HHsearch alignment for GI: 254780456 and conserved domain: TIGR01953
>TIGR01953 NusA transcription termination factor NusA; InterPro: IPR010213 This entry describes NusA, or N utilisation substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents a region of NusA shared by all bacterial forms, and includes the S1 (IPR003029 from INTERPRO) and KH RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this entry, with two repeats of 50-residue domain rich in acidic amino acids.; GO: 0003723 RNA binding, 0030528 transcription regulator activity.
Probab=98.18 E-value=2.1e-05 Score=50.00 Aligned_cols=111 Identities=21% Similarity=0.338 Sum_probs=61.0
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCEEECCCCCC-CCCCCCCCCCCCCC--CCCCCEEEEEEEE--EECCC----CEEEE-
Q ss_conf 334555553023111335432331122121112-22221211100011--2223302467887--53147----17774-
Q gi|254780456|r 148 RDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVL-EESRAEQRSEIVQK--LEEGQVIEGTVKN--ITDYG----VFVDL- 217 (576)
Q Consensus 148 ~d~~~~vG~~i~~~Ii~~d~~~~~ivvS~k~~l-~~~~~~~~~~~~~~--l~~G~~v~g~V~~--i~~~g----~~V~~- 217 (576)
T Consensus 94 ~~p~~~iGd~~~~~~~~~~FgR~a~-~~a~Q~~~Qk~re~e~~~~~~ef~~~~g~~i~g~V~r~d~~~~~~~~g~~v~l~ 172 (366)
T TIGR01953 94 IDPDVQIGDEVKKEINPENFGRIAA-QAAKQVITQKIREAERERVYDEFKSKVGEIISGTVKRVDVNKEGNETGLIVELA 172 (366)
T ss_pred CCCCCCCCCEEEEECCCCCCCHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEECCCCCCCEEEEEEC
T ss_conf 0779621537887427666447899-999999988889999876776643331808999999975257875210799985
Q ss_pred CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCC----CEEEEEE
Q ss_conf 48315788642024444433113326972589999874765----2799852
Q gi|254780456|r 218 SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQET----HRISLGM 265 (576)
Q Consensus 218 ~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~----~~i~lsl 265 (576)
T Consensus 173 g~~e~~lp~~e~------iP~E~~~~Gd~i~~~~~eV~~~~~g~~~~i~lSR 218 (366)
T TIGR01953 173 GKTEAILPKKEQ------IPGEKFRIGDRIKAYVYEVRKTAKGGLPQIILSR 218 (366)
T ss_pred CCEEEECCHHHC------CCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEEC
T ss_conf 750252135337------8887523588899999999986889668999970