5N5Z,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: 398596
Aligned: 24 rows
Threshold Bit Score: 371.686
Threshold Setting Gi: 75462932
Created: 11-May-2020
Updated: 7-Aug-2020
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:
5N5Z_A        989 GIKPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLTKQLEGVHVSYDNSIRDADGTLVQFMYGGDAIDITKESHMTQFEF 1068 baker's yeast
Q9AW39        935 GIHPNCYFFHCMAGREGLLDTAIKTSQSGYIQRNIIKHLENLKINYDFTLRMSHNKINSFIFSDDGQRITSIDFISKIRW 1014 Guillardia theta
O95602        958 GIKPPEFFFHCMAGREGLVDTAVKTSRSGYLQRCIIKHLEGLVVQYDLTVRDSDGSVVQFLYGEDGLDIPKTQFLQPKQF 1037 human
P15398       1002 GIAPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEGLCVQYDHTVRDSDGSIVQFHYGEDSLDVTKQKHLTQFEF 1081 Schizosacchar...
P16356        824 GLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSLAQMVQLRYGEDGLDGMWVENQNMPTM 903  Caenorhabditi...
3H0G_M        813 GLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEYQVFDSL 892  Schizosacchar...
4V1M_A        807 GLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTI 886  baker's yeast
XP_002479200  828 GLTPTEFYFHAMGGREGLIDTAVKTAETGYIQRKLVKALEELMVKYDGTVRNSLGDIIQFLYGEDGLDGAHIENQRVDII 907  Talaromyces s...
BAE57665      827 GLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMVKYDGTVRNSLGDIIQFIYGEDGLDGAHIENQRVDII 906  Aspergillus o...
Q9AVW8        796 GLFPDEFFFHSMGGREGLIDTAIKTSETGYIQRRLSKSMEDIVVEYDFSVRNNQQEIISFLYGEDCFDAVYLENQKIFLG 875  Guillardia theta
5N5Z_A       1069 CLDNYYALLKKYNPSALIEHLDVEsalkyskktlkyrkkhskephyk--------------------------------- 1115 baker's yeast
Q9AW39       1015 KFQNSLRTENDDNNLFNNMKLNSNft------------------------------------------------------ 1040 Guillardia theta
O95602       1038 PFLASNYEVIMKSQHLHEVLSRADpkkalhhfraikkwqskhpntllrrgaflsysqkiqeavkalklesenrngr---- 1113 human
P15398       1082 SAKNYKSLIQKYKVKSVLSAVDSEtassyakkalkkpykydpvld----------------------------------- 1126 Schizosacchar...
P16356        904 KPNNAVFERDFRMDLTDNKFLRKNysedvvreiqesedgislvesewsqleedrrllrkifprgdakivlpcnlqrli-- 981  Caenorhabditi...
3H0G_M        893 RLSTKQFEKKYRIDLMEDRSLSLYmensiendssvqdlldeeytqlvadrellckfifpkgdarwplpvnvqriiq---- 968  Schizosacchar...
4V1M_A        887 GGSDAAFEKRYRVDLLNTDHTLDPsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirrii-- 964  baker's yeast
XP_002479200  908 KCSDEQFRDRFRVDLMDPERTLGPevleqaaeiegdvevqryldeeweallkdreflrsvakgdeemmqlplnvqril-- 985  Talaromyces s...
BAE57665      907 KCSDDQFRDRFRIDLMDPERSLGPevleqaneiagdvevqryldeeweqllkaraflrtvakedeemmqlpinvqril-- 984  Aspergillus o...
Q9AVW8        876 KMSDIEMNMVYKVTQSSPCFGLAIdssllflsnksynskianieynqllkdreflrklmldqndiniplpvnldrivska 955  Guillardia theta
5N5Z_A       1116 ---------------------------------qsvkydpvlakynpakylgsvseNFQDKLESFLDKNSKLFKSSDGVN 1162 baker's yeast
Q9AW39       1041 ------------------------------------------------------kkNINFHKINFKQIISKRSCKKNFGS 1066 Guillardia theta
O95602       1114 -----spgtqemlrmwyeldeesrrkyqkkaaacpdpslsvwrpdiyfasvsetfeTKVDDYSQEWAAQTEKSYEKSELS 1188 human
P15398       1127 -----------------------------------kyppsrylgsvsekfqravdeYTQKNPDKLIASKKESKLDDSLLN 1171 Schizosacchar...
