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. 2008 Mar;72(1):13–53. doi: 10.1128/MMBR.00026-07

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Copyright © 2008, American Society for Microbiology

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FIG. 6. — Snapshots of character state features. Eighteen panels are shown as mini-semblances of the bifurcated tree of cohesion groups portrayed in Fig. 2. Various character states of interest are displayed on these trees to facilitate comparisons. The organisms in all three domains of life that host the various TyrA cohesion groups are profiled in panels 1 to 8. The numbers at the branch ends in panels 2 to 8 indicate the total number of sequences within the cohesion group. An appropriate fraction of a given branch is color coded if the cohesion group has a “mixed” membership. Thus, in panel 3, the proximal half of the TyrCG-13 branch is color coded for the nine sequences of the Epsilonproteobacteria. In panel 6, the other (distal) half of the branch is color coded to indicate the nine TyrA sequences from the class Flavobacteria (Bacteroidetes). The locations of cohesion groups containing intruder sequences are identified in panel 9, e.g., the Flavobacteria mentioned above. TyrA character states associated with cofactor and cyclohexadienyl substrate specificities are displayed in accord with the color-coded legends (panels 10 and 11). In panel 10, “?NADP or NAD(P)?” means that whether the enzyme is NADP⁺ specific or whether it can use either cofactor is unknown, but we know that it cannot be NAD⁺ specific. The amino acid lengths of trimmed core supradomain TyrA sequences are given at the branch ends of panel 12. TyrA enzymes encoded by tyrA genes fused to other genes are depicted in panel 13. TyrA enzymes encoded by tyrA genes which are isolated from other aromatic pathway genes are shown in panel 15. The color-coded legends for panels 17 and 18 show conserved motifs (Fig. 3), which are disrupted or absent in the indicated cohesion groups (or a fraction thereof). These panels can be accessed at http://theseed.uchicago.edu/FIG/Html/TyrAPanels.html, where they can be expanded and sorted in order to facilitate comparisons. The interactive panels are linked to the extended table in order to quickly view the membership of any cohesion group of interest.

FIG. 6. — Snapshots of character state features. Eighteen panels are shown as mini-semblances of the bifurcated tree of cohesion groups portrayed in Fig. 2. Various character states of interest are displayed on these trees to facilitate comparisons. The organisms in all three domains of life that host the various TyrA cohesion groups are profiled in panels 1 to 8. The numbers at the branch ends in panels 2 to 8 indicate the total number of sequences within the cohesion group. An appropriate fraction of a given branch is color coded if the cohesion group has a “mixed” membership. Thus, in panel 3, the proximal half of the TyrCG-13 branch is color coded for the nine sequences of the Epsilonproteobacteria. In panel 6, the other (distal) half of the branch is color coded to indicate the nine TyrA sequences from the class Flavobacteria (Bacteroidetes). The locations of cohesion groups containing intruder sequences are identified in panel 9, e.g., the Flavobacteria mentioned above. TyrA character states associated with cofactor and cyclohexadienyl substrate specificities are displayed in accord with the color-coded legends (panels 10 and 11). In panel 10, “?NADP or NAD(P)?” means that whether the enzyme is NADP⁺ specific or whether it can use either cofactor is unknown, but we know that it cannot be NAD⁺ specific. The amino acid lengths of trimmed core supradomain TyrA sequences are given at the branch ends of panel 12. TyrA enzymes encoded by tyrA genes fused to other genes are depicted in panel 13. TyrA enzymes encoded by tyrA genes which are isolated from other aromatic pathway genes are shown in panel 15. The color-coded legends for panels 17 and 18 show conserved motifs (Fig. 3), which are disrupted or absent in the indicated cohesion groups (or a fraction thereof). These panels can be accessed at http://theseed.uchicago.edu/FIG/Html/TyrAPanels.html, where they can be expanded and sorted in order to facilitate comparisons. The interactive panels are linked to the extended table in order to quickly view the membership of any cohesion group of interest.