>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit; InterPro: IPR012756 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.

Probab=100.00 E-value=0 Score=1272.29 Aligned_cols=759 Identities=41% Similarity=0.669 Sum_probs=609.4 Q ss_pred EECCHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 75110020136669999999808178999875588999999985398613212326836999999999789999998864 Q gi|254780142|r 591 ICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYND 670 (1398) Q Consensus 591 ~~~~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~k~~~i~~a~~~~~~~~~~~~~ 670 (1398) T Consensus 2 F~N~~vDK~~L~~Li~way~~~GtA~ta~~AD~lKdLGF~yAT~AgVSISVdDL~vP~~K~~lle~AE~~I~~te~rY~~ 81 (1252) T TIGR02388 2 FKNRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPEKQDLLEAAEKEIRATEERYRR 81 (1252) T ss_pred CCEEEEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 31005414678889999874058325788877765200011322401698705548878999999888876778876305 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCHHHEEEEEEECCCCCCCCCC Q ss_conf 89766788878864234658999999999987611565432222468837642255557842411200100002464434 Q gi|254780142|r 671 GLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGE 750 (1398) Q Consensus 671 G~~t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~qi~ql~Gqq~l~gkp~G~ 750 (1398) T Consensus 82 GEITEVERf~KVIDTW~~T~E~L~d~V~~~F~~~---------dpLNSVyMMAfSGARGN~SQVRQLVGMRGLMA~PQGE 152 (1252) T TIGR02388 82 GEITEVERFQKVIDTWNGTNEELKDEVVNNFRQT---------DPLNSVYMMAFSGARGNLSQVRQLVGMRGLMADPQGE 152 (1252) T ss_pred CCEEEEECCEEEEECCCCCCHHHHHHHHHHHHCC---------CCCCEEEEECCCCCCCCHHHHHHHHCCCCCCCCCCCC T ss_conf 8613530200476455661168899999864205---------8732110002168756634565543131225689976 Q ss_pred CCCCCCCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEEE Q ss_conf 44566630111088898976405761032210121015674011015423014327751388766651211100884886 Q gi|254780142|r 751 IIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVY 830 (1398) Q Consensus 751 ~~~~PV~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~ 830 (1398) T Consensus 153 IIDLPIkTNFREGLTVTEYvISSYGARKGLVDTALRTADSGYLTRRLVDVsQDVIvRE~DCgT~R~i~~~~mt~g~k~~~ 232 (1252) T TIGR02388 153 IIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKVVI 232 (1252) T ss_pred EEECCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHCCCCCHHHEEEEEECCEEEECCCCCCCCCEEEEEECCCCEEEE T ss_conf 78468544653685356456632354422034554312553101101333231589614688524358876247872799 Q ss_pred EECCCCCCCCCHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHH Q ss_conf 50001012211442017789718851786578999999997598402023310003551865788754201785200010 Q gi|254780142|r 831 SLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGE 910 (1398) Q Consensus 831 ~l~~~~~~r~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe 910 (1398) T Consensus 233 ~l~~RL~GR~~~~Dv~~p~tge~i~~~N~~I~~~Lak~i~~~~~~~V~vRSPLTCEA~rSVC~~CYGWsLAH~~~VDlGE 312 (1252) T TIGR02388 233 KLADRLLGRLVAEDVLHPETGEVIVPKNTAIDEDLAKKIEKAGIEEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGE 312 (1252) T ss_pred EECCCCEEEEEHHHCCCCCCCEEEECCCCCCCHHHHHHHHHHHHCEEEECCCCCCCCCCCCCCCCCCHHHHHCCCEECCC T ss_conf 86254022332100247654606611676021899999975111576871687401252210045422555356010222 