P16356        982 ---wnaqkifkvdlrkpvnlsplhvisgvrelskkliivsgndeiskqaqynatllMNILLRSTLCTKNMCTKSKLNSEA 1058 Caenorhabditi...
3H0G_M        969 ----nalqifhleakkptdllpsdiinglneliakltifrgsdritrdvqnnatllFQILLRSKFAVKRVIMEYRLNKVA 1044 Schizosacchar...
4V1M_A        965 ---qnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlFCCLLRSRLATRRVLQEYRLTKQA 1041 baker's yeast
XP_002479200  986 ---esakttfhikegtisdlhpaevipqvqalldrlvivrgddviskeaqtsatllFKAQLRSRLAFKRLVTQYSMNKLA 1062 Talaromyces s...
BAE57665      985 ---emarttfriregtisdlhpaevipqvqalldrllivrgddpisqeaqenatllFKAQLRSRLAFRRLVTEYSMNKLA 1061 Aspergillus o...
Q9AVW8        956 svlfknhknsslinfketirslkflrnyflelinfkisfnqkksdnkqlinrdnflLAIYIRSSLSLKIIYTKFNLNQHA 1035 Guillardia theta
5N5Z_A       1163 EKKFRALMQLKYMRSLINPGEAVGIIASQSVGEPSTQMTLNTFHFAGHGAANVTLGIPRLREIVMTaSAAIKTPQMTLPI 1242 baker's yeast
Q9AW39       1067 FVSYQNILNSNYFENLIEPGESTGILCGQAIGEPCTQMTLNTFHYAGKISSHGKQGLPRLKEM-----LLYNSKNSTNFL 1141 Guillardia theta
O95602       1189 LDRLRTLLQLKWQRSLCEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMVaSANIKTPMMSVPV 1268 human
P15398       1172 ESKFKALMQLRYQQSLVDPGESVGVLASQSIGEPSTQMTLNTFHFAGFGAKNVTLGIPRLREIIMTaSANIQTPTMTLRL 1251 Schizosacchar...
P16356       1059 FDWLLGEIESRFQQAIAQPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKEIINV-SKTLKTPSLTVFL 1137 Caenorhabditi...
3H0G_M       1045 FEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNV-AKNIKTPSLTIYL 1123 Schizosacchar...
4V1M_A       1042 FDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNV-AKNMKTPSLTVYL 1120 baker's yeast
XP_002479200 1063 FNHVLGAIEMRFARAQANPGEMVGVLAAQSIGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEILNV-ATNIKTPSMTVYQ 1141 Talaromyces s...
BAE57665     1062 FQHVIGAIESRFAKANAPAGEMVGVLAAQSIGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEILNV-ATNIKTPSMTVYQ 1140 Aspergillus o...
Q9AVW8       1036 LNWIVNEICLSIRKSLIQPGEMVGTISAQSIGQPATQMTLNTFHFAGVSAKNVTLGVPRLKEIIDI-QKNIKSPSLTIFL 1114 Guillardia theta
5N5Z_A       1243 WNDVsDEQAD-----TFCKSISKVLLSEVIDKVIVTETTGTSNTAGGNAARSYVIHMRFFDNNEYSEEYDVSKEELQNVI 1317 baker's yeast
Q9AW39       1142 VNCRlKSIINrkyleKVKRNFSNYKLFDLVESIELYYNYEKKRINLSLKFKIKKKKVFVAQKLMENNNIFKCFTNQIKNF 1221 Guillardia theta
O95602       1269 LNTK-KALKRv---kSLKKQLTRVCLGEVLQKIDVQESFCMEEKQNKFQVYQLRFQFLPHAYYQQEKCLRPEDILRFMET 1344 human
P15398       1252 NDGVsDKRAS-----AFCKEVNKLVLSEVVRQVRVTEKISGQGSDEQSKTYAIRLDLYSRDEYQDEYGVLQEEIESTFSN 1326 Schizosacchar...
P16356       1138 TGAAaKDPEKa---kDVLCKLEHTTLKKVTCNTAIYYDPDPKNTVIAEDEEWVSIFYEMPDHDLSRTSPWLLRIELDRKR 1214 Caenorhabditi...
3H0G_M       1124 MPWIaANMDLa---kNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLEL 1200 Schizosacchar...
