Conserved Protein Domain Family
RNA_pol_Rpb1_5

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pfam04998: RNA_pol_Rpb1_5 
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: 368228
View PSSM: pfam04998
Aligned: 24 rows
Threshold Bit Score: 371.686
Threshold Setting Gi: 75462932
Created: 6-May-2019
Updated: 18-Jul-2019
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
O95602    958 GIKPPEFFFHCMAGREGLVDTAVKTSRSGYLQRCIIKHLEGLVVQYDLTVRDSDGSVVQFLYGEDGLDIPKTQFLQPKQF 1037 human
P17545    810 GLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYDGTVRNANDELIQFMYGEDGLDGARIEGGQLFPL 889  Trypanosoma bruce...
Q9NJR9    786 GLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVRNANQELIQLAYGEDGLDGARIEGNQAFPI 865  Leishmania donovani
Q9AXN0    795 GLTATEFFFHAMGGREGLIDTAVKTSETGYIQRRLIKALEDVMVKYDGTVRNSTGLIVQFLYGEDGMDGAMVEDQNLRTL 874  Glaucosphaera vac...
P16356    824 GLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSLAQMVQLRYGEDGLDGMWVENQNMPTM 903  Caenorhabditis el...
P36594    813 GLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEYQVFDSL 892  Schizosaccharomyc...
P04050    807 GLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTI 886  Saccharomyces cer...
EED22237  828 GLTPTEFYFHAMGGREGLIDTAVKTAETGYIQRKLVKALEELMVKYDGTVRNSLGDIIQFLYGEDGLDGAHIENQRVDII 907  Talaromyces stipi...
BAE57665  827 GLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMVKYDGTVRNSLGDIIQFIYGEDGLDGAHIENQRVDII 906  Aspergillus oryza...
Q9AVW8    796 GLFPDEFFFHSMGGREGLIDTAIKTSETGYIQRRLSKSMEDIVVEYDFSVRNNQQEIISFLYGEDCFDAVYLENQKIFLG 875  Guillardia theta
O95602   1038 PFLASNYEVIMKSQHLHEVLSRADpkkalhhfraikkwqskhpntllrrgaflsysqkiqeavkalklesenrngr---- 1113 human
P17545    890 PFRDDKEMEDTYKYEYDVDGTFSGkvggnymdphvrkmlradpqnvrklqeeyeqltadrewsrkmldledrdklklnlp 969  Trypanosoma bruce...
Q9NJR9    866 PHMTNSEMADKYRYEYNDEGSFSEnmgghymdpfvrdsllrdpqsvlkvqeefeqlmkdramsrlvidmedknklkmnlp 945  Leishmania donovani
Q9AXN0    875 SMNDAKLEQTFHLDPFDLDFGIGEnrrsylaqeviddvrndpqlikaledefaqikldrdrlqreiirsreskwplavni 954  Glaucosphaera vac...
P16356    904 KPNNAVFERDFRMDLTDNKFLRKNysedvvreiqesedgislvesewsqleedrrllrkifprgdakivlpcnlqrli-- 981  Caenorhabditis el...
P36594    893 RLSTKQFEKKYRIDLMEDRSLSLYmensiendssvqdlldeeytqlvadrellckfifpkgdarwplpvnvqriiq---- 968  Schizosaccharomyc...
P04050    887 GGSDAAFEKRYRVDLLNTDHTLDPsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirrii-- 964  Saccharomyces cer...
EED22237  908 KCSDEQFRDRFRVDLMDPERTLGPevleqaaeiegdvevqryldeeweallkdreflrsvakgdeemmqlplnvqril-- 985  Talaromyces stipi...
BAE57665  907 KCSDDQFRDRFRIDLMDPERSLGPevleqaneiagdvevqryldeeweqllkaraflrtvakedeemmqlpinvqril-- 984  Aspergillus oryza...
Q9AVW8    876 KMSDIEMNMVYKVTQSSPCFGLAIdssllflsnksynskianieynqllkdreflrklmldqndiniplpvnldrivska 955  Guillardia theta
O95602   1114 ------------------------------spgtqemlrmwyeldeesrrkyqkkaaacpdpslsvwrpdiyfasvsetf 1163 human
P17545    970 vnpgrli------------qnarstmgkrsqvsnlspitiidhvrklqedlmklfpsyhrggdgyirntlsreriesalt 1037 Trypanosoma bruce...
