>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.

Probab=100.00 E-value=0 Score=1833.32 Aligned_cols=801 Identities=49% Similarity=0.791 Sum_probs=711.3 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCC--CCCEEEEEEEEEECCCC---------CCHHHHHHCCCC Q ss_conf 8899999999986246652211122589997663780767--98589999978980985---------889999983997 Q gi|254780143|r 29 LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPK---------FDVDDCLWRDLT 97 (1386) Q Consensus 29 Li~iQ~~Sf~~Flq~~~~~~~r~~~GL~~v~~~~fPI~d~--~~~~~Lef~~y~l~~Pk---------~tp~ECRlR~lT 97 (1386) T Consensus 1 Lv~~qidSFn~Fi----------~~gl~~ii~~~~~i~~~~~~~~~~i~~~~i~i~~P~~~~~~~~~~l~P~eaRlr~lT 70 (866) T cd00653 1 LVKQQIDSFNYFL----------NVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEGGVTRKLTPNECRLRDLT 70 (866) T ss_pred CCHHHHHHHHHHH----------HHHHHHHHHHCCCEEEECCCCEEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHCCCC T ss_conf 9427889999999----------983999998569889708995599999889980780157897564699999854995 Q ss_pred EEEEEEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEECCEECC------------------------CCCEEECCEEEEE Q ss_conf 5335899999999317876655200012236787510000268------------------------9628986821468 Q gi|254780143|r 98 YAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------------------------DGTFVIKGIQRIV 153 (1386) Q Consensus 98 YsapL~V~i~l~v~~~~~~~~~k~~~~ike~~V~lG~IPiMt~------------------------~GyFIING~ERVI 153 (1386) T Consensus 71 Ys~~l~v~i~~~~~~~~---------~~~~~~v~iG~IPIMvkS~~C~L~~~~~~~l~~~gEcp~D~GGYFIInG~EKVI 141 (866) T cd00653 71 YSAPLYVDIRLTVNDKG---------KIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVI 141 (866) T ss_pred EEEEEEEEEEEEECCCC---------CEEEEEEEEEECCEEECCCCCCCCCCCHHHHHHCCCCCCCCCEEEEECCEEEEE T ss_conf 30479999999997777---------179999998417378278743367999889976188877898089987789999 Q ss_pred EEEECCCCCEEECCCCCCCCCCCCEEEEEEEEC----CCCCEEEEEECC-CCEEEEEECCCCCHHHHHHHHHCCCCHHHH Q ss_conf 665122785212023465157785679999811----887236899758-982999971878703998998809984799 Q gi|254780143|r 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP----DQGLWMDIEFDS-KDIIHVRIDRRRKVPVTSFLMALGMDSEEI 228 (1386) Q Consensus 154 VsQl~RSPGVyf~~~k~k~~~s~k~~ysa~IIP----~RGSwLe~e~d~-kd~iyvrIdr~rKIPi~ilLrALG~ssdeI 228 (1386) T Consensus 142 i~qe~~~~N~~~~~~~-----~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~i~~~i~~~------------------- 197 (866) T cd00653 142 INQEQRSPNVIIVEDS-----KGKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLK------------------- 197 (866) T ss_pred EEEECCCCCEEEEECC-----CCCEEEEEEECCCCCCCCCEEEEEEECCCCCEEEEEECCC------------------- T ss_conf 9999058987999748-----9837999998656677760699999536687699984158------------------- Q ss_pred HHHHCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCHHHHHHHHHHHHCCCCCCCCCHHHHCCCCC Q ss_conf 99738740577306731023545666421012232112445845440221020799887876360001026677347410 Q gi|254780143|r 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308 (1386) Q Consensus 229 l~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~ 308 (1386) T Consensus 198 -------------------------------------------------------------------------------- 197 (866) T cd00653 198 -------------------------------------------------------------------------------- 197 (866) T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred CCCCCCCCCCEEEEECCCCCCHHHHHHHHHCCCCCEEEEEECCCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHCCCCCCH Q ss_conf 00013666776999623459989999998656541024420244455200000110234588999999887605776310 