HHsearch alignment for GI: 254780617 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=523.92 Aligned_cols=243 Identities=19% Similarity=0.261 Sum_probs=225.9
Q ss_pred HCCHHHHHCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCC
Q ss_conf 41602331011115683365524778861158999999988630246678760699995167767899999851146742
Q gi|254780617|r 147 STGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSVARFVKALEDRGAL 226 (509)
Q Consensus 147 ~TGI~~ID~l~pigrGQR~~I~g~~g~GKt~l~~~~I~nq~~~~~~~~~~~~v~~V~~~IGer~~ev~~~~~~l~~~~~~ 226 (509)
T Consensus 1 d~~~r~ID~l~pigkGQR~gI~g~~gvGKT~L-l~~i~~~~~~~-----~~~~~~v~~lIGER~rEv~e~~~~~~----- 69 (249)
T cd01128 1 ELSTRVVDLFAPIGKGQRGLIVAPPKAGKTTL-LQSIANAITKN-----HPEVYLIVLLIDERPEEVTDMQRSVK----- 69 (249)
T ss_pred CCCCEEEEEECCCCCCCEEEEECCCCCCHHHH-HHHHHHHHHHH-----CCCEEEEEEEEECCHHHHHHHHHHHC-----
T ss_conf 97410154324616786778878999889999-99999999985-----89849999997165799999999716-----
Q ss_pred CEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 11589972887888999998876666667542046884799616478999998754530378754333752001246788
Q gi|254780617|r 227 SYSIVVVASASDPAPMQLLAPFAGCAMGEYFRDNGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLL 306 (509)
Q Consensus 227 ~~tvvv~a~a~~~~~~r~~ap~~a~aiAEyfr~~G~~VLi~~Ddltr~A~a~reisl~~~~pp~~~gyp~~vf~~~s~l~ 306 (509)
T Consensus 70 --~~vv~st~d~~p~~r~~~a~~a~~iAEyfr~~G~dVLl~~DslTR~A~A~rEis~~~ge~~~-~g~~~~~~~~~~~~~ 146 (249)
T cd01128 70 --GEVIASTFDEPPERHVQVAEMVLEKAKRLVEHGKDVVILLDSITRLARAYNTVVPPSGKILS-GGVDANALHKPKRFF 146 (249)
T ss_pred --EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHCCCCCCCCC-CCCCHHHHHHHHHHH
T ss_conf --16999569999899999999999999999987997799951488999998663024698788-997913545548999
Q ss_pred HHHHHCCCCCCCCCEEEEEEEECC-CCCCCCCHHHHHHHHHCCEEEEECCHHHHCCCCCCCCCCCHHHCCCCCCCHHHHH
Q ss_conf 887504544588735675310036-7664431146688540616996150122102665433444122034343898877
Q gi|254780617|r 307 ERAAKMSDALGAGSLTALPVIETQ-VNDVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVGSAAQVKAMKQ 385 (509)
Q Consensus 307 ERa~~~~~~~g~GSiT~~~~v~~~-~~D~~~~i~~~~~si~DG~i~l~~~l~~~g~~Paid~~~S~SRv~~~~~~~~~~~ 385 (509)
T Consensus 147 ~~a~~~e~---~GSiT~~~tvlve~~d~~d~~I~~~~~~i~Dg~IvLsr~la~~g~yPAIDv~~S~SR~~~~i~~~~~~~ 223 (249)
T cd01128 147 GAARNIEE---GGSLTIIATALVDTGSRMDDVIFEEFKGTGNMELVLDRRLAERRIFPAIDILKSGTRKEELLLDPEELQ 223 (249)
T ss_pred HHCCCCCC---CCEEEEEEEEEECCCCCCCCHHHHHHHHCCCEEEEECHHHHHCCCCCCCCCCCCCCCCCHHHCCHHHHH
T ss_conf 85267889---953799888876377666726899986517749996399997599986463346210340109999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 556788879988767879876
Q gi|254780617|r 386 VSGAVKGELAQYREMSSFSKF 406 (509)
Q Consensus 386 ~a~~lr~~laqy~Ele~f~~f 406 (509)
T Consensus 224 ~a~~~R~~l~~y~~~e~m~~l 244 (249)
T cd01128 224 RMWLLRRVLSDMDPIEAMEFL 244 (249)
T ss_pred HHHHHHHHHHCCCHHHHHHHH
T ss_conf 999999999668778999999