HHsearch alignment for GI: 254780142 and conserved domain: pfam00623
>pfam00623 RNA_pol_Rpb1_2 RNA polymerase Rpb1, domain 2. 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 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Probab=100.00 E-value=0 Score=449.16 Aligned_cols=143 Identities=50% Similarity=0.711 Sum_probs=121.5
Q ss_pred CCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHHH--------HHHHHHCCCCCC-----CC---CCCCEEE-----
Q ss_conf 51004577403412554354620034898776128999--------999998798666-----30---0010012-----
Q gi|254780142|r 346 GKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFL--------YAQLEKKGYVST-----VK---QAKKFVE----- 404 (1398)
Q Consensus 346 GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~~--------~~~L~~~g~~~~-----i~---~~k~~i~----- 404 (1398)
T Consensus 1 GKRvd~saRsVItpdP~L~i~evGiP~~iA~~Lt~pe~V~~~N~~~l~~~v~~g~~~~~~~~~~~~~~~~~~~l~~~~~~ 80 (165)
T pfam00623 1 GKRVDFSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPGAKYIKRIKGAKRDLEYKKRI 80 (165)
T ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCHHHHHHCCCHHEEHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEECCCC
T ss_conf 99877489754617998838874697999986281032379899999999972986566650677178858887505631
Q ss_pred -CCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHHHHHHH
Q ss_conf -2488250132666569789975763101114012358994495479731225454678775456997468999999999
Q gi|254780142|r 405 -KERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEAR 483 (1398)
Q Consensus 405 -~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~~vc~pyNADFDGDEMnlHvPqs~eAraEa~ 483 (1398)
T Consensus 81 ~~~l~~g~~v~R~l~dGD~Vl~NRqPTLHr~si~a~~v~i~~~~tirlnp~vc~~fNADFDGDeMnih~pqs~~a~~E~~ 160 (165)
T pfam00623 81 AIELWYGDIVLRHVIDGDVVLLNRQPTLHRMSIMAHRPRVLEGKTIRLNPSVCSPYNADFDGDEMNLHVPQSEEARAEAR 160 (165)
T ss_pred CHHHCCCHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEEECCCEEEECCCCCCCCCCCCCCCEEEEECCCCHHHHHHHH
T ss_conf 11212351156576479889992785225142036688996897058776546770588787247876689999999999
Q ss_pred HHHHH
Q ss_conf 98767
Q gi|254780142|r 484 VLMLS 488 (1398)
Q Consensus 484 ~Lm~~ 488 (1398)
T Consensus 161 ~Lm~v 165 (165)
T pfam00623 161 ELMLV 165 (165)
T ss_pred HHHCC
T ss_conf 87249