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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 (%)

Neisseria

      

   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

Pasteurellaceae

      

   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.