HHsearch alignment for GI: 254780788 and conserved domain: TIGR01954

>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214 NusA, or N utilisation substance protein A, is 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 an acidic 50-residue region found in two copies toward the C terminus of most proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic ; GO: 0030528 transcription regulator activity.
Probab=98.60  E-value=6.1e-08  Score=77.62  Aligned_cols=50  Identities=38%  Similarity=0.507  Sum_probs=47.8

Q ss_pred             CCHHHHHHHHHCCCCCHHHHHHCCHHHHCC--CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             998999999987984788965326775212--312344432112453343588999999999984122578
Q gi|254780788|r  443 IDSKIKVALGENGIKTMEDLAGCSVDDLLG--WSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGW  511 (526)
Q Consensus       443 l~~~~~~~L~e~gIktleDlAels~dEL~~--~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~gW  511 (526)
T Consensus         1 ~~e~~a~~Lv~eGf~t~EdlAy~~~~EL~~fGIe-----------------G~~Ee~A~~L~~~Ar~~--~   52 (52)
T TIGR01954         1 IDEEIAQLLVEEGFTTVEDLAYVPVDELLSFGIE-----------------GLDEETAKELINRARNA--L   52 (52)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHCCCHHHHHHHCCC-----------------CCCHHHHHHHHHHHHHH--C
T ss_conf             9578899999736731788750455668863589-----------------98878899999998752--9