Q9NJR9    946 vnvarli-----------qnarttmgkrsqvsnlnrittvinrvrelqedlvqlfpsyhkdysgrfanvlsqqrveralt 1014 Leishmania donovani
Q9AXN0    955 drliwnvktlfnirqdsvsdlnprdilkgvqillsrcnvvalppksiklldegdgdqvaevdtnsvsrqlaveaqenatl 1034 Glaucosphaera vac...
P16356    982 ----------------------------wnaqkifkvdlrkpvnlsplhvisgvrelskkliivsgndeiskqaqynatl 1033 Caenorhabditis el...
P36594    969 -----------------------------nalqifhleakkptdllpsdiinglneliakltifrgsdritrdvqnnatl 1019 Schizosaccharomyc...
P04050    965 ----------------------------qnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavt 1016 Saccharomyces cer...
EED22237  986 ----------------------------esakttfhikegtisdlhpaevipqvqalldrlvivrgddviskeaqtsatl 1037 Talaromyces stipi...
BAE57665  985 ----------------------------emarttfriregtisdlhpaevipqvqalldrllivrgddpisqeaqenatl 1036 Aspergillus oryza...
Q9AVW8    956 -------------------------svlfknhknsslinfketirslkflrnyflelinfkisfnqkksdnkqlinrdnf 1010 Guillardia theta
O95602   1164 eTKVDDYSQEWAAQTEKSYEKSELSLDRLRTLLQLKWQRSLCEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTL 1243 human
P17545   1038 lFNVHLRQLLASKRVLKEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTL 1117 Trypanosoma bruce...
Q9NJR9   1015 lFGIHLRQILGSKRVLKEYKLNDKAFEYLLKEIRTKYQESLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTL 1094 Leishmania donovani
Q9AXN0   1035 lWSIHIRAFLASKVILKEYRLDKKAFMHLLGEIENRFLHAKCPPGEMIGAVAPQSIGEPATQMTLNTFHFAGVSAKNVTL 1114 Glaucosphaera vac...
P16356   1034 lMNILLRSTLCTKNMCTKSKLNSEAFDWLLGEIESRFQQAIAQPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTL 1113 Caenorhabditis el...
P36594   1020 lFQILLRSKFAVKRVIMEYRLNKVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTL 1099 Schizosaccharomyc...
P04050   1017 lFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTS 1096 Saccharomyces cer...
EED22237 1038 lFKAQLRSRLAFKRLVTQYSMNKLAFNHVLGAIEMRFARAQANPGEMVGVLAAQSIGEPATQMTLNTFHFAGVSSKNVTL 1117 Talaromyces stipi...
BAE57665 1037 lFKAQLRSRLAFRRLVTEYSMNKLAFQHVIGAIESRFAKANAPAGEMVGVLAAQSIGEPATQMTLNTFHFAGVSSKNVTL 1116 Aspergillus oryza...
Q9AVW8   1011 lLAIYIRSSLSLKIIYTKFNLNQHALNWIVNEICLSIRKSLIQPGEMVGTISAQSIGQPATQMTLNTFHFAGVSAKNVTL 1090 Guillardia theta
O95602   1244 GIPRLREILMVaSANIKTPMMSVPVLNTK-KALKRVKSLKKQLTRVCLGEVLQKIDVQESFCMEEKQNKFQVYQLRFQFL 1322 human
P17545   1118 GVPRLLELLNV-SRNQKHASMTVSLFPPY-DEKRNAQKAQHLIEYCTLESITRRIQFIYDPDPRHTVVEADRDILELEWN 1195 Trypanosoma bruce...
Q9NJR9   1095 GVPRLLELLNV-SKNQRNASVAVCLIREY-QKRNKAQEAQQFIEYCTLANITTTVQIIYDPDPRNTVVAEDEEMIRWEQA 1172 Leishmania donovani
Q9AXN0   1115 GVPRLKEIINV-AKHCKTPSLTVYLRGEAaRDAERAKQVQAELQHTTLNHVTQSTEIYYDPNPQDTVIEADQELVRSYYE 1193 Glaucosphaera vac...
P16356   1114 GVPRLKEIINV-SKTLKTPSLTVFLTGAAaKDPEKAKDVLCKLEHTTLKKVTCNTAIYYDPDPKNTVIAEDEEWVSIFYE 1192 Caenorhabditis el...
P36594   1100 GVPRLKEILNV-AKNIKTPSLTIYLMPWIaANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFA 1178 Schizosaccharomyc...
P04050   1097 GVPRLKEILNV-AKNMKTPSLTVYLEPGHaADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFS 1175 Saccharomyces cer...
