The SORGOdb “”search by BlastP”" tool therefore allows the accuracy of public SOR annotations to be checked and allows suggestions of their possible SORGOdb classification. Figure 4 Repartition of superoxide reductase (SOR) and superoxide dismutase (SOD) genes regarding the 16S rRNA gene distance tree of all Crenarchaeota described in SORGOdb. All of the sequences were retrieved from SILVA [60] when available or GenBank (http://​www.​ncbi.​nlm.​nih.​gov/​). The Thermoproteales are highlighted in red, the Sulfolobales in blue and the Desulfurococcales in green. Organisms having at least one SOR, or one SOD or none of both (any SOD and any SOR) are respectively

represented in red, blue and dark. Thermococcus and Pyrococcus are obligate anaerobes

that live click here in environments where there is no oxygen and both produce a SOR-type superoxide reductase that is catalytically active at temperatures below the optimum growth temperature but representing conditions likely corresponding to zones of oxygen exposure [23]. Archaeoglobus is a true archaeal sulphate reducer, reducing SO4 2- to H2S in hot marine sediments. Two complete Archaeoglobus genomes are available, A. fulgidus and A.profundus, The A. fulgidus genome contains one SOR and one Dx-SOR, and the two enzymes have similar kinetics of learn more the superoxide reduction. This raises the question of functional redundancy as Dx-SOR is GDC-0449 absent from A. profundus and from the related Ferroglobus placidus, an iron-oxidising nitrate-reducing species that lives in anoxic (oxygen free) and hot (85°C) environments [70]. The A. profundus genome (1.6 Mb) Ribose-5-phosphate isomerase is significantly smaller than those of A. fulgidus (2.2 Mb) and F. placidus (2.2 Mb). Using the SORGOdb “”by organism name search”" option, it is easy to compare the genomic locations (GC view map) and the genes contexts (gview synteny map) of the SOR of these three

species. This visualization reveals that these genes have different genetic locations and, although the neighbouring genes encode related functions, the genetic organization and order, are not conserved. Again using the “”Browse by phylogeny”" option of SORGOdb, we get quickly all archaeal SOR amino acid sequences (using check all then get all amino acid sequence) can be selected and used to cluster by Maximum Likelihood using ClustalW to produce a protein distance-tree (Figure 3). This tree shows the position of each four proteins considered (AF0833, AF0344, Arcpr_0633 and Ferp_1979) and indicate that the two A. fulgidus SOR (Figure 5, point 3 and 5) are very distant from those of A. profundum and F. placibus, which by contrast are closely related (Figure 5, point 4). This proximity cannot be linked to the origin of the organisms as A. fulgidus and F. placibus originate from a shallow marine hydrothermal system at Volcano, Italy [70, 71] whereas A.