HHsearch alignment for GI: 254780143 and conserved domain: pfam04563

>pfam04563 RNA_pol_Rpb2_1 RNA polymerase beta subunit. 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Probab=100.00  E-value=0  Score=486.33  Aligned_cols=355  Identities=29%  Similarity=0.484  Sum_probs=284.4

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCC--EEEEEEEEEECCCCC----------CHHHHHHCC
Q ss_conf             08899999999986246652211122589997663780767985--899999789809858----------899999839
Q gi|254780143|r   28 DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDPPKF----------DVDDCLWRD   95 (1386)
Q Consensus        28 ~Li~iQ~~Sf~~Flq~~~~~~~r~~~GL~~v~~~~fPI~d~~~~--~~Lef~~y~l~~Pk~----------tp~ECRlR~   95 (1386)
T Consensus         1 gLv~~qi~Sfn~Fi----------~~gl~~ii~~~~~I~~~~~~~~~~l~~~~~~i~~P~~~e~~~~~~~i~P~eaR~r~   70 (394)
T pfam04563         1 GLVEQQLDSFNWFL----------DEGLQEEIDEFPPIEDEDEEPEFSLKVGQIKLAKPKIKESDGKTREIYPREARLRN   70 (394)
T ss_pred             CCHHHHHHHHHHHH----------HHHHHHHHHHCCCEEECCCCEEEEEEEEEEEECCCCEEECCCCCCCCCHHHHHHCC
T ss_conf             94478889999999----------97189999865998815998699999878998378056156755778979999619


Q ss_pred             CCEEEEEEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEECCEECCC------------------------CCEEECCEEE
Q ss_conf             9753358999999993178766552000122367875100002689------------------------6289868214
Q gi|254780143|r   96 LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQR  151 (1386)
Q Consensus        96 lTYsapL~V~i~l~v~~~~~~~~~k~~~~ike~~V~lG~IPiMt~~------------------------GyFIING~ER  151 (1386)
T Consensus        71 lTYs~~i~v~v~~~~~~~---------~~~~~~~V~iG~iPiMv~S~~C~L~~~~~~el~~~~Ec~~D~GGYFIING~Er  141 (394)
T pfam04563        71 LTYSSPLYVPAELTVNNT---------EEIEKQKVFIGKIPLMLRSNACILNGASESELVKLGECPLDPGGYFIVNGIEK  141 (394)
T ss_pred             CCCCEEEEEEEEEEECCC---------CEEEEEEEEEECCCEEECCCEEECCCCCHHHHHHCCCCCCCCCCEEEECCHHH
T ss_conf             965304899999999788---------64899999850252460466224689998998652667668980899846777


Q ss_pred             EEEEEECCCCCEEECCCCCCCCCCCCEEEEEEEECCCCCEEEEEECCCCEEEEEECCCCCHHHHHHHHHCCCCHHHHHH-
Q ss_conf             6866512278521202346515778567999981188723689975898299997187870399899880998479999-
Q gi|254780143|r  152 IVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS-  230 (1386)
Q Consensus       152 VIVsQl~RSPGVyf~~~k~k~~~s~k~~ysa~IIP~RGSwLe~e~d~kd~iyvrIdr~rKIPi~ilLrALG~ssdeIl~-  230 (1386)
T Consensus       142 VIi~qe~~~~n~~~~~~~~---~~~~~~~~~~i~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~  218 (394)
T pfam04563       142 VIINQIQRSPNIYYVFKKD---KNGIRIYSASIISNRGRSVRLEITSKGKIYARINSGAKLIIFVLLLALGLNPVEIILI  218 (394)
T ss_pred             HHHHHHHCCCCCEEEEECC---CCCCEEEEEEEECCCCCCCCCEEEEEEEEEEEECCCCCCCEEEEHHHHCCCCHHHHHH
T ss_conf             8788761078744899748---9982788899953677753211440005999936998640588338555886899998


Q ss_pred             HHCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCHHHHHHHHHHHHCCCCCCCCCHHHHCCCCCCC
Q ss_conf             73874057730673102354566642101223211244584544022102079988787636000102667734741000
Q gi|254780143|r  231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE  310 (1386)
Q Consensus       231 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~~  310 (1386)
T Consensus       219 ~~~~~~~~--------------e~------~~~~~------------------------~~-------------------  235 (394)
T pfam04563       219 VLVPEFDL--------------EI------IDDIG------------------------VN-------------------  235 (394)
T ss_pred             HHCCCCHH--------------HH------HHHHH------------------------CC-------------------
T ss_conf             50444449--------------99------99875------------------------24-------------------


Q ss_pred             CCCCCCCCEEEEECCCCCCHHHHHHHHHCCCCCEEEEEECCCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHCCCCCCHHH
Q ss_conf             01366677699962345998999999865654102442024445520000011023458899999988760577631045
Q gi|254780143|r  311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS  390 (1386)
Q Consensus       311 ~~~d~~~gei~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~d~~~~~~eAl~~I~k~lr~~~~~~~~  390 (1386)
T Consensus       236 ~~----------------~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~i~~~----------  267 (394)
T pfam04563       236 LE----------------EDEFLTL----------------------KLELEEKFYIQTQDEALSFIGKL----------  267 (394)
T ss_pred             CC----------------HHHHHHH----------------------HHHHHHHHCCCCCHHHHHHHHHH----------
T ss_conf             31----------------1156666----------------------78899874179837889999998----------


Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCHHHH
Q ss_conf             68888620245302333455557776542036677677066189988889888763048764344010153323333578
Q gi|254780143|r  391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM  470 (1386)
Q Consensus       391 ~~~~~~~~~~~~~~~y~l~~vgr~~~n~~l~~~~~~~~~~Lt~~d~~~~i~~L~~l~~g~~~~DdiDhlgnkRvr~vgeL  470 (1386)
T Consensus       268 -----~~~~~~~~~~~~~~~~~~l~~~~lphl~~~~~~~~~k~~~l~~mi~~Ll~~~~g~~~~DD~D~~~NKRv~~~G~L  342 (394)
T pfam04563       268 -----GSARGFQRERRILGAVGILRLNVLPHLGVSENKRTLKAQDIGYMIHRLLLLALGRGPLDDIDHLGNKRLRLAGEL  342 (394)
T ss_pred             -----HHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf             -----730478811578899899998777098998765404299999999999998639899988511168122759999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCC--CCCCCCCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             7898888889999887653113--4433435211222023465554202667
Q gi|254780143|r  471 LKNQYRLGLLRMERSIKERISS--VDIDSVMPQDLINAKPVVSAVCEFFCSS  520 (1386)
Q Consensus       471 l~~~fr~~l~rl~r~i~~~~~~--~~~~~~~~~~~in~~~i~~~i~~ff~t~  520 (1386)
T Consensus       343 l~~lFr~~~~r~~r~ik~~~~~~~~~~~~~~~~~~i~~~~it~~i~~~~~TG  394 (394)
T pfam04563       343 LQSQFRILLNRLERDVRERIQKCLKKNFDFTLQNLVNSKPITSGIRYFLGTG  394 (394)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCHHHHHHHHHHHCCC
T ss_conf             9999999999999999999998860478789999838365999999985389