                                                                        Gene putatively regulated by attenuation in C_burnetii

                                                                        Characteristics of the secondary structures
Terminator:    Distance from promoter:102 nt.    Distance to gene:12 nt.     Distance to run of Ts=0 nt.   Size=28 nt.     Delta G= -9.10 kcal/mol
Antiterminator:    Distance from promoter:76 nt. Size=37 nt.     Delta G=-11.10 kcal/mol
Anti-antiterminator:    Distance from promoter:55 nt.    Size=25 nt.     Delta G= -7.50 kcal/mol

                                                                        Nomenclature/Definitions
The most likely promoter is: ttgtca-tataat. It has a score value of 76.31 and is shown in blue
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

ttgtcatttcattgatttctctataatataatccagcattgaTGCGGGGTGGAGCAGTCTGGCAGCTCGTCGGGCT
CATAACCCGAAGGTCGTAGGTTCAAATCCTACCCCCGCTACCAattttgcatcgggtttaagagtggg
gctatgtgcccttttttgttttttgaggtaaggtaATG

    CBU1434 --- nusA --- infB Gene: CBU1434     GI: 29654725     BI number: CBU1434     GOG: COG0779     Description: conserved hypothetical protein Gene: nusA     GI: 29654724     BI number: CBU1433     GOG: COG0195     Description: N utilization substance protein A Gene: infB     GI: 29654723     BI number: CBU1432     GOG: COG0532     Description: translation initiation factor IF-            tg           t  c           t  a           t  t           a  c           A  g            Cg         t            Cg       a  g   A        At       t  t C  A      |  t       cg T  A      |  t       gc T  T      |  a       gc GC       |  a       gc GC       |  g       gt AT        Ta       t  | TA        Cg        gt GC        Gt        at C  C       Cg        gt T  C       Cg        at GC        Cg        at GC        Cg        tg                         ttttttgaggtaaggtaATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [S] COG0779 Uncharacterized protein conserved in bacteria ... can be seen here [K] COG0195 Transcription elongation factor ... can be seen here [J] COG0532 Translation initiation factor 2 (IF-2; GTPase) ... can be seen here     ..................................................................................................................                                                                         Gene putatively regulated by attenuation in C_burnetii                                                                         Characteristics of the secondary structures Terminator:    Distance from promoter:109 nt.    Distance to gene:19 nt.     Distance to run of Ts=0 nt.   Size=15 nt.     Delta G= -8.00 kcal/mol Antiterminator:    Distance from promoter:68 nt. Size=37 nt.     Delta G=-11.10 kcal/mol Anti-antiterminator:    Distance from promoter:55 nt.    Size=25 nt.     Delta G= -7.50 kcal/mol                                                                         Nomenclature/Definitions The most likely promoter is: ttgtca-tataat. It has a score value of 76.31 and is shown in blue 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 ttgtcatttcattgatttctctataatataatccagcattgaTGCGGGGTGGAGCAGTCTGGCAGCTCGTCGGGCT CATAACCCGAAGGTCGTAGGTTCAAATCCTACCCCCGCTACCAattttgcatcgggtttaagagtggg gctatgtgcccttttttgttttttgaggtaaggtaATG     CBU1434 --- nusA --- infB Gene: CBU1434     GI: 29654725     BI number: CBU1434     GOG: COG0779     Description: conserved hypothetical protein Gene: nusA     GI: 29654724     BI number: CBU1433     GOG: COG0195     Description: N utilization substance protein A Gene: infB     GI: 29654723     BI number: CBU1432     GOG: COG0532     Description: translation initiation factor IF-            AC           T  C           C  A           G  a           C  t           C  t            Ct            Ct   A        Cg C  A      |  c T  A      |  a T  T      |  t GC       |  c GC       |  g        t AT        Ag       a  g TA        Tg       t  t GC        Ct        cg C  C       Ct        gc T  C       Tt        gc GC        Aa        gc GC        Aa        gt                         tttttgttttttgaggtaaggtaATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [S] COG0779 Uncharacterized protein conserved in bacteria ... can be seen here [K] COG0195 Transcription elongation factor ... can be seen here [J] COG0532 Translation initiation factor 2 (IF-2; GTPase) ... can be seen here     ..................................................................................................................