                                                                        Gene putatively regulated by attenuation in S_typhimurium_LT2

                                                                        Characteristics of the secondary structures
Terminator:    Distance from promoter:118 nt.    Distance to gene:23 nt.     Distance to run of Ts=0 nt.   Size=27 nt.     Delta G=-20.20 kcal/mol
Antiterminator:    Distance from promoter:75 nt. Size=54 nt.     Delta G=-19.00 kcal/mol
Anti-antiterminator:    Distance from promoter:47 nt.    Size=49 nt.     Delta G=-11.81 kcal/mol

                                                                        Nomenclature/Definitions
The most likely promoter is: ttgaca-tactgt. It has a score value of 64.93 and is shown in blue
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

ttgacaggattaaaacagtacgggtactgtacttacgtacacaaaggaaacagttATGAAGCTCACCCGGTTTTTCTTCGC
ATTCTTTTTTATCTTCCCCTGAccgggaggcgtttcgtcatgtgataaagaatgcgaagacgaacaagaaggcctcccccaccg
ggaggccttttttattgataacaaaaaaggcaacactATG

    pheA Gene: pheA     GI: 16765982     BI number: STM2667     GOG: COG0077,COG1605     Description: chorismate mutase P/prephenate dehydratas            aa           a  g           t  a           a  a           g  t GA        tg T  c       gc C  c       tg Cg       |  a Cg       a  a Cg        cg Ta        ta Tg        gc Cg        cg T  c       ta A  g      |  a T  t      |  c        a T  t      |  a      c  c T  t      |  a      c  c T  c      |  g       cg T  g       ta        cg T  t       ta        cg C  c      g  g       ta T  |       cg        cg Ta        gc        cg At        gc        gc Cg        at        gc Gt        gc        at Cg        gc        at Ta        gc        gt                         tttattgataacaaaaaaggcaacactATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [E] COG0077 Prephenate dehydratase ... can be seen here [E] COG1605 Chorismate mutase ... can be seen here     ..................................................................................................................                                                                         Gene putatively regulated by attenuation in S_typhimurium_LT2                                                                         Characteristics of the secondary structures Terminator:    Distance to gene:202 nt.     Distance to run of Ts=0 nt.   Size=20 nt.     Delta G=-16.70 kcal/mol Antiterminator: Size=43 nt.     Delta G= -4.80 kcal/mol Anti-antiterminator:   Size=29 nt.     Delta G= -4.20 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 CCACCGCATCGGTGAAAGATGCCAGCTTCGTCGAAGCAGAAGAAGAGTAGtcccttacattga gtgtatcgccaacgcgccttcgggcgcgttttttgttgacaggattaaaacagtacgggtactgtacttacgtacacaaaggaaacagttATGAAG CTCACCCGGTTTTTCTTCGCATTCTTTTTTATCTTCCCCTGAccgggaggcgtttcgtcatgtgataaa gaatgcgaagacgaacaagaaggcctcccccaccgggaggccttttttattgataacaaaaaaggcaacactATG     pheA Gene: pheA     GI: 16765982     BI number: STM2667     GOG: COG0077,COG1605     Description: chorismate mutase P/prephenate dehydratas             g           t  a            tg            at            cg            at            ta           |  t AA       |  c G  G      t  g G  A      c  c TG       c  c AT       c  a tA        ta cG        Gc        tc at       |  g      t  g c  c      A  c       cg a  |       Tg        cg a  |       Gc        gc c  |      A  |       cg gc        Gc        gc gc        At        cg at        At        at at        Gc        at                         ttttgttgacaggattaaaacagtacgggtactgtacttacgtacacaaaggaaacagttATGAAGCTCACCCGGTTTTTCTTCGCATTCTTTTTTATCTTCCCCTGAccgggaggcgtttcgtcatgtgataaagaatgcgaagacgaacaagaaggcctcccccaccgggaggccttttttattgataacaaaaaaggcaacactATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [E] COG0077 Prephenate dehydratase ... can be seen here [E] COG1605 Chorismate mutase ... can be seen here     ..................................................................................................................