                                                                        Gene putatively regulated by attenuation in B_halodurans

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:205 nt.     Distance to run of Ts=0 nt.   Size=23 nt.     Delta G=-10.70 kcal/mol
Antiterminator: Size=45 nt.     Delta G= -3.25 kcal/mol
Anti-antiterminator:   Size=56 nt.     Delta G= -9.80 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

AGTCACCTGTCCCATATAAAAAGGTAGAACCGGTTGAAGAATAGttttgtaagcgctttatatatgg
gaaaaccgctattttagcggttttttatttgcaatcatttaaaagctactatcgcattttttatggatagagagcgaccctgcaaaatgtaaattcagaa
aaatgattttattcaatattgaaataattttgactaaataactaccaaattcaatatacatccttgcaggcagatactatacttttttacagttcggtat
taattagccaatgcggtgaaaggggtttccaaaATG

    BH0213 --- BH0214 --- BH0215 --- BH0216 --- BH0217 --- pdh Gene: BH0213     GI: 15612776     BI number: BH0213     GOG: COG1071     Description: pyruvate dehydrogenase E1 (lipoamide) alpha subunit Gene: BH0214     GI: 15612777     BI number: BH0214     GOG: COG0022     Description: pyruvate dehydrogenase E1 (lipoamide) beta subunit Gene: BH0215     GI: 15612778     BI number: BH0215     GOG: COG0508     Description: pyruvate dehydrogenase E2 (dihydrolipoamide acetyltransferase) Gene: BH0216     GI: 15612779     BI number: BH0216     GOG: COG1249     Description: pyruvate dehydrogenase E3 (dihydrolipoamide dehydrogenase) Gene: BH0217     GI: 15612780     BI number: BH0217     GOG: COG0733     Description: sodium-dependent transporter Gene: pdh     GI: 15612781     BI number: BH0218     GOG: COG0334     Description: phenylalanine dehydrogenas             a           a  a AA       g  a G  G       gc TA        gc TA       t  | GT       a  | G  A      t  | C  |      a  | CG       t  | At       a  | At       t  | Gt       t  | At       t  | |  g      c  | |  t      g  | |  a      c  | |  a      g  | Tg       a  | Gc       a  | |  g      t  | Gc       g  |        t At       t  |      t  t At       t  |       at At       t  |       ta A  a       tg        cg At        Gc        gc Ta        At        cg At        Ta        cg Ta        At        at At        At        at Cg        Gt        at Cg        At        at                         ttatttgcaatcatttaaaagctactatcgcattttttatggatagagagcgaccctgcaaaatgtaaattcagaaaaatgattttattcaatattgaaataattttgactaaataactaccaaattcaatatacatccttgcaggcagatactatacttttttacagttcggtattaattagccaatgcggtgaaaggggtttccaaaATG                                                                         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 [C] COG1249 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes ... can be seen here [R] COG0733 Na+-dependent transporters of the SNF family ... can be seen here [E] COG0334 Glutamate dehydrogenase/leucine dehydrogenase ... can be seen here     ..................................................................................................................