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=98.19  E-value=2.3e-06  Score=55.84  Aligned_cols=107  Identities=28%  Similarity=0.435  Sum_probs=60.1

Q ss_pred             CCCCCCEEECCCCEEEEEEEEECCCCCEEEE-EECCCCCC-----CCCCCCCCC--CCCCEEEEEEEE--ECCCE----E
Q ss_conf             4443311332697258999987476527998-52155543-----210000000--489665899998--15966----9
Q gi|254780456|r  233 RILHPSKVLSIGQQVKVKIIRINQETHRISL-GMKQLEKN-----PWDDVQDKY--VEGSKVSGVVTN--LTDYG----V  298 (576)
Q Consensus       233 ~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~l-slK~l~~d-----p~~~~~~~~--~~G~~v~g~V~~--v~~~G----~  298 (576)
T Consensus        92 ~~~~p~--~~iGd~~~~~~~~~~F--gR~a~~~a~Q~~~Qk~re~e~~~~~~ef~~~~g~~i~g~V~r~d~~~~~~~~g~  167 (366)
T TIGR01953        92 REIDPD--VQIGDEVKKEINPENF--GRIAAQAAKQVITQKIREAERERVYDEFKSKVGEIISGTVKRVDVNKEGNETGL  167 (366)
T ss_pred             HHCCCC--CCCCCEEEEECCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEECCCCCCCEE
T ss_conf             210779--6215378874276664--478999999999888899998767766433318089999999752578752107


Q ss_pred             EEEE-CCCCEEEEECCCCCCCCCCCCCCCEECCCCEEEEEEEEEECCCC----EEEEE
Q ss_conf             9985-14200000011110111355742100378457999998621550----47875
Q gi|254780456|r  299 FVEL-QSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARK----RISLG  351 (576)
Q Consensus       299 ~V~l-~~~v~G~i~~sels~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~----~i~lS  351 (576)
T Consensus       168 ~v~l~g-~~e~~lp~~e~-------iP~E~~~~Gd~i~~~~~eV~~~~~g~~~~i~lS  217 (366)
T TIGR01953       168 IVELAG-KTEAILPKKEQ-------IPGEKFRIGDRIKAYVYEVRKTAKGGLPQIILS  217 (366)
T ss_pred             EEEECC-CEEEECCHHHC-------CCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEE
T ss_conf             999857-50252135337-------888752358889999999998688966899997