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Figure 4 | BMC Evolutionary Biology

Figure 4

From: Phylogenomic analysis of glycogen branching and debranching enzymatic duo

Figure 4

Bayesian phylogeny of CBM_48—Alpha-amylase containing branching and debranching enzymes. Only select protein names are shown (such as human GBE1 and E. coli GlgB and GlgX). The CBM_48 domain is shown in red, Alpha-amylase in blue, Alpha-amylase_C in light blue, and DUF3372 and PUD in gray. The E-value cutoff used for domains was 10-3 (exceptions are indicated in parentheses). For this figure, only representative species were analyzed (see Additional file 4); some taxonomy-dependent colors are: red—animals, bright green—green plants, light blue—Alveolata, light gray—Archaea, dark gray—Bacteria. The tree shown was inferred by MrBayes [49] based on a MAFFT [50] multiple sequence alignment. The support values shown are: minimal-evolution based bootstrap values normalized to 1.0 (ML distances calculated by TREE-PUZZLE [51], tree inference by FastME [52]) /ML based probabilities inferred by PhyML [53] /posterior probabilities calculated by MrBayes. Support values are only shown for branches for which all three values are at least 0.5. Branch length distances are proportional to expected changes per site. High-confidence gene duplications are shown as red circles [54].

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