Conserved Protein Domain Family
POLBc_Pol_II

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cd05537: POLBc_Pol_II 
Click on image for an interactive view with Cn3D
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Statistics
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PSSM-Id: 99920
View PSSM: cd05537
Aligned: 17 rows
Threshold Bit Score: 569.977
Threshold Setting Gi: 162453773
Created: 11-Sep-2007
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
active sitemetal-binding
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:Based on similarity to bacteriophage RB69 POLBc (1Q9Y)

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                             #  ###                                                    
1Q8I_A      397 HASPGGYVMDSRPGLYDSVLVLDYKSLYPSIVRTFLIDPVGLVEgmaqp----------------dpehsTEGFLDAWFS 460
gi 87119943 393 IASPGGFVMSSKPGLYKNVLVFDFKSLYPSIIRTFLIDPFARVKpsd---------------------rrVEGFLGASYD 451
gi 94500920 398 FKAPGGLVLDSKPGLYKDVLVLDFKSLYPSIIRTFKIDPLGLIEglkaqqe-------------ghsedcIAGFHDAFFH 464
gi 89094696 395 LSAPGGYVMDSKPGLYRQVLVLDFKSLYPSIIRTFKIDPYGLAEglktsv---------------paddlIPGFNHAIFS 459
gi 71279212 413 LVSPGGYVMDSKPGLYKNVLVLDFKSLYPSIIRTFKIDPMGLIEglkavseqksahskseklsddcfddvIRGFDGAYFS 492
gi 24373385 419 IESPGGYVMDSVPGFYQHILVFDFKSLYPSIIRTFLIDPKGLIEglgddsl------------vldesetVTGFLGARFS 486
gi 91793780 437 IESPGGYVMDSVPGFYKDVLVLDFKSLYPSIIRTFLIDPKGLVTgmqer-----------------peqtVPGFLGASFS 499
gi 88857892 397 FNSPGGYVMNSQPGLYQNVIVLDFKSLYPSIIRTFLIDPIGMVEglla------------------ptqsIAGFHDAYFS 458
gi 77360914 425 FESPGGYVMESTPGLYKNVLVLDFKSLYPSIMRTFCIDPLGLIEglns------------------pekaVAGFNDALFS 486
gi 88798884 397 SSSPGGHVMDSTPGIYRDVIVLDFKSLYPSIIRTFLIDPMGLLEglnad-----------------eaesIPGFLGARFH 459
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                       #               #   #                                           
1Q8I_A      461 RekhCLPEIVTNIWHGRDEAKRQGnkpLSQALKIIMNAFYGVLGTTaCRFFDPRLASSITMRGHQIMRQTKALIEAQ-GY 539
gi 87119943 452 KdsgILPDLISELAQAREQAKQEDnqiLSYAIKIIMNSFYGVLGSNlCRFYHPELASSITMRGHQILNLTKAWFEEA-QA 530
gi 94500920 465 RekhFLPNIITQLWAERDLAKKRNdaaQSYAIKIIMNSFYGILGSTgCRFFDARLASSITERGHSIINQSATWIEQQ-GF 543
gi 89094696 460 RsktILPELIERLWAARDQAKQSSnsaLSQAIKIIMNSFYGVLGSNvCRFFDQRLSSSITLRGHEILIKTRDIIEEEfGF 539
gi 71279212 493 RtehFLPDIIKSLWLERDKAKLQKdaaLSQAIKIIMSSFYGVLGSTgCRFFDPRLSGSITKRSHEILKKTSVWIEKL-GY 571
gi 24373385 487 RrqpILPKLIQTLSEQREKAKREAnapLSQAIKIIMNSLYGVLGSQgCVFHDAKLASSITMRGHQIMKQTRAWIEEM-GY 565
gi 91793780 500 RespILPTLIASLAAQRELAKLDKnnpLSHAIKIIMNSLYGVLGSKgCVFHDAKLASSITMRGHEIMKQTRRWIEDL-GY 578
gi 88857892 459 RtahHLPNLIATLWQARDVAKQQKnkmLSQAIKIIMNSFYGVLGSTgCRFYDPRLSSSITLRGHEIMLATRAEIERL-GY 537
gi 77360914 487 RelhHLPKLIKHLTRTRQKAKDTNqpmLSQAIKIIMNSLYGVLGSKgCRFYDPRLSSSITLRGHEIMQTTRKWIEEL-GY 565
gi 88798884 460 RtrhILPGLIDQLWAARDQAKREQnapMSQAIKIIMNSFYGVLGSPlCRFFDPRLASSITMRGHDILQRSSEFIESQ-GY 538
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1              #                                                                        
1Q8I_A      540 DVIYGDTDSTFVWlkg------ahsEEEAAKIGRALVQHVNAWWAETLQKqrl-tsaLELEYETHFCRFLMPTIRGADt- 611
gi 87119943 531 EVIYGDTDSLFVVfedp-----glsDAKIRDKGKQLCSEINQKWKTWCLQtyqvdcyLELEFERMYNRFFMPTIRGQAe- 604
gi 94500920 544 QVIYGDTDSVFVSlhtgngniidvdHSIAQQIGNQLSDGLNQYWRHKLQHefgldshLEIEFENHYGDFLMPTIRGSDk- 622
