>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.

Probab=100.00 E-value=0 Score=605.91 Aligned_cols=401 Identities=21% Similarity=0.228 Sum_probs=259.6 Q ss_pred CCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEE- Q ss_conf 1000355186578875420178520001014602111100788987764202454322211220240148768972113- Q gi|254780142|r 882 ALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN- 960 (1398) Q Consensus 882 ~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~- 960 (1398) T Consensus 2 ~~s~~~~~~~~~~~--~~ky~rslV~pGEaVGiIAAQSIGEPgTQlTLrTFH~gG~as~-------~vT~GipRl~Ei~~ 72 (410) T cd02584 2 RLNKEAFDWILGEI--ETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAK-------NVTLGVPRLKEIIN 72 (410) T ss_pred CCCHHHHHHHHHHH--HHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCHHHH-------CEECCCHHHHHHHH T ss_conf 77889999999999--9999983879875889998873473698898874604013101-------04457405676765 Q ss_pred EEECCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCC Q ss_conf 46517887789742760466406776000000110000135678553225078621354311320246368975312783 Q gi|254780142|r 961 VCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGI 1040 (1398) Q Consensus 961 ~~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~ 1040 (1398) T Consensus 73 ~~k~~kt~~~~i~------l~~~~~~~~~~~~~~~~~i~~~~l~d~~~~~~i~~~~~~~~~~i~~~~~~i~~~~~~~~~~ 146 (410) T cd02584 73 VAKNIKTPSLTVY------LEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDED 146 (410) T ss_pred HCCCCCCCEEEEE------ECCCCCCCHHHHHHHHHEEEEEEHHHEEEEEEEEECCCCCCEEEEECCEEEEEEEEECCCC T ss_conf 4057777607999------7577542188887776500155444511245899627777427873140388768833410 Q ss_pred EEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHH Q ss_conf 20012302368602677510110122123853477427782532247884202137784454136761354842221013 Q gi|254780142|r 1041 SVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPI 1120 (1398) Q Consensus 1041 ~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~ 1120 (1398) T Consensus 147 ~---~~~~~~~~~~~~~~~~~~-----~~~~~i~~~~~~~~i-------~~~~~~~~~~~~~~~~~~~---~~~~~r~~~ 208 (410) T cd02584 147 V---EQDRLSPWLLRIELDRKK-----MTDKKLSMEQIAKKI-------KEEFKDDLNVIFSDDNAEK---LVIRIRIIN 208 (410) T ss_pred C---CCCCCCCEEEEEEECHHH-----HCCCCCCHHHHHHHH-------HHHCCCCCEEEECCCCCCE---EEEEEECCC T ss_conf 2---213335437999953355-----303787788889999-------8752898469841577653---699998047 Q ss_pred HHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEE-CCCCEEEEECCCEE Q ss_conf 20245543367732889887525111101113478678633127944999983689840268981-38965898419877 Q gi|254780142|r 1121 SSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFI-PKNKHFYLQDGDHV 1199 (1398) Q Consensus 1121 ~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~i-p~~~~l~v~dgd~V 1199 (1398) T Consensus 209 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-~~~~~~l~t~g~n--l~~il~~ 283 (410) T cd02584 209 -DDEEKEEDSEDDVFLKKIESNMLSDMTLKGIEGIRKVFIR-EENKKKVDIETGEFK-KREEWVLETDGVN--LREVLSH 283 (410) T ss_pred -CCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCEEEEEEE-ECCCEEEEECCCCCC-CCEEEEEECCCCC--HHHEECC T ss_conf -7655555676245535666336666469764665999989-717279980378767-6507998048832--6333243 Q ss_pred ECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHH Q ss_conf 40864643899999998752799999999999999999809700612560124762861489418864545664106999 Q gi|254780142|r 1200 EKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIE 1279 (1398) Q Consensus 1200 ~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~ 1279 (1398) T Consensus 284 ~~vd~~~~~sNdi~eil~~~GiEAar~~iv~Ei~~V~~~~Gv~In~rHi~lI~d~Mt~~G~~~----------------- 346 (410) T cd02584 284 PGVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLM----------------- 346 (410) T ss_pred CCCCCCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEE----------------- T ss_conf 575333002576314666414999999988888899984595516999999888872178265----------------- Q ss_pred HHHHHHHHHHCCCCCCCEEEEEECHHHHHH--CCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCC Q ss_conf 999999999728987520121000014530--231077650402589999997452855236653221550730565535 Q gi|254780142|r 1280 VEELNRSLAQQGKKLVSFSPILQGITKASL--QTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTG 1357 (1398) Q Consensus 1280 ~~~~Nr~~~~~g~~pa~~~p~llGITKasl--~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG 1357 (1398) T Consensus 347 -----------------------~itR~gi~k~s~S~isaASFqeTt~vLt~AAi~G~~D~L~GlkenVIvG~lipaGTG 403 (410) T cd02584 347 -----------------------AITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTG 403 (410) T ss_pred -----------------------EECHHHCCCCCCCHHHHHHCHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCCCCCC T ss_conf -----------------------401764466986888872046289999999862896667780887445897578777 Q ss_pred HHH Q ss_conf 466 Q gi|254780142|r 1358 AIL 1360 (1398) Q Consensus 1358 ~f~ 1360 (1398) T Consensus 404 ~fd 406 (410) T cd02584 404 CFD 406 (410) T ss_pred CEE T ss_conf 378

HHsearch alignment for GI: 254780142 and conserved domain: cd02584