EED22237 1118 GVPRLKEILNV-ATNIKTPSMTVYQEPHRkHDKESAKQLRSVVEHTSLRSVTEATEIYYDPDIQSTVIENDRDMVESYFI 1196 Talaromyces stipi...
BAE57665 1117 GVPRLKEILNV-ATNIKTPSMTVYQEPGRtHDKEGAKQLRSVVEHTSLRSVTEATEIYYDPDIQSTVIENDRDMVESYFI 1195 Aspergillus oryza...
Q9AVW8   1091 GVPRLKEIIDI-QKNIKSPSLTIFLHKKCsNDPRKVKKIQESIESVRLNRISNYFEIIYDPDFFFSISKCNRILVKNYME 1169 Guillardia theta
O95602   1323 PHAYYQQEKCLRPEDILRFMETRFFKLLMESIKKKnnkasafrnvntrratqrdldnagelgrsrgeqegdeeeeghivd 1402 human
P17545   1196 VMDESDAELRIQEVVAGSPWVVRLELDVDMV------------------------------------------------- 1226 Trypanosoma bruce...
Q9NJR9   1173 VMNEEDEEPDAEQPPSPFIARLILDNDLF--------------------------------------------------- 1201 Leishmania donovani
Q9AXN0   1194 LPDDENSSANLSPWLLRLNLSKEMMTDRKLSMNHV--------------------------------------------- 1228 Glaucosphaera vac...
P16356   1193 MPDHDLSRTSPWLLRIELDRKRMVDKKLTMEM------------------------------------------------ 1224 Caenorhabditis el...
P36594   1179 IPDEEVEENLYKQSPWLLRLELDRAKMLDKKLS----------------------------------------------- 1211 Schizosaccharomyc...
P04050   1176 LLDEEAEQSFDQQSPWLLRLELDRAAMNDKDL------------------------------------------------ 1207 Saccharomyces cer...
EED22237 1197 IPEDVADDSSRQSKWLLRIVLSRPKLLDKGLT------------------------------------------------ 1228 Talaromyces stipi...
BAE57665 1196 IPEDVTDDSSRQSKWLLRIILSRPKLLDKGLT------------------------------------------------ 1227 Aspergillus oryza...
Q9AVW8   1170 IPDEDINFLQASSWILKLKLLTEEFVEKGLFSNYIietikkkikpip--------------------------------- 1216 Guillardia theta
O95602   1403 aeaeegdadasdakrkekqeeevdyeseeeeeregeenddedmqeernphregarktqeqdeevglgteedpslpalltq 1482 human
P17545        -------------------------------------------------------------------------------- Trypanosoma bruce...
Q9NJR9        -------------------------------------------------------------------------------- Leishmania donovani
Q9AXN0        -------------------------------------------------------------------------------- Glaucosphaera vac...
P16356        -------------------------------------------------------------------------------- Caenorhabditis el...
P36594        -------------------------------------------------------------------------------- Schizosaccharomyc...
P04050        -------------------------------------------------------------------------------- Saccharomyces cer...
EED22237      -------------------------------------------------------------------------------- Talaromyces stipi...
BAE57665      -------------------------------------------------------------------------------- Aspergillus oryza...
Q9AVW8   1217 ----------------------------------------------------------------------fliiasdens 1226 Guillardia theta
O95602   1483 pRKPTHSQEPQGPEAMERRVQAVREIHPFIDDYQYDTEESLWCQVTVKLPLMKINFDMSSLVVSLAHGAVIYATKGITRC 1562 human
P17545   1227 ------TDKALDMKDVKQAILRVDESYIIETGMANNVRQRTIRMRSRYNEGADSIPKLKREIPALLARVHLRGIPGVRRA 1300 Trypanosoma bruce...
Q9NJR9   1202 -------NDKRLNMKDVKSAIRQVDDTYMVQANMENDGQRIVRLRPRKCTGADSVPALTKAVAQLLQSVHHRGIPGIKKT 1274 Leishmania donovani
Q9AXN0   1229 -KNKIHHDLGGDVNVMASEDNDANLVLRIRIAAQKEPEKMAEGEEHAQEEEEDECLFLRKVEGSLLSEMNLGGVPDIKKV 1307 Glaucosphaera vac...
P16356   1225 -----IADRIHGGFGNDVHTIYTDDNAEKLVFRLRIAGEDKGEAQEEQVDKMEDDVFLRCIEANMLSDLTLQGIPAISKV 1299 Caenorhabditis el...
