Supplementary Table 2. Trna Genes and Associated Anticodons Encoded by the Genome of C

Supplementary Table 1. The top BLAST search hits of the inferred C. calidirosea proteome to different bacterial phyla. Only the top three phyla are shown, and only hits detected above an E value cutoff of e-10 are considered. The entire C. calidirosea proteome was searched against the non-redundant NCBI database and against a more balanced database consisting of 10 Firmicutes, 5 Chloroflexi and 5 Cyanobacteriaproteomes. The tendency for Firmicutes to arise as the top BLAST hits against the nr database contradicts the phylogenetic analysis, and points to an obvious bias toward Firmicutes in the database. This bias is removed by using a more balanced BLAST reference database.

1The balanced BLAST database consisted of the Firmicutes: Bacillus cereus ATCC 10987 (AE017194), Clostridium perfringens ATCC 13124 (CP000246.1), Enterococcus faecalis V583 (AE016833.1), Geobacillus thermodenitrificans NG80-2 (CP000558.1) Staphylococcus aureus RF122 (J938182.1), Lactobacillus acidophilus NCFM (CP000033), Leuconostoc citreum KM20 (DQ489736), Streptococcus agalactiae 2603V/R (AE009948), Eubacterium eligens ATCC 27750 (CP001104); Thermoanaerobacter ethanolicus CCSD1 (ACXY0000000); the Chloroflexi: Chloroflexus aggregans DSM 9485 (CP001337), Herpetosiphon aurantiacus ATCC 23779 (CP000875), Dehalococcoides ethenogenes 195 (CP000027), Thermobaculum terrenum ATCC BAA-798 (CP001825, CP001826), Ktedonobacter racemifer SOSP1-21 (ADVG00000000); and the Cyanobacteria: CS-328 (ABYK00000000), Cyanothece sp. CCY 0110 (AAXW00000000), Nostoc sp. PCC 7120 (BA000019), Prochlorococcus marinus MIT 9312 (CP000111), Synechococcus elongatus PCC 6301 (AP0082314).

Supplementary Table 2. tRNA genes and associated anticodons encoded by the genome of C. calidirosea T49T.

Supplemental Table 3: Genome content similarities of C. calidirosea T49T with selected species from the core eggNOG database, based on 3 similarity coefficients: Bray-Curtis, Jaccard, and Sørensen (Legendre & Legendre 1998). Species are sorted based on highest Bray-Curtis similarities to C. calidirosea T49T.

Legendre P, Legendre LFJ. (1998). Numerical Ecology. 2nd ed. Elsevier: Amsterdam, New York.

Supplemental Table 5: Bray-Curtis similarity coefficients from comparison of the genome contents of Chthonomonas calidirosea T49 T and selected bacteria from the core eggNOG database (Muller et al. 2010). For all cells except those comparing C. calidirosea T49T, data are averages of multiple species in a particular phylum or class. The numbers in parentheses indicate the number of species in each group. The diagonal (bold numbers) shows average within-group similarities.

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, et al. (2010). eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic acids research 38:D190–5.

Supplementary Table 6. Sigma factors (σ) identified from the genome of Chthonomonas calidirosea T49T.

1Phylogenetic position of sigHbetween Group 3 and Group 4 is currently unclear(Schmid et al. 2012), 2 Group 4 sigmas are highly diverse,sigE prediction was based on BLASTP search with the KEGG ortholog database(Kanehisa et al. 2012).

Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. (2012). KEGG for integration and interpretation of large-scale molecular data sets. Nucleic acids research 40:D109–14.

Schmid S, Bevilacqua C, Crutz-Le Coq A-M. (2012). Alternative sigma factor σH activates competence gene expression in Lactobacillus sakei. BMC microbiology 12:32.