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