4C3H,3H0G,4V1M


Conserved Protein Domain Family
RNA_pol_Rpb1_5

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pfam04998: RNA_pol_Rpb1_5 
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RNA polymerase Rpb1, domain 5
RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Statistics
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PSSM-Id: 309920
View PSSM: pfam04998
Aligned: 24 rows
Threshold Bit Score: 371.686
Threshold Setting Gi: 75462932
Created: 17-Jul-2016
Updated: 4-Aug-2016
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4C3H_A        989 GIKPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLTKQLEGVHVSYDNSIRDADGTLVQFMYGGDAIDITKESHMTQFEF 1068
gi 75272883   935 GIHPNCYFFHCMAGREGLLDTAIKTSQSGYIQRNIIKHLENLKINYDFTLRMSHNKINSFIFSDDGQRITSIDFISKIRW 1014
gi 215273873  958 GIKPPEFFFHCMAGREGLVDTAVKTSRSGYLQRCIIKHLEGLVVQYDLTVRDSDGSVVQFLYGEDGLDIPKTQFLQPKQF 1037
gi 3334489   1002 GIAPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEGLCVQYDHTVRDSDGSIVQFHYGEDSLDVTKQKHLTQFEF 1081
gi 380865455  824 GLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSLAQMVQLRYGEDGLDGMWVENQNMPTM 903
3H0G_M        813 GLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEYQVFDSL 892
4V1M_A        807 GLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTI 886
gi 75272823   796 GLFPDEFFFHSMGGREGLIDTAIKTSETGYIQRRLSKSMEDIVVEYDFSVRNNQQEIISFLYGEDCFDAVYLENQKIFLG 875
gi 75261693   802 GLDSKEFFFHSMAGREGLIDTAVKTAEIGYLQRRLVKSLEDISIMNDSTVRDSFGRIYQFTFGGDNVNPENFSKFYSINS 881
gi 9955855    827 GLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMVKYDGTVRNSLGDIIQFIYGEDGLDGAHIENQRVDII 906
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4C3H_A       1069 CLDNYYALLKKYNPSALIEHLDVEsalkyskktlkyrkkhskephyk--------------------------------- 1115
gi 75272883  1015 KFQNSLRTENDDNNLFNNMKLNSNft------------------------------------------------------ 1040
gi 215273873 1038 PFLASNYEVIMKSQHLHEVLSRADpkkalhhfraikkwqskhpntllrrgaflsysqkiqeavkalklesenrngr---- 1113
gi 3334489   1082 SAKNYKSLIQKYKVKSVLSAVDSEtassyakkalkkpykydpvld----------------------------------- 1126
gi 380865455  904 KPNNAVFERDFRMDLTDNKFLRKNysedvvreiqesedgislvesewsqleedrrllrkifprgdakivlpcnlqrli-- 981
3H0G_M        893 RLSTKQFEKKYRIDLMEDRSLSLYmensiendssvqdlldeeytqlvadrellckfifpkgdarwplpvnvqriiq---- 968
4V1M_A        887 GGSDAAFEKRYRVDLLNTDHTLDPsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirrii-- 964
gi 75272823   876 KMSDIEMNMVYKVTQSSPCFGLAIdssllflsnksynskianieynqllkdreflrklmldqndiniplpvnldrivska 955
gi 75261693   882 FDFSLKLKKSTDNYLLYVFLRAHFlrff---------------------------------------------------- 909
gi 9955855    907 KCSDDQFRDRFRIDLMDPERSLGPevleqaneiagdvevqryldeeweqllkaraflrtvakedeemmqlpinvqril-- 984
