HHsearch alignment for GI: 254780142 and conserved domain: cd02736
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=0 Score=560.80 Aligned_cols=293 Identities=27% Similarity=0.380 Sum_probs=203.6
Q ss_pred CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEE-EEECCCCCEEEEECCCCEE
Q ss_conf 178520001014602111100788987764202454322211220240148768972113-4651788778974276046
Q gi|254780142|r 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN-VCRNSTNDLISMGRNTTLQ 979 (1398)
Q Consensus 901 ~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~-~~~n~~~~~i~vs~~~~~~ 979 (1398)
T Consensus 2 y~~slv~pGEaVGiIAAQSIGEPgTQlTLrTFH~aGvas~-------~vT~GvpRl~El~~a~k~~~tp~i~~~l~---- 70 (300)
T cd02736 2 YMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASM-------NITLGVPRIKEIINASKNISTPIITAKLE---- 70 (300)
T ss_pred CCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCCE-------EEECCCCEEEEEEECCCCCCCCEEEEEEE----
T ss_conf 5415279986378776773386488888885635220030-------35437651799886555677877999974----
Q ss_pred EEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEE
Q ss_conf 64067760000001100001356785532250786213543113202463689753127832001230236860267751
Q gi|254780142|r 980 ILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVID 1059 (1398)
Q Consensus 980 i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~ 1059 (1398)
T Consensus 71 --~--~~~~~~~~~v~~~i~k~~l~~v~~~~~~~~~~~~~~~~i~~~~-------------------------------- 114 (300)
T cd02736 71 --N--DRDEKSARIVKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDK-------------------------------- 114 (300)
T ss_pred --C--CCCHHHHHEECCEEEEEEEECCCCEEEEEECCCCEEEEEEECH--------------------------------
T ss_conf --2--5325432201146889985201122799988983489998467--------------------------------
Q ss_pred HHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHH
Q ss_conf 01101221238534774277825322478842021377844541367613548422210132024554336773288988
Q gi|254780142|r 1060 WRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELF 1139 (1398)
Q Consensus 1060 ~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLF 1139 (1398)
T Consensus 115 -~~i~~-~---------------------------------------------------------------~l~~~~~~~ 129 (300)
T cd02736 115 -KIIEK-L---------------------------------------------------------------QLSKSNLYF 129 (300)
T ss_pred -HHHHH-C---------------------------------------------------------------CCCHHHHHH
T ss_conf -67753-3---------------------------------------------------------------787477888
Q ss_pred HHHCCCC---CCEECCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHH
Q ss_conf 7525111---1011134786786331279449999836898402689813896589841987740864643899999998
Q gi|254780142|r 1140 EARRPKN---HAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDIL 1216 (1398)
Q Consensus 1140 Ear~pk~---~aiisei~Giv~i~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl 1216 (1398)
T Consensus 130 ~~~~~~~~l~~v~i~Gi~~i~~----------~~i~~-~~~~~~~~~~~~g~~l~~v~~~~~vd~~~~~---sn~i~~i~ 195 (300)
T cd02736 130 LLQSLKRKLPDVVVSGIPEVKR----------AVINK-DKKKGKYKLLVEGYGLRAVMNTPGVIGTRTT---SNHIMEVE 195 (300)
T ss_pred HHHHHHHHCCCEEEECCCCCCE----------EEEEE-CCCCCEEEEEECCCCCEEEECCCCEECCEEC---CCCHHHHH
T ss_conf 8888884458559946678547----------99960-2788538999538771024313867323412---37888888
Q ss_pred HHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCC
Q ss_conf 75279999999999999999980970061256012476286148941886454566410699999999999972898752
Q gi|254780142|r 1217 RIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVS 1296 (1398)
Q Consensus 1217 ~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~ 1296 (1398)
T Consensus 196 ~~lGiEAar~~ii~Ei~~v~~~~Gv~in~rHi~li~d~Mt~~g~~----------------------------------- 240 (300)
T cd02736 196 KVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEV----------------------------------- 240 (300)
T ss_pred HHHHHHHHHEEEEECCCEEEECCCCEECHHHHHHHCCEEEECCEE-----------------------------------
T ss_conf 774366532156411520330365100034476534430574789-----------------------------------
Q ss_pred EEEEEECHHHHHHC--CCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHH
Q ss_conf 01210000145302--3107765040258999999745285523665322155073056553546
Q gi|254780142|r 1297 FSPILQGITKASLQ--TKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359 (1398)
Q Consensus 1297 ~~p~llGITKasl~--t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f 1359 (1398)
T Consensus 241 -----~~itr~gl~~~~~S~ls~ASFeeT~~vLt~AAi~g~~D~L~GlkenVi~G~~ip~GTG~F 300 (300)
T cd02736 241 -----LGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300 (300)
T ss_pred -----EEECHHHCCCCCCCHHHHCCCHHHHHHHHHHHHHCCCCCCCCHHHHEECCCCCCCCCCCC
T ss_conf -----610143176799998897031879999999997189776788288665289767886889