>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit; InterPro: IPR010243 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. This entry describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.

Probab=96.20 E-value=0.00031 Score=47.99 Aligned_cols=266 Identities=20% Similarity=0.161 Sum_probs=148.6 Q ss_pred HCCCEEECCCCC-CCCCCCCCCEEEECCCCCCCCCCCCCEEECCCC-----------CCCCCCCCCCCCCCCCCCCCEEE Q ss_conf 065301021244-343356553025215665564446630111465-----------55445473224453044797720 Q gi|254780143|r 722 SSGAAIVAKRAG-IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK-----------FQRSNQNTCVNQRPLVKVGDEVR 789 (1386) Q Consensus 722 ~s~~~i~a~~~g-~v~~vd~~~i~i~~~~~~~~~~~~~~~~y~~~~-----------~~~~~~~~~~~q~p~V~~g~~~~ 789 (1386) T Consensus 705 i~~d~V~~R~~G~e~~~~~~~~VdyMDVSP~Q~VSVaAaLIPFLEHDDANRALMGsNMQRQAVPLL~seaP~VGTGmE~~ 784 (1449) T TIGR02013 705 IVEDLVVARYRGDEITLVSPDEVDYMDVSPKQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAK 784 (1449) T ss_pred CCCCEEEEEECCCCCCCCCCCCEEEEEECCHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHCCCCCCCCCCCCCCHHHHH T ss_conf 52356888654773221167602476518323556655426332354145665412531236777877988232027898 Q ss_pred CCCEECCCCCCCCCC-CCCCCCCEEEEEECCCCCCCCCEECCHHHHHCCCCCEEEEEEEEHHHHHCCCCC----CCCCCC Q ss_conf 785203552235786-022237515553135544444200001344258731034666531121147884----002466 Q gi|254780143|r 790 RNDIIADGPSTDLGD-LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP----EEITRD 864 (1386) Q Consensus 790 ~~~~l~~~~~~~~~e-l~~G~N~~VA~m~~~GYN~EDaiiin~~~v~rg~~~s~h~~~y~~~~~~~~~g~----~~~~~~ 864 (1386) T Consensus 785 ~---A~D-----SG~~i~A~~~GvV~~Vd---------------------a~~I~v~~~~~~~~~~~~g~DPd~~~~~Y~ 835 (1449) T TIGR02013 785 V---ARD-----SGAVIVAKRAGVVEYVD---------------------AKRIVVRYKEKEEEETVSGDDPDAAIDIYR 835 (1449) T ss_pred H---HHC-----CCEEEEECCCCEEEEEE---------------------CCEEEEEECCCCCCCCCCCCCCCCCEEEEE T ss_conf 8---623-----54089970697899984---------------------778899314776665557788322025750 Q ss_pred CCC-CCHHHHHHCCCCCCCCCCCEECCCCCEE-ECCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCEECCC------CCC Q ss_conf 654-6867841024137413773313676111-01246777767703466543035555443233202278------853 Q gi|254780143|r 865 IPN-VSEEGLKNIDECGIICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVS 936 (1386) Q Consensus 865 ~~~-~~~~~~~~ld~~Giv~~G~~V~~gDilv-gk~tp~~~~~~~pe~~~l~~i~~~~~~~~~d~~~~~~~------g~~ 936 (1386) T Consensus 836 L~Ky~RSNQ~TC~nQ~PiV~~GDrV~~GdvlADGPsT~~G--ELALGrNvlVAFMPW~GYNyEDAIliSERlVkdDvFTS 913 (1449) T TIGR02013 836 LLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLG--ELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTS 913 (1449) T ss_pred CCCCCCCCCCCEECCEEECCCCCEECCCCEEECCCCCCCC--CCCCCCCEEEEEECCCCCCHHHHHHHHHHHEECCCCEE T ss_conf 4676314788401453550148681021277347666443--20116710367522788653356355000101376203 Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCC Q ss_conf 22001210145654202667888899999998728889998878889888886258534566555554321135764014 Q gi|254780143|r 937 GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016 (1386) Q Consensus 937 g~v~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1016 (1386) T Consensus 914 IHI~E~e~~aRdTKLG~EEiTrDIPNVsE~ALrnL-DE~GIvrIGAeV~~GDILVGKvTPKGEs~~TPEEkLLRAIFGEK 992 (1449) T TIGR02013 914 IHIEEFEVEARDTKLGPEEITRDIPNVSEEALRNL-DENGIVRIGAEVKAGDILVGKVTPKGESELTPEEKLLRAIFGEK 992 (1449) T ss_pred EEEEEEEECCEECCCCCCCCCCCCCCCCHHHHHCC-CCCCEEEEEEEECCCCEEEEEECCCCCCCCCHHHHHHHHCCCCC T ss_conf 78999983010347887012345798408888258-95775887338707747772121889888875677542003341 Q ss_pred CHH Q ss_conf 854 Q gi|254780143|r 1017 PRS 1019 (1386) Q Consensus 1017 ~~~ 1019 (1386) T Consensus 993 A~d 995 (1449) T TIGR02013 993 ARD 995 (1449) T ss_pred HHH T ss_conf 145

HHsearch alignment for GI: 254780143 and conserved domain: TIGR02013