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:
4C3H_A    989 GIKPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLTKQLEGVHVSYDNSIRDADGTLVQFMYGGDAIDITKESHMTQFEF 1068 baker's yeast
Q9AW39    935 GIHPNCYFFHCMAGREGLLDTAIKTSQSGYIQRNIIKHLENLKINYDFTLRMSHNKINSFIFSDDGQRITSIDFISKIRW 1014 Guillardia theta
O95602    958 GIKPPEFFFHCMAGREGLVDTAVKTSRSGYLQRCIIKHLEGLVVQYDLTVRDSDGSVVQFLYGEDGLDIPKTQFLQPKQF 1037 human
P15398   1002 GIAPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEGLCVQYDHTVRDSDGSIVQFHYGEDSLDVTKQKHLTQFEF 1081 Schizosaccharomyc...
P16356    824 GLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSLAQMVQLRYGEDGLDGMWVENQNMPTM 903  Caenorhabditis el...
3H0G_M    813 GLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEYQVFDSL 892  Schizosaccharomyc...
4V1M_A    807 GLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTI 886  baker's yeast
Q9AVW8    796 GLFPDEFFFHSMGGREGLIDTAIKTSETGYIQRRLSKSMEDIVVEYDFSVRNNQQEIISFLYGEDCFDAVYLENQKIFLG 875  Guillardia theta
Q98RN1    802 GLDSKEFFFHSMAGREGLIDTAVKTAEIGYLQRRLVKSLEDISIMNDSTVRDSFGRIYQFTFGGDNVNPENFSKFYSINS 881  Guillardia theta
BAB12227  827 GLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMVKYDGTVRNSLGDIIQFIYGEDGLDGAHIENQRVDII 906  Aspergillus oryzae
4C3H_A   1069 CLDNYYALLKKYNPSALIEHLDVEsalkyskktlkyrkkhskephyk--------------------------------- 1115 baker's yeast
Q9AW39   1015 KFQNSLRTENDDNNLFNNMKLNSNft------------------------------------------------------ 1040 Guillardia theta
O95602   1038 PFLASNYEVIMKSQHLHEVLSRADpkkalhhfraikkwqskhpntllrrgaflsysqkiqeavkalklesenrngr---- 1113 human
P15398   1082 SAKNYKSLIQKYKVKSVLSAVDSEtassyakkalkkpykydpvld----------------------------------- 1126 Schizosaccharomyc...
P16356    904 KPNNAVFERDFRMDLTDNKFLRKNysedvvreiqesedgislvesewsqleedrrllrkifprgdakivlpcnlqrli-- 981  Caenorhabditis el...
3H0G_M    893 RLSTKQFEKKYRIDLMEDRSLSLYmensiendssvqdlldeeytqlvadrellckfifpkgdarwplpvnvqriiq---- 968  Schizosaccharomyc...
4V1M_A    887 GGSDAAFEKRYRVDLLNTDHTLDPsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirrii-- 964  baker's yeast
Q9AVW8    876 KMSDIEMNMVYKVTQSSPCFGLAIdssllflsnksynskianieynqllkdreflrklmldqndiniplpvnldrivska 955  Guillardia theta
Q98RN1    882 FDFSLKLKKSTDNYLLYVFLRAHFlrff---------------------------------------------------- 909  Guillardia theta
BAB12227  907 KCSDDQFRDRFRIDLMDPERSLGPevleqaneiagdvevqryldeeweqllkaraflrtvakedeemmqlpinvqril-- 984  Aspergillus oryzae
4C3H_A   1116 ---------------------------------qsvkydpvlakynpakylgsvseNFQDKLESFLDKNSKLFKSSDGVN 1162 baker's yeast
Q9AW39   1041 ------------------------------------------------------kkNINFHKINFKQIISKRSCKKNFGS 1066 Guillardia theta
O95602   1114 -----spgtqemlrmwyeldeesrrkyqkkaaacpdpslsvwrpdiyfasvsetfeTKVDDYSQEWAAQTEKSYEKSELS 1188 human
P15398   1127 -----------------------------------kyppsrylgsvsekfqravdeYTQKNPDKLIASKKESKLDDSLLN 1171 Schizosaccharomyc...
P16356    982 ---wnaqkifkvdlrkpvnlsplhvisgvrelskkliivsgndeiskqaqynatllMNILLRSTLCTKNMCTKSKLNSEA 1058 Caenorhabditis el...
3H0G_M    969 ----nalqifhleakkptdllpsdiinglneliakltifrgsdritrdvqnnatllFQILLRSKFAVKRVIMEYRLNKVA 1044 Schizosaccharomyc...
