>gnl|CDD|144229 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII). Length = 373

Score = 264 bits (677), Expect = 1e-70 Identities = 101/234 (43%), Positives = 128/234 (54%), Gaps = 58/234 (24%) Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116 ++ ++ D+ PG ++ VKV++ KR Q GDK A RHG KG+VS+ILP EDMPF +DG Sbjct: 196 VDDVKI--DLNPGGIKKVKVYIRQKRKPQVGDKFASRHGQKGVVSKILPQEDMPFTEDGI 253 Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176 P DI+LNP GVPSRM +GQ+ E+ LG A LGK I D +P Sbjct: 254 PPDIILNPHGVPSRMTIGQLLESLLGKAAALLGKFI-----------DATP--------- 293 Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE--EAINSMLRMADLDESGQS 1234 FDGA E E I +L+ A + G+ Sbjct: 294 ----------------------------------FDGASEVVEDIGELLKEAGYNAYGKE 319 Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288 +LYDG TGEPF P+ VG IY KL HMV DK++ARSTG YSL+TQQPLGG+S Sbjct: 320 VLYDGRTGEPFKAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTQQPLGGRSR 373

RPSBLAST alignment for GI: 254780143 and conserved domain: pfam00562