Input a UniProt ID to identify its cluster.
For all but Megacluster-1-1 (SFLD Subgroup-17, SPASM/Twitch domain), Megacluster-2-1 (SFLD Subgroup 5, B12-binding domain), Megacluster-2-2 (SFLD Subgroup 2, anaerobic coproporphyrinogen-III oxidase-like), or Cluster-7 ((SFLD Subgroup 16, PLP-dependent), the search opens the Explore page for the cluster that contains the user-specified UniProt ID.
For Megacluster-1-1 (SFLD Subgroup-17, SPASM/Twitch domain), Megacluster-2-1 (SFLD Subgroup 5, B12-binding domain), Megacluster-2-2 (SFLD Subgroup 2, anaerobic coproporphyrinogen-III oxidase-like), or Cluster-7 ((SFLD Subgroup 16, PLP-dependent), the search identifies the cluster (if ≥3 nodes/UniRef50 IDs) in each “diced” SSN that contains the ID. The number of UniProt IDs, number of cluster nodes, and UniProt ID convergence ratio (CR; described on the Subgroups tab) are provided for each identified cluster.
In the generation of the megaclusters and clusters, some UniProt IDs for a singleton may be deleted. The Search will report: "ID not found".
Input a sequence to find clusters that contain homologues. The sequence is used to query the HMMs for the clusters (≥3 UniRef IDs/nodes).
The results reports matches for the “top” three clusters if the e-value is ≤1e-10. The cluster is a link to the Explore page for the cluster.
For Megacluster-1-1 (SFLD Subgroup-17, SPASM/Twitch domain), Megacluster-2-1 (SFLD Subgroup 5, B12-binding domain), Megacluster-2-2 (SFLD Subgroup 2, anaerobic coproporphyrinogen-III oxidase-like), or Cluster-7 ((SFLD Subgroup 16, PLP-dependent), the second section reports matches for clusters in the “diced” SSNs; the clusters with the three smallest e-values are listed. The number of UniProt IDs, number of cluster nodes, and UniProt ID convergence ratio (CR; described on the Subgroups tab) are provided for each identified cluster.
The “Exploring Subgroups” subtab under the “Functionally Diverse Subgroups” tab provides advice about interpreting the search results for these subgroups.
The EFI-GNT web tools allow users to lookup genome neighborhood diagrams (GNDs) for lists of UniProt IDs. Users may find it convenient to be able to access the GNDs for members of the RSS within RadicalSAM.org.
The GND Viewer can be accessed with the button below. The input is a list of UniProt IDs. The GNDs will be displayed.
Input the genus/species/strain for an organism.
If only the genus is entered, a pop-up list of matching genus-species-strains is provided for selection of the desired genus/species/strain. If the genus and species are entered, a pop-up list of matching genus-species-strains is provided for selection of the desired genus/species/strain.
The search provides a list of sequences in the RSS. The list provides the UniProt ID (link to the UniProt page for sequence), UniProt description, organism name, UniProt annotation status (SwissProt or TrEMBL), and link to its Explore page.