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