Conserved Protein Domain Family
RNAP_I_Rpa1_C

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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.
Statistics
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PSSM-Id: 132722
View PSSM: cd02735
Aligned: 30 rows
Threshold Bit Score: 261.743
Threshold Setting Gi: 65304964
Created: 9-Jun-2005
Updated: 17-Jan-2013
Structure
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Aligned Rows:
  next features
Feature 1:Rpb1 (Rpa1) - Rpb2 (Rpa2) interaction site [polypeptide binding site]
Evidence:
  • Comment:based on similarity to yeast RNAP II
  • Comment:The two largest subunits of eukaryotic RNAP I, Rpa1 and Rpa2, correspond to subunits Rpb1 and Rpb2, respectively, of yeast RNAP II.
  • Comment:The two largest subunits of yeast RNAP II, Rpb1 and Rpb2, form distinct masses with a deep cleft between them. Each of the small subunits occurs in a single copy, arrayed around the periphery.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                    #  #                                                                 
gi 15230368  1146 KFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTAAanIKTPIMTCPLLkgktke--- 1222
gi 65304964  1392 YFERCKCDPGEAVGCIAGQSIGEPATQMTLNTFHLAGHGAANVTLGIPRLVEILQNTSh-CSTPYFSVPILgknedei-- 1468
gi 159117294 1605 KFIRSLVAPGSAVGVIAAQSTGEPSTQLTLNTFHLAGHGGVNATMGVPRLREIIMTRN--TSSPIITMSFKdkhrvsvlk 1682
gi 145529488 1222 RYLRALMHPGEAVGCVAAQSIGEPSTQMTLNTFHLAGHGEKNVTLGIPRLREILMTATkkQKTPTMSLQFLnaniek--- 1298
gi 118363248 1255 KYLNSLIHPGDSVGCLAAQAIGEPSTQMTLNTFHLAGHGGVNLTLGIPRLREILMTATdkLKTPVMLLNLSnpevaqn-- 1332
gi 46098565  1263 LYHRGLVDPGEAVGLLAAQGVGEPSTQMTLNTFHFAGHGAANVTLGIPRLREIVMTASqhIKTPIMRLPVLdgitad--- 1339
gi 74860727  1128 YYSRSMVSPGESVGLLCAQSIGEPSTQMTLNTFHLAGRGEANVTLGIPRLRELIMTATtkPITPLMEFQINdstnkv--- 1204
gi 162606436 1077 NYFENLIEPGESTGILCGQAIGEPCTQMTLNTFHYAGKISSHGKQGLPRLKEMLLYNSknSTNFLVNCRLKsiinrk--- 1153
gi 19068861   953 RYICSLADPGESVGVIAAQSVGEPSTQMTLNTFHLAGVGAKNVTLGVPRLREILITASksIRTPLITVPIKrrvs----- 1027
gi 183232815 1120 KYNKSLINPGEPVGVLAGQSIGEPSTQMTLNTFHLAGRGDVNVTLGMPRIKELVMFAKkeIATPSMILYLKepnqk---- 1195
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 15230368  1223 ------------------dandiTDRLRKITVADIIKSMELSVvpytvyenevcsihklki------nlykpehypkhtd 1278
gi 65304964  1469 ----------------aenaenaINALRKIYLSDIVQSVGMETnvyvnknsekeweysatiq-----fddfnlfrkvigh 1527
gi 159117294 1683 gdslhhktvslgpnetmrackslQQQLRKIYLRDVLRSFVLREcpisdgsvryeltmkl-----------ltlsellhef 1751
gi 145529488 1299 -----------------sqadryAKRMSKLVFLELVNNIKVREykrltengiplhsllrgviyeidveledlnqikyvfg 1361
gi 118363248 1333 ----------------keqvqnhARKLQKINLLELVNNIEVKEqkiivvdnnilpfnerfrhyeikinledleaihfafq 1396
gi 46098565  1340 ------------------qiktfCKDGSRLVLSQVIDEAIVTEkispksegtgfhrqktytvr---lnfypadeckeeyn 1398
gi 74860727  1205 ------------------etekmAKYLEILKLSDIIKDITVQEyfqdtnrnydieiefiptlq---qvlslhrikekqln 1263
gi 162606436 1154 ------------------ylekvKRNFSNYKLFDLVESIELYYnyekkrinlslkfkik-----------kkkvfvaqkl 1204
gi 19068861  1028 --------------------fdiTECLRRVTLKDCVKRFGVTEeivmvsgvfqkkv-----------------kimfeld 1070
gi 183232815 1196 ------------------nteklAKLLTKVTLANIIEGIKCLDsiivhegqrrrqyt--------------idltlidky 1243
