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Comparative genomics can be used to identify the mechanisms underlying lineage-specific protein innovations and the biological functions of the resulting proteins. We compared the number and classification of CD-like genes in the complete genomes of 10 unrelated bacteria and one alga. Among the 10 bacteria, 5 species carry a single CD gene, and 3 species carry two or three CD genes, the latter being the most common genome organization. The single CD genes are categorized into a clade of the six families of CDP-alcohols. The phylogeny of the families shows congruence with their different physical locations (chromosomal and plasmid) and of their organization in operon-like clusters. The second group of 3 bacteria share homologous CD genes, which belong to a single family and cluster within a 12 kb neighborhood with only one other gene, which is a putative γ-glutamyl carboxylase. The organization of these three bacteria is similar to that of the Proteobacteria. In addition, the CD-like genes of plants and algae show homology to the 3 CD families. In contrast, the prokaryotic CD-like genes do not cluster among the eukaryotic homologs in the phylogenetic tree. We propose that CD-like genes were originally generated by a gene duplication event, after which they were separated to bacteria, plants and possibly animals and fungi.

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