>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, 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 assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the

Probab=99.61 E-value=6.6e-16 Score=123.24 Aligned_cols=82 Identities=28% Similarity=0.303 Sum_probs=76.6 Q ss_pred EECCCCCEECCCCCCCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHH Q ss_conf 74687632034444655754302124311114422357764116887762189999993896177799999999999988 Q gi|254780237|r 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228 (340) Q Consensus 149 ie~G~GY~~~e~~~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l 228 (340) T Consensus 4 i~~~~~~~tf~~~~EDHTlgN~Lr~~l~~~PV~~~~Y~v~hp~~~~~t~~dk~~l~IqT~g~i~p~eAl~~A~~~L~~~l 83 (86) T cd00460 4 LEKEKNYVDFVLENEDHTLGNSLRRILLKSPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKKL 83 (86) T ss_pred EECCCCEEEEEEECCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHH T ss_conf 85289859999947885278899999801983789987588765543676617999998999999999999999999987 Q ss_pred HH Q ss_conf 87 Q gi|254780237|r 229 GM 230 (340) Q Consensus 229 ~~ 230 (340) T Consensus 84 ~~ 85 (86) T cd00460 84 EH 85 (86) T ss_pred HC T ss_conf 14

HHsearch alignment for GI: 254780237 and conserved domain: cd00460