Figure 1.
Venn Diagram Showing the Distribution of Transporter Families across the Three Domains of Life
Figure 2.
Numbers of Recognized Transport Proteins and Percentage of Total ORFs
The overall numbers of recognized transport proteins (A) and percentage of total ORFs encoding transport proteins (B) were compared for the 141 organisms analyzed. Species from distinct phylogenetic groups are labeled with different colors. The prokaryotic and eukaryotic obligate intracellular parasites/pathogens are marked with red stars.
Figure 3.
Number of Total ORFs versus Number of Distinct Transporter Families or Average Number of Paralogs per Family
The number of total ORFs in the genome for each of the 141 sequenced prokaryotic and eukaryotic organisms (x-axis) was plotted as a function of either the number of distinct transporter families (A) or the average number of paralogs per family (B) (y-axis). Blue diamonds represent prokaryotic organisms and red squares represent eukaryotic organisms. Trend line and power correlation R2 value are shown for prokaryotes and eukaryotes, respectively. A group of α-Proteobacteria are enclosed by a circle (see text for discussion).
Table 1.
The Relative Percentage of Each Transporter Type within Major Phylogenetic Groups
Figure 4.
Phylogenetic Profiling of Transporter Families
Phylogenetic profiles were created for each transporter family. Each profile is a string with 141 entries (number of organisms analyzed). If a given family is present in an organism, the value one is assigned at this position (red). If not, zero is assigned (black). Organisms and transporter families were clustered according to the similarity of their phylogenetic profiles.
Figure 5.
Hierarchial Clustering of Phylogenetic Profiles of Obligate Intracellular Pathogens/Symbionts versus Soil/Plant-Associated Microbes
Detailed view of two clusters of organisms generated by hierarchical clustering of their phylogenetic profiles of transporter families: obligate intracellular pathogens/symbionts and soil/plant-associated microbes.
Figure 6.
Venn Diagrams Showing the Distribution of Transporter Families among Species Belonging to the Same Genus
(A) Transporter family distribution among three Pseudomonas species.
(B) Transporter family distribution among three Corynebacterium species.