                                                                        Gene putatively regulated by attenuation in A_tumefaciens_C58_UWash_pl-AT

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:16 nt.     Distance to run of Ts=0 nt.   Size=27 nt.     Delta G= -6.80 kcal/mol
Antiterminator: Size=22 nt.     Delta G= -5.20 kcal/mol
Anti-antiterminator:   Size=61 nt.     Delta G= -9.90 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

ctaacgctgttccaatctccgctcattggctactagcagctactcccctggtggccccggaagcccggcaaaacgaaccgtcgtccctcaataaggaatt
ttagtgcgttaggtctggcctaattgcagggccgacggttcgtatccgttcaaggtgaagcatggacactcggttctcgccggtgccagacacgagcgct
gatcgaacctgtcatcaaaacgtcgcaagaccttcaagaaagtgtctcctgcaattgctagacagccgtcattgcaattctttttgcacaggagatacgg
ATG

    ugpB --- ugpA --- ugpE --- glpQ --- ugpC --- Atu5063 Gene: ugpB     GI: 17938646     BI number: Atu5058     GOG: COG1653     Description: ABC transporter, substrate binding protein [glycerol-3-phosphate] Gene: ugpA     GI: 17938647     BI number: Atu5059     GOG: COG1175     Description: ABC transporter, membrane spanning protein [glycerol-3-phosphate] Gene: ugpE     GI: 17938648     BI number: Atu5060     GOG: COG0395     Description: ABC transporter, membrane spanning protein [glycerol-3-phosphate] Gene: glpQ     GI: 17938649     BI number: Atu5061     GOG: COG0584     Description: glycerophosphoryl diester phosphodiesterase Gene: ugpC     GI: 17938650     BI number: Atu5062     GOG: COG3839     Description: ABC transporter, nucleotide binding/ATPase protein [glycerol-3-phosphate] Gene: Atu5063     GI: 17938651     BI number: Atu5063     GOG: COG1737     Description: transcriptional regulator, RpiR famil ca g  a cg ta gc c  c a  t a  t a  c a  a c  a t  | a  | c  | t  | g  | t  | c  | c  | a  | a  | g  | cg ta                  gc a  a                a  c g  |       at        cg ta       a  t       at cg        cg        gc gt        gc       |  a cg       t  t      a  t |  t      c  |      t  t gc       c  |       cg at        ta        gc gc        cg        ta c  c       ta        ta at        gc        at cg        ta        at                         ctttttgcacaggagatacggATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [G] COG1653 ABC-type sugar transport system, periplasmic component ... can be seen here [G] COG1175 ABC-type sugar transport systems, permease components ... can be seen here [G] COG0395 ABC-type sugar transport system, permease component ... can be seen here [C] COG0584 Glycerophosphoryl diester phosphodiesterase ... can be seen here [G] COG3839 ABC-type sugar transport systems, ATPase components ... can be seen here [K] COG1737 Transcriptional regulators ... can be seen here     ..................................................................................................................