4V1M_A       1121 EPGHaADQEQa---kLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLEL 1197 baker's yeast
XP_002479200 1142 EPHRkHDKESa---kQLRSVVEHTSLRSVTEATEIYYDPDIQSTVIENDRDMVESYFIIPEDVADDSSRQSKWLLRIVLS 1218 Talaromyces s...
BAE57665     1141 EPGRtHDKEGa---kQLRSVVEHTSLRSVTEATEIYYDPDIQSTVIENDRDMVESYFIIPEDVTDDSSRQSKWLLRIILS 1217 Aspergillus o...
Q9AVW8       1115 HKKCsNDPRKv---kKIQESIESVRLNRISNYFEIIYDPDFFFSISKCNRILVKNYMEIPDEDINFLQASSWILKLKLLT 1191 Guillardia theta
5N5Z_A       1318 SNQFIHLLEAAIVkeikkqkrttgpdigvavprlqtdvansssnskrleedndeeqshkktk------------------ 1379 baker's yeast
Q9AW39       1222 HKNVMINYKN---------------------------------------------------------------------- 1231 Guillardia theta
O95602       1345 RFFKLLMESIKKKnnkasafrnvntrratqrdldnagelgrsrgeqegdeeeeghivdaeaeegdadasdakrkekqeee 1424 human
P15398       1327 RFLKILNRIIKSYlakskqrksggkddtvpevgqalkpledideapiegraqealededndatnekmv------------ 1394 Schizosacchar...
P16356       1215 MVDKKLTMEM---------------------------------------------------------------------- 1224 Caenorhabditi...
3H0G_M       1201 DRAKMLDKKLS--------------------------------------------------------------------- 1211 Schizosacchar...
4V1M_A       1198 DRAAMNDKDL---------------------------------------------------------------------- 1207 baker's yeast
XP_002479200 1219 RPKLLDKGLT---------------------------------------------------------------------- 1228 Talaromyces s...
BAE57665     1218 RPKLLDKGLT---------------------------------------------------------------------- 1227 Aspergillus o...
Q9AVW8       1192 EEFVEKGLFSNYIietikkkikpip------------------------------------------------------- 1216 Guillardia theta
5N5Z_A       1380 ----------qavsydepdedeietmreaekssdeegidsdkesdsdsededvdmneqiNKSIVEANNNMNKVQRDRQSA 1449 baker's yeast
Q9AW39       1232 ---------------------------------------------------------------PFKRLFNNNGDTKIFLN 1248 Guillardia theta
O95602       1425 vdyeseeeeeregeenddedmqeernphregarktqeqdeevglgteedpslpalltqpRKPTHSQEPQGPEAMERRVQA 1504 human
P15398       1395 -----srskqhasyegpdeadkvalrqlkgsnkvedvnmdeeedegfksdesvsdfkerKLLEKQNTVSISERRELQLKT 1469 Schizosacchar...
P16356       1225 ---------------------------------------------------------------IADRIHGGFGNDVHTIY 1241 Caenorhabditi...
3H0G_M       1212 -------------------------------------------------------------MSDVAGKIAESFERDLFTI 1230 Schizosacchar...
4V1M_A       1208 ---------------------------------------------------------------TMGQVGERIKQTFKNDL 1224 baker's yeast
XP_002479200 1229 ---------------------------------------------------------------VQDVATRIKEQYPRDIA 1245 Talaromyces s...
BAE57665     1228 ---------------------------------------------------------------VQDVATRIKQAYPKDIA 1244 Aspergillus o...
Q9AVW8       1217 ------------------------------------------------fliiasdensgSIEFLVRFIWPEFINNYNSEK 1248 Guillardia theta
5N5Z_A       1450 IISHHRFITKYNFDDESGKWCEFKLELAADTEKLLMVNIVEEICRKSIIRQIPHIDRCVHP--EPE-NGKRVlvt----- 1521 baker's yeast
Q9AW39       1249 LNMISLEIINKKKKFRIDLGKLFQMNFNITSNFLLSNIILDYFTKRIQIS----GNNIEIF------------------- 1305 Guillardia theta
O95602       1505 VREIHPFIDDYQYDTEESLWCQVTVKLPLMKINFDMSSLVVSLAHGAVIYATKGITRCLLN--ETT-NNKNEkelvl--- 1578 human
P15398       1470 AKEILSNCKHLDFDYVNGEWATVELVFPINTEKLLMVSLVEKACSETVIHEIPGITRCFSK--PPDsALDTVpkvi---- 1543 Schizosacchar...