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4C3H_A       1116 ---------------------------------qsvkydpvlakynpakylgsvseNFQDKLESFLDKNSKLFKSSDGVN 1162
gi 75272883  1041 ------------------------------------------------------kkNINFHKINFKQIISKRSCKKNFGS 1066
gi 215273873 1114 -----spgtqemlrmwyeldeesrrkyqkkaaacpdpslsvwrpdiyfasvsetfeTKVDDYSQEWAAQTEKSYEKSELS 1188
gi 3334489   1127 -----------------------------------kyppsrylgsvsekfqravdeYTQKNPDKLIASKKESKLDDSLLN 1171
gi 380865455  982 ---wnaqkifkvdlrkpvnlsplhvisgvrelskkliivsgndeiskqaqynatllMNILLRSTLCTKNMCTKSKLNSEA 1058
3H0G_M        969 ----nalqifhleakkptdllpsdiinglneliakltifrgsdritrdvqnnatllFQILLRSKFAVKRVIMEYRLNKVA 1044
4V1M_A        965 ---qnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlFCCLLRSRLATRRVLQEYRLTKQA 1041
gi 75272823   956 svlfknhknsslinfketirslkflrnyflelinfkisfnqkksdnkqlinrdnflLAIYIRSSLSLKIIYTKFNLNQHA 1035
gi 75261693   910 -----------------------------------------------------dslTFSINLRNKINFEKILNIKSNFGY 936
gi 9955855    985 ---emarttfriregtisdlhpaevipqvqalldrllivrgddpisqeaqenatllFKAQLRSRLAFRRLVTEYSMNKLA 1061
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4C3H_A       1163 EKKFRALMQLKYMRSLINPGEAVGIIASQSVGEPSTQMTLNTFHFAGHGAANVTLGIPRLREIVMTaSAAIKTPQMTLPI 1242
gi 75272883  1067 FVSYQNILNSNYFENLIEPGESTGILCGQAIGEPCTQMTLNTFHYAGKISSHGKQGLPRLKEM-----LLYNSKNSTNFL 1141
gi 215273873 1189 LDRLRTLLQLKWQRSLCEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMVaSANIKTPMMSVPV 1268
gi 3334489   1172 ESKFKALMQLRYQQSLVDPGESVGVLASQSIGEPSTQMTLNTFHFAGFGAKNVTLGIPRLREIIMTaSANIQTPTMTLRL 1251
gi 380865455 1059 FDWLLGEIESRFQQAIAQPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKEIINV-SKTLKTPSLTVFL 1137
3H0G_M       1045 FEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNV-AKNIKTPSLTIYL 1123
4V1M_A       1042 FDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNV-AKNMKTPSLTVYL 1120
gi 75272823  1036 LNWIVNEICLSIRKSLIQPGEMVGTISAQSIGQPATQMTLNTFHFAGVSAKNVTLGVPRLKEIIDI-QKNIKSPSLTIFL 1114
gi 75261693   937 FEILIKKYFQTFKLVIIDPGTGVGCISAQSLGEPGTQMTLQTFHSAGTGSQNITSGIPRINEI----LSNSKNTKFPLIS 1012
gi 9955855   1062 FQHVIGAIESRFAKANAPAGEMVGVLAAQSIGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEILNV-ATNIKTPSMTVYQ 1140
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4C3H_A       1243 WNDVsDEQAD-----TFCKSISKVLLSEVIDKVIVTETTGTSNTAGGNAARSYVIHMRFFDNNEYSEEYDVSKEELQNVI 1317
gi 75272883  1142 VNCRlKSIINrkyleKVKRNFSNYKLFDLVESIELYYNYEKKRINLSLKFKIKKKKVFVAQKLMENNNIFKCFTNQIKNF 1221
gi 215273873 1269 LNTK-KALKRv---kSLKKQLTRVCLGEVLQKIDVQESFCMEEKQNKFQVYQLRFQFLPHAYYQQEKCLRPEDILRFMET 1344
gi 3334489   1252 NDGVsDKRAS-----AFCKEVNKLVLSEVVRQVRVTEKISGQGSDEQSKTYAIRLDLYSRDEYQDEYGVLQEEIESTFSN 1326
gi 380865455 1138 TGAAaKDPEKa---kDVLCKLEHTTLKKVTCNTAIYYDPDPKNTVIAEDEEWVSIFYEMPDHDLSRTSPWLLRIELDRKR 1214
