Table 1 ssu rRNA 3′ ends that are free to base-pair with SD motifs in E. coli and B. subtilis and their compatible motifs
Species and 3′ TAIL SequenceaSD Motifsb
E. coliUAAG
3′-AUUCCUCCACUAG-5′UAAGG
UAAGGA
UAAGGAG
UAAGGAGG
UAAGGAGGUG
B. subtilisUAGAAGAA
3′-AUCUUUCCUCCACUAG-5′UAGAAAGAAA
UAGAAAAGAAAG
UAGAAAGAGAAAGG
UAGAAAGGAGAAAGGA
UAGAAAGGAAGAAAGGAG
UAGAAAGGAGAGAAAGGAGG
UAGAAAGGAGGAGAAAGGAGGU
UAGAAAGGAGGUAGAAAGGAGGUG
AAAGGAAA
AAAGGGAAAG
AAAGGAGAAAGG
AAAGGAGGAAAGGA
AAAGGAGGGAAAGGAG
AAAGGAGGUGAAAGGAGG
AAAGGAGGUGGAAAGGAGGU
AAAGGAGGUGAGAAAGGAGGUG
AAAGGAGGUGAUGAAAGGAGGUGA
  • a Bolded letters show the differences in the base composition between two species. (E. coli ends with A whereas B. subtilis ends with UCU or AUCU). The underlined nucleotides denote the alternative 3′-AUCU-5′ TAIL and motifs exclusively compatible with it.

  • b The SD motifs shown are derived from differences in 3′TAIL (boldface) for both species.