HHsearch alignment for GI: 254780615 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=559.39 Aligned_cols=241 Identities=23% Similarity=0.339 Sum_probs=225.7
Q ss_pred CCCCCCCCCCCCCCCCCCEECCCCCCCCHHHHHHHHHHHHHHCCCC-CEEEEEECCCHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 0231100235570215410036756666248999999988505788-526876216434599999985424420012223
Q gi|254780615|r 134 TTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGG-YSVFAGVGERTREGNDLYHEMIDSKVNIDPRKN 212 (478)
Q Consensus 134 ~TGIkaID~l~pig~Gqr~gIfgg~GvGKT~l~~~~i~n~~~~~~~-v~V~~~iGER~rEv~e~~~e~~~~~~~~~~~~~ 212 (478)
T Consensus 1 d~~~r~ID~l~pigkGQR~gI~g~~gvGKT~Ll~~i~~~~~~~~~~~~~v~~lIGER~rEv~e~~~~~------------ 68 (249)
T cd01128 1 ELSTRVVDLFAPIGKGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSV------------ 68 (249)
T ss_pred CCCCEEEEEECCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEEEEECCHHHHHHHHHHH------------
T ss_conf 97410154324616786778878999889999999999999858984999999716579999999971------------
Q ss_pred CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHCCCCHHHHCCHHHHH
Q ss_conf 44433231699971766896787777777877689998669967999715599987601245531144101101223566
Q gi|254780615|r 213 NGSAVGSKCSLLYGQMNEPPGARSRVALTGLTVAEHFRDQGQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLAL 292 (478)
Q Consensus 213 ~~~~~~~~tv~v~~~~~~~~~~r~~~~~~a~tiAEyfrd~g~dVll~~Dsltr~a~A~rEisl~~g~~P~~~gYp~~~f~ 292 (478)
T Consensus 69 -------~~~vv~st~d~~p~~r~~~a~~a~~iAEyfr~~G~dVLl~~DslTR~A~A~rEis~~~ge~~~-~g~~~~~~~ 140 (249)
T cd01128 69 -------KGEVIASTFDEPPERHVQVAEMVLEKAKRLVEHGKDVVILLDSITRLARAYNTVVPPSGKILS-GGVDANALH 140 (249)
T ss_pred -------CEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHCCCCCCCCC-CCCCHHHHH
T ss_conf -------616999569999899999999999999999987997799951488999998663024698788-997913545
Q ss_pred HHHHHHHHHCCCC-CCCEEEEEEEEEC-CCCCCCHHHHHHHHHCCCEEEEEHHHHHCCCCCCCCCCCCCCCCCCCEECCH
Q ss_conf 6578887631777-6532566654304-7664410589999750342564115663188675322355431116201289
Q gi|254780615|r 293 EMGELQERITTTL-KGSITSVQAIYVP-ADDLTDPAPATSFTHLDATTVLSRQISEKGIYPAIDPLDSNSSMLEIDIVGQ 370 (478)
Q Consensus 293 ~~~~l~ERag~~~-~GSIT~~~tV~~~-~dD~~dpi~~~~~si~Dg~ivLsr~la~~g~~PAId~~~S~Sr~~~~~i~~~ 370 (478)
T Consensus 141 ~~~~~~~~a~~~e~~GSiT~~~tvlve~~d~~d~~I~~~~~~i~Dg~IvLsr~la~~g~yPAIDv~~S~SR~~~-~i~~~ 219 (249)
T cd01128 141 KPKRFFGAARNIEEGGSLTIIATALVDTGSRMDDVIFEEFKGTGNMELVLDRRLAERRIFPAIDILKSGTRKEE-LLLDP 219 (249)
T ss_pred HHHHHHHHCCCCCCCCEEEEEEEEEECCCCCCCCHHHHHHHHCCCEEEEECHHHHHCCCCCCCCCCCCCCCCCH-HHCCH
T ss_conf 54899985267889953799888876377666726899986517749996399997599986463346210340-10999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999989989999997
Q gi|254780615|r 371 EHYDVARRVQEILQRYKSLQDIIAI 395 (478)
Q Consensus 371 ~h~~~a~~~r~~l~~y~el~~~i~~ 395 (478)
T Consensus 220 ~~~~~a~~~R~~l~~y~~~e~m~~l 244 (249)
T cd01128 220 EELQRMWLLRRVLSDMDPIEAMEFL 244 (249)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999999999668778999999