HHsearch alignment for GI: 254780142 and conserved domain: cd02735
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP 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=540.69 Aligned_cols=303 Identities=22% Similarity=0.313 Sum_probs=195.8
Q ss_pred CCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEE--EEEECCCCCEEEEECCCCE
Q ss_conf 17852000101460211110078898776420245432221122024014876897211--3465178877897427604
Q gi|254780142|r 901 ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNR--NVCRNSTNDLISMGRNTTL 978 (1398)
Q Consensus 901 ~~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi--~~~~n~~~~~i~vs~~~~~ 978 (1398)
T Consensus 2 y~~slV~pGEaVGiIAAQSIGEPgTQlTLrTFH~aGv~~-------~~vT~GvpRl~EIl~~~sk~~ktp~~~v~l~--- 71 (309)
T cd02735 2 YMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGE-------MNVTLGIPRLREILMTASKNIKTPSMTLPLK--- 71 (309)
T ss_pred CCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-------EEEEECCCCEEEEEEECCCCCCCCEEEEEEE---
T ss_conf 200447997689999988638558888887663076045-------1145156631677752378887876999961---
Q ss_pred EEEECCCCEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEE
Q ss_conf 66406776000000110000135678553225078621354311320246368975312783200123023686026775
Q gi|254780142|r 979 QILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVI 1058 (1398)
Q Consensus 979 ~i~d~~~~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i 1058 (1398)
T Consensus 72 ---~~~--~~~~~~~~~~~~~~~~l~dv~~~i~i~~i~~~------------------------------~~~~------ 110 (309)
T cd02735 72 ---NGK--SAERAETLKKRLSRVTLSDVVEKVEVTEILKT------------------------------IERV------ 110 (309)
T ss_pred ---CCC--CHHHHHHHHHHCCCEEEEEECCCEEEEEEHHH------------------------------HHHH------
T ss_conf ---783--07899999862373999871472799995232------------------------------0001------
Q ss_pred EHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHH
Q ss_conf 10110122123853477427782532247884202137784454136761354842221013202455433677328898
Q gi|254780142|r 1059 DWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAEL 1138 (1398)
Q Consensus 1059 ~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eL 1138 (1398)
T Consensus 111 ----------~~~~---~~---~~--------~~~~--------~-------------~~~----------~~~~~~~~~ 135 (309)
T cd02735 111 ----------FKKL---LG---KW--------CEVT--------I-------------KLP----------LSSPKLLLL 135 (309)
T ss_pred ----------EECC---CC---CE--------EEEE--------E-------------EEC----------CCCCHHHHH
T ss_conf ----------0013---48---53--------8999--------9-------------816----------888402677
Q ss_pred HHHHCCCCCCEECCCCCEEEEEEECCCCE-EEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHH
Q ss_conf 87525111101113478678633127944-99998368984026898138965898419877408646438999999987
Q gi|254780142|r 1139 FEARRPKNHAILAEISGTIRIKRNYKNKS-RVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILR 1217 (1398)
Q Consensus 1139 FEar~pk~~aiisei~Giv~i~~~~~~k~-~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~ 1217 (1398)
T Consensus 136 ~~~~~~~~~~~i~~i~gI~~~~~~~~~~~~~~~~~~~t~g~n~~~~~---------~~~~~id~~~~~---sndi~di~~ 203 (309)
T cd02735 136 SIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALW---------KFSDILDVNRIY---TNDIHAMLN 203 (309)
T ss_pred HHHHHHHHHCEEECCCCEEEEEEEECCCCCEEEEEECCCCCCHHHHC---------CCCCEECCCCCC---CCCHHHHHH
T ss_conf 88876541038967899179999703798138999546872276610---------137767677555---688999998
Q ss_pred HHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCE
Q ss_conf 52799999999999999999809700612560124762861489418864545664106999999999999728987520
Q gi|254780142|r 1218 IKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSF 1297 (1398)
Q Consensus 1218 vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~ 1297 (1398)
T Consensus 204 ~~GIEAar~~li~Ei~~V~~~~Gv~in~rHi~li~d~Mt~~G~~~~------~~R~g----------------------- 254 (309)
T cd02735 204 TYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRP------FNRIG----------------------- 254 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCEEE------CCHHC-----------------------
T ss_conf 7579999999999999997435865674776657665000685731------01221-----------------------
Q ss_pred EEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHHH
Q ss_conf 121000014530231077650402589999997452855236653221550730565535466
Q gi|254780142|r 1298 SPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAIL 1360 (1398)
Q Consensus 1298 ~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f~ 1360 (1398)
T Consensus 255 ------i~~----~~s~L~~aSFeet~~vL~~AAi~g~~D~l~Gl~enVi~G~~ip~GTG~~~ 307 (309)
T cd02735 255 ------MES----STSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFD 307 (309)
T ss_pred ------CCC----CCCHHHHHHCHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCCCCCCCEE
T ss_conf ------025----98898984267599999999863896777880776442898778776435