Table 1.
General genome statistics.
Figure 1.
Proposed pathway for methanogenesis in Methanomicrobiales.
Methanomicrobiales are predicted to couple formylmethanofuran formation and CoM-CoB heterodisulfide reduction to ion gradients. Fd: ferredoxin; MF: methanofuran; H4MPT: tetrahydromethanopterin.
Table 2.
Hydrogenases in methanogen genomes.
Figure 2.
Alternate pathways for synthesis of 2-oxoglutarate from oxaloacetate.
Class I methanogens and Methanomicrobiales use a partial reductive citric acid cycle while Methanosarcinales use a partial oxidative citric acid cycle.
Figure 3.
Phylogenetic tree of methanogens based on seven core enzymes of methanogenesis and cofactor biosynthesis.
See Materials and Methods for a list of the proteins and organisms included. Protein sequences were concatenated and aligned with Clustal W. The tree was generated with MrBayes 3.1.2 and viewed with TreeView.
Figure 4.
Venn diagram of signature clusters.
The clusters were generated using a spectral clustering procedure (see Materials and Methods section for details). Signature protein clusters were identified as clusters for which a member protein was present in every analyzed species from one or more classes of methanogens. The number of exclusive, shared, and common signature clusters associated with each methanogen class are shown. The functions of characterized proteins belonging to exclusive signature clusters and to clusters shared between the Methanomicrobiales and the Methanosarcinales are also noted.