1CEZ


Conserved Protein Domain Family
RPOL_N
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pfam14700: RPOL_N (this model, PSSM-Id:291372 is obsolete and has been replaced by 464270)
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DNA-directed RNA polymerase N-terminal
This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex.
Links
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Statistics
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PSSM-Id: 291372
Aligned: 189 rows
Threshold Bit Score: 101.86
Created: 27-Jun-2015
Updated: 5-Aug-2015
Structure
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Program:
Drawing:
Aligned Rows:
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PubMed ReferencesClick to see Conserved Features Help
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
1CEZ_A         35 EQLALEH------E------SYEMGEARFRKMFERQLkagevadnaaakplittllpKMIARINDWFEEVKAKRGKRPTA 102  Enterobacteri...
XP_006101869  391 QQLSVEMativtvD------SVEKAPSLTEEVLQARk--------------------TLQELRTRWEAELCLALQQTKAR 444  little brown bat
XP_005331993  385 QQLHVELttsvyiQ------SVEKAPSLTKEMLQARk--------------------TLKALRAQWEAALRRVLQETKAS 438  thirteen-line...
XP_005209315  391 QQLGVEMattvtvE------SVEKAPLLTEEVLQARk--------------------TLAALRAEWESVLSLELQETKES 444  cattle
XP_003735468  395 QQLRVELastvcvK------SVEKPVAQSKEVRRARE--------------------TLKVLRLQWEKALYEALQETKER 448  white-tufted-...
EGV99464      370 QQLHVEL------SanvcvqSVEKAPVMTKEVIEARk--------------------TLKTLQGQWEAELLRVLQQTKAT 423  Chinese hamster
XP_010600150  397 QQLRVELattvqvQ------SVDKAPPLTSEVLHARE--------------------TLRSLQAQWEAALCQELQEIKAN 450  African savan...
NP_001100236  366 lqdlfyqqlhvelsssvsvqsveeAPVMTKEVIEARk--------------------TLKALRSKWEVELLRVLRETKAK 425  Norway rat
XP_004778191  397 QQLRVEMattvavE------SVEQARVLTEEVLRARn--------------------TLQQLRAEWVEALCLGL------ 444  domestic ferret
XP_004866078  486 QQLSVELasivhvE------SVEKTLSPTQETLEARk--------------------TLAALHTTWESELHSQLQKAKAH 539  naked mole-rat

1CEZ_A        103 FQ-------------------FLQEIKPEAVAYITIKTTLACLTSADntTVQAVASAIGRAIEDEARFGRIRDleakhfk 163  Enterobacteri...
XP_006101869  445 eaqaare-------grpslfpYLCLLSEGELTQLMLQTLQVLSQQGE--SLLSLAQELGMRIFNRHVVQRKQlndevqal 515  little brown bat
XP_005331993  439 LAhqaheg-------rpslfpFLCLLSERELVRMLLQALYALPAQGE--SLVVVAKDLGLRTFNRHMVQQKRlnnqvqal 509  thirteen-line...
XP_005209315  445 EAraaaeg-------rpslfpYLCLLSEKELVGLLLQTLQALPSHGE--SLFFLAHELGVRVlkrkrlrnqveeleqryf 515  cattle
XP_003735468  449 LEreahtg-------lpsmfpFLCLLGEQEMVQMLLQALQALPAQGEsf--mgLARDLGARTFSRHEVQRQQfsgqveal 519  white-tufted-...
EGV99464      424 MAhqaqeg-------qptlypFLCLLSEGEFVSMLMQVLRLLPAQGE--PLLHLAHDLGLRVLNRHLVKQKQAtnhvqkl 494  Chinese hamster
XP_010600150  451 LArtahgg-------rptlypHLCLLSERQMAQMLLQVLQVLPPQGE--SLIHLAHELGMRTFNRYVVQRKQRehqvqal 521  African savan...
NP_001100236  426 MGsqayeg-------qptlypFLCLLSEGEFVSILMQALQVLPAQGE--PLFQLAQNLGLQVFNRHLVKQKQvtnhvqkl 496  Norway rat
XP_004778191  445 -RnlkasevcaartgrpsvfpFLCVLPEKELAELLLQALQVLPPQGE--SLLSLAQQLGMRVFGRHAVRRQQRssrlqal 521  domestic ferret
XP_004866078  540 LAkvtsyg-------hptlypFLCTVPEDELVQMLLQFLHTMPAQGE--PFVYVVHRLAMQTFQRHIVQQrrcrgqllal 610  naked mole-rat

