RPSBLAST alignment for GI: 254780788 and conserved domain: TIGR01953

>gnl|CDD|162623 TIGR01953, NusA, transcription termination factor NusA. This model describes NusA, or N utilization 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 E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids. Length = 341
 Score =  438 bits (1128), Expect = e-123
 Identities = 179/341 (52%), Positives = 252/341 (73%), Gaps = 2/341 (0%)

Query: 8   ELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLE 67
           E L   +A+A EK I  + V+  + +++++A +  +G   ++ V I+ +TGDI+++R  E
Sbjct: 1   EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKE 60

Query: 68  VVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAER 127
           VVEEVE+ + +ISL+ AR+ DP + IG  V   +PP +FGR+A Q+AKQVI+QK+REAER
Sbjct: 61  VVEEVEDPSLEISLEDAREIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAER 120

Query: 128 DRQYLEFKDKVGEIISGTVKRVEY-GNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYI 186
           +R Y EF  K GEIISGTVKRV   GN+ V+LG ++G++ + E I  E  R GDR+K+Y+
Sbjct: 121 ERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPKKEQIPGEKFRIGDRIKAYV 180

Query: 187 YDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDS 246
           Y+VR+  +GPQ++LSRTHP+F+ +L  +EVPEI +GI+++K ++R+PG R K+AV S+D 
Sbjct: 181 YEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDE 240

Query: 247 SIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKV-VLDEDV 305
           +IDPVGACVG +GSR+QA+  EL  EKIDI+ +S D A F+ NAL PA V  V VLDED 
Sbjct: 241 NIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVEVLDEDK 300

Query: 306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE 346
              EV+VP +QLSLAIG+ GQNVRLAS+LTGW ID+ TE +
Sbjct: 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTESQ 341