HHsearch alignment for GI: 254780143 and conserved domain: pfam04560
>pfam04560 RNA_pol_Rpb2_7 RNA polymerase Rpb2, domain 7. 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Probab=99.93 E-value=8.1e-27 Score=210.98 Aligned_cols=77 Identities=57% Similarity=0.941 Sum_probs=71.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCC-CCCCHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf 784320789999999869899998611100110159999887638787899-78667789999999854200276406
Q gi|254780143|r 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSIDLENS 1366 (1386)
Q Consensus 1290 GGlRfGEMErwaL~AyGAa~~LqE~Lt~kSDdv~gr~~~~~~iv~g~~~~~-~~~pesf~vl~~El~~l~l~~~~~~~ 1366 (1386)
T Consensus 1 GGlR~GEMErd~l~~hGas~~LkErl~~~SD~vc~~cg~~~~~c~~~~~~~~v~iPyafKLL~qEL~am~I~~rl~~~ 78 (78)
T pfam04560 1 GGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRCGAYAAICKGKTIIEPGDIPESFKLLLQELRSLGLDIRLFLE 78 (78)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHCCCCCEEECCCCHHHHHHHHHHHHCCCCEEEECC
T ss_conf 996301679999999959999999842578733125376989869899634667887999999999977777177339