Tion. Gray indicates additional evidence of function by way of synteny evaluation. Bold font indicates gene numbers for proteins detected in proteomic information. “split” indicates a split gene. “fusion” indicates a fused gene. Additional file 13: Structural alignment of blue copper proteins. -Strands (cupredoxin fold) predicted by YASPIN [118] are highlighted (cyan for -strand 1, yellow and light green for -strand two, pink for -strand 3, dark blue for -strand 4, dark green for -strand five, purple for -strand 6 and red for -strand 7). Amicyanin from Paracoccus denitrificans [GenBank: CAA39199] and Plastocyanin from Synechococcus elongatus GenBank: ABB57 [118] serve as references. Red circles indicate copper-binding ligands. Residues highlighted by light grey correspond to further -strands and these in bold orange correspond to -helices. Sulfocyanin-specific motifs are boxed in red. Black arrows indicate copper-binding ligands. Further loops are indicated at the bottom with the alignment by a light orange line. Further file 14: Blue-copper protein motifs discovered in AMD plasma genes. Additional file 15: AMD plasma blue-copper protein tree. bcp indicates a blue-copper protein of unknown function. Extra file 16: AMD plasma CODH gene tree. Extra file 17: Active internet site alignment of aerobic CODH catalytic subunit genes. The red box indicates the active site residues. H. pseudoflava is Hydrogenophaga pseudoflava, O. carboxidovorans is Oligotropha carboxidovorans, M. loti is Mesorhizobium loti, B. japonicum is Bradyrhizobium japonicum, and B. fungorum is Burkholderia fungorum. Extra file 18: Ni-CODH catalytic subunit alignment. Genes within this alignment will be the Ni-CODH catalytic subunits from R. rubrum (CooS, PDB:1JQK), M. thermoacetica (AcsA, PDB:1MJG) and Fer2 (fer2_31_0047).NPX800 fer2_31_0047’s secondary structure was predicted by YASPIN [118].Glycyrrhizic acid strands are shown in green and -helices are highlighted in cyan.PMID:26760947 Residues belonging to the D-cluster are boxed in yellow (Cys41 and Cys49). Ligands from the B-cluster are boxed in black (Cys50, Cys53, Cys58 and Cys72). Catalytic residues binding the Ni-Fe-S cluster from C-cluster are boxed in purple (His265, Cys300, Cys338, Cys451, Cys481, and Cys531) and catalyze the oxidation of carbon. His95 and Lys568 (boxed in dark red) are non-coordinating residues conserved in Ni-CODHs and have been suggested to be involved in facilitating the reaction [119]. Residue numbering is from the R. rubrum Ni-CODH. More file 19: Cytochrome c oxidase subunit II alignment. * indicates the copper-binding motif found in other cytochrome c oxidase proteins. S. acidocaldarius is Sulfolobus acidocaldarius, A. pernix is Aeropyrum pernix, P. oguniense is Pyrobaculum oguniense, T. thermophilus is Thermus thermophilus, P. denitrificans is Paracoccus denitrificans.Additional file 20: Amino acid identity of AMD plasma cytochrome c oxidase subunit II genes with closely connected genes. More file 21: AMD plasma gene homologs to genes overexpressed or overtranscribed below anaerobic situations in T. volcanium and T. acidophilum [75,76]. Bold font indicates gene numbers for proteins detected in proteomic information. Further file 22: AMD plasma putative hydrogenase four gene tree. Accession numbers are towards the left with the species names. Extra file 23: Pili genes in the AMD plasmas. * indicates a putative annotation. ** indicates a probable annotation. *** indicates a doable annotation. Gray indicates extra evidence of function via.