HHsearch alignment for GI: 254780142 and conserved domain: pfam04997
>pfam04997 RNA_pol_Rpb1_1 RNA polymerase Rpb1, domain 1. 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 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Probab=100.00 E-value=0 Score=587.93 Aligned_cols=310 Identities=41% Similarity=0.581 Sum_probs=235.3
Q ss_pred CCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 64053689845886788501448971755425456875688733621368566772156641563448835675788530
Q gi|254780142|r 15 DRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGVEVT 94 (1398)
Q Consensus 15 ~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg~~~~ 94 (1398)
T Consensus 1 ~k~i~~i~f~l~S~eeI~k~Sv~eVt~~~t~~~~~~~P~~gGL~D~rlG~~~~~---------------~~C~TCg~~~~ 65 (330)
T pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEPGGLLDERMGTIKKK---------------SICETCGVEVT 65 (330)
T ss_pred CCCCCEEEEEECCHHHHHHHCEEEECCCCCEECCCCCCCCCCCCCCCCCCCCCC---------------CCCCCCCCCCC
T ss_conf 974163899817899999744799837566638999747899865001799999---------------86889999877
Q ss_pred CCCCCCCCCCCCCCCCCCEEECHHHHHHH---HHHHHHCCCHHHHHHHHHHCCEEEECC-CCCCHHHHCCCCHHH-HHHH
Q ss_conf 47757876772002776220130122578---999980999656301332111232178-865104322369999-9886
Q gi|254780142|r 95 LSSVRRDRMAHIDLASPVAHPWFLKSLPS---RISTLLGMSLRDVERVLYFESYVVVDP-GLSSLEKYQILTEEE-YVEA 169 (1398)
Q Consensus 95 ~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~---~i~~~l~~~~~~~~~v~y~~~~~~~~~-~~~~~~~~~~~~~~~-~~~~ 169 (1398)
T Consensus 66 ~Cp---GHfGhIeL~~PV~h~~f~~~i~~iL~~iC~~C~~~ll~~~~~~~~-~~~~~~~~~~~~~~~~~~i~~~~~~~~~ 141 (330)
T pfam04997 66 ECP---GHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSLLLNESVKYFF-LKVVIDPKGKNSKKRLKKINNLCKKKSI 141 (330)
T ss_pred CCC---CCCEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH-HHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 179---856268865312019899999999999875065503656678899-9988621678878999999999977654
Q ss_pred HHHCCC--------------CCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 763585--------------550611552677888772674889999998731032203478864477888666634898
Q gi|254780142|r 170 VSQFGQ--------------DQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNN 235 (1398)
Q Consensus 170 ~~~~~~--------------~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ 235 (1398)
T Consensus 142 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ilk~I~~~d~~llg~~~~~~~ 220 (330)
T pfam04997 142 CSKCGEDNGGLKAFEGCGKYQPKISKDGAEAIKALLKNIEIEE-LKEKLRKLNPEKVLQIFKKISKEDEEILGFNPSGNR 220 (330)
T ss_pred HHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHH-HHHHHHHCCHHHHHHHHHHCCHHHHHHHCCCCCCCC
T ss_conf 0146601343110378666787045507999999986275166-678875358999999998556989998577677999
Q ss_pred CCEEEEEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 51128630450762235138846973131003789999999869999998739835677769999999888874277678
Q gi|254780142|r 236 PGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHK 315 (1398)
Q Consensus 236 Pewmil~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~ 315 (1398)
T Consensus 221 Pe~mil~~lPVpPp~~RP~v~~~~~~~~edDlt~~~~~Ii~~N~~L~~~~~~~~~~~~i~~~~~~LQ~~V~~lidn~~~~ 300 (330)
T pfam04997 221 PEWMILTVLPVPPPCIRPSVQLDGGRFAEDDLTHKLRDIIKRNNRLKKMLEEGAPSHIIREEKRLLQEHVATLFDNDIPG 300 (330)
T ss_pred CCEEEEEECCCCCCCCCCCEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 77688775358989999977719985206831799999999999999999749968899999999999999995499889
Q ss_pred CCC-CCCCCCHHHHHHHHHCCCCCCEEECC
Q ss_conf 772-47876506789986102378200034
Q gi|254780142|r 316 RVV-TGANRRPLKSLSDMLKGKQGRFRTNL 344 (1398)
Q Consensus 316 ~~~-~~~~~rp~ks~~~rlkgK~GrfR~nl 344 (1398)
T Consensus 301 ~~~~~~~~~kp~k~i~qrLkgKeGrfR~NL 330 (330)
T pfam04997 301 QPPALQKSGRPLKSISQRLKGKEGRFRGNL 330 (330)
T ss_pred CCCCCCCCCCCCCCHHHHHCCCCCCCCCCC
T ss_conf 986668897914329999678877578899