P36594   1212 ---MSDVAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRV 1288 Schizosaccharomyc...
P04050   1208 -----TMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERV 1282 Saccharomyces cer...
EED22237 1229 -----VQDVATRIKEQYPRDIAVIFSDNNADEQVIRIRQLHDAKEDEDEEDMEYDVTLKKLEQHLLDTLTLRGVAGVERA 1303 Talaromyces stipi...
BAE57665 1228 -----VQDVATRIKQAYPKDIAVIFSDNNADEQVIRIRQIQDHKEDEDDDDIEYDVTLKKLEQHLLDTLTLRGVNGVERA 1302 Aspergillus oryza...
Q9AVW8   1227 gSIEFLVRFIWPEFINNYNSEKIEKLFSRSNANTFFEYIKRANQKVSENLFLEPNYFKKIKHYFYNYNLKPYGSQKLTKL 1306 Guillardia theta
O95602   1563 LLN--ETT-NNKNE--------------KELvlntegINLPE----LFKYAE--VLDLRRLYSNDIHAIANTYGIEAALR 1619 human
P17545   1301 LLK--DTT-EFTVDqatgk-----msgnKIWaidtdgTALRRafigVVGEDGknIINAVKTSSNKVPEVCSLLGIEAARS 1372 Trypanosoma bruce...
Q9NJR9   1275 LLK--EGN-TFRVDpetgg-----ikneSSWmvdtegTALQRifvgVVNNEGknIIDFSKTSSNKIPEVVTVLGIEAARR 1346 Leishmania donovani
Q9AXN0   1308 YMR--EAD-RIVPDprtgg-----lsveKEWvldtdgTNLLA----VMSHKD---VDYTRTVSNDVVEMFVTLGIEGVRA 1372 Glaucosphaera vac...
P16356   1300 YMNqpNTDdKKRIIitpeg----gfksvADWiletdgTALLR----VLSERQ---IDPVRTTSNDICEIFEVLGIEAVRK 1368 Caenorhabditis el...
P36594   1289 YMM--EHK-IVRQIedgt------feraDEWvletdgINLTE----AMTVEG---VDATRTYSNSFVEILQILGIEATRS 1352 Schizosaccharomyc...
P04050   1283 VMM--KYD-RKVPSptge------yvkePEWvletdgVNLSE----VMTVPG---IDPTRIYTNSFIDIMEVLGIEAGRA 1346 Saccharomyces cer...
EED22237 1304 FIN--EKD-NVRVMedgslfqsktdplcKEWvletsgSALAD----VLTIPG---VDTSRTYSNQFIEVFEVFGIEAART 1373 Talaromyces stipi...
BAE57665 1303 FIN--EKS-KVRVLedgslftskvdplcKEWvletsgSALGE----VLAVPG---VDATRTYSNQFIEVFEVFGIEAART 1372 Aspergillus oryza...
Q9AVW8   1307 YPR--RID-IIEPEpnqsg----klknnFEFvletegVDLRF----VMNYNG---IDYSRCTTNDLLESLKVLGIEATRK 1372 Guillardia theta
O95602   1620 VIEKEIKDVFAVYGIAVDPRHLSLVADYMCFEGVYKPLNRFGIRSNSSPLQ 1670 human
P17545   1373 KMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSDTSGP 1423 Trypanosoma brucei brucei
Q9NJR9   1347 KLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRSETSGP 1397 Leishmania donovani
Q9AXN0   1373 ALLNEIRGVISFDGAYVNYRHLAILADIMTCRGHIMSITRHGINRVETGAL 1423 Glaucosphaera vacuolata
P16356   1369 AIEREMDNVISFDGSYVNYRHLALLCDVMTAKGHLMAITRHGINRQEVGAL 1419 Caenorhabditis elegans
P36594   1353 ALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGAL 1403 Schizosaccharomyces pombe 972h-
P04050   1347 ALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGAL 1397 Saccharomyces cerevisiae S288C
EED22237 1374 AVLRELTQVLAFDGSYVNHRHLALLVDVMTVRGYLTPVTRHGINRADNGAL 1424 Talaromyces stipitatus ATCC 10500
BAE57665 1373 AVLRELTQVLAFDGSYVNHRHLALLVDVMTVRGYLTPVTRHGINRADNGAL 1423 Aspergillus oryzae RIB40
Q9AVW8   1373 ILIQELRNLISFDGSYVNYRHLCTLVDLITFRGSLMSINRHGINKCNSGPI 1423 Guillardia theta
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