>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and

Probab=99.78 E-value=5.3e-17 Score=130.31 Aligned_cols=185 Identities=18% Similarity=0.288 Sum_probs=142.9 Q ss_pred CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHHC Q ss_conf 3678881589999616975667888999998741698306889998---------8714431466462444999998401 Q gi|254780237|r 20 LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIK 90 (340) Q Consensus 20 ~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNLK 90 (340) T Consensus 5 i~~~~~~~~~F~l~g----~d~s~aNaLRRi~iseVPt~AId~V~i~~NTSvl~DE~laHRLGLIPl~s~~~~~~~~~~~ 80 (212) T cd07028 5 IREADKDNVDFILSG----VDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAHRLGLIPLQSMDILQLYRSPE 80 (212) T ss_pred EEECCCCEEEEEEEC----CCHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCCHHHHHEECCCCCCCCCCHHHHCCCC T ss_conf 997589779999968----9999999999999875974267799999788626546665130352013451023320733 Q ss_pred C-CEEEEC-CCCCEEEEEEEECCE----EEEEEEEECCC------CEEEECCCEEEEEECCCCEEEEEEEEECCCCCEEC Q ss_conf 1-417772-798279999994471----69963351389------85998888089997789649999997468763203 Q gi|254780237|r 91 G-INLKMS-GDSHKRVTIFKRGPG----VVTAGDIQTVN------DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158 (340) Q Consensus 91 ~-I~~k~~-~~~~~~~~l~~~Gp~----~vtA~Di~~p~------~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~ 158 (340) T Consensus 81 ~~~~~~~~~~~~~v~~~l~~~~~~~~~~~V~s~dl~~~~~~~~~~~~~pv~~~I~I~kL~~gQ~I~l~a~a~kG~Gk~H- 159 (212) T cd07028 81 EDCECEDHCDKCSVVLTLQAFAESESTTNVYSKDLVIVSNLMGRNIGHPIIQDILICKLRKGQEIKLTCVAKKGIGKEH- 159 (212) T ss_pred CCCCCCCCCCCEEEEEEEECCCCCCCCCEEECHHCEECCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEEEEECCCCCC- T ss_conf 3775567776469999996458999874498400788477777887633699958999389998999999994405646- Q ss_pred CCCCCCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 44446557543021243111144223577641168877621899999938961777999999999999888762 Q gi|254780237|r 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232 (340) Q Consensus 159 e~~~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~ 232 (340) T Consensus 160 ----------------AKwsPvs~~~y~~~p~~-------d~f~f~vES~G~l~p~~i~~~A~~iL~~K~~~~~ 210 (212) T cd07028 160 ----------------AKFGPVAAIEFRYDPVA-------DTYIMNVESVGSLPPDQVVVEAIKTLQKKVASIL 210 (212) T ss_pred ----------------EEECCCEEEEEEEEECC-------CEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHH T ss_conf ----------------08677168999984048-------6699999851799989999999999999999985

HHsearch alignment for GI: 254780237 and conserved domain: cd07028