Ctocarpi,” plus a second sequence with only 97 identity, suggesting the existence of various species related with algae inside this candidate genus.Altogether, these BLAST analyses indicate that “Ca. P. ectocarpi” belongs for the class Alphaproteobacteria. To ascertain the exact taxonomic position of “Ca. P. ectocarpi” within the Alphaproteobacteria, two phylogenetic analyses were performed: one with a representative sample of 236 full-length 16S rDNA sequences comprising all orders of the class, and a second, extended analysis, comprising all offered families. In the resulting phylogenetic trees, “Ca. P. ectocarpi” was situated in a well-supported clade composed of sequences from the uncultured bacterial clone 47-S-68 and of the Alphaproteobacteria GMD21A06 and GMD21D06 (Figure 1). It was linked towards the species Parvibaculum via a node with moderate help (85 and 63 in NJ and ML analyses respectively) inside the decreased phylogenetic tree (Figure 1) but not in the full tree (Data sheet 1). Given that the genus Parvibaculum is presently classified as Rhizobiales, and in agreement with all the automatic classification obtained by way of RDP classifier, we could assumeFIGURE 1 | Taxonomic position of “Ca. Phaeomarinobacter ectocarpi” Ec32 within the Alphaproteobacteria. The figure shows a neighbor-joining tree of 236 16S rDNA sequences with bootstrap support values obtained for this and a corresponding maximum likelihood tree, respectively (onlyvalues 50 are shown). Pyrroloquinoline quinone Endogenous Metabolite Hyper-variable regions had been masked in the alignment. The Gammaproteobacterium Escherichia coli was made use of as outgroup. A far more exhaustive tree of Alphaproteobacteria determined by 790 taxa is obtainable in Information sheet 1.Frontiers in Genetics | Systems BiologyJuly 2014 | Volume 5 | Write-up 241 |Dittami et al.The “Ca. Phaeomarinobacter ectocarpi” genomethat “Ca. Phaeomarinobacteraceae” also belongs to the order of Rhizobiales. Nevertheless, as seen from the phylogenetic tree presented by Gruber-Vodicka et al. (2011), as well as the lack of bootstrap help for an expanded order of Rhizobiales (which includes Parvibaculum) in our analyses (Figure 1, Information sheet 1), we are able to conclude that the clade like “Ca. P. ectocarpi” and its relatives likely represents a new order. In any case it represents a new household, “Ca. Phaeomarinobacteraceae” fam. nov., like “Ca. Phaeomarinobacter spp.” with species “Ca. Phaeomarinobacter ectocarpi,” and the strains “Ca. Phaeomarinobacter sp.” GMD21A06 and GMD21D06.A COMPACT AND FUNCTIONAL GENOME Without having THE Characteristics OF NODULE-FORMING RHIZOBIALESThe circular genome of “Ca. P. ectocarpi” features a total size of three.four Mbp and includes 3298 predicted open reading frames (Table 2, Figure 2). No plasmid replication initiator sequences were identified within the E. siliculosus genome information, offering a loose indication on the absence of functional plasmids in the bacterium. At the time of submission, the metabolic network of “Ca. P. ectocarpi” comprised 1558 enzymatic reactions 4′-Methoxychalcone Protocol organized in 279 pathways having a rather comprehensive set of genes and pathways associated to primary metabolism. They contain 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) which includes cyclopropane fatty acids (PWY0-541) and fatty acid elongation (FASYN-ELONG-PWY), as well as the synthesis of all main amino acids (IND-AMINO-ACID-SYN).