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Figure 5 | BMC Genomics

Figure 5

From: Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus

Figure 5

Maximum likelihood phylogeny of PDC domain protein sequences. 303 PDC domain sequences identified from 28 Gram-positive bacterial genomes are included. The phylogeny is shown in two color schemes: based on PDC/PAS domain architectures (A) and based on bacterial genera (B). "Distal" and "Proximal" PDCs are the first and second, respectively, domains in the two-PDC proteins (shown as "PDC = 2" in Figure 3). Black and green circles at internal nodes represent those supported by bootstrap values greater than 60% and those supported by all three phylogenetic methods although bootstrap values were 60% or lower. Seven PDC domain sequences whose structures are known and used as the search queries were included in the phylogeny and they are labeled with black letters. One PAS domain sequence, 1D06 (FixL, Rhizhobium meliloti), was included as the outgroup and is shown in black. See Table 1 and (Additional file 1: Table S1) and (Additional file 3: Table S2) for the species name abbreviations and protein IDs. Species abbreviations not listed in Table 1 are Gs (Geobacter sulfurreducens), Rm (Rhizobium meliloti), and Vp (Vibrio parahaemolyticus).

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