HHsearch alignment for GI: 254780148 and conserved domain: TIGR01955
>TIGR01955 RfaH transcriptional activator RfaH; InterPro: IPR010215 This entry represents the transcriptional activator protein, RfaH . This protein is most closely related to the transcriptional termination/antitermination protein NusG (IPR001062 from INTERPRO) and contains the KOW motif (IPR005824 from INTERPRO) . This protein appears to be limited to the proteobacteria. In Escherichia coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=100.00 E-value=9.7e-40 Score=257.94 Aligned_cols=160 Identities=25% Similarity=0.441 Sum_probs=143.5
Q ss_pred EEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCC-CCHHHHHCCC
Q ss_conf 189995288538999999999997798111432663131012772020356641203309999996186-5224442033
Q gi|254780148|r 5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTD-KVYHTIKDTP 83 (177)
Q Consensus 5 Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~-~~~~~i~~t~ 83 (177)
T Consensus 1 WYLlYcKpr~e~RA~~hL~r---------Q~~e~~~P~~~~ek~~rG~~~~v~ePLFP~YLFi~fD~~~G~~~~~irSTR 71 (162)
T TIGR01955 1 WYLLYCKPRQEQRAEEHLER---------QDVECYLPMVSVEKIKRGKKQLVEEPLFPNYLFIEFDPEKGDSWTPIRSTR 71 (162)
T ss_pred CCCCCCCCHHHHHHHHHHHH---------CCCCCCCHHHHHHHHHHCCHHEECCCCCCCEEEEEECCCCCCCCCEEEEEE
T ss_conf 96310081457999998861---------681001005678887620201121578987326770456788121254110
Q ss_pred EEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCC-CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCC
Q ss_conf 036643278861002588999999765322210000-1234789779995187789719999982889889999981687
Q gi|254780148|r 84 KVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVS-SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGR 162 (177)
Q Consensus 84 gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~-~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr 162 (177)
T Consensus 72 GVS~~VrfG~~P~~v~~~~I~~l~~~~~~~~~~~~~~P~~~~~G~~V~i~~G~fag~EAIF~~~dG~-~R~~~Llnm~~~ 150 (162)
T TIGR01955 72 GVSRIVRFGGHPAPVPDDLIHQLRQKELEASVPAKKTPLLFKKGDKVRITDGSFAGLEAIFLEPDGE-KRSVLLLNMIGK 150 (162)
T ss_pred CCEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCHHHCCCCCCCCCEEEEEECCCCCCCEEEECCCCC-HHHHHHHHHHCC
T ss_conf 5144460489772236689898640343225583135657789887998628713600354078842-477665466365
Q ss_pred EEEEEECHHHHE
Q ss_conf 047885678712
Q gi|254780148|r 163 VTPVELAYNQVE 174 (177)
Q Consensus 163 ~~~v~l~~~~ie 174 (177)
T Consensus 151 ~~~~~vp~~s~~ 162 (162)
T TIGR01955 151 QVKVSVPNTSVE 162 (162)
T ss_pred EEEEEEECCCCC
T ss_conf 046886145459