TABLE 1.

Features of the prokaryotic genomes studied

GenomeaG+C%Anti-SDbGenescSD%dOASe
Bacteria
    Proteobacteria
        γ-Type
            ESCCO50.8AUCACCUCCUUA3,90857.17, 8, 9
            HAEIN38.2AUCACCUCCUUA1,53353.77, 8, 9
            VIBCH47.5AUCACCUCCUUA3,26048.37, 8, 9
            PSEAE66.6AUCACCUCCUUA5,24669.27, 8, 9
        ε-Type
            CAMJE30.5AUCACCUCCUUU1,50258.76, 7, 8
            HELPY38.9AUCACCUCCUUU1,39159.46, 7, 8
        α-Type
            RICPR29.0AUCACCUCCUUA77318.67, 8, 9
        β-Type
            NEIME51.5AUCACCUCCUUU1,67449.36, 7, 8
    Chlamydiae
            CHLPN40.6AUCACCUCCUUU96542.87, 8, 9
            CHLTR41.3AUCACCUCCUUU83146.87, 8, 9
    Spirochetes
            BORBU28.6AUCACCUCCUUU77152.36, 7, 8
            TREPA52.8AUCACCUCCUUU91660.06, 7, 8
    Fermicutes (gram-positive)
        Bacilli
            BACSU43.5AUCACCUCCUUU3,62489.49, 10, 11
        Mollicutes
            MYCGE31.7AUCACCUCCUUU44810.86, 7, 8*
            MYCPN40.0AUCACCUCCUUU65817.511, 12, 13
            UREUR25.5AUCACCUCCUUU55657.47, 8, 9
        Actinobacteria
            MYCTU65.6AUCACCUCCUUU3,67747.77, 8, 9
    Cyanobacteria
        SYNSQ47.7AUCACCUCCUUU2,90626.09, 10, 11
    Thermus/Deinococcus
        DEIRA66.6AUCACCUCCUUU2,92342.07, 8, 9
    Gram-negative thermophiles
        AQUAE43.5AUCACCUCCUUU1,48748.18, 9, 10
        THEMA46.2AUCACCUCCUUU1,68590.19, 10, 11
Archaea
    Euryarchaea
        Methanogens
            METJA31.4AUCACCUCCU1,47148.89, 10, 11
            METTH49.5AUCACCUCCUUA1,64160.78, 9, 10
            ARCFU48.6AUCACCUCCUAA2,08346.29, 10, 11
        Hyperthermophiles
            PYRAB44.7AUCACCUCCUAU1,68671.39, 10, 11
            PYRHO41.9AUCACCUCCUAU1,99954.99, 10, 11
            THEAC46.0AUCACCUCC1,38623.59, 10, 11
        Halobacteriales
            HALSP67.9AUCACCUCCUAA1,75526.69, 10, 11
    Crenarchaea
        SULSO35.8AUCACCUCAU2,74123.010, 11, 12
        PYRAE51.4AUCACCUCC2,13722.94, 5, 6*
  • a For abbreviations, see Fig. 2 legend.

  • b 3′ end of the 16S rRNA sequence; the core anti-SD sequence CCUCC is in bold.

  • c Number of genes with at least 100 codons.

  • d Fraction of genes having an SD sequence.

  • e OAS for the SD sequences (see the text for a formal definition of OAS). *, OAS that may not reflect real optimal spacings as in other genomes (see text for details).