The Classification Viewer
is a component designed to show the kinase classification created
by the PKR team and can be used for navigation, loading entries
into the viewers or finding a kinase's place in the hierarchical
view of the superfamily.
The classification is based on the
original clustering work done at Kinase
Sequence Database. The entire kinase superfamily was clustered
into approximately 300 distinct families and sequence alignments
were created for all of them (reference).
Each family alignment was then used to generate a consensus sequence,
which were combined into a multiple sequence alignment as a subset
of the master alignment of the database content. As the next step,
CLUSTALW and PHYLIP packages were used to produce a phylogeny tree.
The latter was then manually edited and the families were mapped
to kinase groups present in the Protein Kinase Resource and compared
to the human kinome classification (Manning
The resulting classification covers
almost the entire content of the Protein Kinase Resource and features
eight distinct classes of protein kinases. Seven of them are found
in the human kinome classification, and the eighth is a class specific
to plant kinases with no close relation to the other classes. At
this point, a more detailed refinement is being done, and this preliminary
classification is provided as a test case in order to solicit your
input on the quality and possible changes in the existing tree.
The Classification Viewer uses a simple
tree representation model, which dynamically reflects the content
of the database. We plan to use a different graphical representation
for the classification tree at the Protein Kinase Resource web site.
In any event, any comments as to usability and accuracy of the viewer
and the classification content will be most welcome.
If you would like to contribute any
suggestions or ideas regarding the kinase clasification and the
viewer, please email us.