Phylogenetic relationship and protein clusters of 12 genomes from the order Legionellales. (A) The phylogenetic tree was inferred using maximum likelihood from a concatenated alignment of 285 single copy orthologous genes. The numbers on each node represent the support of 1,000 bootstrap replicates. (B) Venn diagram depicting numbers of protein clusters in five specified groups or genomes, Rg, Rickettsiella grylli; 5 Cb, All 5 C. burnetii genomes; 4 Lb, all four Legionella genomes. *includes both clusters and single proteins not found in any cluster. (C) A comparison between COG assignment for coding genes (green) and pseudogenes (blue) found in CRt. A: RNA processing and modification; J: translation, ribosomal structure and biogenesis; K: transcription; L: replication, recombination, and repair; C: energy production and conversion; M: cell wall/membrane biogenesis; D: cell cycle control, cell division; F: nucleotide transport and metabolism; H: coenzyme transport and metabolism; G: carbohydrate transport and metabolism; O: posttranslational modification, protein turnover, and chaperones; U: intracellular trafficking; T: signal transduction mechanisms; I: lipid transport and metabolism; V: defense mechanisms; P: inorganic ion transport and metabolism; Q: secondary metabolites biosynthesis, transport, and catabolism; N: cell motility; R: general function predicted only; S: function unknown; X: not assigned.
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