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