Conserved Protein Domain Family
POLBc_delta

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cd05533: POLBc_delta 
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Statistics
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PSSM-Id: 99916
View PSSM: cd05533
Aligned: 25 rows
Threshold Bit Score: 678.988
Threshold Setting Gi: 71033557
Created: 23-May-2007
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
active sitemetal-binding
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                                #  ###                                                   
gi 13124199   551 EGYEGATVIDPIRGFYNEPIATLDFASLYPSIMIAHNLCYTTLLKSPQgven---------------------------- 602
gi 232011     575 EKYEGATVLEPIKGYYIEPISTLDFASLYPSIMIAHNLCYSTLIKSNHevsdlq-------------------------- 628
gi 71033557   570 NSYEGATVLEPLKGYHKNPISVLDFQSLYPSIMIAHNICYSTLLNYNTinnyk--------------------------- 622
gi 66809121   585 EKFQGAIVIEPTPGFYDTPIATLDFTSLYPSIMMAHNLCYSTLLSAEEakklp--------------------------- 637
gi 67478112   529 DKYVGATVINPIKGFYKVPISTLDFSSLYPSIMISHNLCYSTLIDGIKtrkdipsieflktseseedrklydqimkklkd 608
gi 134065298  510 RGYEGATVIDPIKGFYNCPVATLDFASLYPSIIIAHNLCYSTLVRPADarlyp--------------------------- 562
gi 123496446  517 DQYQGATVIEPSTGYYTTPIPTLDFNSLYPSIMIGHNICYSTLMTKPDpnv----------------------------- 567
gi 145514650  428 QEYQGAFVLDPVKNFYKVPIATLDFASLYPSIMMAHNMCYSTLLNTSPfkvgl--------------------------- 480
gi 85014201   462 KTFEGGFVIEPRKGFYNKPVSVMDFSSLYPSIMISHNLCYTTLLTKEQyri----------------------------- 512
gi 118400060  573 DKFEGAFVLQPKKGFYDKPIATLDFASLYPSIMMAHNLCYSTLISKNVamsmn--------------------------- 625
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                #                           #   #        
gi 13124199   603 -----edyIRTP--SGQYFATKSKRRGLLPEILEDILAARKRAKNDMKN-EKDEFKRMVYNGRQLALKISANSVYGFTGA 674
gi 232011     629 --nddittIQGK--NNLKFVKKNVKKGILPLIVEELIEARKKVKLLIKN-EKNNITKMVLNGRQLALKISANSVYGYTGA 703
gi 71033557   623 ----pediVTVPgyNDICFINVKKRKGILPIIVENLINERKKAKKMMNE-CKDEMLKKVYDGRQLALKITTNSVYGYTGA 697
gi 66809121   638 ----peiyTTTP--FGDHFIKSDTKKGLLPRILEELLSARKKAKDELKN-EKDPFKRAVLDGRQLALKISANSVYGFTGA 710
gi 67478112   609 kqlnvedvELSP--NGDLFVKSSKRKGILPEILENLLAARKQAKKDMAA-ATDPFKITVLNGRQLALKVSANSVYGFTGA 685
gi 134065298  563 ----edalDRSP--TSDVFVKKDVFPGILPEVLQDLLAARKHARAMMKDvPMHSLEYKVLNGRQLALKVSANSVYGFTGA 636
gi 123496446  568 ------qyEKSP--NHCFFAKHDEFPGVLPEILKELLAARKATKKLMEE-ATDPMQKKVFDKRQLALKISANSVYGFTGA 638
gi 145514650  481 ---adeqvTVSPe-TNAIFVKPNVRKGMLPLILEDLINARKKAKNQLAQ-ETDPFKKAVLDGRQLALKISANSVYGFTGA 555
gi 85014201   513 -----lggTKTP--TGNYFCSAERKKGLLPRILTDLLTSRKRIKEELER-EKDSALRACLNGRQLAFKLCANSLYGFTGA 584
