HHsearch alignment for GI: 254780142 and conserved domain: pfam05000
>pfam05000 RNA_pol_Rpb1_4 RNA polymerase Rpb1, domain 4. 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, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Probab=98.83 E-value=4.7e-10 Score=93.59 Aligned_cols=89 Identities=31% Similarity=0.435 Sum_probs=57.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCCCCCCCCCEEEEECCCCCCC---HHHEEEEEEECCCCCC
Q ss_conf 6678887886423465899999999998761----15654322224688376422555578---4241120010000246
Q gi|254780142|r 674 TRGEKYNKVVDLWGKTTDKVTEEMMARIKRV----EFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGGMRGLIAK 746 (1398)
Q Consensus 674 t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ql~Gqq~l~gk 746 (1398)
T Consensus 2 ~~~~~~~~~~~~~~~s~~~~~E~~i~~~l~~~~~~~~~~~~~~~~~~N~~~~Mv~SGsKGs~~Ni~Qi~g~~GQQ~v~g~ 81 (108)
T pfam05000 2 TDAERYGKLEDIWGMTLEEVFEALINNILNKARDPAGNIASKSLDLNNSIYMMADSGAKGSIINISQIAGCRGQQNVEGK 81 (108)
T ss_pred CCHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCHHHHHHHHHHHCCEEECCC
T ss_conf 16544885347999988999999999999999999999999865866659999883377654529999986352147782
Q ss_pred CCCCCCCCCCCCHHHC
Q ss_conf 4434445666301110
Q gi|254780142|r 747 PSGEIIESPIRSHFKG 762 (1398)
Q Consensus 747 p~G~~~~~PV~~sF~~ 762 (1398)
T Consensus 82 Ri~~~~~~Rtlp~f~~ 97 (108)
T pfam05000 82 RIPFGFSGRTLPHFKK 97 (108)
T ss_pred CCCCCCCCCCCCCCCC
T ss_conf 1678989987999999