                                                                        Gene putatively regulated by attenuation in A_fulgidus

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:167 nt.     Distance to run of Ts=1 nt.   Size=33 nt.     Delta G=-10.10 kcal/mol
Antiterminator: Size=34 nt.     Delta G= -3.80 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

TTTAGCCTTCCTTGAAAAGCACATCGCCAAGTACAAGCTACCGAGGATAATTGAGTTT
ACGGATAAACCTCTGCCAAGAACACCCACAGGAAAGCTGCTGAGAAGGCTGTTGAAGC
AGAGTAGCTGAtttttctttttttaaaaagaatattttttattttttgatgtcgattttaacattttctaaattggccgcgttcttgagaaa
tcttcaatttctacaaattttcttaaaaattcttcagtaaattctctaattcatgcaaaaaacttttaaatctggcatgaaatcctgagtacATG

    acs --- 4 Gene: amt-1     GI: 11498582     BI number: AF0977     GOG: COG0004     Description: ammonium transporter (amt-1) Gene: glnB-1     GI: 11498583     BI number: AF0978     GOG: COG0347     Description: nitrogen regulatory protein P-II (glnB-1             T AC       T  G C  A      G  A CG        TA CG        CG A  A       GC C  A      G  A A  A      A  G A  G      A  | GC       G  | AT       A  | A  |      G  | C  |       TA CG        CG GC        GT T  T       TA CG        CG TA        GC CG        AT             GAtttttctttttttaaaaagaatattttttattttttgatgtcgattttaacattttctaaattggccgcgttcttgagaaatcttcaatttctacaaattttcttaaaaattcttcagtaaattctctaattcatgcaaaaaacttttaaatctggcatgaaatcctgagtacATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [P] COG0004 Ammonia permease ... can be seen here [E] COG0347 Nitrogen regulatory protein PII ... can be seen here     ..................................................................................................................