4V1M_A    965 ---qnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlFCCLLRSRLATRRVLQEYRLTKQA 1041 baker's yeast
Q9AVW8    956 svlfknhknsslinfketirslkflrnyflelinfkisfnqkksdnkqlinrdnflLAIYIRSSLSLKIIYTKFNLNQHA 1035 Guillardia theta
Q98RN1    910 -----------------------------------------------------dslTFSINLRNKINFEKILNIKSNFGY 936  Guillardia theta
BAB12227  985 ---emarttfriregtisdlhpaevipqvqalldrllivrgddpisqeaqenatllFKAQLRSRLAFRRLVTEYSMNKLA 1061 Aspergillus oryzae
4C3H_A   1163 EKKFRALMQLKYMRSLINPGEAVGIIASQSVGEPSTQMTLNTFHFAGHGAANVTLGIPRLREIVMTaSAAIKTPQMTLPI 1242 baker's yeast
Q9AW39   1067 FVSYQNILNSNYFENLIEPGESTGILCGQAIGEPCTQMTLNTFHYAGKISSHGKQGLPRLKEM-----LLYNSKNSTNFL 1141 Guillardia theta
O95602   1189 LDRLRTLLQLKWQRSLCEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMVaSANIKTPMMSVPV 1268 human
P15398   1172 ESKFKALMQLRYQQSLVDPGESVGVLASQSIGEPSTQMTLNTFHFAGFGAKNVTLGIPRLREIIMTaSANIQTPTMTLRL 1251 Schizosaccharomyc...
P16356   1059 FDWLLGEIESRFQQAIAQPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKEIINV-SKTLKTPSLTVFL 1137 Caenorhabditis el...
3H0G_M   1045 FEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNV-AKNIKTPSLTIYL 1123 Schizosaccharomyc...
4V1M_A   1042 FDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNV-AKNMKTPSLTVYL 1120 baker's yeast
Q9AVW8   1036 LNWIVNEICLSIRKSLIQPGEMVGTISAQSIGQPATQMTLNTFHFAGVSAKNVTLGVPRLKEIIDI-QKNIKSPSLTIFL 1114 Guillardia theta
Q98RN1    937 FEILIKKYFQTFKLVIIDPGTGVGCISAQSLGEPGTQMTLQTFHSAGTGSQNITSGIPRINEI----LSNSKNTKFPLIS 1012 Guillardia theta
BAB12227 1062 FQHVIGAIESRFAKANAPAGEMVGVLAAQSIGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEILNV-ATNIKTPSMTVYQ 1140 Aspergillus oryzae
4C3H_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 Schizosaccharomyc...
P16356   1138 TGAAaKDPEKa---kDVLCKLEHTTLKKVTCNTAIYYDPDPKNTVIAEDEEWVSIFYEMPDHDLSRTSPWLLRIELDRKR 1214 Caenorhabditis el...
3H0G_M   1124 MPWIaANMDLa---kNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLEL 1200 Schizosaccharomyc...
4V1M_A   1121 EPGHaADQEQa---kLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLEL 1197 baker's yeast
Q9AVW8   1115 HKKCsNDPRKv---kKIQESIESVRLNRISNYFEIIYDPDFFFSISKCNRILVKNYMEIPDEDINFLQASSWILKLKLLT 1191 Guillardia theta
Q98RN1   1013 YDINfFEFNKkksrlKFF--LKKIKIGFLINSIEIFLHRGFVSVKIHFIKKIYEYLDQSKIYYFIIKKFHDNTK------ 1084 Guillardia theta
BAB12227 1141 EPGRtHDKEGa---kQLRSVVEHTSLRSVTEATEIYYDPDIQSTVIENDRDMVESYFIIPEDVTDDSSRQSKWLLRIILS 1217 Aspergillus oryzae
4C3H_A   1318 SNQFIHLLEAAIVkeikkqkrttgpdigvavprlqtdvansssnskrleedndeeqshkktk------------------ 1379 baker's yeast
Q9AW39   1222 HKNVMINYKN---------------------------------------------------------------------- 1231 Guillardia theta
O95602   1345 RFFKLLMESIKKKnnkasafrnvntrratqrdldnagelgrsrgeqegdeeeeghivdaeaeegdadasdakrkekqeee 1424 human
P15398   1327 RFLKILNRIIKSYlakskqrksggkddtvpevgqalkpledideapiegraqealededndatnekmv------------ 1394 Schizosaccharomyc...
P16356   1215 MVDKKLTMEM---------------------------------------------------------------------- 1224 Caenorhabditis el...
3H0G_M   1201 DRAKMLDKKLS--------------------------------------------------------------------- 1211 Schizosaccharomyc...
