The SUPERFAMILY web site provides a number of comparative
genomics tools for the analysis of superfamily, and family, domains from across the
tree of life.
Unusual domains
It is now possible to compare the domain composition of a
given genome with that of other genomes and thereby detect superfamilies that are
over- or under-represented. The group of genomes for comparison consists of several
predefined choices, such as eukaryotes or archaebacteria, or any user-defined set
of genomes (or a single genome), e.g. other strains of the same species.
Over-represented superfamilies have typically expanded as
the organism specialised for its environmental niche; e.g. in Shewanella oneidensis,
a Gram-negative bacterium with diverse respiratory strategies that are of potential
use in bioremediation, the five most unusual superfamilies include multiheme cytochromes,
porins and transferrins. Proteins in these superfamilies may provide interesting
targets for investigation.
Links to the unusual superfamily and family domains are
provided at the top of each genome page.
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Adjacent domain pair lists and graphs
For each genome, lists of pairs of superfamilies that occur next to each other
in its domain architectures, can be accessed by clicking on the "domain combinations" link at the top
of each genome page. This list can be visualised in the form of a graph, by clicking on the Adjacent
domain pairs logo (shown above) at the top of the domain pairs list pages. Nodes represent superfamilies
labelled according to their SCOP classification, edges indicate superfamilies that occur next to each
other in domain architectures, and arrows show the N-to-C terminal order. Node size and edge thickness
are proportional to the number of proteins.
Users can remove from the initial list those pairs that are already present in proteins of known structure,
or which also occur in other genomes. Lists, and graphs, for adjacent domain pairs in custom sets of
genomes can be obtained by entering two letter genome codes into the "Custom genome sets" form on the
adjacent domain pairs list page.
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Domain combinations in groups of genomes
Starting from a superfamily of interest, users can get a visual representation of all
domain architectures the superfamily occurs in. From this representation, a clear picture of partner
domains occuring with the superfamily of interest can be gained. Five groups of genomes
are available for comparison: all, eukaryotic, bacterial, eubacterial and archaeal.
These pages can be navigated to by selecting the superfamily of
interest from one of the genome assignment pages, and then following the
Domain Combinations icon link at the top of the page. Finally, select one of the five
groups of genomes.
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Taxonomic visualisation of domain distribution
The TaxViz tool displays the distribution of domain superfamilies,
or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives
an immediate impression of how superfamilies/families are restricted to certain kingdoms
of life.
The TaxViz pages can be navigated to by selecting the superfamily,
or family, of interest from one of the genome assignment pages, and then following the
TaxViz logo (shown above) at the top of the page.
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Domain occurrence networks
Undirected domain occurrence networks are available for all superfamilies.
Nodes in these networks represent genomes. Connections between nodes represent the presence of
domain architectures, which contain the superfamily of interest, in both
genomes. These networks convey the co-occurrence of domain architectures, for each superfamily,
across the genomes included in SUPERFAMILY.
Again, the Domain occurrence network pages can be navigated to by selecting the superfamily
of interest from one of the genome assignment pages, and then clicking the
network logo (shown above) at the top of the page.
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