Conserved Protein Domain Family
RNA_pol_Rpb1_6

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pfam04992: RNA_pol_Rpb1_6 (This model is not part of the current CDD release)
RNA polymerase Rpb1, domain 6
RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Statistics
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PSSM-Id: 516555
Aligned: 109 rows
Threshold Bit Score: 115.31
Created: 14-Feb-2025
Updated: 28-Apr-2025
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:
XP_001007918  884 LAGEFIE-TQKIGEVDYKEEDFQKEYRFvkanksdDWlfqytkldqmenqIskEISRDVLI----------AIKEEFmrM 952 
A0BYP5        879 MAAEFIE-HQEIKCVNLSNAQLEEKYEL-------IKeqwfgseirqkyqN--------------------ILTEDVikD 930  Paramecium te...
XP_004027344  336 LAGEYIE-TQKIAEIEYSNEQFEKEYRFi-----------------------rDFENQVSIkeflereyerKLNKDVisE 391 
XP_001467585  852 LDGARIEgNQAFPIPHMTNSEMADKYRY-------EY-------------NdeGSFSENMGg--------hYMDPFVrdS 903 
Q57YU2        875 LDGARIEgGQLFPLPFRDDKEMEDTYKY-------EY-------------DvdGTFSGKVGg--------nYMDPHVrkM 926  Trypanosoma b...
Q4DDX5        859 LDGARIEgGQLFPLPFRDNKEMESTYKY-------EY-------------DetGAFNEKVGg--------aYMDPHVkkM 910  Trypanosoma c...
Q7T6X5        869 GINTENQvDQKIDLISANDNKVRNDYVYt-----------------------eDEIKYLIKn------------------ 907  Acanthamoeba ...
XP_001580050  891 LDATGLE-TQRLALVTLNDEDFMKKYHL-------AT-------------E--DPTFGQV-----------EMDDFVldE 936 
XP_002674498  860 MDAHKVE-SQSIDIMNLSDAKFQDKYWY-------NSlgs--------spSftNPTESSVSmpsggilkesFISTKVydE 923 
XP_002674726  864 MDPIKLE-SQSFEMLSLSDEIFEEKYKWstkledhNI------------------------------------PESDlnE 906 
XP_001007918  953 ineRNEGEdPKFI-----LEQEYEELIEARNLFRKNFYFyaQe---GKLDinLPVNIGRMIESAKIEMSQknktYTRDQ- 1023
A0BYP5        931 i--EEDFE-GQAL-----LKGEFDEIKKIRNELRRLFLIdsApkeeLFTHyyLVVNIERIISTIKINKKI----SDREK- 997  Paramecium te...
XP_004027344  392 i--DESARqSRQKyepfcLEEEYRDLLEARDLFRKCFYFysFk---QSLDlnIPVNIDRMLRSTKIEMSKnnriYDKDE- 465 
XP_001467585  904 l--LRDPQ-SVLK-----LQEEFEQLMKDRAMSRLVIDMed----kNKLKmnLPVNVARLIQNARTTMGK------RSQv 965 
Q57YU2        927 l--RADPQ-NVRK-----LQEEYEQLTADREWSRKMLDLed----rDKLKlnLPVNPGRLIQNARSTMGK------RSQv 988  Trypanosoma b...
Q4DDX5        911 l--RADPE-NVRK-----LQSEFDQLMADRDWARRMMDLee----rEKLKlnLPVNIGRLIQNARSTMGK------RSQv 972  Trypanosoma c...
Q7T6X5        908 --hKTDKRyTTDL-----NNSLYRKLISMRDQLRRIQRLvnLtsaeFKETykMPVDIQQFIFNIINR-------DVRNNn 973  Acanthamoeba ...
XP_001580050  937 f--LKTPN-KDKF-----LKEEENRLREYREILQKEIFPngS----NTVV--VPVNIARIIESSQRQFDI----NVHVSk 998 
XP_002674498  924 i--LKDPAtYLSK-----VREEYKTLMEDRHILRTEIFPnaE----NKIV--MPVNLKRIIKNAQKEYGIhp--siGKP- 987 
XP_002674726  907 i--SLDFAnYLMK-----LNDEYKKLQEYRHLVRDEILQsvD----SKIV--FPVNLSRLIKRVQREYGRkhs-tfNNS- 971 
XP_001007918 1024 CKTNPIQVYKSLLELF-KNLD--------------DYAVKRGMEYESLALFKAHIRLHLGSKKIVLRHKLSMEVFDKLTK 1088
A0BYP5        998 CRLNPIYVTQQVDELI-QKVDkl-------------lsYDLEERKDCINLFRTHLKVSLASKDLCCRHRLTPEAFQELIS 1063 Paramecium te...
XP_004027344  466 SRLSPIYVYRVINELF-TKLD--------------NDAINRGVDPNALMLFKAHVRLHLSSKKIVIKHKINKEKFEQLVR 530 
XP_001467585  966 SNLNPITVINRVRELQ-EDLAqlfpsyhkdyngrfANVLSQQRVERALTLFGIHLRQILGSKRVLKEYKLNDKAFEYLLK 1044
Q57YU2        989 SNLSPITIIDHVRKLQ-EDLMklfpsyhrggdgyiRNTLSRERIESALTLFNVHLRQLLASKRVLKEYKLNDRAFEYLLK 1067 Trypanosoma b...
Q4DDX5        973 SNLSPVTIIDHVRKLQ-EDMLklfpcyhkgvdgriHNLLSRQRIENALTLFSVHLRQLLASKRVLREYKLNDKAFEYLLK 1051 Trypanosoma c...
Q7T6X5        974 VVVDPYYVLKMIKDMYyGSDSkimk------ynnrTSRIKKEDEKRIKFLMKIYLYDVLAPKKCTHVYKFSKQEFDEIVD 1047 Acanthamoeba ...
XP_001580050  999 SDLNPLDIISRVDECV-NSLIvv----------kgNDNISRTEQENATLLLRIMLYSHLSAKQCIFEYRLNEQAFKYILG 1067
XP_002674498  988 SDMNPIYVIEKIKKLC-DDLVvi----------kgTDELSTEAQTNATLLFSMFLRSTFSSKVVLKELCLTQEAFDFLVG 1056
XP_002674726  972 SDLNPLYVIKKVNSTC-EELLii----------kgKDKLSEEAQRNAILLFSIFLKFSLASKVVMNELNLTRESLEYLLG 1040
XP_001007918 1089 EIFDKFKKA 1097
A0BYP5       1064 EIIYKLKKS 1072 Paramecium tetraurelia
XP_004027344  531 EVEARYKQA 539 
XP_001467585 1045 EIRTKYQQS 1053
Q57YU2       1068 EIRTKYHQS 1076 Trypanosoma brucei
Q4DDX5       1052 EIRTKYLQS 1060 Trypanosoma cruzi
Q7T6X5       1048 -----YFKK 1051 Acanthamoeba polyphaga mimivirus
XP_001580050 1068 SIKDRFYRS 1076
XP_002674498 1057 EIRMRFHNC 1065
XP_002674726 1041 EVKYTFLNG 1049
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