HHsearch alignment for GI: 254780237 and conserved domain: pfam03118

>pfam03118 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal.
Probab=99.76  E-value=7.2e-19  Score=142.41  Aligned_cols=60  Identities=50%  Similarity=0.734  Sum_probs=57.4

Q ss_pred             HHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             233311122101105888989883983718887449888861889886449999999998
Q gi|254780237|r  253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT  312 (340)
Q Consensus       253 ~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~  312 (340)
T Consensus         3 ~~~l~~~I~~L~LS~R~~N~Lk~~~I~tv~dL~~~s~~dLl~i~N~G~kSl~EI~~~L~~   62 (62)
T pfam03118         3 LALLSIPIEELELSVRSYNCLKRAGINTVGDLLSKSEEDLLKIKNFGKKSLEEIKEKLEE   62 (62)
T ss_pred             HHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf             888639899816868999999894996799998589999974889868579999999829