                                                                        Gene putatively regulated by attenuation in C_pneumoniae_J138

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:168 nt.     Distance to run of Ts=0 nt.   Size=22 nt.     Delta G= -8.80 kcal/mol
Antiterminator: Size=34 nt.     Delta G= -8.10 kcal/mol
Anti-antiterminator:   Size=46 nt.     Delta G=-16.50 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

TTGAATTGCGTGGGTCATCTCGCAATTACAATGTAGACTTAGGAGCAAAATACCAATT
CTAAtgcgttagctttggtaaagagctccatacatcgaagggaaaagagcttttaagatttcttgaaggctcttttcgatttcgatttccattttag
tgttttgctaaaacactttctaatttttttcttttgttttctacattgaaaaaaagagagttacggcagctgtaaagtttttaatattgctccctttgtt
ccatttatgtagcgttcagactttgcactaaaacgagggtgtcatATG

    pmp_4_1 --- pmp_4_1_2 --- pmp_4_2 Gene: pmp_4_1     GI: 15835552     BI number: CPj0016A     GOG: -------     Description: polymorphic outer membrane protein G Family Gene: pmp_4_1_2     GI: 15835553     BI number: CPj0016B     GOG: -------     Description: polymorphic outer membrane protein G Family Gene: pmp_4_2     GI: 15835554     BI number: CPj0017     GOG: -------     Description: Pmp_ gc t  g At At Ta Cg        aa T  c      g  g T  t       cg At        tg At       a  a Cg       c  a Cg       a  a At       t  a       tt Ta       a  |      a  t A  a      c  |       gc A  a       cg        at A  g       ta        at A  a       cg        tg Cg        gc        ta Gc        at        ta At        gt        tg Gc        at        cg Gc        at        gc                         tcttttcgatttcgatttccattttagtgttttgctaaaacactttctaatttttttcttttgttttctacattgaaaaaaagagagttacggcagctgtaaagtttttaatattgctccctttgttccatttatgtagcgttcagactttgcactaaaacgagggtgtcatATG     ..................................................................................................................