3H0G_M       1124 MPWIaANMDLa---kNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLEL 1200
4V1M_A       1121 EPGHaADQEQa---kLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLEL 1197
gi 75272823  1115 HKKCsNDPRKv---kKIQESIESVRLNRISNYFEIIYDPDFFFSISKCNRILVKNYMEIPDEDINFLQASSWILKLKLLT 1191
gi 75261693  1013 YDINfFEFNKkksrlKFF--LKKIKIGFLINSIEIFLHRGFVSVKIHFIKKIYEYLDQSKIYYFIIKKFHDNTK------ 1084
gi 9955855   1141 EPGRtHDKEGa---kQLRSVVEHTSLRSVTEATEIYYDPDIQSTVIENDRDMVESYFIIPEDVTDDSSRQSKWLLRIILS 1217
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4C3H_A       1318 SNQFIHLLEAAIVkeikkqkrttgpdigvavprlqtdvansssnskrleedndeeqshkktk------------------ 1379
gi 75272883  1222 HKNVMINYKN---------------------------------------------------------------------- 1231
gi 215273873 1345 RFFKLLMESIKKKnnkasafrnvntrratqrdldnagelgrsrgeqegdeeeeghivdaeaeegdadasdakrkekqeee 1424
gi 3334489   1327 RFLKILNRIIKSYlakskqrksggkddtvpevgqalkpledideapiegraqealededndatnekmv------------ 1394
gi 380865455 1215 MVDKKLTMEM---------------------------------------------------------------------- 1224
3H0G_M       1201 DRAKMLDKKLS--------------------------------------------------------------------- 1211
4V1M_A       1198 DRAAMNDKDL---------------------------------------------------------------------- 1207
gi 75272823  1192 EEFVEKGLFSNYIietikkkikpip------------------------------------------------------- 1216
gi 75261693       --------------------------------------------------------------------------------
gi 9955855   1218 RPKLLDKGLT---------------------------------------------------------------------- 1227
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4C3H_A       1380 ----------qavsydepdedeietmreaekssdeegidsdkesdsdsededvdmneqiNKSIVEANNNMNKVQRDRQSA 1449
gi 75272883  1232 ---------------------------------------------------------------PFKRLFNNNGDTKIFLN 1248
gi 215273873 1425 vdyeseeeeeregeenddedmqeernphregarktqeqdeevglgteedpslpalltqpRKPTHSQEPQGPEAMERRVQA 1504
gi 3334489   1395 -----srskqhasyegpdeadkvalrqlkgsnkvedvnmdeeedegfksdesvsdfkerKLLEKQNTVSISERRELQLKT 1469
gi 380865455 1225 ---------------------------------------------------------------IADRIHGGFGNDVHTIY 1241
3H0G_M       1212 -------------------------------------------------------------MSDVAGKIAESFERDLFTI 1230
4V1M_A       1208 ---------------------------------------------------------------TMGQVGERIKQTFKNDL 1224
gi 75272823  1217 ------------------------------------------------fliiasdensgSIEFLVRFIWPEFINNYNSEK 1248
gi 75261693  1085 -------------------------------------------------------------------------------I 1085
gi 9955855   1228 ---------------------------------------------------------------VQDVATRIKQAYPKDIA 1244