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE---EEEECCCCCE-EEEECCCCEEEEECCCC Q ss_conf 1460211110078898776420245432221122024014876897211---3465178877-89742760466406776 Q gi|254780142|r 911 AVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR---NVCRNSTNDL-ISMGRNTTLQILDMSGQ 986 (1398) Q Consensus 911 ~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi---~~~~n~~~~~-i~vs~~~~~~i~d~~~~ 986 (1398) T Consensus 313 AVGIIAAQSIGEPGTQLTMRTFHTGGVfTgEva~~~r~~~~G~v~~g~kl~~R~~RTrHG~dA~~vE~~g~l~~~~~~~~ 392 (1252) T TIGR02388 313 AVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDGTVEFGKKLRIRKYRTRHGEDAKQVEVAGLLILKPEGKK 392 (1252) T ss_pred CEEEEEEECCCCCCCCCCCEEEECCCEEECCCCEEEECCCCCEEECCCCCEECCCCCCCCCCCEEEEEEEEEEECCCCCC T ss_conf 01200210368797533220342386431332202214545337558721234556887644002333106898357654 Q ss_pred ----EEEEEECCCHHCCCCCCCCEEECCEEEEECC-----------CCCCEEEECCCCEEEEEEEC-------------- Q ss_conf ----0000001100001356785532250786213-----------54311320246368975312-------------- Q gi|254780142|r 987 ----EQYSHRIMYGAKLFVDDGGVIECGQRISEWD-----------PHTFPIITEVSGTVGFEDLV-------------- 1037 (1398) Q Consensus 987 ----~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~D-----------p~~~~i~~e~~~~v~~~~~~-------------- 1037 (1398) T Consensus 393 ~~~~~~Q~~~~t~GS~~~v~DG~~v~~g~l~a~~~~~~r~~~~~~Eka~KDV~~DLAGeV~f~~~~~p~e~~DRQGn~T~ 472 (1252) T TIGR02388 393 TETAAAQEIEVTQGSLLFVEDGQTVKAGQLLAEIALGARAVRKSTEKATKDVASDLAGEVKFDKVVQPEEKTDRQGNTTR 472 (1252) T ss_pred CCCCCCCEEEECCCCEEEEECCCCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCHHH T ss_conf 45656544772377389986376100061000134410244443222222123103473353221062203367763113 Q ss_pred -------------------------------------------------------------------------------- Q ss_conf -------------------------------------------------------------------------------- Q gi|254780142|r 1038 -------------------------------------------------------------------------------- 1037 (1398) Q Consensus 1038 -------------------------------------------------------------------------------- 1037 (1398) T Consensus 473 ~A~rgGl~WvLsGeVYNLPPgA~pVV~~~~~vE~g~vlAEt~~~t~~GG~VRL~e~~~~k~~REv~IiTaSvlLd~~~v~ 552 (1252) T TIGR02388 473 IAQRGGLIWVLSGEVYNLPPGAEPVVKNGDRVEAGTVLAETKLSTEHGGVVRLPESVDSKDSREVEIITASVLLDQAKVI 552 (1252) T ss_pred HHHCCCEEEEEECCEECCCCCCEEEECCCCEECCCCEEEEEEEEECCCCEEEECCCCCCCCCCEEEEEEEEEEECCCEEE T ss_conf 32026758998332103888871164068775124266423542047875872245788876458888722100111235 Q ss_pred -------------------------------------------------------------------------------- Q ss_conf -------------------------------------------------------------------------------- Q gi|254780142|r 1038 -------------------------------------------------------------------------------- 1037 (1398) Q Consensus 1038 -------------------------------------------------------------------------------- 1037 (1398) T Consensus 553 ~es~~gre~y~i~t~~~~~f~L~a~PGtKv~~g~vvAeLiDdRyrT~TGG~~kyApg~~V~K~g~~K~GyEV~~GGTLLW 632 (1252) T TIGR02388 553 EESSQGREQYLIETADGQRFRLKAAPGTKVQNGQVVAELIDDRYRTTTGGLLKYAPGVEVAKKGKAKQGYEVVKGGTLLW 632 (1252) T ss_pred EECCCCCEEEEEECCCCCEEEEECCCCCCCCCCCEEEEECCCCCCCCCCCEEEECCCCEEEECCCCCCCCEEECCCEEEE T ss_conf 