Figure 1.
Phylogenetic Distribution of the Fap Systems and Operon Structure.
Taxonomic analysis was performed based on the NCBI taxonomy and visualized using MEGAN [37]. The number of strains containing Fap systems within each genus is indicated next to the taxa and illustrated through the diameter of the circle. Note that these numbers are highly influenced by the number of sequenced strains within each phylogenetic group and do not reflect the prevalence of Fap systems within these groups. Organization of the fap operons is illustrated for each genus.
Figure 2.
Comparison of Homologous FapB and FapC Repeat Regions.
The phylogeny is based on the NCBI taxonomy. Bold residues represent 50% (black), 80% (blue) and 100% (red) conserved residues. Note that the conservation is highly biased by the number of sequenced strains and internal repeat units within the Fap proteins of each genus.
Figure 3.
Comparison of phylogenetic trees based on the FapA, FapD and FapF protein sequences and corresponding 16S rRNA genes. The phylogenetic trees were estimated using the neighbor-joining method. Full-length 16S rRNA gene sequences could not be obtained for all Fap containing strains due to gaps in genome sequences. The phylogenetic tree is colored according to taxonomy. Betaproteobacteria (blue), Gammaproteobacteria (brown), and Deltaproteobacteria (red). Nonparametric bootstrap values are shown for each node. No bootstrap value represent 100% bootstrap support.
Figure 4.
Fap Systems within Metagenomes.
FapA homologs were identified using the respective HMMs within 10 large metagenomes from a diverse range of habitats, see Table 2. The hits were aligned with the FapA homologs identified within the refseq protein database and phylogenetic trees were estimated using the neighbor-joining method. The phylogenetic tree is colored according to taxonomy. Betaproteobacteria (blue), Gammaproteobacteria (brown), and Deltaproteobacteria (red). Metagenome hits are highlighted in red text. Nonparametric bootstrap values are shown for each node. The absence of a bootstrap value represent 100% bootstrap support.