>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=92.60 E-value=0.19 Score=29.86 Aligned_cols=55 Identities=15% Similarity=0.229 Sum_probs=43.7 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 0001112258884678888773211147775058888776530588999999999 Q gi|254780788|r 358 RTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGR 412 (526) Q Consensus 358 ~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~r 412 (526) T Consensus 5 ~l~~~I~~L~LS~R~~N~Lk~~~I~tv~dL~~~s~~dLl~i~N~G~kSl~EI~~~ 59 (62) T pfam03118 5 LLSIPIEELELSVRSYNCLKRAGINTVGDLLSKSEEDLLKIKNFGKKSLEEIKEK 59 (62) T ss_pred HHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH T ss_conf 8639899816868999999894996799998589999974889868579999999

HHsearch alignment for GI: 254780788 and conserved domain: pfam03118