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.
RadicalSAM.org, our resource for investigating sequence-function space in the radical SAM superfamily, has been updated with sequences from the UniProt Release 2024_01 and InterPro Release 98 databases (January 24, 2024) !!
A minimum sequence similarity threshold that specifies the sequence pairs
connected by edges is needed to generate the SSN. This threshold also
determines the segregation of proteins into clusters. The threshold is applied
to the edges in the SSN using the alignment score, an edge node attribute that
is a measure of the similarity between sequence pairs.
The taxonomy distribution for the UniProt IDs in the input dataset is displayed.
For UniRef90 and UniRef50 cluster datasets, these are retrieved from the lookup
table provided by UniProt/UniRef.
The UniRef90 and UniRef50 clusters containing the UniProt IDs then are
identified using the lookup table provided by UniProt/UniRef. These UniRef90
and UniRef50 clusters may contain UniProt IDs from other families; in addition,
the UniRef90 and UniRef50 clusters in the selected taxonomy category may
contain UniProt IDs from other categories. This results from conflation of
UniProt IDs in UniRef90 and UniRef50 clusters that share ≥90% and ≥50% sequence
identity, respectively.
The numbers of UniProt IDs, UniRef90 cluster IDs, and UniRef50 cluster IDs for
the selected category are displayed.
The sunburst is interactive, providing the ability to zoom to a selected
taxonomy category by clicking on that category; clicking on the center circle
will zoom the display to the next highest rank.
Root
Superkingdom
Kingdom
Phylum
Class
Order
Family
Genus
Species
415 UniProt, 341 UniRef90, 87 UniRef50 IDs
Preparing Downloads
This download may take a long time.
This tab provides histograms and box plots with statistics about the sequences
in the input dataset as well as the BLAST all-by-all pairwise comparisons that
were computed.
The descriptions for the histograms and plots guide the choice of the values
for the "Alignment Score Threshold" and the Minimum and Maximum "Sequence
Length Restrictions" that are applied to the sequences and edges to generate
the SSN.
Sequences as a Function of Full Length Histogram (First Step for Alignment Score Threshold Selection)
This histogram describes the length distribution for all sequences (UniProt
IDs) in the input dataset.
Inspection of the histogram permits identification of fragments, single
domain proteins, and multidomain fusion proteins. This histogram is used to
select Minimum and Maximum "Sequence Length Restrictions" in the "SSN
Finalization" tab to remove fragments, select only single domain proteins, or
select multidomain proteins. The sequences in the "Sequences as a Function of
Full-Length Histogram (UniRef90 Cluster IDs)" (last histogram) are used to
calculate the edges.
Alignment Length vs Alignment Score Box Plot (Second Step for Alignment Score Threshold Selection)
This box plot describes the relationship between the query-subject alignment
lengths used by BLAST (y-axis) to calculate the alignment scores (x-axis).
This plot shows a monophasic increase in alignment length to a constant
value for single domain proteins; this plot shows multiphasic increases in
alignment length for datasets with multidomain proteins (one phase for each
fusion length). The value of the "Alignment Score Threshold" for generating
the SSN (entered in the "SSN Finalization" tab) should be selected (from the
"Percent Identity vs Alignment Score Box Plot"; next box plot) at an alignment
length ≥ the minimum length of single domain proteins in the dataset
(determined by inspection of the "Sequences as a Function of Full-Length
Histogram"; previous histogram). In that region, the
"Alignment Length" should be independent of the "Alignment Score".
Percent Identity vs Alignment Score Box Plot (Third Step for Alignment Score Threshold Selection)
This box plot describes the pairwise percent sequence identity as a function
of alignment score.
Complementing the "Alignment Length vs Alignment Score Box Plot" (previous
box plot), this box plot describes a monophasic increase in sequence identity
for single domain proteins or a multiphasic increase in sequence identity for
datasets with multidomain proteins (one phase for each fusion length). In the
"Alignment Length vs Alignment Score" box plot (previous box plot), a
monophasic increase in sequence identity occurs as the alignment score
increases at a constant alignment length; multiphasic increases occur as the alignment
score increases at additional longer constant alignment lengths.
For the initial SSN, we recommend that an alignment score corresponding to
35 to 40% pairwise identity be entered in the "SSN Finalization" tab (for the
first phase in multiphasic plots).
Edge Count vs Alignment Score Plot (Preview of Full SSN Size)
Invalid data
This plot shows the number of edges in the full SSN for the input dataset (a
node of each sequence) as a function of alignment score. By moving the cursor
over the plot, the number of edges for each alignment score is displayed.
This plot helps determine if the full SSN generated using the initial
alignment score can be opened with Cytoscape on the user’s computer. As a rough guide,
SSNs with ~2M edges can be opened with 16GB RAM, ~4M edges with 32GB RAM, ~8M
edges with 64GB RAM, ~15M edges with 128GB RAM, and ~30M edges with 256GB RAM.
If the number of edges for the full SSN is too large to be opened, a
representative node (rep node) SSN can be opened. In a rep node SSN, sequences
are grouped into metanodes based on pairwise sequence identity (from 40 to 100%
identity, in 5% intervals). The download tables on the "Download Network Files"
page provide the numbers of metanodes and edges in rep node SSNs. The rep node
SSNs are lower resolution than full SSNs; clusters of interest in rep node SSNs
can be expanded to provide the full SSNs.
Edges as a Function of Alignment Score Histogram (Preview of SSN Diversity)
This histogram describes the number of edges calculated at each alignment
score. This plot is not used to select the alignment score for the initial SSN;
however, it provides an overview of the functional diversity within the input
dataset.
In the histogram, edges with low alignment scores typically are those
between isofunctional clusters; edges with large alignment scores typically are
those connecting nodes within isofunctional clusters.
The histogram for a dataset with a single isofunctional SSN cluster is
single distribution centered at a "large" alignment score; the histogram for a
dataset with many isofunctional SSN clusters will be dominated by the edges
that connect the clusters, with the number of edges decreasing as the alignment
score increases.
Sequences as a Function of Full Length Histogram (UniRef90 Cluster IDs)
This histogram describes the distribution of the full-length UniRef cluster
IDs in the input dataset. The sequences of the cluster IDs displayed do not
accurately reflect the distribution of fragments, single domain proteins, and
multidomain full-length proteins in the input dataset.
Portions of these data are derived from the Universal Protein Resource (UniProt) databases.