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 15230368  1279 iteedWEETMRAVFLRKLedaiethmkmlhrirgihndvtgpiagnetdnddsvsgkqneddgdddgegtevddlgsdaq 1358
gi 65304964  1528 fdtsdIIKVCSHSLIKSFmkrvlgqmivtmdinvpfelsdktdqleefwnmfvmekqivkrdklstrirkmilssgsssd 1607
gi 159117294 1752 nfnvvVLKKLFAVAIPKHlarvltkevlahkatiqslqnklpsdtsfpeyvekvagprnstgkedsdaqedtskenssvs 1831
gi 145529488 1362 isedqIKNKVNHVFIPLLlkiiqaelnknssrcvektsflktkeneakkqrkgsddeeeddedqqeeqddlselnqd--- 1438
gi 118363248 1397 lnidtINRRIEKVFLPNLfqyinkelkrdqkselqtrvlkkkenessgmeteglvsdfdkeaasdgeelkkaadalv--- 1473
gi 46098565  1399 cttahILHGLQETFAPNLensinnemrkqkrehalqaaaigkgrvfsdnapagdnadedgerangvvgrsqtrsrgnead 1478
gi 74860727  1264 klfgeFNKVIKRQVKSQGklkvnngdiglgskvrgsdlveddsltindddapanddttnndentsqqqpssqnkkskskv 1343
gi 162606436 1205 mennnIFKCFTNQIKNFHknvminyknpfkrlfnnngdtki--------------------------------------- 1245
gi 19068861  1071 nfvdlAGEVLDRKFLKLLgnkmkglakakytlgmseapkddckevdenkenegedesdsdkesdpegdn----------- 1139
gi 183232815 1244 eevvdFNTTEITKKIKSVlmneiakrqqskvgididykgvsgeeaeekvneesedvqekinkgkvieeevpee------- 1316
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 15230368  1359 kqkkqetdemdyeens---------------------------------------------------------------- 1374
gi 65304964  1608 ipkgvggqditdtvfpsledsvcdshggdededseggtessveesevdeevgeeedeghgeeelqeeeqekeddldeeee 1687
gi 159117294 1832 nptdsepnldtdasdttdstqhaqeq------------------------------------------------------ 1857
gi 145529488      --------------------------------------------------------------------------------
gi 118363248      --------------------------------------------------------------------------------
gi 46098565  1479 sddeedassdagdgdaddakrkqks------------------------------------------------------- 1503
gi 74860727  1344 itqddd-------------------------------------------------------------------------- 1349
gi 162606436      --------------------------------------------------------------------------------
gi 19068861       --------------------------------------------------------------------------------
gi 183232815      --------------------------------------------------------------------------------
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 15230368  1375 --------------edetnepssisgvedpemdsenedtevskedtpepqeesmepqkevkgvknvkeqskkkrrkfvra 1440
gi 65304964  1688 geeefevldasqsssatvedipmdldketgdpnlmnldeqddtlsgvddfnsptlsptrmrnessgikegkqkiftinrk 1767
gi 159117294 1858 ---hdteesalhaetdpslndidqhrghealslidsninlsakakdflkewvfpdidklievaqkavnttcitlkrisft 1934
gi 145529488 1439 ---------------------------------eevlniinqtfeqsaqqydifeeshqqqesqkkqtpkkeqqqtpqtt 1485
gi 118363248 1474 ---------------------------------seveygiftetedelkskskpqsaepvkrvptrtskaelfeaspyyn 1520
gi 46098565  1504 ----aahasyeegddeemggpsttedieaafsnggskkrssdvmdvdsdsesdssedgsineewaeqtcaleralqensk 1579
gi 74860727  1350 -----------------------svaaksknkkkqnvnyedgeeeaeekdsdegeseaeesddksdvdsdsdeisnsrss 1406
gi 162606436 1246 ---------------------------------------------------------------------flnlnmislei 1256
gi 19068861  1140 ----------------------------------------vcleattgengdkdsedhstsyleatdetdqtddsgntee 1179
gi 183232815 1317 ------------------------------------eqnemseeeieteeksgssssseeeekeekkspleeekeeikek 1360
