Is there a phylogenetic signal in prokaryote proteins?

Using the sequence information from nine completely sequenced bacterial gen omes, we extract 32 protein families that are thought to contain orthologou s proteins from each genome. The alignments of these 32 families are used t o construct a phylogeny with the neighbor-joining algorithm. This tree has several topological features that are different from the conventional phylo geny, yet it is highly reliable according to its bootstrap values. Upon clo ser study of the individual families used, it is clear that the strong phyl ogenetic signal comes from three families, at least two of which are good c andidates for horizontal transfer. The tree from the remaining 29 families consists almost entirely of noise at the level of bacterial phylum division s, indicating that, even with large amounts of data, it may not be possible to reconstruct the prokaryote phylogeny using standard sequence-based meth ods.