1CEZ_A        164 knveeqlnkrvghvykkaf--mqvveadmlskgllggeawsswhkeDSIHVGVRCIE----------MLIESTGMVSLHR 231  Enterobacteri...
XP_006101869  516 qeryfkylhllasdtqvv--msrlprqhwealgtteasqdqpwpltVVVQLGKQLAE----------VLVQTVKMPSNLA 583  little brown bat
XP_005331993  510 eqryaqylhllacdtqva--spclprqyweslgppeappqqpwplpVLMQLGKQLAE----------MLVQAVHMPLGLA 577  thirteen-line...
XP_005209315  516 eylhllasdtq-------vaepclprqhwealgvpeappeqpwpvsVLVQLGKQLAE----------VLVRAVQMPSSLA 578  cattle
XP_003735468  520 krhyrqylhllaadtevp--epylprqywealgvseppqeqpwplpVQVELGRLLAE----------ILVQATKMPSNLA 587  white-tufted-...
EGV99464      495 gqhysqylrllasdtqvea--pclpreyweslgpletpmqqpwsltVLLHLGKQLAE----------MLVQAVQMPRNLs 562  Chinese hamster
XP_010600150  522 qrryseylrllacdtqvdpprlprqhwemlggpggepppeqpwplpVLLQLGKQLAE----------VLVRAVHMPRNLG 591  African savan...
NP_001100236  497 gqqysqylrllasdtqva---pclpreywdslgsletpaqqpwsvpVLLQLGKQLAE----------LLVQAVQMPRSLa 563  Norway rat
XP_004778191  522 qeryyqyvrllasdtqvea--pqlprqywealgppeapheqpwplsVLVQLGKKLAE----------MLVEAVRMPGSVA 589  domestic ferret
XP_004866078  611 eqrymqylqllasdtq------------vaepclprqhwetlgppepappqvwpLMEllslgkllleILVQSVQLPPSLA 678  naked mole-rat

1CEZ_A        232 qna------------------gvvGQDSETIELAPEYAEAIaTRAGALAGIs--P--MFQPCVVPPKPWTGITGGGYWAN 289  Enterobacteri...
XP_006101869  584 qqqdtqklip----vlyhvysfqsFRQIGILKPHPAFIQ-L-QETAAERTMt--FesAEVPMLCPPLPWTSPHSGAFLLS 655  little brown bat
XP_005331993  578 vpqgscrpip----vlyhvysfrsYRQIGILKPHPAFTQLL-V-AAADPTLt--FetVDVPMLCPPLPWTSPHTGAFLLS 649  thirteen-line...
XP_005209315  579 aprgpstlip----vlyhvysfrsFRQIGILKPHPAFTQ-L-QETAAERTLi--FesTEVPMLCPPLPWTSPHSGAFLLS 650  cattle
XP_003735468  588 kprnssrlvp----llyhvysfrnVYQIGFLKPHPAYVQLL-AT-AAEPTVt--FeaVDVPMLCPPLPWTSPHTGAFLLN 659  white-tufted-...
EGV99464      563 tpqasrhlip----vlyhvysfrsYRQIGILKPHPAFSKLL--ETAAEPTLileT--TEVPMLCPPLPWTTPHTGAYLLS 634  Chinese hamster
XP_010600150  592 apagkgagteplipvlyhvysfrsVRQIGILKPHPAFSQLL-A-AAAEPTLt--FeaAEVPMLCPPLPWTSPHSGAFLLS 667  African savan...
NP_001100236  564 arhgaqnfip----vlyhvysfrsYRQVGILKPHPAFTHLL--ETAAEPTLt--FetTEVPMLCPPLPWTSLHSGAYLLS 635  Norway rat
XP_004778191  590 apqgpgtlip----vlyhvysfrsFRQIGILKPHPAFIELL-AT-AAEHTLt--FeaAEVPMLCPPLPWTSPHTGAFLLS 661  domestic ferret
XP_004866078  679 lpqssssqpvp---vlyhvytfrgIRQIGFLRPHPAFIQLL--DDAAEPLMi--FeaTDMPMLCPPLPWASSQSGGFLLS 751  naked mole-rat

1CEZ_A        290 GRrplALVRTHS---------KKAlmryedvYMPEVYKAINIAQ 324  Enterobacteria phage T7
XP_006101869  656 PT---KLMRSLEgtiqhqrllEGCpp----tELHGALDALTQLG 692  little brown bat
XP_005331993  650 PT---KLMRAVEgttqhqrllERCpp----tNLHGALDTLTQLG 686  thirteen-lined ground squirrel
XP_005209315  651 PT---KMMRSLEgtqqhqlllERCpp----aELHGALDALTQLG 687  cattle
XP_003735468  660 PT---KLMRAVDgtmhhqrllENCpp----aaLHGALDTLTQLG 696  white-tufted-ear marmoset
EGV99464      635 ST---KLMRATEgttqhqhllERCap----aQLHGALDALTQLG 671  Chinese hamster
XP_010600150  668 PA---KLMRAVEgtmlhqqrlEHCpp----aaLHGAFDALTQLG 704  African savanna elephant
NP_001100236  636 ST---KIMRATEgttqhqrllERCpp----aQLHGALDALTQLG 672  Norway rat
XP_004778191  662 PT---KLMRSLEgtvqhqrllDSCpp----aDLHGALDALTQLG 698  domestic ferret
XP_004866078  752 PT---KLMRSVDgslqhqnllDSWpp----tELHGALDTLTQLG 788  naked mole-rat
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