HHsearch alignment for GI: 254780784 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=95.20  E-value=0.15  Score=31.27  Aligned_cols=91  Identities=19%  Similarity=0.287  Sum_probs=71.3

Q ss_pred             EEEEEECCHHHHHHHHHHHHHHCCC-----------CCCCCEEEEEEEE--EEECC----EEEECCCCCCEEEEEEECCC
Q ss_conf             8999968989999999999985247-----------5468678999999--94153----69982879710488663144
Q gi|254780784|r  592 TVKIASSSLAEIEAAREMIRSITDV-----------PEVNKIYKGQVVK--VMDFG----AFVHFCGARDGLVHISQLST  654 (699)
Q Consensus       592 ~v~i~~~~~~~~~~a~~~i~~~~~~-----------~e~g~~y~~~v~~--i~~fG----afve~~~g~~gl~HiS~l~~  654 (699)
T Consensus       107 ~~~~~~FgR~a~~~a~Q~~~Qk~re~e~~~~~~ef~~~~g~~i~g~V~r~d~~~~~~~~g~~v~l~g~~e~~lp~~----  182 (366)
T TIGR01953       107 EINPENFGRIAAQAAKQVITQKIREAERERVYDEFKSKVGEIISGTVKRVDVNKEGNETGLIVELAGKTEAILPKK----  182 (366)
T ss_pred             ECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEECCCCCCCEEEEEECCCEEEECCHH----
T ss_conf             4276664478999999999888899998767766433318089999999752578752107999857502521353----


Q ss_pred             CCCCCHHHHCCCCCEEEEEEEEECC--CC---CEEEEEE
Q ss_conf             4547855603259889999997868--99---8666873
Q gi|254780784|r  655 ERVAKTSDVVKEGDTVWVKLLDFDD--RG---KIKLSMK  688 (699)
Q Consensus       655 ~~v~~~~d~~~~Gd~i~vk~~~~d~--~g---~i~lSrk  688 (699)
T Consensus       183 --e~iP~E~~~~Gd~i~~~~~eV~~~~~g~~~~i~lSRt  219 (366)
T TIGR01953       183 --EQIPGEKFRIGDRIKAYVYEVRKTAKGGLPQIILSRT  219 (366)
T ss_pred             --HCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEECC
T ss_conf             --3788875235888999999999868896689999708