21127750478981787189986588861126646465215651014575478628732721676667707613873752 Q ss_pred -------------------------------------------------------------------------------- Q ss_conf -------------------------------------------------------------------------------- Q gi|254780142|r 1038 -------------------------------------------------------------------------------- 1037 (1398) Q Consensus 1038 -------------------------------------------------------------------------------- 1037 (1398) T Consensus 633 IP~ETHE~NKDISLL~vED~~yvEAGTEVVKDIFcQ~SG~V~V~QKNDILREi~vk~G~~~~~~D~e~~~rf~~~g~L~~ 712 (1252) T TIGR02388 633 IPEETHEINKDISLLLVEDGQYVEAGTEVVKDIFCQNSGIVEVVQKNDILREIIVKPGELHEVDDPEAVKRFLEEGTLLQ 712 (1252) T ss_pred CCCCCCCCCCCEEEEEEECCCEEEECCEEEEEEEECCCCEEEEEECCCCEEEEEEECCCEEEECCHHHHHHHHHCCCCCC T ss_conf 67532100243468775266345406347764551588669998527505788971782244358799999873684027 Q ss_pred ------------------------------------------------------------------------------CC Q ss_conf ------------------------------------------------------------------------------78 Q gi|254780142|r 1038 ------------------------------------------------------------------------------DG 1039 (1398) Q Consensus 1038 ------------------------------------------------------------------------------~~ 1039 (1398) T Consensus 713 PGe~~~~G~~~~~l~~~~~~E~~p~G~~lLlRpV~Ey~vp~ep~~P~~~~~~~~~G~~i~lravQRL~YKd~e~vKSVeG 792 (1252) T TIGR02388 713 PGEEVLPGVVVDELSQVQYLEDTPEGKGLLLRPVEEYKVPDEPEVPSQSSVSQEKGRSIELRAVQRLPYKDGERVKSVEG 792 (1252) T ss_pred CHHHHHCCCCHHHHHHHHHHHCCCCCCEEEECCEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEECC T ss_conf 81666288302454544654148898735533302331578756786344112578668887664134447861355448 Q ss_pred CEEH------H---HHHC---CCCCEE----------------------------------------------------- Q ss_conf 3200------1---2302---368602----------------------------------------------------- Q gi|254780142|r 1040 ISVI------E---SIGE---STGIAK----------------------------------------------------- 1054 (1398) Q Consensus 1040 ~~~~------~---~~~~---~t~~~~----------------------------------------------------- 1054 (1398) T Consensus 793 v~LL~T~LvlE~~~~~~~~~~~s~l~~DiE~~~D~~d~~~~RL~LVILESl~~RRD~~~D~~~Gst~T~L~v~dgd~i~p 872 (1252) T TIGR02388 793 VELLRTQLVLEIEDEGPQEHNISHLAADIELIQDEEDKDIQRLQLVILESLVLRRDIASDSTQGSTKTSLLVKDGDLIKP 872 (1252) T ss_pred CHHHCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCHHCCCCCCCEEEEEECCCCEECC T ss_conf 11001024677424573000753036777764487543102555554345444302000356884125788416876167 Q ss_pred -----------------------------EEEEEHH-------------------HCCCCCCCCCCEEEECCCCCEEECC Q ss_conf -----------------------------6775101-------------------1012212385347742778253224 Q gi|254780142|r 1055 -----------------------------RKVIDWR-------------------FASRSQNLKPAIVVTDENGVVLKSA 1086 (1398) Q Consensus 1055 -----------------------------~~~i~~~-------------------~~~~~~~~~~~~~i~d~~~~~~~~~ 1086 (1398) T Consensus 873 G~V~A~T~I~~Ke~G~v~g~~~~~~E~~RR~lv~r~~D~~~~~~~g~kp~VK~Gdl~v~G~~l~~G-v~~~~~g~~~~v~ 951 (1252) T TIGR02388 873 GAVVARTQILCKEAGVVRGIKKGEGESIRRVLVERNSDRLKVNIKGAKPKVKTGDLVVAGDELAKG-VKAEESGEVLEVK 951 (1252) T ss_pred CCEEEEEEECCCCCCEEEECCCCCCCCEEEEEEEECCCEEEEEECCCCCCCCCCCEEECCCHHCCC-CCCCCCCEEEEEC