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Table S1. Pseudogenes found in the M. thermoacetica genome.

Table S2. Parameters for blast alignments of some M. thermoacetica sequences mentioned in the text with GenBank sequences.

Table S3. Genes belonging to alcohol and aldehyde dehydrogenase COGs and pfams.

Table S4. Five M. thermoacetica gene clusters made up of COGs found in pyruvate:ferredoxin oxidoreductase.

Table S5. Dissimilatory sulfite reductase gene cluster.

Table S6. COGs with greater representation in the M. thermoacetica genome than in genomes of two closely related bacteria.

Table S7. Transporters encoded in the genome of M. thermoacetica.

Fig. S1. Circular representations of the genome of M. thermoacetica ATCC 39073. The outermost two circles indicate start sites of genes and assigned function (coloured by COG categories). Circle 1 consists of forward-strand gene products. Circle 2 consists of reverse-strand gene products. Colours represent the following functional categories: amino acid biosynthesis, cyan; biosynthesis of cofactors, brown; cell envelope, light gray; cellular processes, light blue; central intermediary metabolism, dark salmon; energy metabolism, green; fatty acid and phospholipid metabolism, orange; other categories, salmon; protein fate, dark gray; purines, pyrimidines, nucleosides, and nucleotides, light green; regulatory functions, light salmon; replication, blue; transcription and translation, magenta; transport and binding proteins, yellow; unassigned, black; unknown function, red; circle 3, RNA genes (tRNAs green, sRNAs red); circle 4, pseudogenes, circle 5, IS elements; circle 6, G+C content; circle 7, GC skew [(G-C/G+C), khaki indicates values > 1, purple < 1].

Fig. S2. Pathway proposed for metabolism of xylose. Locus tags for genes encoding individual steps are shown.

Fig. S3. Pathway proposed for metabolism of glucose and fructose. Locus tags for genes encoding individual steps are shown.

Fig. S4. Pyruvate from sugar metabolism provides electrons and carbon for acetate synthesis by the Wood–Ljungdahl pathway.

Fig. S5. Tetrahydrofolate synthesis. Moorella thermoacetica genes which could be involved in synthesis of tetrahydrofolate from guanosine triphosphate and chorismate. The sequences of genes encoding enzymes which catalyse the transformations of 7,8-dihydroneopterin 3′-triphosphate to dihydroneopterin phosphate and dihydroneopterin phosphate to dihydroneopterin are not known.

Fig. S6. Synthesis of molybdenum cofactor and bis-molybdopterin guanine dinucleotide cofactor from guanine triphosphate. No M. thermoacetica genes were found with homology to the large subunit of molybdopterin synthase, MoaE.

Fig. S7. Components of the bacterial flagellar proteins in M. thermoacetica. The figure was derived from the KEGG web server (Kanehisa et al., 2006; http://www.genome.jp/kegg/). The gene IDs that correspond to the labelled flagellar proteins are as follows: FlgB (Moth_0768), FlgC (Moth_0769), FlgD (Moth_0777), FlgE (Moth_0779), FlgG (Moth_0764), FlgK (Moth_0746), FlgL (Moth_0747), FlgL (Moth_0760), FlgM (Moth_0744), FlgN (Moth_0745), FlhA (Moth_0790), FlhB (Moth_0789), FliD (Moth_0765), FliE (Moth_0770), FliF (Moth_0771), FliG (Moth_0772), FliH (Moth_0773), FliI (Moth_0774), FliJ (Moth_0775), FliK (Moth_0776), FliM (Moth_0804), FliN (Moth_0784), FliO (Moth_0785), FliP (Moth_0786), FliQ (Moth_0787), FliR (Moth_0788), FliS (Moth_0766). Genes encoding FlgA, FlhC, FlhD, FliT proteins could not be identified in the M. thermoacetica genome. However, additional putative flagellar genes with unknown functions are encoded in the genome, such as Moth_0780 (FlbD), Moth_0783 (FliL), Moth_0791 (FlhF), Moth_0797 (FlgE-like), Moth_0798 (FlgE-like).

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