                                                                        Gene putatively regulated by attenuation in C_perfringens

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:163 nt.     Distance to run of Ts=0 nt.   Size=30 nt.     Delta G=-11.50 kcal/mol
Antiterminator: Size=23 nt.     Delta G= -3.10 kcal/mol

                                                                        Nomenclature/Definitions
Bases shared by the antitermination and termination structures are shown in red
The sequences of the antiterminator and terminator structures are underlined
Coding regions are in CAPS, non-coding regions are in lower case

CAGTTTTAAAAGTTGATATTTCACCTATAATATCAGATTCAAGCATAGAAAAAAGATA
TATTTATTAGaagcaaaaatttatagttttaagaaacataaggctaaacaaatctagtcttatgttttttttattttttgtaatattttaaga
gttaaaacactaccttttaatatagcctaaaaagaaaataatgctaatgaaatattgatttattaaaatcacaattaactagtatttttaaagtagtgta
ctaaggattttagatttttaaattatttatttatgggagggaaaatatcATG

    CPE1062 --- nqrD --- nqrE --- CPE1065 Gene: CPE1062     GI: 18310044     BI number: CPE1062     GOG: COG4659     Description: conserved hypothetical protein Gene: nqrD     GI: 18310045     BI number: CPE1063     GOG: COG4660     Description: probable Na-translocating NADH-quinone reductase Gene: nqrE     GI: 18310046     BI number: CPE1064     GOG: COG4657     Description: probable Na-translocating NADH-quinone reductase Gene: CPE1065     GI: 18310047     BI number: CPE1065     GOG: COG2878     Description: ferredoxin-like protei            aa           c  a           a  t   a       a  c a  a       at g  c       ta a  a       cg at        gt ta        gc ta        at tg        at tg        ta gc        at at        cg ta        at             tttttttattttttgtaatattttaagagttaaaacactaccttttaatatagcctaaaaagaaaataatgctaatgaaatattgatttattaaaatcacaattaactagtatttttaaagtagtgtactaaggattttagatttttaaattatttatttatgggagggaaaatatcATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [C] COG4659 Predicted NADH:ubiquinone oxidoreductase, subunit RnfG ... can be seen here [C] COG4660 Predicted NADH:ubiquinone oxidoreductase, subunit RnfE ... can be seen here [C] COG4657 Predicted NADH:ubiquinone oxidoreductase, subunit RnfA ... can be seen here [C] COG2878 Predicted NADH:ubiquinone oxidoreductase, subunit RnfB ... can be seen here     ..................................................................................................................                                                                         Gene putatively regulated by attenuation in C_perfringens                                                                         Characteristics of the secondary structures Terminator:    Distance to gene:170 nt.     Distance to run of Ts=0 nt.   Size=36 nt.     Delta G=-14.60 kcal/mol Antiterminator: Size=23 nt.     Delta G= -3.10 kcal/mol                                                                         Nomenclature/Definitions Bases shared by the antitermination and termination structures are shown in red The sequences of the antiterminator and terminator structures are underlined Coding regions are in CAPS, non-coding regions are in lower case CAGTTTTAAAAGTTGATATTTCACCTATAATATCAGATTCAAGCATAGAAAAAAGATA TATTTATTAGaagcaaaaatttatagttttaagaaacataaggctaaacaaatctagtcttatgttttttttattttttgtaatattttaaga gttaaaacactaccttttaatatagcctaaaaagaaaataatgctaatgaaatattgatttattaaaatcacaattaactagtatttttaaagtagtgta ctaaggattttagatttttaaattatttatttatgggagggaaaatatcATG     CPE1062 --- nqrD --- nqrE --- CPE1065 Gene: CPE1062     GI: 18310044     BI number: CPE1062     GOG: COG4659     Description: conserved hypothetical protein Gene: nqrD     GI: 18310045     BI number: CPE1063     GOG: COG4660     Description: probable Na-translocating NADH-quinone reductase Gene: nqrE     GI: 18310046     BI number: CPE1064     GOG: COG4657     Description: probable Na-translocating NADH-quinone reductase Gene: CPE1065     GI: 18310047     BI number: CPE1065     GOG: COG2878     Description: ferredoxin-like protei            aa           c  a           a  t           a  c            at            ta   a        cg a  g       gt G  c       gc A  a       at Ta        at Ta        ta Aa        at Ta        cg Tt        at Tt        at At        at Ta        gt             ttttattttttgtaatattttaagagttaaaacactaccttttaatatagcctaaaaagaaaataatgctaatgaaatattgatttattaaaatcacaattaactagtatttttaaagtagtgtactaaggattttagatttttaaattatttatttatgggagggaaaatatcATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [C] COG4659 Predicted NADH:ubiquinone oxidoreductase, subunit RnfG ... can be seen here [C] COG4660 Predicted NADH:ubiquinone oxidoreductase, subunit RnfE ... can be seen here [C] COG4657 Predicted NADH:ubiquinone oxidoreductase, subunit RnfA ... can be seen here [C] COG2878 Predicted NADH:ubiquinone oxidoreductase, subunit RnfB ... can be seen here     ..................................................................................................................