Links to the phylogenetic trees and associated data I have shown on the AAA meetings in San Diego and in Kyoto

San Diego Meeting 1999

The phylogenetic tree of the AAA superfamily I have presented on the 3rd AAA meeting is available as a GIF file or as the original layered Canvas file. The tree has been constructed from almost 200 sequences. Name labels have been replaced by "letter number" (A1, A2,...A9, A0, B1...S9) to allow for a maximal resolution of the tree (the tree drawing program fits name labels and tree on one page - the shorter the names, the larger the tree). The tree still looks nicer without the 200 labels, so they can be hidden in the Canvas file (and have been omitted from the GIF file). Sequence names correlating to the shortcuts are available as a text file.

To construct the tree, I started with a text file of the AAA box sequences (in NBRF/PIR-format), had Clustal W align the sequences and calculate the tree data, and produced the drawing using TreeView. The picture was modified in Canvas by moving the name labels to another drawing layer (to allow hiding them), and by adding a layer containing the names of families and subfamilies. The tree drawing was colorized, but not altered otherwise.

To view just a representative sample of the AAA proteins, have a look at a tree showing the complete set of AAA members of C. elegans (representing metazoan eukaryotes), S. cerevisiae (representing unicellular eukaryotes), E. coli (representing eubakteria), and M. janaschii (representing archaea).

Kyoto Meeting 2001

The trees I showed at the Kyoto meeting were derived from searches of the genome databases of C. elegans, D. melanogaster, H. sapiens, and A. thaliana with archaean AAA boxes (Methanococcus proteasomal cap subunit and CDC48 D1). The sequences returned from the blast search were extracted with a computer macro and directly used for alignment and tree construction, combined with a representative set of AAA boxes (all yeast sequences, a eubacterium, an archaeon). In a second round, duplicated sequences and far relatives were omitted and the tree recalculated:
Species Sequences (AAA boxes, MS Word file)Tree (PICT format)
C. elegans C. e. sequence file C. e. AAA tree
D. melanogaster D. s. sequence file D. s. AAA tree
H. sapiens H. s. sequence file H. s. AAA tree
A. thaliana A. t. sequence file A. t. AAA tree
The color of the branches indicates the AAA (sub)family, the sequence names are colored according to the host organism: red for animals, green for the plant, brown for eu- and black for arche-bacteria, and blue for yeast (Do you still remember the reason?).

The statistics of the search results (numbers of the AAA members in each of these species) and the Web addresses of the databases used are listed on a separate page.

Specific remarks:


The tree drawing showing all currently known AAA proteins and the corresponding data (sequences, alignment, bootstrapping data) can be accesssed from a separate page. The tree is published as a poster in the Journal of Cell Science in the section Science at a Glance.
Last edited: February 22, 2002 by KaiFr

Dr. Kai-Uwe Fr?hlich
IMBM
Universitätsplatz 2
8010 Graz
Austria