>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun

Probab=99.48 E-value=2.2e-11 Score=93.93 Aligned_cols=197 Identities=22% Similarity=0.277 Sum_probs=121.3 Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEEC---CC------CCCCCCCCCCHHHHHHHHHHHCCC Q ss_conf 788815899996169756678889999987416983068899988---71------443146646244499999840114 Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID---GV------LHEISSIKGVHEDLTDIILNIKGI 92 (340) Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~---gv------~HEfs~i~GV~EDV~eIiLNLK~I 92 (340) T Consensus 7 ~~~~~~~~F~L~----~~d~s~aNaLRR~~lseVPtlAId~V~i~eNtS~l~DE~iaHRLglIPl~~-d-------~~~~ 74 (291) T cd07032 7 SLSDEELEFDLI----GVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLIPIKA-D-------PRLF 74 (291) T ss_pred ECCCCEEEEEEE----CCCHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCHHHHHHHHCCCCCCC-C-------HHHC T ss_conf 668977999995----798999999999998739857899999997786361489887643633233-8-------6661 Q ss_pred EEEEC------CCCCEEEEEEEECC------------------EEEEEEEEE-----------CCCCEEEECCCEEEEEE Q ss_conf 17772------79827999999447------------------169963351-----------38985998888089997 Q gi|254780237|r 93 NLKMS------GDSHKRVTIFKRGP------------------GVVTAGDIQ-----------TVNDIEVLNPDHVICNL 137 (340) Q Consensus 93 ~~k~~------~~~~~~~~l~~~Gp------------------~~vtA~Di~-----------~p~~veivNpd~~IaTl 137 (340) T Consensus 75 ~~~~~~~~~~~~~~~v~~~l~v~~~~~~~~~~~~~~~~~~~~~~~V~s~dl~~~p~~~~~~~~~~~~~~~~~~~I~I~kL 154 (291) T cd07032 75 EYREDSDDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLKWVPIGSQEKRFADNPIRPVHPDILIAKL 154 (291) T ss_pred CCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCEECCCCCCCCCCCCCCCCCCCCCCEEEEE T ss_conf 35564023689875799999966367866555545654234675698000666467753434668886546899669993 Q ss_pred CCCCEEEEEEEEECCCCCEECCCCCC--------------------------CCCCCCEECCCCCHHEEEEEEEEEEEE- Q ss_conf 78964999999746876320344446--------------------------557543021243111144223577641- Q gi|254780237|r 138 DVDAVVRMELTVSKGHGYVPAKHHRT--------------------------ENDPIGLITIDALYSPIKKVSYTVESA- 190 (340) Q Consensus 138 ~~~~~l~iel~ie~G~GY~~~e~~~~--------------------------~~~~ig~i~iDa~FsPV~~Vny~Ve~~- 190 (340) T Consensus 155 ~~gQ~l~l~a~a~~G~GkeHAKw~Pv~~~~y~~~p~i~i~~~~~~~~~~~l~~~~p~~v~~~~~~~~---~~~~~v~~~~ 231 (291) T cd07032 155 RPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPITGEDAEKLQKCFPPGVIDIEEVKG---KKKAVVANPR 231 (291) T ss_pred CCCCEEEEEEEEEECCCCCCCCCCCCEEEEEEECCEEEECCCCCHHHHHHHHHHCCCCCEECCCCCC---CCEEEECCCH T ss_conf 7999899999998555440562277168999642115773523477899999758787332146777---6527864711 Q ss_pred ---------CC-------CCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf ---------16-------88776218999999389617779999999999998887622 Q gi|254780237|r 191 ---------RE-------GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 (340) Q Consensus 191 ---------rv-------g~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340) T Consensus 232 ~c~~~~e~~~~~~~~~~i~~~~~~~~F~F~VES~G~l~p~~Iv~~A~~~L~~Kl~~l~~ 290 (291) T cd07032 232 KDTLSREVLRHEEFKDKVELGRVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE 290 (291) T ss_pred HCCHHHHHHCCCCCCCCEEEEECCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 15412655103101565257764997999996647769999999999999999999964

HHsearch alignment for GI: 254780237 and conserved domain: cd07032