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