T ss_conf 755873000015676685033467761358999725764898405788612467654176121277-3444662056731 Q ss_pred CCC---------CCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEE Q ss_conf 788---------42021377844541367613548422210132024554336773288988752511110111347867 Q gi|254780142|r 1087 RGT---------DARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTI 1157 (1398) Q Consensus 1087 ~~~---------~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv 1157 (1398) T Consensus 952 ~~~~~~~v~lR~~RPY~VSPgaVL~i~dGDLV~RGDnL~LLVFER~KTGDIvQGLPRIEELLEAR~Pke~c~La~~~G~~ 1031 (1252) T TIGR02388 952 NADDNYAVILRIARPYRVSPGAVLHIEDGDLVQRGDNLVLLVFERAKTGDIVQGLPRIEELLEARKPKEACVLAKRPGVV 1031 (1252) T ss_pred CCCCCCEEEEECCCCCEECCCCEEEEECCCEEEECCCEEEEEEECCCCCCEECCCCCHHHHHHCCCCCCCEEEECCCCEE T ss_conf 58885079996178843478654775458566517855899873046686211885068886227972113662279769 Q ss_pred EEEEECCCC--EEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHH---------------- Q ss_conf 863312794--49999836898402689813896589841987740864643899999998752---------------- Q gi|254780142|r 1158 RIKRNYKNK--SRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIK---------------- 1219 (1398) Q Consensus 1158 ~i~~~~~~k--~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vl---------------- 1219 (1398) T Consensus 1032 ~v~~~~~desv~i~ViE--~dg-~~~eY~ll~GQN~~v~DG~~v~~g~~LtDGp~nPH~iL~~~F~~~~~~~g~~~aA~~ 1108 (1252) T TIGR02388 1032 QVKYGEDDESVEIKVIE--EDG-TVSEYPLLPGQNIMVSDGQKVDVGEPLTDGPINPHDILDVFFSYYKDKDGLLEAAQE 1108 (1252) T ss_pred EEEECCCCCEEEEEEEE--CCC-CEEECCCCCCCCCEEECCCEECCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHH T ss_conf 99886887568999980--588-361213568785222078551367423688987378999887523575247999999 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEE Q ss_conf 79999999999999999980970061256012476286148941886454566410699999999999972898752012 Q gi|254780142|r 1220 GVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSP 1299 (1398) Q Consensus 1220 GIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p 1299 (1398) T Consensus 1109 ~l~k~Q~~lVNEVQ~VY~SQGv~I~DKHIEVIVRQMT~KVRIdD~GDT~lLpGEL~~LRQvE~~N~aM~iTGgApA~yTP 1188 (1252) T TIGR02388 1109 SLQKVQKFLVNEVQSVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPAQYTP 1188 (1252) T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEEECCCEEEEECCCCEEECCCCEEEEECHHCCCCCCCCCCCCCCCCCC T ss_conf 99999887635554232107814533448999962465236635887055373202200021035521013678652331 Q ss_pred EEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHHHH Q ss_conf 100001453023107765040258999999745285523665322155073056553546653 Q gi|254780142|r 1300 ILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHE 1362 (1398) Q Consensus 1300 ~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~~~ 1362 (1398) T Consensus 1189 VLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGf~~~~ 1251 (1252) T TIGR02388 1189 VLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSYE 1251 (1252) T ss_pred EEEECHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCEEEEEEEEECCCCCCCCCCC T ss_conf 320001121021013443100014566655430576023146600178863126888777577

HHsearch alignment for GI: 254780142 and conserved domain: TIGR02388