EFI - Training Resources: 2022

This web resource is supported by a Research Resource from the National Institute of General Medical Sciences (R24GM141196-01).
SSNs for Taxonomy Categories: Taxonomy Tool and Filter by Taxonomy

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.

A manuscript has been submitted that describes the Taxonomy Tool and Filter by Taxonomy feature that we have developed. The manuscript also 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).

The manuscript and supplementary figures and table are both available for download.

On this page we provide access to the EFI-EST, EFI-GNT, EFI-CGFP, and Taxonomy Tool jobs described in the manuscript.

GRE

Filter by Taxonomy Analysis Step

EFI-EST

ID Job Name Date Completed
26123 IP91_IPR004184_UniRef90_NoFragments
11/6 07:25 PM
IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS240
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Minlen650 AS240 full ssn.xgmml
11/7 12:35 PM
26123 IP91 IPR004184 UniRef90 NoFragments Minlen650 AS240 full ssn.xgmml
11/9 08:55 PM
26123 IP91 IPR004184 UniRef90 NoFragments Minlen650 AS240 full ssn.xgmml
11/7 01:21 PM
26123 IP91 IPR004184 UniRef90 NoFragments Minlen650 AS240 full ssn.xgmml
11/7 11:56 AM
IP91_IPR004184_UniRef90_NoFragments_Bacteria_Minlen650_AS240
;
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Bacteria Minlen650 AS240 SB full ssn.xgmml
11/12 02:40 PM
IP91_IPR004184_UniRef90_NoFragments_Actinobacteria_Minlen650_AS240
;
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Actinobacteria Minlen650 AS240 PA full ssn.xgmml
11/12 01:45 PM
IP91_IPR004184_UniRef90_NoFragments_Bacteroidetes_Minlen650_AS240
;
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Bacteroidetes Minlen650 AS240 PB full ssn.xgmml
11/12 01:40 PM
IP91_IPR004184_UniRef90_NoFragments_Firmicutes_Minlen650_AS240
;
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Firmicutes Minlen650 AS240 PF full ssn.xgmml
11/12 02:15 PM
IP91_IPR004184_UniRef90_NoFragments_Proteobacteria_Minlen650_AS240
;
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Proteobacteria Minlen650 AS240 PP full ssn.xgmml
11/12 02:05 PM
IP91_IPR004184_UniRef90_NoFragments_Fungi_Minlen650_AS240
;
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Fungi Minlen650 AS240 PAPBPFPu full ssn.xgmml
11/12 01:35 PM
IP91_IPR004184_UniRef90_NoFragments_Archaea_Minlen650_AS240
;
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Archaea Minlen650 AS240 SA full ssn.xgmml
11/12 01:40 PM
IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS90
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Minlen650 AS90 full ssn.xgmml
11/7 12:10 PM
IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS120
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Minlen650 AS120 full ssn.xgmml
11/7 12:05 PM
IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS150
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Minlen650 AS150 full ssn.xgmml
11/7 12:00 PM
IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS210
11/7 10:30 AM
26123 IP91 IPR004184 UniRef90 NoFragments Minlen650 AS210 full ssn.xgmml
11/7 12:05 PM
IP91_IPR004184_UniRef90_NoFragments_Minlen650_AS180
11/7 10:25 AM
26123 IP91 IPR004184 UniRef90 NoFragments Minlen650 AS180 full ssn.xgmml
11/7 12:05 PM