Q gi|254780143|r 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388 (1386) Q Consensus 309 ~~~~~d~~~gei~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~d~~~~~~eAl~~I~k~lr~~~~~~ 388 (1386) T Consensus 198 ------------------------------------------------------------~~e~al~yIg~k~------- 210 (866) T cd00653 198 ------------------------------------------------------------RQEEALKYIGKRF------- 210 (866) T ss_pred ------------------------------------------------------------CHHHHHHHHHHHH------- T ss_conf ------------------------------------------------------------8899999999999------- Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCHH Q ss_conf 45688886202453023334555577765420366776770661899888898887630487643440101533233335 Q gi|254780143|r 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468 (1386) Q Consensus 389 ~~~~~~~~~~~~~~~~~y~l~~vgr~~~n~~l~~~~~~~~~~Lt~~d~~~~i~~L~~l~~g~~~~DdiDhlgnkRvr~vg 468 (1386) T Consensus 211 ---------------------------------------------~~L~~mi~kLl~~~~g~~~~DD~D~~~NKRv~~~G 245 (866) T cd00653 211 ---------------------------------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAG 245 (866) T ss_pred ---------------------------------------------HHHHHHHHHHHHHHCCCCCCCCCCCCCCCEECCHH T ss_conf ---------------------------------------------99999999999986699998886434587764599 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCC--CCCCCCCCCCCCHHHHHHHHHHHCCCCC------------CEEECCCCCCHHH Q ss_conf 7878988888899998876531134--4334352112220234655542026675------------0354155421023 Q gi|254780143|r 469 EMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ------------LSQLEEHVNSLSR 534 (1386) Q Consensus 469 eLl~~~fr~~l~rl~r~i~~~~~~~--~~~~~~~~~~in~~~i~~~i~~ff~t~~------------lsq~ld~~n~ls~ 534 (1386) T Consensus 246 ~Ll~~lFr~~l~~~~~~ik~~i~k~~~~~~~~~~~~~~~~~~It~~i~~~~~TGnw~~~~~~~~~~GvsQ~l~r~N~ls~ 325 (866) T cd00653 246 ELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSE 325 (866) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCHHHH T ss_conf 99999999999999999999998764036657888863762789999999971887666776565418999536888998 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEECEEEEEEECCCCCCCCEEEEEECCCCCCCE Q ss_conf 22001122344444322346655432211110444303566765210210001224424687644106986225534816 Q gi|254780143|r 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614 (1386) Q Consensus 535 lth~RR~s~lgpggl~r~~~~~evR~ih~s~~GriCPieTPEG~n~GLv~~la~~a~in~~g~ie~py~~v~~~~~~~~i 614 (1386) T Consensus 326 lSh~Rri~~---g~~~~~~k~~~~R~Lh~s~~G~iCPveTPEG~~cGLvknLal~a~It--Grl~rP~~~v~-------- 392 (866) T cd00653 326 LSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE-------- 392 (866) T ss_pred HHHHHEECC---CCCCCCCCCCCCCCCCHHHCEEECCCCCCCCCCEEEEEEEEEEEEEE--EEEECCEEEEC-------- T ss_conf 666642136---78474556775533460126242355589998431000001048864--69854479946-------- Q ss_pred EECCHHHHCCEEEECCCCEECCCCCCCCCCEEECCCCCCCCCCHHHEEECCCCCCCEEEECCCCCCCHHHCCHHHHHHHH Q ss_conf 64296773763796165341146840222000000233332257872202367211023112333201101002211222 Q gi|254780143|r 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694 (1386) Q Consensus 615 ~~l~~~~e~~~~Ia~~~~~l~~~~~~~~~~~~~r~~~~~~~~~~~~v~~~~i~p~~i~sv~aslIPflehdda~R~l~g~ 694 (1386) T Consensus 393 --------------------------------------------~~~th~ei~p~~~l~~~aslIPF~~hNqspRn~yq~ 428 (866) T cd00653 393 --------------------------------------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428 (866) T ss_pred --------------------------------------------CCEEEEECCHHHHHHHHHHCCCCCCCCHHHHHHHHH T ss_conf --------------------------------------------860799728778344664246773468136777766 Q ss_pred HHHHHHHCCCCCCCCEECCCCCHHHHHHCCCEEECCCCCCCCCCCCCCEEEECCCCCCCCCCCCCEEECCCCCCCCCCCC Q ss_conf 34443210136654111266201110106530102124434335655302521566556444663011146555445473 Q gi|254780143|r 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774 (1386) Q Consensus 695 nm~rQav~l~~~~~~~v~tg~E~~~~~~s~~~i~a~~~g~v~~vd~~~i~i~~~~~~~~~~~~~~~~y~~~~~~~~~~~~ 774 (1386) T Consensus 429 ~M~kQa~g~~~~n~~-----------------------------------------~r~D~~~--------------~~L 453 (866) T cd00653 429 NMQKQAVGTPALNQQ-----------------------------------------YRMDTKL--------------YLL 453 (866) T ss_pred HHHHCCCCEEECCCC-----------------------------------------EECCCCC--------------EEE T ss_conf 644031420101340-----------------------------------------4403510--------------353 Q ss_pred CCCCCCCCCCCCEEECCCEECCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEECCHHHHHCCCCCEEEEEEEEHHHHHC Q ss_conf 22445304479772078520355223578602223751555313554444420000134425873103466653112114 Q gi|254780143|r 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854 (1386) Q Consensus 775 ~~~q~p~V~~g~~~~~~~~l~~~~~~~~~el~~G~N~~VA~m~~~GYN~EDaiiin~~~v~rg~~~s~h~~~y~~~~~~~ 854 (1386) T Consensus 454 ~ypQ~Plv~t~~~----------~~~~~~e~p~G~N~iVAv~~y~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~ 523 (866) T cd00653 454 LYPQKPLVGTGIE----------EYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKT 523 (866) T ss_pred CCCCCCEEECCHH----------HHHCCCCCCCCEEEEEEEECCCCCCCCCEEEECHHHHHHHHCEEEEEEEEEEEEEEC T ss_conf 3687754405768----------874898677745579999657787743058961989873213169999889998715 Q ss_pred CCCCCCCCC-CCCCCCHHHHHHCCCCCCCCCCCEECCCCCEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCEECCC Q ss_conf 788400246-6654686784102413741377331367611101246777767703466543035555443233202278 Q gi|254780143|r 855 KLGPEEITR-DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933 (1386) Q Consensus 855 ~~g~~~~~~-~~~~~~~~~~~~ld~~Giv~~G~~V~~gDilvgk~tp~~~~~~~pe~~~l~~i~~~~~~~~~d~~~~~~~ 933 (1386) T Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdvligk~~~~~~~~~~~-------~~~~~~~~~~d~s~~~~~ 596 (866) T cd00653 524 KNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPG 596 (866) T ss_pred CCCCCEECCCCCCCCCHHHHHHCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCC-------CCCCCCCEEEEEEEEECC T ss_conf 8986313468999898678742374577579989779998999966787666664-------445566503575799359 Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHH Q ss_conf 85322001210145654202667888899999998728889998878889888886258534566555554321135764 Q gi|254780143|r 934 GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013 (1386) Q Consensus 934 g~~g~v~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1013 (1386) T Consensus 597 ~~~g~V~~V~~~~~~----------------------------------------------------------------- 611 (866) T cd00653 597 GEKGIVDDVKIFSRE----------------------------------------------------------------- 611 (866) T ss_pred CCCEEEEEEEEECCC----------------------------------------------------------------- T ss_conf 984899999995255----------------------------------------------------------------- Q ss_pred HCCCHHHHHEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEECCCCCCCCCCCC Q ss_conf 01485431001415867899999999989999999999989887631258867747276999999875588552314336 Q gi|254780143|r 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093 (1386) Q Consensus 1014 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~ki~~~~~~~~gv~~~vKV~ir~~R~p~iGDKfasR 1093 (1386) T Consensus 612 ----------------------------------------------------~~~~~~~~vkV~~r~~R~p~iGDKfssR 639 (866) T cd00653 612 ----------------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASR 639 (866) T ss_pred ----------------------------------------------------CCCCCCEEEEEEEEEECCCCCCCCCCCC T ss_conf ----------------------------------------------------6878737999998153466546521245 Q ss_pred CCCCCEEEEEECCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 67873588863000078793587156986689867507089999999999998719622433343222210246777877 Q gi|254780143|r 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173 (1386) Q Consensus 1094 HGqKGVis~i~p~eDMPf~~dG~~pDIIlNPhgvPSRMtIGqllE~~lGka~~~~G~~~~~~~f~~~~~~~~~~~~~~~~ 1173 (1386) T Consensus 640 HGqKGvi~~i~~~~DmPft~~G~~pDiI~NPhg~PSRMtiGql~E~~~gk~~~~~g~~~d-------------------- 699 (866) T cd00653 640 HGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGD-------------------- 699 (866) T ss_pred CCCCCEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCEE-------------------- T ss_conf 576622567875203982889987717446665755561999999998899985497353-------------------- Q ss_pred HHCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCCCHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCEEEEE Q ss_conf 63154322100001352567776653026840025655788999999999986868998699986898840268504884 Q gi|254780143|r 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253 (1386) Q Consensus 1174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~aTP~F~g~~~~~i~~~L~~aG~~~~Gke~lydG~TGe~~~~~IfvG~ 1253 (1386) T Consensus 700 ---------------------------------~t~-F~~~~~~~i~~~l~~~g~~~~G~e~l~~G~tG~~~~~~i~~G~ 745 (866) T cd00653 700 ---------------------------------ATP-FDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGP 745 (866) T ss_pred ---------------------------------ECC-CCCCCHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCEEEEE T ss_conf ---------------------------------278-8999889999999985989999989865999988237489962 Q ss_pred EEEEECCCHHHHHCCCCCCCCCCCEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 64541011021100002368731103079986233178432078999999986989999861110011015999988763 Q gi|254780143|r 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333 (1386) Q Consensus 1254 ~YyqkL~HMV~DKiHARstGP~sllTrQP~eGRsr~GGlRfGEMErwaL~AyGAa~~LqE~Lt~kSDdv~gr~~~~~~iv 1333 (1386) T Consensus 746 ~yyqrL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~ahGas~~l~erl~~~SD~~~~~vc~~cg~~ 825 (866) T cd00653 746 VYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGII 825 (866) T ss_pred HHHHCCCHHHHHCCEEECCCCCCCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCC T ss_conf 47640212330061853528997613189997646898501477999999872999999997637887158840367612 Q ss_pred ----------CCCCCCCCCCCHHHHHHHHHHHHCCCCEEEE Q ss_conf ----------8787899786677899999998542002764 Q gi|254780143|r 1334 ----------AGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364 (1386) Q Consensus 1334 ----------~g~~~~~~~~pesf~vl~~El~~l~l~~~~~ 1364 (1386) T Consensus 826 ~~~~~c~~c~~~~~~~~~~~Py~~kll~~EL~~m~i~~~l~ 866 (866) T cd00653 826 LSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866 (866) T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEC T ss_conf 24543344679981670689889999999998788777609

HHsearch alignment for GI: 254780143 and conserved domain: cd00653