                                                                        Gene putatively regulated by attenuation in C_muridarum

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:118 nt.     Distance to run of Ts=0 nt.   Size=25 nt.     Delta G= -7.10 kcal/mol
Antiterminator: Size=39 nt.     Delta G= -7.75 kcal/mol
Anti-antiterminator:   Size=49 nt.     Delta G=-12.20 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

GAAGAAAAATGCTAAAAAACCATCTGTAAAACACTCTGAGCAAAGAAAATAAATCTTT
GAAAGAAAAAACGACCCAATCCGTTTTTCTGGGTAGTGCTGAAAAATTGTTTTGTGTA
GCATAGGCTTTTCGCCCAGCGACATatataatattgcggaggccaaaacttttctggtttctttttatcgctggccgtgcat
agcaagagaagcttttaaaagtttttatttagacttgattcaaatagaattttttaaaatctattctaaaattttttagaaaccttttatccaagagaat
ctATG

    pdhA --- pdhB --- TC0518 Gene: pdhA     GI: 15835134     BI number: TC0516     GOG: COG1071     Description: pyruvate dehydrogenase, E1 component, alpha subunit Gene: pdhB     GI: 15835135     BI number: TC0517     GOG: COG0022     Description: pyruvate dehydrogenase, E1 component, beta subunit Gene: TC0518     GI: 15835136     BI number: TC0518     GOG: COG0508     Description: pyruvate dehydrogenase, E2 component, dihydrolipoamide acetyltransferase, putativ TG T  T AT AT AT |  G A  T A  G GT TA        Ta CG       A  t GC       C  a TA       A  t GT       G  a |  A      C  a |  G      G  t |  G      A  a        t |  C      C  t      c  t |  T      C  t      a  t |  T       Cg       a  t |  T       Gc       a  c |  T       Cg        at A  C      T  |       cg TG        Tg        cg GC        Ta        gt GC        Tg        gt GC        Cg        at TA        Gc        gc CG        Gc        gt                         ttttatcgctggccgtgcatagcaagagaagcttttaaaagtttttatttagacttgattcaaatagaattttttaaaatctattctaaaattttttagaaaccttttatccaagagaatctATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [C] COG1071 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit ... can be seen here [C] COG0022 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit ... can be seen here [C] COG0508 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes ... can be seen here     ..................................................................................................................