>gnl|CDD|132719 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 channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria. Length = 158

 Score = 95.9 bits (239), Expect = 7e-20
 Identities = 42/149 (28%), Positives = 69/149 (46%), Gaps = 42/149 (28%)

Query: 1212 PQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYIL 1271
              ++L   G+EA    +I E+Q+V   +GV+++ +HIE++   M                
Sbjct: 50   IHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMT--------------- 94

Query: 1272 GDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASL--QTKSFISAASFQETTKVLTE 1329
                                     +S  L+G+T++       S +  ASF++TTK L +
Sbjct: 95   -------------------------YSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLLD 129

Query: 1330 AAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358
            AA AG+ D L+G  EN+I+GR  P GTG+
Sbjct: 130  AAAAGEKDELEGVSENIILGRPAPLGTGS 158