Filter by Taxonomy Generate Step

ID Job Name Date Completed
26129 IP91_IPR004184_UniRef90_NoFragments_Bacteria
11/7 11:50 AM
IP91_IPR004184_UniRef90_NoFragments_Bacteria_Minlen650_AS240
11/8 09:45 AM
26130 IP91_IPR004184_UniRef90_NoFragments_Actinobacteria
11/7 11:20 AM
IP91_IPR004184_UniRef90_NoFragments_Actinobacteria
11/8 09:40 AM
26131 IP91_IPR004184_UniRef90_NoFragments_Bacteroidetes
11/7 11:20 AM
IP91_IPR004184_UniRef90_NoFragments_Bacteroidetes_Minlen650_AS240
11/8 09:55 AM
26131 IP91 IPR004184 UniRef90 NoFragments Bacteroidetes Minlen650 AS240 full ssn.xgmml
11/12 10:20 AM
26132 IP91_IPR004184_UniRef90_NoFragments_Firmicutes
11/7 11:30 AM
IP91_IPR004184_UniRef90_NoFragments_Firmicutes_Minlen650_AS240
11/8 09:45 AM
26133 IP91_IPR004184_UniRef90_NoFragments_Proteobacteria
11/7 11:25 AM
IP91_IPR004184_UniRef90_NoFragments_Proteobacteria_Minlen650_AS240
11/8 09:40 AM
26134 IP91_IPR004184_UniRef90_NoFragments_Fungi
11/7 11:15 AM
IP91_IPR004184_UniRef90_NoFragments_Fungi_Minlen650_AS240
11/8 09:40 AM
26135 IP91_IPR004184_UniRef90_NoFragments_Archaea
11/7 11:15 AM
IP91_IPR004184_UniRef90_NoFragments_Archaea_Minlen650_AS240
11/8 09:40 AM

Taxonomy Tool Transfer to Option D

ID Job Name Date Completed
26146 IP91_IPR004184_NoFragments Bacteria UniRef90_NoFragments_IPR004184_Bacteria
11/7 12:35 PM
IP91_IPR004184_NoFragments_Bacteria_UniRef90_NoFragments_IPR004184_Bacteria_Minlen650_AS240
11/8 09:45 AM
26147 IP91_IPR004184_NoFragments Actinobacteria UniRef90_NoFragments_IPR004184_Actinobacteria
11/7 12:05 PM
IP91_IPR004184_NoFragments_Actinobacteria_UniRef90_NoFragments_IPR004184_Actinobacteria_Minlen650_AS240
11/8 09:45 AM
26148 IP91_IPR004184_NoFragments Bacteroidetes UniRef90_NoFragments_IPR004184_Bacteroidetes
11/7 12:05 PM
IP91_IPR004184_NoFragments_Bacteroidetes_UniRef90_NoFragments_IPR004184_Bacteroidetes
11/8 09:45 AM
26149 IP91_IPR004184_NoFragments Firmicutes UniRef90_NoFragments_IPR004184_Firmicutes
11/7 12:15 PM
IP91_IPR004184_NoFragments_Firmicutes_UniRef90_NoFragments_IPR004184_Firmicutes_Minlen650_AS240
11/8 09:45 AM
26150 IP91_IPR004184_NoFragments Proteobacteria UniRef90_NoFragments_IPR004184_Proteobacteria
11/7 12:05 PM
IP91_IPR004184_NoFragments_Proteobacteria_UniRef90_NoFragments_IPR004184_Proteobacteria_Minlen650_AS240
11/8 09:45 AM
26151 IP91_IPR004184_NoFragments Eukaryota UniRef90_NoFragments_IPR004184_Fungi
11/7 12:00 PM
IP91_IPR004184_NoFragments_Eukaryota_UniRef90_NoFragments_IPR004184_Fungi_Minlen650_AS240
11/8 09:45 AM
26152 IP91_IPR004184_NoFragments Archaea UniRef90_NoFragments_IPR004184_Archaea
11/7 12:05 PM
IP91_IPR004184_NoFragments_Archaea_UniRef90_NoFragments_IPR004184_Archaea_Minlen650_AS240
11/8 09:45 AM

RSS

Filter by Taxonomy Generate Step

ID Job Name Date Completed
26155 IP91_RSS_UniRef50_NoFragments
11/7 05:25 PM
IP91_RSS_UniRef50_NoFragments_Minlen140_AS11
11/10 07:45 PM
26156 IP91_RSS_UniRef90_NoFragments_Actinobacteria
11/7 03:25 PM
IP91_RSS_UniRef90_NoFragments_Actinobacteria_Minlen140_AS11
11/8 10:15 AM
26157 IP91_RSS_UniRef90_NoFragments_Bacteroidetes
11/7 03:15 PM
IP91_RSS_UniRef90_NoFragments_Bacteroidetes_Minlen140_AS11
11/8 10:15 AM
26158 IP91_RSS_UniRef90_NoFragments_Firmicutes
11/7 04:40 PM
IP91_RSS_UniRef90_NoFragments_Firmicutes_Minlen140_AS11
11/10 07:20 PM
26160 IP91_RSS_UniRef90_NoFragments_Fungi
11/7 02:00 PM
IP91_RSS_UniRef90_NoFragments_Fungi_Minlen140_AS11
11/8 09:45 AM
26161 IP91_RSS_UniRef90_NoFragments_Archaea
11/7 03:10 PM
IP91_RSS_UniRef90_NoFragments_Archaea_Minlen140_AS11
11/8 10:25 AM
26238 IP91_RSS_UniRef90_NoFragments_EukaryotaNoFungi
11/12 02:55 PM
IP91_RSS_UniRef90_NoFragments_EukaryotaNoFungi_Minlen140_AS11
11/12 04:30 PM

