HHsearch alignment for GI: 254780709 and conserved domain: cd01128
>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.
Probab=95.49 E-value=0.13 Score=31.67 Aligned_cols=89 Identities=18% Similarity=0.280 Sum_probs=52.0
Q ss_pred CEEECCCCCCCCHHHHHHHHHHHHHHCCCC--EEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHH---HHHHHH
Q ss_conf 123113544444247899999998522674--267743451245688999997530353212235866124---542289
Q gi|254780709|r 112 HVILVVGVNGVGKTTVIGKLSKKMSDAGLK--VMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAAA---LAYEAF 186 (321)
Q Consensus 112 ~vil~vG~nG~GKTTT~aKLA~~~~~~g~k--V~lva~DtfR~aA~eQL~~~a~~~~v~~~~~~~~~dp~~---v~~~a~ 186 (321)
T Consensus 17 QR~gI~g~~gvGKT~Ll~~i~~~~~~~~~~~~~v~~lIG-ER~rEv~e~---~~~~~~~vv~st~d~~p~~r~~~a~~a~ 92 (249)
T cd01128 17 QRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLID-ERPEEVTDM---QRSVKGEVIASTFDEPPERHVQVAEMVL 92 (249)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEEEEE-CCHHHHHHH---HHHHCEEEEEECCCCCHHHHHHHHHHHH
T ss_conf 677887899988999999999999985898499999971-657999999---9971616999569999899999999999
Q ss_pred ---HHHHHHCCCEEEE-ECCCC
Q ss_conf ---9996514875998-65433
Q gi|254780709|r 187 ---KQAQAKKVDVLII-DTAGR 204 (321)
Q Consensus 187 ---~~a~~~~~Dvvli-DTAGR 204 (321)
T Consensus 93 ~iAEyfr~~G~dVLl~~DslTR 114 (249)
T cd01128 93 EKAKRLVEHGKDVVILLDSITR 114 (249)
T ss_pred HHHHHHHHCCCCEEEEEHHHHH
T ss_conf 9999999879977999514889