>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 = 248 bits (636), Expect = 7e-66 Identities = 113/224 (50%), Positives = 140/224 (62%), Gaps = 26/224 (11%) Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT---CVNQRPLVK 783 IVA V+ + RI + G + IY L K+ RS+QNT C Q+PLVK Sbjct: 2 IVASLIPFVDHNQSPRITYQCAMGK-----QAIGIYTLNKYNRSDQNTYLLCYPQKPLVK 56 Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843 G V + G+L LG+N LVA M + GYN ED+++I++ V +FTSIH Sbjct: 57 TGA-VEKGGF---------GELPLGQNALVAVMSYTGYNQEDAIIINKSSVDRGLFTSIH 106 Query: 844 IEEFEVMARDTKLGP-EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902 I+E+E+ AR TKLGP EEITRD PNVSEE + +DE GI+ VGAEV PGDILVGK+TPKG Sbjct: 107 IKEYEIEARKTKLGPIEEITRDPPNVSEEAYRKLDEDGIVRVGAEVKPGDILVGKVTPKG 166 Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946 EKLLRAIFGEKA DV+DTSL+V G G V DV+I Sbjct: 167 -------EKLLRAIFGEKARDVKDTSLKVKHGEEGRVDDVKIDL 203

RPSBLAST alignment for GI: 254780143 and conserved domain: pfam00562