                                                                        Gene putatively regulated by attenuation in B_aphidicola_Sg

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:157 nt.     Distance to run of Ts=2 nt.   Size=22 nt.     Delta G= -6.10 kcal/mol
Antiterminator: Size=78 nt.     Delta G= -8.22 kcal/mol
Anti-antiterminator:   Size=40 nt.     Delta G= -5.30 kcal/mol

                                                                        Nomenclature/Definitions
Bases shared by the antitermination and termination structures are shown in red
Bases shared by the anti-antitermination and antitermination structures are shown in green
The sequences of the anti-antiterminator, antiterminator and terminator structures are underlined
Coding regions are in CAPS, non-coding regions are in lower case

TATATAAAAATCTAAAAAGAAAAATTCCTATTATCGGAGTAGGCGGTATTAATTCTAT
AAATTCTGCTAGAGAAAAAATTATGTGTGGAGCTAATTTAATACAAGTATATTCTGGA
TTGATATATCACGGTCCAAATTTTATTAGAGAAATAATTAGAAATCTATGAattaagtaaga
gtatgaagatcaattaacaatctattttaaacaaaaattactgattttttatattaacaaatctttttagatgttaatttttttaaaaaattttaaatat
ttaatcaaataaaagtaaaaaaATG

    ycbY --- uup Gene: ycbY     GI: 21672626     BI number: BUsg351     GOG: COG0116,COG1092     Description: hypothetical 78.9 kDa protein Gene: uup     GI: 21672627     BI number: BUsg352     GOG: COG0488     Description: ABC transporter ATP-binding protein Uu             G           T  G           G  A            TG            GC           T  |            AT            TA            TA            AT            AT            AT           A  A           A  A           A  T           G  A           A  C           G  A           A  |            TA            CG   T        GT A  T       TA A  C      C  T T  T      T  | TA        TA AT        AT TA        AT G  A      A  C G  A      T  T C  T      A  | GT       T  |       TA GC        CG       A  T AT        TG       T  C TG        TA       A  A GC        AT        GC AT        AT        TG |  A       TG        TG G  G       TA        AT G  A       AT        GC CG        TA        GC TA        GT        TA                         AATTTTATTAGAGAAATAATTAGAAATCTATGAattaagtaagagtatgaagatcaattaacaatctattttaaacaaaaattactgattttttatattaacaaatctttttagatgttaatttttttaaaaaattttaaatatttaatcaaataaaagtaaaaaaATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [L] COG0116 Predicted N6-adenine-specific DNA methylase ... can be seen here [R] COG1092 Predicted SAM-dependent methyltransferases ... can be seen here [R] COG0488 ATPase components of ABC transporters with duplicated ATPase domains ... can be seen here     ..................................................................................................................