HHsearch alignment for GI: 254780456 and conserved domain: TIGR00448

>TIGR00448 rpoE DNA-directed RNA polymerase; InterPro: IPR004519 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to Escherichia coli RpoE.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription, 0005634 nucleus.
Probab=98.55  E-value=3.2e-07  Score=61.07  Aligned_cols=73  Identities=38%  Similarity=0.736  Sum_probs=54.0

Q ss_pred             CCCCCEEEEEEEEEECCCCEEE-ECCCEEEEEEEECCCCCCC-CC-------------CEEECCCCEEEEEEEEEC----
Q ss_conf             2223302467887531471777-4483157886420244444-33-------------113326972589999874----
Q gi|254780456|r  195 LEEGQVIEGTVKNITDYGVFVD-LSGVDGLLHVTDIAWHRIL-HP-------------SKVLSIGQQVKVKIIRIN----  255 (576)
Q Consensus       195 l~~G~~v~g~V~~i~~~g~~V~-~~g~~g~i~~~~ls~~~~~-~~-------------~~~~~~G~~v~~~Vl~~d----  255 (576)
T Consensus        79 P~l~EiVeGev~~~~efG~fV~LlGp~D~l~h~sq~~ddy~~YdPk~~~liGPmD~Etk~~ld~gd~vRaRIv~~slk~~  158 (184)
T TIGR00448        79 PELGEIVEGEVIEIVEFGAFVSLLGPFDGLLHVSQVLDDYVVYDPKESALIGPMDKETKKVLDVGDKVRARIVALSLKDR  158 (184)
T ss_pred             CCCEEEEEEEEEEEEECCCEEEEECCCCCEEEEEEEEECCEEECCCCCCEECCCCHHCCCEEECCCEEEEEEEEEEECCC
T ss_conf             35216786589989852742675223132344100113563662656604567401217351016756678888764041


Q ss_pred             -C-CCCEEEEEECC
Q ss_conf             -7-65279985215
Q gi|254780456|r  256 -Q-ETHRISLGMKQ  267 (576)
Q Consensus       256 -~-~~~~i~lslK~  267 (576)
T Consensus       159 ~pk~~~k~~LtmRq  172 (184)
T TIGR00448       159 RPKEGSKIGLTMRQ  172 (184)
T ss_pred             CCCCCCEEEEECCC
T ss_conf             37888511001157