Another type of rare genomic changes (RGCs) that are useful for taxonomic classification as well as for understanding evolutionary relationships among different organisms are whole proteins that are uniquely present in particular groups or subgroups of bacteria but not found anywhere else. Recent analyses of genomic sequences have indicated that such signature proteins, which are also referred to as ORFans (i.e. ORFs that have no known homologs), are present at different phylogenetic depths. Although most identified signature proteins are of hypothetical functions, it is highly likely that these proteins specify functions or characteristics that distinguish species belonging to a given phylogenetic clades from all other. Hence, functional studies on these proteins should prove instrumental in identifying important physiological characteristics that are unique to particular groups of organisms. Similar to other important RGCs, these signature proteins once acquired are generally vertically transmitted, and based upon their phylogenomic analyses, it should again be possible to draw robust phylogenetic inferences as with the conserved inserts or deletions.

Whole genomic analyses of proteins from many different groups of prokaryotes have led to identification of larte numbers of proteins or ORFs that are distinctive characteristics of particular groups of bacteria and archaea. The result of BLAST search for a protein that is specific for certain subgroups of α-proteobacteria is presented below. As seen, other than the α-proteobacteria, no other hits with significant E values were obtained for this protein. The table below shows the results of BLAST analyses for four proteins that are limited to particular groups of α-proteobacteria. The unique presence of these proteins in various species from particular orders of α-proteobacteria indicates that they provide molecular markers for identifying species belonging to these Orders. Based upon the species distribution of these proteins, it is also possible to deduce the branching order or evolutionary relationships among different α-proteobacterial subgroups. [Go to Top]

Results of BLAST search and the deduced branching order (Click to enlarge table and graphical result)

This website describes many group-specific, subgroups-specific as well as main-line conserved indels, as well as whole protein signatures, that have thus far been identified. Based on these signatures a comprehensive and reliable picture of the evolutionary relationships among different phyla of Bacteria and Archaea has began to emerge. These signature indels or proteins can be viewed/explored by clicking at the appropriate phylum on the main page [Home]. Some of the bacterial phyla (e.g., Actinobacteria, Firmicutes) have not yet been studied in detail and information regardig these as well as many other groups will be posted here as they become available. [Go to Top]

Citation for this webpage:
Bacterial (Prokaryotic) Phylogeny Webpage (March 2006). http://www.bacterialphylogeny.com/index.html