>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.

Probab=100.00 E-value=0 Score=571.44 Aligned_cols=356 Identities=25% Similarity=0.320 Sum_probs=239.6 Q ss_pred CCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 57899999999759840202331000355186578875420178520001014602111100788987764202454322 Q gi|254780142|r 860 LILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVT 939 (1398) Q Consensus 860 ~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS 939 (1398) T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~y~~sl-----V~pGEaVGiIAAQSIGEPgTQLTLrTFH~aG~a~ 70 (363) T cd06528 2 LLKEKLEEVLKEHGLTLSEAEEIIK------EVLREYLRSL-----IEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAE 70 (363) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHH------HHHHHHHHCC-----CCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCEEE T ss_conf 5578999999982999999999999------9999987607-----7987388999887327669888898764510001 Q ss_pred CCCCCEEEECCCCEEEEEEEEEEE-CCCCCEEEEECCCCEEEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCC Q ss_conf 211220240148768972113465-1788778974276046640677600000011000013567855322507862135 Q gi|254780142|r 940 VMDRSFIESPCDGIVKIKNRNVCR-NSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDP 1018 (1398) Q Consensus 940 ~~~~~~iknvTlGVPRlkEi~~~~-n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp 1018 (1398) T Consensus 71 -------~~vt~G~pRl~Ei~~a~k~~~tp~~~i~l~------~~~~~~~~~~~~v~~~i~~~~~~~~~~~i~----id~ 133 (363) T cd06528 71 -------INVTLGLPRLIEIVDARKEPSTPTMTIYLE------EEYKYDREKAEEVARKIEETTLENLAEDIS----IDL 133 (363) T ss_pred -------EEEECCCCEEEEEEECCCCCCCCEEEEEEC------CCCCCCHHHHHHHHHHCCEEEEEEEEEEEE----ECC T ss_conf -------006537432699886004766756999960------544551899998886435189870068999----917 Q ss_pred CCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCC Q ss_conf 43113202463689753127832001230236860267751011012212385347742778253224788420213778 Q gi|254780142|r 1019 HTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVD 1098 (1398) Q Consensus 1019 ~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~ 1098 (1398) T Consensus 134 ~~~~i~i~l~~---------------~~~~~~~-----------------i~----~~~i~~~i~~~-~----------- 165 (363) T cd06528 134 FNMRITIELDE---------------EMLEDRG-----------------IT----VDDVLKAIEKL-K----------- 165 (363) T ss_pred CCCEEEEEECH---------------HHHHHCC-----------------CC----HHHHHHHHHHH-C----------- T ss_conf 87079999884---------------6764249-----------------98----89999998764-3----------- Q ss_pred CEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECCCCCEEEEEEECCCCEEEEEEECCCCC Q ss_conf 44541367613548422210132024554336773288988752511110111347867863312794499998368984 Q gi|254780142|r 1099 ALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGV 1178 (1398) Q Consensus 1099 ~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~ 1178 (1398) T Consensus 166 ------~~~~~~~---------~~~~~~~~~~~~~~~~~l~~~~~~~~~~~i~gi~gi~~~~i~~~~~-e~~i~--t~G~ 227 (363) T cd06528 166 ------KGKVGEE---------GDVTLIVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEED-EYVIY--TEGS 227 (363) T ss_pred ------CCCEEEC---------CCCCEEEECCCCCCHHHHHHHHHHCCCEEEECCCCEEEEEEEECCC-EEEEE--ECCC T ss_conf ------8877664---------9952797069999989999987442674793679858999996399-99999--5475 Q ss_pred CEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCE Q ss_conf 02689813896589841987740864643899999998752799999999999999999809700612560124762861 Q gi|254780142|r 1179 EPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQK 1258 (1398) Q Consensus 1179 ~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~k 1258 (1398) T Consensus 228 nl~~~l----------~~~~v---D~~~~~tndi~dI~~i~GiEAar~~lv~Ei~~v~~~qGv~In~rHi~li~d~Mt~~ 294 (363) T cd06528 228 NLKAVL----------KVEGV---DPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYD 294 (363) T ss_pred CHHHHE----------ECCCC---CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCC T ss_conf 567723----------00661---35323358789999886088899999999988886078632057787765344046 Q ss_pred EEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEEC Q ss_conf 48941886454566410699999999999972898752012100001453023107765040258999999745285523 Q gi|254780142|r 1259 VEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDT 1338 (1398) Q Consensus 1259 g~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~ 1338 (1398) T Consensus 295 G~~~~------i~r~g--------------------------------~~~~~~S~ls~ASFqeT~~vLt~AAi~g~~D~ 336 (363) T cd06528 295 GEVRQ------IGRHG--------------------------------IAGEKPSVLARAAFEVTVKHLLDAAVRGEVDE 336 (363) T ss_pred CCEEE------CCHHH--------------------------------HCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 71420------45132--------------------------------23799889997210638999999985389676 Q ss_pred CCCCCEEEECCCCCCCCCCHHH Q ss_conf 6653221550730565535466 Q gi|254780142|r 1339 LDGFKENVIVGRSIPAGTGAIL 1360 (1398) Q Consensus 1339 L~GvSENIIlGqliP~GTG~f~ 1360 (1398) T Consensus 337 L~GlkenVi~G~~ipaGTG~~~ 358 (363) T cd06528 337 LRGVIENIIVGQPIPLGTGDVE 358 (363) T ss_pred CCCCHHHEECCCCCCCCCCCEE T ss_conf 7880888335897568868779

HHsearch alignment for GI: 254780142 and conserved domain: cd06528