HHsearch alignment for GI: 254780142 and conserved domain: pfam04983
>pfam04983 RNA_pol_Rpb1_3 RNA polymerase Rpb1, domain 3. 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 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Probab=99.93 E-value=1e-25 Score=211.53 Aligned_cols=133 Identities=37% Similarity=0.574 Sum_probs=114.9
Q ss_pred CCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEEECC
Q ss_conf 54237887820440258999999873367887446814179999999998889867852365204645667614245217
Q gi|254780142|r 491 NLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKIYDT 570 (1398)
Q Consensus 491 niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~a~i~~~~~~~~~~~~~~~~~~~t 570 (1398)
T Consensus 1 NiisP~~G~Pii~~~QD~ilG~y~LT~~~--------~f~~~~e~~~~~~~~~~~~~~~i~~~~~-~------------~ 59 (158)
T pfam04983 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRD--------TFFDREEVMQLLMYGIVLPHPAILKPIK-P------------L 59 (158)
T ss_pred CCCCCCCCCCEEEEHHHHHHHHHHHHCCC--------CCCCHHHHHHHHHHCCCCCCCCEEECCC-C------------C
T ss_conf 93268998936764028989989972898--------6699999999998379877870576376-6------------7
Q ss_pred CCCCCCCCE-------------------------EEECCCCCEEEEECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 977511220-------------------------5545875101775110020136669999999808178999875588
Q gi|254780142|r 571 TPGRMIIGE-------------------------ILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLM 625 (1398)
Q Consensus 571 t~Gr~~~~~-------------------------ilp~~~~~~~~~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~ 625 (1398)
T Consensus 60 ~tgkq~~s~il~~~~~~~~~~~~~~~~~~~~~~~v~I~~G~l~~G~idk~~~~~~~~~Li~~i~~~~G~~~~~~~ld~i~ 139 (158)
T pfam04983 60 WTGKQTFSRLLPNEINPKGKPKTNEETLCENDSYVLINNGELISGVIDKKLGGKSLGSLIHIIYKEYGPEETVKFLDRLQ 139 (158)
T ss_pred CEEEEEHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCEEEEEEECCHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_conf 23103131102266454757766764457777748985781787453311126528889999999829899999999999
Q ss_pred HHHHHHHHHCCCCCCCCCC
Q ss_conf 9999999853986132123
Q gi|254780142|r 626 RLGFRYACSSGISFGKDDI 644 (1398)
Q Consensus 626 ~l~~~~l~~~GfSigi~D~ 644 (1398)
T Consensus 140 ~l~~~~l~~~GfSvgi~Dl 158 (158)
T pfam04983 140 KLGFRYLTKSGFSIGIDDI 158 (158)
T ss_pred HHHHHHHHHCCEEEEECCC
T ss_conf 9999999977867952059