The SSN for the RSS was generated and segregated into five megaclusters (containing >1 SFLD subgroup) and five clusters (1 SFLD subgroup). These are shown in the image. The megaclusters then were separately segregated to obtain their component SFLD subgroups as well as uncharacterized subgroups. The details for this segregation are provided in the Subgroups tab on the RadicalSAM.org home page.
Cluster is large and functionally diverse. A single alignment score threshold cannot be used to segregate the SSN into isofunctional clusters. To solve this problem, a series of # SSNs was generated with increasing alignment scores (increments). As the alignment score increases, the clusters decrease in complexity and size as they become isofunctional. We refer this process as "dicing".
The "AS Walk-Through" function is provided so that the user can 1) “walk” forward from any cluster in any of the "diced" SSNs to its progeny clusters in the SSN with the next alignment score or 2) "walk" backward to its progenitor cluster in in the SSN with the previous alignment score.
The Explore pages for the clusters provide several types of information for determining whether the cluster is isofunctional: convergence ratio of the UniProt IDs, number of conserved Cys residues, and genome neighborhood diagrams (GNDs).
Information about Cluster is provided below.
No community annotations are available for this cluster.
We are accepting submissions for community-driven annotations.
The clusters in the "diced" SSNs for Megacluster can be viewed by clicking the alignment scores (a cluster contains ≥3 UniRef90 IDs/nodes). As the alignment score increases, the clusters decrease in size and complexity. Also, as the alignment score increases, the number of clusters initially increases as large clusters segregate and then decreases as clusters "dissociate" into individual nodes. The images do not include clusters with ≤2 nodes or singletons because Explore pages are not provided for these.
This link provides access to the Explore page for Megacluster-1 in the SSN generated with an alignment score of #. On that (and any) Explore page, any cluster in the SSN can be selected; also, SSNs generated with other alignment scores can be selected.
Or, select an alignment score for a "diced" cluster in the image and click on its image to access its Megacluster-1 Explore page.
Each Explore page includes the "AS Walk-Through" button above the cluster image. Clicking the button opens a window that identifies 1) the progenitor cluster in the previous SSN ("walk backward") and 2) for the progeny clusters in the next SSN ("walk forward"). The cluster name is a link to its Explore page. These connections may allow the discovery of divergent functions that share mechanistic attributes.
The Search functions enables the user to identify the clusters in the "diced" SSNs that contain a specified UniProt ID or homologues of a specified sequence.
When Find by UniProt ID is used, the Results page provides a list of clusters in the "diced" SSNs that contain the UniProt ID along with the number of UniProt IDs in the cluster, the number of cluster nodes, and the UniProt ID convergence ratio (CR; described on the Explore Pages tab).
As the alignment score continues to increase, the ID may may be located in a cluster with ≤2 nodes or a singleton. No results will be returned for these alignment scores.
When Find by Sequence is used, the Results page provides a list of the three clusters at each alignment score with the smallest e-values along with the number of UniProt IDs in the cluster, the number of cluster nodes, and the UniProt ID convergence ratio.
As the alignment score increases, the "best" e-value typically decreases as the cluster becomes orthologous/isofunctional as nonorthologous sequences are segregated. As the alignment score continues to increase, the "best" cluster can segregates into a cluster with ≤2 nodes or a singleton; the Search results will identify clusters but the e-values likely will be larger than those identified for the clusters with lower alignment scores.
The SSN image was generated with the Color SSN function of the "Cluster Analysis" utility. The clusters are numbered and assigned a unique color in order of decreasing number of UniProt IDs. The Color SSNs generated with increasing alignment scores are colored independently, so clusters in different Color SSNs with the same color need not be related.
The table provides a (mega)cluster directory for locating the SFLD subgroups:
|2||Coproporphyrinogen III oxidase-like||Red||Mega-2|
|3||Antiviral proteins (viperin)||--||Mega-1|
|5||B12-binding domain containing||Blue||Mega-2|
|6||BATS domain containing||Orange||Mega-4|
|9||F420, menaquinone cofactor biosynthesis||Purple||Mega-4|
|10||FeMo-cofactor biosynthesis protein||Mint green||Mega-1|
|11||Lipoyl synthase like||Yellow||Cluster-8|
|13||Methyltransferase Class A||Dark brown||Cluster-6|
|14||Methyltransferase Class D||Light pink||Mega-1|
|15||Organic radical activating enzymes||Cyan||Mega-3|
|17||SPASM/twitch domain containing||Magenta||Mega-1|
|19||Spore photoproduct lyase||Green||Mega-5|
|Protein MJ0683-like||Electric lime||Mega-5|
|Uncharacterized protein family UPF0313||Olive||Cluster-10|
|3',8-Cyclase/Mo cofactor synthesis||Dodger blue||Mega-1|