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Table 3 USS motifs in the best high-confidence terminators following genes

From: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

Organism USS N R G (%) U P (%)
   N. meningitidis Z2491 5'-GCCGTCTGAA-3' 1,892 827 40 469 57
   N. meningitidis MC58 5'-GCCGTCTGAA-3' 1,935 801 39 444 55
   N. gonorrhoeae FA 1090 5'-GCCGTCTGAA-3' 1,965 828 41 451 54
   H. influenzae 5'-AAGTGCGGT-3' 1,471 644 39 148 23
   H. influenzae 86 028NP 5'-AAGTGCGGT-3' 1,516 668 37 147 22
   P. multocida 5'-AAGTGCGGT-3' 927 796 40 133 17
   M. succiniciproducens MBEL55E 5'-AAGTGCGGT-3' 1,485 848 36 248 29
   H. ducreyi 35000HP 5'-AAGCGGT-3' 1,371 530 31 84 16
  1. Column N gives number of USS instances in the genome. Column R gives the number of genes followed by a high-confidence terminator, and column G gives this as a percentage of the total number of genes. These genes are the most likely operon ends. Column U gives the number of these likely operon ends for which the best high-confidence terminator contains at least one exact match to the USS motif or its reverse complement. Column P gives this number as a percentage of the likely operon ends (P = U/G). (Because of the requirements for high-confidence terminators, the USS motif likely pairs with a similar, but perhaps imperfect, USS motif on the opposite side of the hairpin stem.) A large fraction of predicted operon ends have a terminator that contains a USS signal. For H. ducreyi the motif AAGCGGT is not known to be a USS; however, its prevalence in the genome and similarity to the USS motif in other Pasteurellaceae lead us to conjecture that it functions as a USS. Only 1% of the likely operon ends in H. ducreyi had a terminator containing the USS motif found in the other Pasteurellaceae.