                                                                        Gene putatively regulated by attenuation in A_aeolicus

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:113 nt.     Distance to run of Ts=1 nt.   Size=22 nt.     Delta G= -7.30 kcal/mol
Antiterminator: Size=36 nt.     Delta G= -3.10 kcal/mol
Anti-antiterminator:   Size=76 nt.     Delta G= -9.55 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

TACTCTTTAAGGTAATCGAACTTCCCCTTCCAGTCGTCTCCCATAACGAATACATCAA
CGTTGTACTTCTTTATGTCCTCTATCTTCTGCTCCCAGTTCCTTTCGGGAATTACCAG
ATCCACATACTTAATGGAACGTACTATTTCCGCCCTGTGCTCGTAAGGGTAAACAGAT
TTCTTTCCTTTTATAGCGTTAAACTCGTCCGTGGAAACTCCCACTATGAGAAAGTCTC
CGAGGGCTTTTGCCCTCTTCAGTAAGTTCAGATGTCCTATATGAAATAAATCAAAAGT
TCCGTAAGTAATG

    aq_1369 --- rlpA1 --- argH --- nuoH2 --- nuoH3 --- nuoI2 --- nuoJ2 --- nuoK2 --- nuoL3 --- nuoM2 --- nuoN2 --- nuoA1 --- aq_1386 --- arsR Gene: aq_1369     GI: 15606565     BI number: aq_1369     GOG: -------     Description: putative protein Gene: rlpA1     GI: 15606566     BI number: aq_1370     GOG: COG0797     Description: rare lipoprotein A Gene: argH     GI: 15606567     BI number: aq_1372     GOG: COG0165     Description: argininosuccinate lyase Gene: nuoH2     GI: 15606568     BI number: aq_1373     GOG: COG1005     Description: NADH dehydrogenase I chain H Gene: nuoH3     GI: 15606569     BI number: aq_1374     GOG: COG1005     Description: NADH dehydrogenase I chain H Gene: nuoI2     GI: 15606570     BI number: aq_1375     GOG: COG1143     Description: NADH dehydrogenase I chain I Gene: nuoJ2     GI: 15606571     BI number: aq_1377     GOG: COG0839     Description: NADH dehydrogenase I chain J Gene: nuoK2     GI: 15606572     BI number: aq_1378     GOG: COG0713     Description: NADH dehydrogenase I chain K Gene: nuoL3     GI: 15606573     BI number: aq_1379     GOG: COG1009     Description: NADH dehydrogenase I chain L Gene: nuoM2     GI: 15606574     BI number: aq_1382     GOG: COG1008     Description: NADH dehydrogenase I chain M Gene: nuoN2     GI: 15606575     BI number: aq_1383     GOG: COG1007     Description: NADH dehydrogenase I chain N Gene: nuoA1     GI: 15606576     BI number: aq_1385     GOG: COG0838     Description: NADH dehydrogenase I chain A Gene: aq_1386     GI: 15606577     BI number: aq_1386     GOG: COG1752     Description: hypothetical protein Gene: arsR     GI: 15606578     BI number: aq_1387     GOG: COG0640     Description: transcriptional regulator (ArsR family   T T  C T  G CG CG TA TA GT AT C  A C  C C  | T  | C  | GC TA CG TA T  T C  C T  C A  A       AC T  C      T  T C  A      G  A T  T      C  T C  A       AT C  C       AT T  T       GC G  T       GC T  A       TG        TA A  A      A  C      G  A T  T      A  C       CG T  |      T  C       TG TG       T  |       CG CG       C  |       GT TA       A  |      |  A TA       T  |      |  A |  C       AT        TA CG        CG        GC AT        AT        TA TA        CG        CG                         ATTTCTTTCCTTTTATAGCGTTAAACTCGTCCGTGGAAACTCCCACTATGAGAAAGTCTCCGAGGGCTTTTGCCCTCTTCAGTAAGTTCAGATGTCCTATATGAAATAAATCAAAAGTTCCGTAAGTAATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [M] COG0797 Lipoproteins ... can be seen here [E] COG0165 Argininosuccinate lyase ... can be seen here [C] COG1005 NADH:ubiquinone oxidoreductase subunit 1 (chain H) ... can be seen here [C] COG1005 NADH:ubiquinone oxidoreductase subunit 1 (chain H) ... can be seen here [C] COG1143 Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) ... can be seen here [C] COG0839 NADH:ubiquinone oxidoreductase subunit 6 (chain J) ... can be seen here [C] COG0713 NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) ... can be seen here [CP] COG1009 NADH:ubiquinone oxidoreductase subunit 5 (chain L)/Multisubunit Na+/H+ antiporter, MnhA subunit ... can be seen here [C] COG1008 NADH:ubiquinone oxidoreductase subunit 4 (chain M) ... can be seen here [C] COG1007 NADH:ubiquinone oxidoreductase subunit 2 (chain N) ... can be seen here [C] COG0838 NADH:ubiquinone oxidoreductase subunit 3 (chain A) ... can be seen here [R] COG1752 Predicted esterase of the alpha-beta hydrolase superfamily ... can be seen here [K] COG0640 Predicted transcriptional regulators ... can be seen here     ..................................................................................................................                                                                         