4V1M_A   1198 DRAAMNDKDL---------------------------------------------------------------------- 1207 baker's yeast
Q9AVW8   1192 EEFVEKGLFSNYIietikkkikpip------------------------------------------------------- 1216 Guillardia theta
Q98RN1        -------------------------------------------------------------------------------- Guillardia theta
BAB12227 1218 RPKLLDKGLT---------------------------------------------------------------------- 1227 Aspergillus oryzae
4C3H_A   1380 ----------qavsydepdedeietmreaekssdeegidsdkesdsdsededvdmneqiNKSIVEANNNMNKVQRDRQSA 1449 baker's yeast
Q9AW39   1232 ---------------------------------------------------------------PFKRLFNNNGDTKIFLN 1248 Guillardia theta
O95602   1425 vdyeseeeeeregeenddedmqeernphregarktqeqdeevglgteedpslpalltqpRKPTHSQEPQGPEAMERRVQA 1504 human
P15398   1395 -----srskqhasyegpdeadkvalrqlkgsnkvedvnmdeeedegfksdesvsdfkerKLLEKQNTVSISERRELQLKT 1469 Schizosaccharomyc...
P16356   1225 ---------------------------------------------------------------IADRIHGGFGNDVHTIY 1241 Caenorhabditis el...
3H0G_M   1212 -------------------------------------------------------------MSDVAGKIAESFERDLFTI 1230 Schizosaccharomyc...
4V1M_A   1208 ---------------------------------------------------------------TMGQVGERIKQTFKNDL 1224 baker's yeast
Q9AVW8   1217 ------------------------------------------------fliiasdensgSIEFLVRFIWPEFINNYNSEK 1248 Guillardia theta
Q98RN1   1085 -------------------------------------------------------------------------------I 1085 Guillardia theta
BAB12227 1228 ---------------------------------------------------------------VQDVATRIKQAYPKDIA 1244 Aspergillus oryzae
4C3H_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 Schizosaccharomyc...
P16356   1242 TDDNAEKLVFRLRIAGEDKGEAQEEQVDKMEDDVFLRCIEANMLSDLTLQGIPAISKVYMNqpNTDdKKRIIitpeggfk 1321 Caenorhabditis el...
3H0G_M   1231 WSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRVYMM--EHK-IVRQIedgtfera 1307 Schizosaccharomyc...
4V1M_A   1225 FVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMM--KYD-RKVPSptgeyvke 1301 baker's yeast
Q9AVW8   1249 IEKLFSRSNANTFFEYIKRANQKVSENLFLEPNYFKKIKHYFYNYNLKPYGSQKLTKLYPR--RID-IIEPEpnqsgklk 1325 Guillardia theta
Q98RN1   1086 IKKSTVFICKKKKNVVLQFHKNDFKIDDFNLNFINLYNFFRIHFGDIVLTGFYESSKINCN------FLFnnlei----- 1154 Guillardia theta
BAB12227 1245 VIFSDNNADEQVIRIRQIQDHKEDEDDDDIEYDVTLKKLEQHLLDTLTLRGVNGVERAFIN--EKS-KVRVLedgslfts 1321 Aspergillus oryzae
4C3H_A   1522 -------------egVNFQAMWDQEAFIDVDGITSNDVAAVLKTYGVEAARNTIVNEINNVFSRYAISVSFRHLDLIADM 1588 baker's yeast
Q9AW39   1306 ---------------FSLSE------FFKIDEIFTSDILKMSIIFGIEAGREILTIELMNIFKNQGIVISNKHIDTISDY 1364 Guillardia theta
O95602   1579 -----------ntegINLPELFKYAEVLDLRRLYSNDIHAIANTYGIEAALRVIEKEIKDVFAVYGIAVDPRHLSLVADY 1647 human
P15398   1544 ------------tegVNLKAIWEFYNEISMNDIYTNDIAAILRIYGVEAARNAIVHEVSSVFGVYGIAVDPRHLSLIADY 1611 Schizosaccharomyc...
P16356   1322 sv----adwiletdgTALLRVLSERQ-IDPVRTTSNDICEIFEVLGIEAVRKAIEREMDNVISFDGSYVNYRHLALLCDV 1396 Caenorhabditis el...
3H0G_M   1308 d------ewvletdgINLTEAMTVEG-VDATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDV 1380 Schizosaccharomyc...
4V1M_A   1302 p------ewvletdgVNLSEVMTVPG-IDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDV 1374 baker's yeast
Q9AVW8   1326 nn----fefvletegVDLRFVMNYNG-IDYSRCTTNDLLESLKVLGIEATRKILIQELRNLISFDGSYVNYRHLCTLVDL 1400 Guillardia theta
Q98RN1   1155 -----------kisdNRFDILLNIPG-IIFRKLYCNNINSIYNFLGIEASRELIVLEITNTFKSHGIFSDNRHVYLLADY 1222 Guillardia theta
BAB12227 1322 kvdplckewvletsgSALGEVLAVPG-VDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDV 1400 Aspergillus oryzae
4C3H_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
Q9AVW8   1401 ITFRGSLMSINRHGINKCNSGPI 1423 Guillardia theta
Q98RN1   1223 MTFNGFIIGINREGLTCNKESVF 1245 Guillardia theta
BAB12227 1401 MTVRGYLTPVTRHGINRADNGAL 1423 Aspergillus oryzae
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