Over- and under-represented superfamilies for a genome, compared to
groups of genomes.
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.
Lists of pairs of superfamilies that occur next to each other
in the domain architectures for a genome.
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. Warning: for the sake of clarity these graphs are limited to 1500 edges, so they may
not be available for all genomes.
Visual representation of all
domain architectures a 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 (shown above). Alternatively, the logo link is also present on
the SCOP hierarchy pages for each superfamily.
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
Taxonomic Distribution link at the top of the page. Alternatively, the logo link is also present on
the SCOP hierarchy pages for each superfamily and family.
Undirected domain occurrence network for a superfamily.
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. Alternatively, the logo link is also present on
the SCOP hierarchy pages for each superfamily.