Gene putatively regulated by attenuation in A_aeolicus                                                                         Characteristics of the secondary structures Terminator:    Distance to gene:121 nt.     Distance to run of Ts=1 nt.   Size=22 nt.     Delta G= -7.30 kcal/mol Antiterminator: Size=36 nt.     Delta G= -3.10 kcal/mol Anti-antiterminator:   Size=32 nt.     Delta G= -6.50 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 TACTCTTTAAGGTAATCGAACTTCCCCTTCCAGTCGTCTCCCATAACGAATACATCAA CGTTGTACTTCTTTATGTCCTCTATCTTCTGCTCCCAGTTCCTTTCGGGAATTACCAG ATCCACATACTTAATGGAACGTACTATTTCCGCCCTGTGCTCGTAAGGGTAAACAGAT TTCTTTCCTTTTATAGCGTTAAACTCGTCCGTGGAAACTCCCACTATGAGAAAGTCTC CGAGGGCTTTTGCCCTCTTCAGTAAGTTCAGATGTCCTATATGAAATAAATCAAAAGT TCCGTAAGTAATG     aq_1369 --- rlpA1 --- argH --- nuoH2 --- nuoH3 --- nuoI2 --- nuoJ2 --- nuoK2 --- nuoL3 --- nuoM2 --- nuoN2 --- nuoA1 --- aq_1386 --- arsR Gene: aq_1369     GI: 15606565     BI number: aq_1369     GOG: -------     Description: putative protein Gene: rlpA1     GI: 15606566     BI number: aq_1370     GOG: COG0797     Description: rare lipoprotein A Gene: argH     GI: 15606567     BI number: aq_1372     GOG: COG0165     Description: argininosuccinate lyase Gene: nuoH2     GI: 15606568     BI number: aq_1373     GOG: COG1005     Description: NADH dehydrogenase I chain H Gene: nuoH3     GI: 15606569     BI number: aq_1374     GOG: COG1005     Description: NADH dehydrogenase I chain H Gene: nuoI2     GI: 15606570     BI number: aq_1375     GOG: COG1143     Description: NADH dehydrogenase I chain I Gene: nuoJ2     GI: 15606571     BI number: aq_1377     GOG: COG0839     Description: NADH dehydrogenase I chain J Gene: nuoK2     GI: 15606572     BI number: aq_1378     GOG: COG0713     Description: NADH dehydrogenase I chain K Gene: nuoL3     GI: 15606573     BI number: aq_1379     GOG: COG1009     Description: NADH dehydrogenase I chain L Gene: nuoM2     GI: 15606574     BI number: aq_1382     GOG: COG1008     Description: NADH dehydrogenase I chain M Gene: nuoN2     GI: 15606575     BI number: aq_1383     GOG: COG1007     Description: NADH dehydrogenase I chain N Gene: nuoA1     GI: 15606576     BI number: aq_1385     GOG: COG0838     Description: NADH dehydrogenase I chain A Gene: aq_1386     GI: 15606577     BI number: aq_1386     GOG: COG1752     Description: hypothetical protein Gene: arsR     GI: 15606578     BI number: aq_1387     GOG: COG0640     Description: transcriptional regulator (ArsR family            GG           T  A   T       A  A T  C      A  C T  G       TG CG        TT CG        CA TA        AC TA        TT        TA GT       A  A      G  A AT       C  T       CG C  A      A  T       TG C  C      C  |       CG C  |      C  |       GT T  |      T  |      |  A C  |      A  |      |  A GC        GT        TA TA        AC        GC CG        CC        TA TA        CG        CG                         ATTTCTTTCCTTTTATAGCGTTAAACTCGTCCGTGGAAACTCCCACTATGAGAAAGTCTCCGAGGGCTTTTGCCCTCTTCAGTAAGTTCAGATGTCCTATATGAAATAAATCAAAAGTTCCGTAAGTAATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [M] COG0797 Lipoproteins ... can be seen here [E] COG0165 Argininosuccinate lyase ... can be seen here [C] COG1005 NADH:ubiquinone oxidoreductase subunit 1 (chain H) ... can be seen here [C] COG1005 NADH:ubiquinone oxidoreductase subunit 1 (chain H) ... can be seen here [C] COG1143 Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) ... can be seen here [C] COG0839 NADH:ubiquinone oxidoreductase subunit 6 (chain J) ... can be seen here [C] COG0713 NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) ... can be seen here [CP] COG1009 NADH:ubiquinone oxidoreductase subunit 5 (chain L)/Multisubunit Na+/H+ antiporter, MnhA subunit ... can be seen here [C] COG1008 NADH:ubiquinone oxidoreductase subunit 4 (chain M) ... can be seen here [C] COG1007 NADH:ubiquinone oxidoreductase subunit 2 (chain N) ... can be seen here [C] COG0838 NADH:ubiquinone oxidoreductase subunit 3 (chain A) ... can be seen here [R] COG1752 Predicted esterase of the alpha-beta hydrolase superfamily ... can be seen here [K] COG0640 Predicted transcriptional regulators ... can be seen here     ..................................................................................................................