P16356       1242 TDDNAEKLVFRLRIAGEDKGEAQEEQVDKMEDDVFLRCIEANMLSDLTLQGIPAISKVYMNqpNTDdKKRIIitpeggfk 1321 Caenorhabditi...
3H0G_M       1231 WSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRVYMM--EHK-IVRQIedgtfera 1307 Schizosacchar...
4V1M_A       1225 FVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMM--KYD-RKVPSptgeyvke 1301 baker's yeast
XP_002479200 1246 VIFSDNNADEQVIRIRQLHDAKEDEDEEDMEYDVTLKKLEQHLLDTLTLRGVAGVERAFIN--EKD-NVRVMedgslfqs 1322 Talaromyces s...
BAE57665     1245 VIFSDNNADEQVIRIRQIQDHKEDEDDDDIEYDVTLKKLEQHLLDTLTLRGVNGVERAFIN--EKS-KVRVLedgslfts 1321 Aspergillus o...
Q9AVW8       1249 IEKLFSRSNANTFFEYIKRANQKVSENLFLEPNYFKKIKHYFYNYNLKPYGSQKLTKLYPR--RID-IIEPEpnqsgklk 1325 Guillardia theta
5N5Z_A       1522 -------------egVNFQAMWDQEAFIDVDGITSNDVAAVLKTYGVEAARNTIVNEINNVFSRYAISVSFRHLDLIADM 1588 baker's yeast
Q9AW39       1306 ---------------FSLSE------FFKIDEIFTSDILKMSIIFGIEAGREILTIELMNIFKNQGIVISNKHIDTISDY 1364 Guillardia theta
O95602       1579 -----------ntegINLPELFKYAEVLDLRRLYSNDIHAIANTYGIEAALRVIEKEIKDVFAVYGIAVDPRHLSLVADY 1647 human
P15398       1544 ------------tegVNLKAIWEFYNEISMNDIYTNDIAAILRIYGVEAARNAIVHEVSSVFGVYGIAVDPRHLSLIADY 1611 Schizosacchar...
P16356       1322 sv----adwiletdgTALLRVLSERQ-IDPVRTTSNDICEIFEVLGIEAVRKAIEREMDNVISFDGSYVNYRHLALLCDV 1396 Caenorhabditi...
3H0G_M       1308 d------ewvletdgINLTEAMTVEG-VDATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDV 1380 Schizosacchar...
4V1M_A       1302 p------ewvletdgVNLSEVMTVPG-IDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDV 1374 baker's yeast
XP_002479200 1323 ktdplckewvletsgSALADVLTIPG-VDTSRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDV 1401 Talaromyces s...
BAE57665     1322 kvdplckewvletsgSALGEVLAVPG-VDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDV 1400 Aspergillus o...
Q9AVW8       1326 nn----fefvletegVDLRFVMNYNG-IDYSRCTTNDLLESLKVLGIEATRKILIQELRNLISFDGSYVNYRHLCTLVDL 1400 Guillardia theta
5N5Z_A       1589 MTRQGTYLAFNRQGMETSTSSFM 1611 baker's yeast
Q9AW39       1365 MTRLGYLRPFNRN-YMKEEAGIQ 1386 Guillardia theta
O95602       1648 MCFEGVYKPLNRFGIRSNSSPLQ 1670 human
P15398       1612 MTFEGGYKAFNRMGIEYNTSPFA 1634 Schizosaccharomyces pombe 972h-
P16356       1397 MTAKGHLMAITRHGINRQEVGAL 1419 Caenorhabditis elegans
3H0G_M       1381 MTSRGHLMAITRHGINRAETGAL 1403 Schizosaccharomyces pombe 972h-
4V1M_A       1375 MTTQGGLTSVTRHGFNRSNTGAL 1397 baker's yeast
XP_002479200 1402 MTVRGYLTPVTRHGINRADNGAL 1424 Talaromyces stipitatus ATCC 10500
BAE57665     1401 MTVRGYLTPVTRHGINRADNGAL 1423 Aspergillus oryzae RIB40
Q9AVW8       1401 ITFRGSLMSINRHGINKCNSGPI 1423 Guillardia theta
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