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| Title: | Comparing function and structure between entire proteomes |
| Author: | Jinfeng Liu & Burkhard Rost |
| Quote: | Protein Science(2001), 10, 1970-1979 |
More than 30 organisms have been entirely sequenced. Here, we
applied a variety of simple bioinformatics tools to analyse 29
proteomes for representatives from all three kingdoms: eukaryotes,
prokaryotes and archaebacteria. We confirmed that eukaryotes have
relatively more long proteins than prokaryotes and archaes, and
that the overall amino acid composition is similar between the
three. We predicted that about 15-30% of all proteins contained
transmembrane helices. We could not find a correlation between
the content of membrane proteins and the complexity of the organism.
In particular, we did not find significantly higher percentages
of helical membrane proteins in eukaryotes than in prokaryotes
or archae. However, we found more proteins with 7 transmembrane
helices in eukaryotes and more with 6 and 12 in prokaryotes. We
found twice as many coiled-coil proteins in eukaryotes (10%) as
in prokaryotes and archaes (4-5%), and we predicted about 15-25%
of all proteins to be secreted by most eukaryotes and prokaryotes.
Every tenth protein had no known homologue in current databases,
and 30-40% of the proteins fall into structural families with
more than 100 members. A classification by cellular function verified
that eukaryotes had a higher proportion of proteins for communication
with the environment. Finally, we found at least one homologue
of experimentally known structure for about 20%-45% of all proteins;
the regions with structural homology covered 20%-30% of all residues.
These numbers may or may not suggest that there are 1200-2600
folds in the universe of protein structures. All predictions are
available at {http://cubic.bioc.columbia.edu/genomes}.
Key words: protein sequence analysis; analysing entire
genomes; helical membrane proteins; coiled coil proteins; signal
peptides; comparative modelling.
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