                                                                        Gene putatively regulated by attenuation in A_fulgidus

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:126 nt.     Distance to run of Ts=0 nt.   Size=38 nt.     Delta G=-11.30 kcal/mol
Antiterminator: Size=40 nt.     Delta G= -5.30 kcal/mol
Anti-antiterminator:   Size=59 nt.     Delta G= -9.00 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

AGACGGTTTATGCATCTCAGCAAAGTGGATTTTCCGCTTCCAGAAGGCCCTATAATGA
CCACAACCTCTCCTTTTTCTACTTTCATCGTCACGCCTTTGAGAACCTCAAGCTCACC
GAATCTCTTGTGGAGGTCTATGATTTCAAGCTGCGCCATcgcttgaagtttaggtttgttatataaaatct
tttttctcgtgcgtactaatcaatacaaagcatacgaagtgaattttaaagagaggcaacagttagtataatgtttatatagagggattaatagagttaa
acaaggtggtgtaATG

    sdhA --- sdhB --- sdhC --- sdhD Gene: sdhA     GI: 11498289     BI number: AF0681     GOG: COG1053     Description: succinate dehydrogenase, flavoprotein subunit A (sdhA) Gene: sdhB     GI: 11498290     BI number: AF0682     GOG: COG0479     Description: succinate dehydrogenase, iron-sulfur subunit B (sdhB) Gene: sdhC     GI: 11498291     BI number: AF0683     GOG: COG2009     Description: succinate dehydrogenase, subunit C (sdhC) Gene: sdhD     GI: 11498292     BI number: AF0684     GOG: COG2142     Description: succinate dehydrogenase, subunit D (sdhD   A A  C GC AT GC TA TA T  | C  | CG        GG GC       A  T C  T       GC A  C       GT         C C  A       TA       G  C T  C       GT       C  A GC       T  |      G  T CG       T  |      T  c TA       C  |       Cg |  A      T  |       Gc |  T       CG        At A  C       TA        At C  T       AT        Cg T  C       AT        Ta T  T       GT        Ta T  T      C  C       Tg CG       C  A       At AT       A  |       Gt TG       C  |      T  | CG        TA        At TA        CG        Ta TG        GC        Cg TG        AT        Tg                         tttgttatataaaatcttttttctcgtgcgtactaatcaatacaaagcatacgaagtgaattttaaagagaggcaacagttagtataatgtttatatagagggattaatagagttaaacaaggtggtgtaATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [C] COG1053 Succinate dehydrogenase/fumarate reductase, flavoprotein subunit ... can be seen here [C] COG0479 Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit ... can be seen here [C] COG2009 Succinate dehydrogenase/fumarate reductase, cytochrome b subunit ... can be seen here [C] COG2142 Succinate dehydrogenase, hydrophobic anchor subunit ... can be seen here     ..................................................................................................................