HHsearch alignment for GI: 254780810 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=100.00 E-value=0 Score=593.80 Aligned_cols=249 Identities=74% Similarity=1.152 Sum_probs=245.6
Q ss_pred CHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHHCCEEEECCCCCC
Q ss_conf 13688899886551023122204877878999999999986118864699995087878999999840342782366788
Q gi|254780810|r 159 DISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGEVISSTFDES 238 (423)
Q Consensus 159 ~~~~~~id~~~pig~gqr~~i~~~~~~gkt~ll~~ia~~~~~~~~~v~~i~~ligEr~~ev~e~~~~~~~~vv~st~d~~ 238 (423)
T Consensus 1 d~~~r~ID~l~pigkGQR~gI~g~~gvGKT~Ll~~i~~~~~~~~~~~~~v~~lIGER~rEv~e~~~~~~~~vv~st~d~~ 80 (249)
T cd01128 1 ELSTRVVDLFAPIGKGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEP 80 (249)
T ss_pred CCCCEEEEEECCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEEEEECCHHHHHHHHHHHCEEEEEECCCCC
T ss_conf 97410154324616786778878999889999999999999858984999999716579999999971616999569999
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHCHHHHHCCCCCCCCCCCEE
Q ss_conf 88999999999999999997799289998163898776200136677767775202466504687522577777785001
Q gi|254780810|r 239 AARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKILTGGVDANALQRPKRFFGAARNIKEGGSLTI 318 (423)
Q Consensus 239 ~~~~~~~a~~a~~~a~~~~e~G~dVll~~DslTR~ArA~~~~~~~~g~~~~gg~~~~~l~~~~~~~~~ar~~~~~Gs~T~ 318 (423)
T Consensus 81 p~~r~~~a~~a~~iAEyfr~~G~dVLl~~DslTR~A~A~rEis~~~ge~~~~g~~~~~~~~~~~~~~~a~~~e~~GSiT~ 160 (249)
T cd01128 81 PERHVQVAEMVLEKAKRLVEHGKDVVILLDSITRLARAYNTVVPPSGKILSGGVDANALHKPKRFFGAARNIEEGGSLTI 160 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 89999999999999999998799779995148899999866302469878899791354554899985267889953799
Q ss_pred EEEEEECCCCCCCCHHHHHHHHCCCCEEEEEHHHHHCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCHHH
Q ss_conf 21120126765541388988522660789808788479997405335422101551999999999999999612693789
Q gi|254780810|r 319 IGTALVDTGSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIVSSMNSSDA 398 (423)
Q Consensus 319 ~~t~lvetg~~~d~~i~~~~~~~~d~~i~L~r~la~~~~~PAId~~~S~sR~~~~l~~~~~~~~~~~~r~~l~~~~~~e~ 398 (423)
T Consensus 161 ~~tvlve~~d~~d~~I~~~~~~i~Dg~IvLsr~la~~g~yPAIDv~~S~SR~~~~i~~~~~~~~a~~~R~~l~~y~~~e~ 240 (249)
T cd01128 161 IATALVDTGSRMDDVIFEEFKGTGNMELVLDRRLAERRIFPAIDILKSGTRKEELLLDPEELQRMWLLRRVLSDMDPIEA 240 (249)
T ss_pred EEEEEECCCCCCCCHHHHHHHHCCCEEEEECHHHHHCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 88887637766672689998651774999639999759998646334621034010999999999999999966877899
Q ss_pred HHHHHHHHH
Q ss_conf 999999840
Q gi|254780810|r 399 IEFLIDKLK 407 (423)
Q Consensus 399 ~~~l~~~~~ 407 (423)
T Consensus 241 m~~l~~~~~ 249 (249)
T cd01128 241 MEFLLKKLR 249 (249)
T ss_pred HHHHHHHHC
T ss_conf 999999729