
11/7 05:25 PM |
| IP91_RSS_UniRef50_NoFragments_Minlen140_AS11 SSN Threshold=11 Min=140 |
11/10 07:45 PM | |
| IP91_RSS_UniRef50_NoFragments_Minlen140_AS11 SSN Threshold=11 Min=140 |
11/10 07:45 PM | |
| 26155 | IP91_RSS_UniRef50_NoFragments Families; IPR000385, IPR001989, ...; UniRef50; Fragments: no |
11/7 05:25 PM |
| IP91_RSS_UniRef50_NoFragments_Minlen140_AS11 SSN Threshold=11 Min=140 |
11/10 07:45 PM | |
| IP91_RSS_UniRef50_NoFragments_Minlen140_AS11 SSN Threshold=11 Min=140 |
11/10 07:45 PM |
