HHsearch alignment for GI: 254780684 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=548.64 Aligned_cols=241 Identities=26% Similarity=0.381 Sum_probs=226.3
Q ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHH----HCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCEEEEE
Q ss_conf 11245875200223585037526678899999999874----07898389931246522388999986427755328984
Q gi|254780684|r 146 KTGIRVIDIFTPLCHGQRIGVFAGSGIGKSTLLSMFAR----SDCFDKVIISLVGERGREVREFIEDYLGDNLKKSVVVV 221 (438)
Q Consensus 146 ~TGIr~ID~l~pig~GQR~gIfg~~GvGKt~Ll~~i~~----~~~~dv~V~alIGeR~rev~efi~~~~~~~l~~tvvv~ 221 (438)
T Consensus 1 d~~~r~ID~l~pigkGQR~gI~g~~gvGKT~Ll~~i~~~~~~~~~~~~~v~~lIGER~rEv~e~~~~~~------~~vv~ 74 (249)
T cd01128 1 ELSTRVVDLFAPIGKGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSVK------GEVIA 74 (249)
T ss_pred CCCCEEEEEECCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEEEEECCHHHHHHHHHHHC------EEEEE
T ss_conf 974101543246167867788789998899999999999998589849999997165799999999716------16999
Q ss_pred ECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHCCHHHHHHHCCC
Q ss_conf 15778803444444567778888642679889997098999999876654047784323663245542004444431136
Q gi|254780684|r 222 ATSDESPILRKMAPLTAVTIAEYFSSKGDNVLLILDSITRFAHSIREIATNSGELPVARGYPTSVFSELPRLLERIGPSE 301 (438)
Q Consensus 222 ~t~d~~~~~r~~a~~~a~~iAEyfr~~G~~Vll~~Ds~tr~a~A~reis~~~ge~P~~~gyp~~~~~~~~~l~ERag~~~ 301 (438)
T Consensus 75 st~d~~p~~r~~~a~~a~~iAEyfr~~G~dVLl~~DslTR~A~A~rEis~~~ge~~~-~g~~~~~~~~~~~~~~~a~~~- 152 (249)
T cd01128 75 STFDEPPERHVQVAEMVLEKAKRLVEHGKDVVILLDSITRLARAYNTVVPPSGKILS-GGVDANALHKPKRFFGAARNI- 152 (249)
T ss_pred ECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHCCCCCCCCC-CCCCHHHHHHHHHHHHHCCCC-
T ss_conf 569999899999999999999999987997799951488999998663024698788-997913545548999852678-
Q ss_pred CCCCCEEEEEEEEEC-CCCCCCHHHHHHHHHCCCEEEEEHHHHHCCCCCCCCCCCCCCCCCHHCCCHHHHHHHHHHHHHH
Q ss_conf 788523554333421-6764202789998612608987042775897131144564000221208999999999999999
Q gi|254780684|r 302 KEKGNITAVISVLVD-GDNHNDPIADSVRSILDGHIVLNRSLAEEGRYPPVDPLASVSRLADKAWSADEKKLVSSLTHLI 380 (438)
Q Consensus 302 ~~~GSiT~~~~v~~~-~dd~~~pi~~~~~~i~DG~i~L~r~la~~g~~Paid~~~S~SR~~~~~~~~~~~~~~~~~~~~l 380 (438)
T Consensus 153 e~~GSiT~~~tvlve~~d~~d~~I~~~~~~i~Dg~IvLsr~la~~g~yPAIDv~~S~SR~~~~i~~~~~~~~a~~~R~~l 232 (249)
T cd01128 153 EEGGSLTIIATALVDTGSRMDDVIFEEFKGTGNMELVLDRRLAERRIFPAIDILKSGTRKEELLLDPEELQRMWLLRRVL 232 (249)
T ss_pred CCCCEEEEEEEEEECCCCCCCCHHHHHHHHCCCEEEEECHHHHHCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHH
T ss_conf 89953799888876377666726899986517749996399997599986463346210340109999999999999999
Q ss_pred HHHHHHHHHHHHHC
Q ss_conf 99999999998523
Q gi|254780684|r 381 HRFEETRDIRLIGG 394 (438)
Q Consensus 381 ~~y~~~~~l~~~g~ 394 (438)
T Consensus 233 ~~y~~~e~m~~l~~ 246 (249)
T cd01128 233 SDMDPIEAMEFLLK 246 (249)
T ss_pred HCCCHHHHHHHHHH
T ss_conf 66877899999999