From the inside, the 1st and 2nd circles show the GC skew (values greater than zero are indicated in green and smaller in pink) and the G+C % content (values greater than the average percentage in the overall chromosome or plasmid are shown in blue and smaller in sky blue) in a 10-kb window with 100-b step, respectively. The 3rd and 4th circles show the presence of RNAs (rRNA, tRNA, and small RNA genes) and CDSs aligned in the clockwise and counterclockwise directions are indicated in the upper and lower sides of the circle, respectively. Different colors mean different functional categories: red for metabolism; green for genetic information and processing; blue for membrane transport; orange for cellular processes; pink for miscellaneous and mobile elements, gray for poorly characterized function and purple for RNA genes.

Overview of the presence of genes for homologues of key enzymes of the carbon, sulfur and nitrogen metabolism as well as of selected electron-accepting complexes and transporters. The KEGG database was used for the reconstruction of metabolic pathways. Arrows and dot-lined arrows indicate presence and absence of the genes, respectively. The lines indicate general pathways found in methanogens (black), the unique pathways identified in M. paludicola and RC-I_MRE50 (red), the pathways found in RC-I_MRE50 but not in M. paludicola (blue). Fd, ferredoxin; MF, methanofuran; H₄MPT, tetrahydromethanopterin; Fdh, formate dehydrogenase; Fmd, formylmethanofuran dehydrogenase; Ftr, formylmethanofuran:H₄MPT formyltransferase; Mch, methenyl-H₄MPT cyclohydrolase; Mtd, F₄₂₀-dependent methylene-H₄MPT dehydrogenase; Mer, methylene-H₄MPT reductase; Mtr, methyl-H₄MPT: coenzyme M methyltransferase; Mcr, methyl-coenzyme M reductase; Hdr, heterodisulfide reductase; Ech, energy-converting hydrogenase; Frh, F₄₂₀-reducing hydrogenase; Mvh, non F₄₂₀-reducing hydrogenase; Pgm, phosphoglucomutase; PgmB, ß-phosphoglucomutase; Gpi, glucose-6-phosphate isomerase; SuhB, inositol-1-monophosphatase/fructose-1,6- bisphosphatase; Pfp, pyrophosphate–fructose 6-phosphate 1-phosphotransferase; Pfk, 6-Phosphofructokinase; Fba, fructose-bisphosphate aldolase; TriA, triosephosphate isomerase; Gap, glyceraldehyde-3-phosphate dehydrogenase; AcyP, acylphosphatase; Pgk, phosphoglycerate kinase; Gpm, phosphoglycerate mutase; Eno, enolase; PpsA, phosphoenolpyrivate synthase; Pyk, pyruvate kinase; Por; pyruvate ferredoxin oxidoreductase; Pdh, pyruvate dehydrogenase; Acd, acetyl-CoA synthetase (ADP-forming); Acs, acetyl-CoA synthetase; Pyc, pyruvate carboxylase; Icd, isocitrate dehydrogenase; Fum, fumarate hydratase; Phi, 3-hexulose-6-phosphate isomerase; Fae, formaldehyde-activating enzyme; Hps, 3-hexulose-6-phosphate synthase; Rpi, ribose-5-phosphate isomerase; Prs, ribose-phosphate pyrophosphokinase; Apt, adenine phosphoribosyltransferase; Deo, thymidine phosphorylase; eif2B, translation initiation factor; Sat, sulfate adenylyltransferase; CysC, adenylylsulfate kinase; CysH, phosphoadenosine phosphosulfate reductase.

Distances were calculated from gene profiles of 18 representative archaeal genomes, based on protein families by the method described in Materials and Methods. The organisms are color-coded according to their affiliated orders: orange, Methanocellales; red, Methanosarcinales; green, Methanomicrobiales; blue, Methanobacteriales; brown, Methanococcales; purple, Methanopyrales. The organisms are represented with the numbers: 1, M. paludicola SANAE; 2, uncultured methanogenic archaeon RC-I, RC-I_MR50; 3, M. a acetivorans C2A; 4, M. barkeri Fusaro; 5, M. mazei Go1; 6, M. burtonii ACE-M; 7, M. thermophila PT; 8, M. marisnigri; 9, M. palustris E1-9c; 10, M. boonei 6A8; 11, M. hungatei JF-1; 12, M. labreanum Z; 13, M. thermautotrophicus ΔH; 14, M. smithii PS; 15, M. stadtmanae MCB-3; 16, M. jannaschii JAL-1; 17, M. maripaludis S2; 18, M. kandleri AV19.