>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the 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. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe

Probab=100.00 E-value=0 Score=434.70 Aligned_cols=110 Identities=35% Similarity=0.547 Sum_probs=100.3 Q ss_pred CHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHC Q ss_conf 99999875279999999999999999980970061256012476286148941886454566410699999999999972 Q gi|254780142|r 1211 VPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQ 1290 (1398) Q Consensus 1211 d~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~ 1290 (1398) T Consensus 49 di~eil~vlGIEAaR~~Ii~Ei~~V~~~~Gi~Id~RHi~LIaD~MT~~G~i~~------i~R~Gi~~------------- 109 (158) T cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRG------VTRSGFRA------------- 109 (158) T ss_pred CHHHHHHHCCHHHHHHHHHHHHHHHHHHCCEEECHHHHHHHHHHHHCCCCCCC------CCHHHHCC------------- T ss_conf 99999995199999999999999999965935439999999999854786666------72565104------------- Q ss_pred CCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCH Q ss_conf 89875201210000145302310776504025899999974528552366532215507305655354 Q gi|254780142|r 1291 GKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358 (1398) Q Consensus 1291 g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~ 1358 (1398) T Consensus 110 -------------------~~~S~L~~ASFE~T~~~L~~AAi~g~~D~L~gvsenIiiG~~ip~GTGs 158 (158) T cd00630 110 -------------------SKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158 (158) T ss_pred -------------------CCCCHHHHCCHHHHHHHHHHHHHCCCCCCCCCHHHHHCCCCCCCCCCCC T ss_conf -------------------6757888716599999999999818978787819873058987899896

HHsearch alignment for GI: 254780142 and conserved domain: cd00630