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4C3H_A       1450 IISHHRFITKYNFDDESGKWCEFKLELAADTEKLLMVNIVEEICRKSIIRQIPHIDRCVHP--EPE-NGKRVlvt----- 1521
gi 75272883  1249 LNMISLEIINKKKKFRIDLGKLFQMNFNITSNFLLSNIILDYFTKRIQIS----GNNIEIF------------------- 1305
gi 215273873 1505 VREIHPFIDDYQYDTEESLWCQVTVKLPLMKINFDMSSLVVSLAHGAVIYATKGITRCLLN--ETT-NNKNEkelvl--- 1578
gi 3334489   1470 AKEILSNCKHLDFDYVNGEWATVELVFPINTEKLLMVSLVEKACSETVIHEIPGITRCFSK--PPDsALDTVpkvi---- 1543
gi 380865455 1242 TDDNAEKLVFRLRIAGEDKGEAQEEQVDKMEDDVFLRCIEANMLSDLTLQGIPAISKVYMNqpNTDdKKRIIitpeggfk 1321
3H0G_M       1231 WSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRVYMM--EHK-IVRQIedgtfera 1307
4V1M_A       1225 FVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMM--KYD-RKVPSptgeyvke 1301
gi 75272823  1249 IEKLFSRSNANTFFEYIKRANQKVSENLFLEPNYFKKIKHYFYNYNLKPYGSQKLTKLYPR--RID-IIEPEpnqsgklk 1325
gi 75261693  1086 IKKSTVFICKKKKNVVLQFHKNDFKIDDFNLNFINLYNFFRIHFGDIVLTGFYESSKINCN------FLFnnlei----- 1154
gi 9955855   1245 VIFSDNNADEQVIRIRQIQDHKEDEDDDDIEYDVTLKKLEQHLLDTLTLRGVNGVERAFIN--EKS-KVRVLedgslfts 1321
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4C3H_A       1522 -------------egVNFQAMWDQEAFIDVDGITSNDVAAVLKTYGVEAARNTIVNEINNVFSRYAISVSFRHLDLIADM 1588
gi 75272883  1306 ---------------FSLSE------FFKIDEIFTSDILKMSIIFGIEAGREILTIELMNIFKNQGIVISNKHIDTISDY 1364
gi 215273873 1579 -----------ntegINLPELFKYAEVLDLRRLYSNDIHAIANTYGIEAALRVIEKEIKDVFAVYGIAVDPRHLSLVADY 1647
gi 3334489   1544 ------------tegVNLKAIWEFYNEISMNDIYTNDIAAILRIYGVEAARNAIVHEVSSVFGVYGIAVDPRHLSLIADY 1611
gi 380865455 1322 sv----adwiletdgTALLRVLSERQ-IDPVRTTSNDICEIFEVLGIEAVRKAIEREMDNVISFDGSYVNYRHLALLCDV 1396
3H0G_M       1308 d------ewvletdgINLTEAMTVEG-VDATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDV 1380
4V1M_A       1302 p------ewvletdgVNLSEVMTVPG-IDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDV 1374
gi 75272823  1326 nn----fefvletegVDLRFVMNYNG-IDYSRCTTNDLLESLKVLGIEATRKILIQELRNLISFDGSYVNYRHLCTLVDL 1400
gi 75261693  1155 -----------kisdNRFDILLNIPG-IIFRKLYCNNINSIYNFLGIEASRELIVLEITNTFKSHGIFSDNRHVYLLADY 1222
gi 9955855   1322 kvdplckewvletsgSALGEVLAVPG-VDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDV 1400
                         730       740
                  ....*....|....*....|...
4C3H_A       1589 MTRQGTYLAFNRQGMETSTSSFM 1611
gi 75272883  1365 MTRLGYLRPFNRN-YMKEEAGIQ 1386
gi 215273873 1648 MCFEGVYKPLNRFGIRSNSSPLQ 1670
gi 3334489   1612 MTFEGGYKAFNRMGIEYNTSPFA 1634
gi 380865455 1397 MTAKGHLMAITRHGINRQEVGAL 1419
3H0G_M       1381 MTSRGHLMAITRHGINRAETGAL 1403
4V1M_A       1375 MTTQGGLTSVTRHGFNRSNTGAL 1397
gi 75272823  1401 ITFRGSLMSINRHGINKCNSGPI 1423
gi 75261693  1223 MTFNGFIIGINREGLTCNKESVF 1245
gi 9955855   1401 MTVRGYLTPVTRHGINRADNGAL 1423
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