Additional file 2.

The HPT protein family. A, RAxML tree of the HPT proteins. The RAxML bootstrap values (upper) and the MrBayes posterior probability values (lower) are shown on each branch. Thick branches represent BI and ML values not lower than 100 and 95, respectively. Different phylogenetic affiliations are represented as follows: blue, Excavata; orange, Chromalveolata plus Rhizaria; magenta, red algae; green, green plants; gray, unikonts; sky blue, cyanobacteria. B, Partial amino acid alignments showing the unique Indels in the HPT family proteins. RAxML tree of hypothetical proteins. RAxML tree of GLK proteins. ClpP protein family. A, RAxML tree of ClpP proteins. B, Partial amino acid alignments showing the conserved amino acid residues in the ClpP family proteins. RAxML tree of PRK proteins. RAxML tree of FBT proteins. RAxML tree of ZEP proteins. RAxML tree of paltidic FBP proteins. RAxML tree of cytosolic FBP proteins. RAxML tree of GND proteins. Glaucophytes are represented in blue-green. RAxML tree of ADP/ATP transporter proteins. RAxML tree of LepA proteins. RAxML tree of MAT proteins. Fatty acid desaturase protein family. A, RAxML tree of fatty acid desaturase proteins. B, Partial amino acid alignments showing the unique Indels in the fatty acid desaturase family proteins. TIM protein family. A, RAxML tree of TIM proteins. B, Partial amino acid alignments showing the unique Indels in the TIM family proteins.

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Maruyama et al. BMC Evolutionary Biology 2011 11:105   doi:10.1186/1471-2148-11-105