Ctocarpi,” as well as a second sequence with only 97 identity, suggesting the existence of unique species associated with algae inside this candidate genus.Altogether, these BLAST analyses indicate that “Ca. P. ectocarpi” belongs to the class Alphaproteobacteria. To establish the exact taxonomic Activated GerminalCenter B Cell Inhibitors Related Products position of “Ca. P. ectocarpi” within the Alphaproteobacteria, two phylogenetic analyses were performed: a single with a representative sample of 236 full-length 16S rDNA sequences comprising all orders from the class, as well as a second, extended analysis, comprising all readily available households. Inside the resulting phylogenetic trees, “Ca. P. ectocarpi” was positioned in a well-supported clade composed of sequences from the uncultured bacterial clone 47-S-68 and on the Alphaproteobacteria GMD21A06 and GMD21D06 (Figure 1). It was linked for the species Parvibaculum by way of a node with moderate assistance (85 and 63 in NJ and ML analyses respectively) within the lowered phylogenetic tree (Figure 1) but not inside the comprehensive tree (Information sheet 1). Given that the genus Parvibaculum is at present classified as Rhizobiales, and in agreement using the automatic classification obtained via RDP classifier, we could assumeFIGURE 1 | Taxonomic position of “Ca. Phaeomarinobacter ectocarpi” Ec32 inside the Alphaproteobacteria. The figure shows a neighbor-joining tree of 236 16S rDNA sequences with bootstrap help values obtained for this along with a corresponding maximum likelihood tree, respectively (onlyvalues 50 are shown). Hyper-variable regions have been masked in the alignment. The Gammaproteobacterium Escherichia coli was used as outgroup. A more exhaustive tree of Alphaproteobacteria depending on 790 taxa is out there in Data sheet 1.Frontiers in Genetics | Systems BiologyJuly 2014 | Volume 5 | Article 241 |Dittami et al.The “Ca. Phaeomarinobacter ectocarpi” genomethat “Ca. Phaeomarinobacteraceae” also belongs to the order of Rhizobiales. Nonetheless, as observed from the phylogenetic tree presented by Gruber-Vodicka et al. (2011), plus the lack of bootstrap assistance for an expanded order of Rhizobiales (which includes Parvibaculum) in our analyses (Figure 1, Data sheet 1), we are able to conclude that the clade like “Ca. P. ectocarpi” and its relatives probably Methyl p-tert-butylphenylacetate web represents a new order. In any case it represents a brand new family members, “Ca. Phaeomarinobacteraceae” fam. nov., like “Ca. Phaeomarinobacter spp.” with species “Ca. Phaeomarinobacter ectocarpi,” and also the strains “Ca. Phaeomarinobacter sp.” GMD21A06 and GMD21D06.A COMPACT AND FUNCTIONAL GENOME With out THE Characteristics OF NODULE-FORMING RHIZOBIALESThe circular genome of “Ca. P. ectocarpi” features a total size of three.4 Mbp and contains 3298 predicted open reading frames (Table 2, Figure 2). No plasmid replication initiator sequences have been located within the E. siliculosus genome data, providing a loose indication of the absence of functional plasmids within the bacterium. In the time of submission, the metabolic network of “Ca. P. ectocarpi” comprised 1558 enzymatic reactions organized in 279 pathways having a rather complete set of genes and pathways connected to key metabolism. They involve the TCA cycle (PWY-5913, PWY-6969), glycolysis (GLYCOLYSIS), the pentose phosphate pathway (NONOXIPENT-PWY, P21-PWY), purine and pyrimidine de novo synthesis (PWY-7227, PWY-7226, PWY-7184), fatty acid biosynthesis (PWY-4381, PWY-5971, PWY-6282) including cyclopropane fatty acids (PWY0-541) and fatty acid elongation (FASYN-ELONG-PWY), along with the synthesis of all important amino acids (IND-AMINO-ACID-SYN).