gi 89094696 540 KIIYGDTDSVFVWlgd------dfpESQADGKGSELASFLNKWWQDNLEErfqlksqLEIEYETHYCRFLMPTMRHSDk- 612
gi 71279212 572 QVIYGDTDSIFVSiga------ektKTQAKQLGAELRSYINDKWQNRLKRdfdiesqLDIEFETHFTKFLMPTIRGIHtv 645
gi 24373385 566 QVIYGDTDSTFVHlgy------epdLSDISALGKQIAAQINANWQAKITKdfelesfLELQFERHYEQFFMPTLRGSEe- 638
gi 91793780 579 QVIYGDTDSTFVWlge------nhdINNINEFGLNIARQITQQWQQKCAEefniesfLELEFETHYSQFVMPTLRGSEe- 651
gi 88857892 538 QVIYGDTDSTFVQlas------elsAEECKKIGFLLQKKINNFWCDYCEKkykiasyLEIEFETLYSPFFMPTIRGSLe- 610
gi 77360914 566 EVIYGDTDSIFVKvne------rlnATQCNEIGNDVMQVINKRWSDSIKTrfsltsyLEIEFETHYSPFFMPTIRGKKi- 638
gi 88798884 539 PVIYGDTDSLFIHar---------nHAEPKRLGRELADQLNEWWRSLLQEsyglasqLEMEFETHYSRFVMPTIRGTDk- 608
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       
1Q8I_A      612 ------GSKKRYAGLiqe-gdkQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRne----pYQEYVRETIDKLMAGELDA 680
gi 87119943 605 ------GSKKRYAGLa-----eGELIFKGLEAVRSDWTPFARHFQKALFEKLFNde----sPEAFIKEIVEALYQGKFNE 669
gi 94500920 623 ------GSKKRYAGLls----sGELVFKGLEAVRSDWTELAKHIQKELYRLVFEgk----dYHVFIQSTVQELLQGKWDH 688
gi 89094696 613 ------GTKKRYAGMkrsadgtDHMVFKGLENVRTDWTMLARKLQEQLYERVFLgq----eWKPLLKSTVESLLAGELDE 682
gi 71279212 646 kdqksiGTKKRYAGVs-----dGELVFKGLETVRSDWTDLSKDFQQELYRLIFNdq----pIEGYIKKIVDELKQGLHDE 716
gi 24373385 639 ------GSKKRYVGAwrnvsgeLEITFKGMEQVRSDWSPLARKVQAELYERMFNqr----dISGYLADVIGELQAGKRDD 708
gi 91793780 652 ------GSKKRYVGAkvneqgeMSLVFKGMEQVRSDWSPIARRIQYLLYEKLFTge----dPVNFIEQELDALKQGLRNS 721
gi 88857892 611 ------GSKKRYVGQvsd-angDHLVFKGMETVRSDWTELAREFQYNLFTLIFAgd----sVEVYIKQVISDLMAGRLNH 679
gi 77360914 639 ------GSKKRYVGQidk-nnaKQLIFKGMETVRSDWTQFAQEFQTELFKTLFDqqfeieqLNNIIKSYTKKLYAGEFDK 711
gi 88798884 609 ------GSKKRYAGWieg-dgePRLVFKGLEAVRSDWTPMAKAFQHRLYRCVFQee----dYRQVIRSTVQQLHAGELDA 677
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       
1Q8I_A      681 RLVYRKRLRRPLSEYQRNVPPHVRAArLADEENQkrgrplqyqn-rgtikyvwttNGPEPLDYqr--sPLDYEHYLTRQL 757
gi 87119943 670 QLVYQKRLSRPLSEYTKVTPPHVRAArIADQRRMalgvkpefdqgrqsvqyfystQGVEPYTDskdlnNLDYDHYLEKQI 749
gi 94500920 689 ALVYKKRIRKPLNHYKKNIPPQIQAAiAAEPIYQkrnqinpyen-ggwiryvitqQGPMALECan-nlPLDYEHYVDKQI 766
gi 89094696 683 QLVYRKRIRQPLDQYVKNKPPHVQAGlKAEHIYKerglnspfsa-gsyieylmtvNGPEPIEFss--sPIDYQHYLDKQL 759
gi 71279212 717 KLIYKKKIRRKLSDYVNTPPHIKAAL-LANQKLKelgdkptykh-rsliryvitlDGVQPLEFnt--sKLDYDFYVEKQL 792
gi 24373385 709 ELIFSKRMRRNLEEYTAKSSPHVKVArQLCELTGkasyskrga----qidyvitvNGPEPVSHrs--sTIDYQYYIDKQI 782
gi 91793780 722 ELVFRKRLKRNIEDYTAKSSPHVKAAaLRCAATGdesfgrkga----nveyvmtkQGARVIQSak--lDYDYDYYIEKQI 795
gi 88857892 680 LLLYKKRLRQHLSEYVKNIPPHAQAAqKMSMKYPektpkrgq-----wieyvitlDGPVVATEkp--lKLNLQHYLEKQL 752
gi 77360914 712 KLIYRKRLGQNLSDYVKNIPPHVQAVkKFKANNPdfdvkrgq-----iieyvyaiNGAEIYNAn---nTLNYPLYIQRQL 783
gi 88798884 678 ELVYRRRLRRQIDQYEKQAPPHVQAArLKKQHNPnwfgrti--------eyvktvQGWQPLPYvs--aPLDYTHYIEKQL 747
                       410
                ....*....|..
Feature 1                   
1Q8I_A      758 QPVAEGILPFIE 769
gi 87119943 750 EPIADSVLNLFG 761
gi 94500920 767 APVVDSILYFLD 778
gi 89094696 760 EPVCESILTFIG 771
gi 71279212 793 KPIADDILPFIG 804
gi 24373385 783 GPIAEPVFSIMK 794
gi 91793780 796 QPIAEPILGLLN 807
gi 88857892 753 QPIADSILPTLN 764
gi 77360914 784 EPVADMILSALG 795
gi 88798884 748 APIADALLFFFD 759

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