Taxonomy Tool Transfer to Option D

ID Job Name Date Completed
26172 IP91_RSS_NoFragments Actinobacteria UniRef90_NoFragments_RSS_Actinobacteria
11/8 10:45 AM
IP91_RSS_NoFragments_Actinobacteria_UniRef90_NoFragments_RSS_Actinobacteria_Minlen140_AS11
11/10 06:35 PM
26173 IP91_RSS_NoFragments Bacteroidetes UniRef90_NoFragments_RSS_Bacteroidetes
11/8 10:40 AM
IP91_RSS_NoFragments_Bacteroidetes_UniRef90_NoFragments_RSS_Bacteroidetes_Minlen140_AS11
11/10 05:30 PM
26174 IP91_RSS_NoFragments Firmicutes UniRef90_NoFragments_RSS_Firmicutes
11/8 12:35 PM
IP91_RSS_NoFragments_Firmicutes_UniRef90_NoFragments_RSS_Firmicutes_Minlen140_AS11
11/10 07:30 PM
26175 IP91_RSS_NoFragments Proteobacteria UniRef90_NoFragments_RSS_Proteobacteria
11/8 07:10 PM
IP91_RSS_NoFragments_Proteobacteria_UniRef90_NoFragments_RSS_Proteobacteria_Minlen140_AS11
11/10 11:45 PM
26176 IP91_RSS_NoFragments Archaea UniRef90_NoFragments_RSS_Archaea
11/8 10:40 AM
IP91_RSS_NoFragments_Archaea_UniRef90_NoFragments_RSS_Archaea_Minlen140_AS11
11/10 05:45 PM
26177 IP91_RSS_NoFragments Eukaryota UniRef90_NoFragments_RSS_Fungi
11/8 09:35 AM
IP91_RSS_NoFragments_Eukaryota_UniRef90_NoFragments_RSS_Fungi_Minlen140_AS11
11/8 09:50 AM
26191 IP91_RSS_NoFragments Alphaproteobacteria UniRef90_NoFragments_RSS_Alphaproteobacteria
11/10 06:50 PM
IP91_RSS_NoFragments_Alphaproteobacteria_UniRef90_NoFragments_RSS_Alphaproteobacteria_Minlen140_AS11
11/10 07:40 PM
26192 IP91_RSS_NoFragments Betaproteobacteria UniRef90_NoFragments_RSS_Betaproteobacteria
11/10 05:45 PM
IP91_RSS_NoFragments_Betaproteobacteria_UniRef90_NoFragments_RSS_Betaproteobacteria_Minlen140_AS11
11/10 06:20 PM
26194 IP91_RSS_NoFragments Deltaproteobacteria UniRef90_NoFragments_RSS_Deltaproteobacteria
11/10 06:30 PM
IP91_RSS_NoFragments_Deltaproteobacteria_UniRef90_NoFragments_RSS_Deltaproteobacteria_Minlen140_AS11
11/10 07:05 PM
26195 IP91_RSS_NoFragments Epsilonproteobacteria UniRef90_NoFragments_RSS_Epsilonproteobacteria
11/10 05:30 PM
IP91_RSS_NoFragments_Epsilonproteobacteria_UniRef90_NoFragments_RSS_Epsilonproteobacteria_Minlen140_AS11
11/10 06:20 PM
26219 IP91_RSS_NoFragments Eukaryota UniRef90_NoFragments_RSS_EukaryotaNoFungi
11/11 02:05 PM
IP91_RSS_NoFragments_Eukaryota_UniRef90_NoFragments_RSS_EukaryotaNoFungi_Minlen140_AS11
11/11 02:45 PM

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