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 15230368  1441 ksdrhifvkgeGEKFEVHFKFAtd----dpHILLAQIAQQTAQKVYIQNSGKIERctvancgdpqviyhgdnpkerreis 1516
gi 65304964  1768 vfhfaksleysEETSTMVLKFGwpvikcpyFLDLLPLLKQEISQLVLRDSYGIRQsrivfqtvddkeeytl--------- 1838
gi 159117294 1935 ledtalgvspdQLPLSVTIQFVnsd---psHVIALATIEKAIRSLVLKEVRGITRcfiryelpadryvmd---------- 2001
gi 145529488 1486 qhkylekaevqKQLIKVVIKLPln----skKMLMTNVVKKTLSNTVINEIKGINKakiikndksggasfm---------- 1551
gi 118363248 1521 vsyqqifktikGERIVCNIKLPld----skKLLMVNLVEKILKKTLVYEVKNISNatvlkkdnkgatsyq---------- 1586
gi 46098565  1580 yinafrfddvkARWAEFDLTLNtq----sqKLLLINIVERVCRQSVIHEIPNIARvmkpppkageegvsl---------- 1645
gi 74860727  1407 nsfsdesiefdQKKLTFTISVAsd----skKVLMLGIVETEASKFVLKSCKGITRcfvnekqvggkthys---------- 1472
gi 162606436 1257 inkkkkfridlGKLFQMNFNITs-------NFLLSNIILDYFTKRIQISGNNIEIffs---------------------- 1307
gi 19068861  1180 eedfmnfakksKNVLTFEILYPsg-----fNEMISSVVESILPTIVVREVKGMEKasvsgsqlfvksssiys-------- 1246
gi 183232815 1361 pnlvekeekgkKQHLVVSVLLNvn-----dKVSMVSVVEKVIEKIILYECPHIVRgiplskkkegrtiyy---------- 1425
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 15230368  1517 ndekkaspalhasgvdfpalwefqDKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYM 1596
gi 65304964  1839 ---------hcdgtnlkrlfmlreNIVDFNRIKMNDVATVFKYYGIEAARSCIVSELQKVFSVYGIKVDYRHLTLIADFM 1909
gi 159117294 2002 ----------ieggnlralfylsnPFINFDNIYTNNISQIFEIYGIEAARNAIIEEIHRVFSTYHIEVDERHLSLIADSM 2071
gi 145529488 1552 ----------iytegvnlnkirnfDFINLNNIDCNDIVAIMNAFGIEAARNAIIKEILAVFGAYGVAVDYRHLYLIADYM 1621
gi 118363248 1587 ----------iqtegvnfkqiwkmDHFDSNTIDSNDIAALNKCYGIEAARNAIVKEIVTVFGVYGVVVDYRHLYLIADYL 1656
gi 46098565  1646 ---------taeginfrdlwdfgfGVIDLDNLYTNDIGAVLHTYGVEAARAAIVAEMRGIFDTYGIAVSPRHLFLIADYQ 1716
gi 74860727  1473 ---------iqsegvnlseifelrDKLKIDEIYTNDIYAILQKYGVEACRQAVTSEISNVFAAYGISVDKRHLILLGDYM 1543
gi 162606436 1308 ----------------------lsEFFKIDEIFTSDILKMSIIFGIEAGREILTIELMNIFKNQGIVISNKHIDTISDYM 1365
gi 19068861  1247 --------ltrmievspgvyedllDILDIYNAESNDIYDVYLTLGVEAARHAIINEVVKVFDVYGISIDIRHLLLIADYM 1318
gi 183232815 1426 ---------vmtegvnfraalqfgNLVDVDTVETNDVYAVLNMYGVEAARTVLIHEIDSVFKAYGIDVDPRHLNLVADYM 1496
                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
Feature 1                                           #         ###     ## # #    #      
gi 15230368  1597 TFSGGYRPMSRMGgiAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLM 1665
gi 65304964  1910 TQKGDVRTFTRYGm-ARHTSPLLQMSFESTMKFLMDASERGAYDNLKSPAGGLMTGKPVHVGSSLCRLM 1977
gi 159117294 2072 TLSGCVRGLNRLEm-RHQTEELLKASFESACTSLAAGALTSGFDSLRAPAGAVTVGQYPSQGTGSFDLL 2139
gi 145529488 1622 TFGGQIRAMNRIYm-DFNTAPFGKMTFETSTQFLTNACLNRETDTFNNLSSQLVIGRVPKVGSNLCDVL 1689
gi 118363248 1657 TFSGEMKAMNRVWm-DESISPFLKMSFETCVKFLTNAATNNEIDTLSTPSSSIVLGRVPQVGTGVFDIL 1724
gi 46098565  1717 TAAGGFRPFNRSGi-SESSSTLLKASFEMTMAFIGGSALHGEVDMLKTPSSKLVVGRPVNSGTGTPEIR 1784
gi 74860727  1544 TFEGGYRALNRIGi-ENNTSPFQKMSFETTFSFLSKASLMGDYDTVTSPSSRIVLGQIVKNGTGSFTIV 1611
gi 162606436 1366 TRLGYLRPFNRNY--MKEEAGIQEISYETALLHLKKYALGKKIESIECISDKIAFGLPCNIGTGLFEIN 1432
gi 19068861  1319 TRKGSYSPFSRHGl-GADDSPIQRISFESCYSNFKTAATFHLEDKLSNPSASLTVGNPVRCGTGCFDLI 1386
gi 183232815 1497 TYEGEYKSLNRSGm-DHNPSPFTKITFETSLGFLAKTCVSGQKDNLRSPSGSVVMGKNMVFGTGAFDIY 1564

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