                                                                        Gene putatively regulated by attenuation in A_tumefaciens_C58_UWash_linear

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:152 nt.     Distance to run of Ts=2 nt.   Size=28 nt.     Delta G=-10.00 kcal/mol
Antiterminator: Size=48 nt.     Delta G=-26.90 kcal/mol
Anti-antiterminator:   Size=75 nt.     Delta G=-29.80 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

CATTGTAACCAGATCGAAGGACTGCTGGCCGCCTTTCCGGACCTTGCCGCCGGGATCG
ATATCCACCGTGTCGGTTTTCAGCGCCCGCGAGAAGCGGTCATTGCCGTCGCGGGCGA
GGAAAACCAGTCGCTGCCGCTGTTTGTTTTTGCCGGCGATGCGCCCGCCGATGCGGCA
AGCCACGGCGACACGCACTTCATTCAGGACACGAAACGAATTTTGCAAATCCTCGCCG
AACGCCACGGGTTCCCGCAGCTCCATTGAGCTGCCGCACCTGCGCATcggattttttcggagaca
gacATG

    Atu3442 --- Atu3441 Gene: Atu3442     GI: 17937150     BI number: Atu3442     GOG: COG0747     Description: ABC transporter, substrate binding protein [oligopeptide] Gene: Atu3441     GI: 17937149     BI number: Atu3441     GOG: COG2141     Description: nitrilotriacetate monooxygenas   A C  C C  C TG AT TG AT GC CG TG AT GT GT GT |  C C  A CG        AT GC       C  T C  |       TG CG        GC GC        GC T  |       CG T  |       GT C  |      A  | C  |      A  | A  |      G  | GC       A  |       AA GC        GC       A  A CG        CG        GC |  C       GC        GC CG        CG       |  A TA        CG       |  G TG        CG        AT TA        GC        GC C  A       CG        CG CG       G  A       GC GC       A  G      |  T CG        CG       |  G CG        TA        GC GT        TA        GC GC        TA        CG TA        TA        GC                         TGTTTGTTTTTGCCGGCGATGCGCCCGCCGATGCGGCAAGCCACGGCGACACGCACTTCATTCAGGACACGAAACGAATTTTGCAAATCCTCGCCGAACGCCACGGGTTCCCGCAGCTCCATTGAGCTGCCGCACCTGCGCATcggattttttcggagacagacATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [E] COG0747 ABC-type dipeptide transport system, periplasmic component ... can be seen here [C] COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases ... can be seen here     ..................................................................................................................