gi 118400060  626 ----kddyTLTP--HGDYFAKPHVRQGILPDILKDLLAARKKAKNELAK-ETDPLRKAVLDGRQLALKISANSVYGFTGA 698
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                               #                         
gi 13124199   675 TVG-KLPCLEISQSVTAFGRKMIDMTKLEVERIYKkgaldgkcpaDAKVIYGDTDSVMVK-------FGVETVAQAMEIG 746
gi 232011     704 SSGgQLPCLEVAVSITTLGRSMIEKTKERVESFYCksng---yehNSTVIYGDTDSVMVK-------FGTNNIEEAMTLG 773
gi 71033557   698 TSGgFLPCIDVATAITSFGRNMIVNTKDLIEEHFSrkng---fkfDSKVIYGDTDSVMIN-------FGTDDIQEAIDLG 767
gi 66809121   711 RVG-KLPCLEISRSVTSFGREMLDKTKKIVEERYTiang---ykhDAVIIYGDTDSVMVK-------FGVKTVAEAMEMG 779
gi 67478112   686 QIG-KLPCMQIASSVTSYGRTMIELTKTTVEEKYSkkng---fpwDAQVVYGDTDSVMVK-------FGTSDLAEAIRLG 754
gi 134065298  637 QVG-KLPCLEISASVTAYGRQMIDKTKNLVEQLYP----------GTRVLYGDTDSVMVKcvtdekaSDKERLQAAMDFG 705
gi 123496446  639 TVG-KLPCLQISESVTAYGRSMIEMTKELVENKYNkqng---ysdDAHVIYGDTDSVMVN-------FGNITLEEAIKRG 707
gi 145514650  556 QVG-QLPCLEISASITSFGRQMIQFTRDTVLEHYSkkng---aefDAEVIYGDTDSVMVK-------FGDYSVEKAMALG 624
gi 85014201   585 SRG-KLPCFEISQSVTGFGREMIILTKKLIEENFSrkng---ythDSVVIYGDTDSVMVD-------FDEQDIEKVFKMS 653
gi 118400060  699 QVG-QLPCLEISSSVTSFGRQMIEATRDFVLNHYNkang---ynyDSDVIYGDTDSVMVK-------FGCDSIEEAMKYG 767
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 13124199   747 LDAAKEVSKI-FTPPIKLEFEKVYSPYLLINKKRYAGLYFTKPDVHDKMDCKGLETVRRDNCPLVAKVLGVCLEKLLIER 825
gi 232011     774 KDAAERISKE-FLSPIKLEFEKVYCPYLLLNKKRYAGLLYTNPNKHDKMDCKGIETVRRDFCILIQQMMETVLNKLLIEK 852
gi 71033557   768 KSAADLITSK-SVRPITLLFEKVYKPLLLLSKKRYAGLYYVNSENYEKIDCKGIESVRRDFCLLIQQMLEKILYLLLVKL 846
gi 66809121   780 RDAAKFVTTT-FIRPINLDFEKVYYPYLLMAKKKYAGLYWTKPDIHDRMDVKGLEMVRRDTCLLVRNVVSTILKKILIEK 858
gi 67478112   755 KEAAVFVTTK-FPRPINLEFEKVFFPYLLISKKRYAGLYFNRADKWDHVDTKGIETVRRDNCLLVKYVIENVLNKILLDS 833
gi 134065298  706 IEAAERVSSD-FLKPIKLEFEKVYFPYLLMNKKRYAGLLWTNTDQFDKLDAKGIETVRRDNCPLVARMVSGVLNRILIHR 784
gi 123496446  708 KEAANYVSDH-FPPPIHIDFEKAYKPYLLISKKHYAGLLWTNHIKYDKIDAKGIEAVRRDNCRLVQGLVQKVLTLLLVKE 786
gi 145514650  625 REAAALISKK-FIQPIKLEFEKVYYPYLLMNRKRYAGQLWTKPDKPDKIDTKGIESVRRDNCFLIRKMVTEILNFLLIKQ 703
gi 85014201   654 KEISEFITSK-FVKPVSLEFEKVYYPYLLINKKRYAGLLYSNPENPSKIDTRGIETVRRDNCRLVKEVVETVLEMILYQK 732
gi 118400060  768 KEAAEMISKKlFINPIKLEFEKVYYPYLLISKKRYAGCFYTKPDKYDKIDTKGMENVRRDNCQFIREMMNTCLRYILVEH 847
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 13124199   826 DQQ---SALDFAKRTISDLLCNKIDISLLIISKELTKsg------------------------------dKYQAKQAHVE 872
gi 232011     853 NLN---SAIEYTKSKIKELLTNNIDMSLLVVTKSLGKt--------------------------------DYETRLPHVE 897
gi 71033557   847 DLD---GAIEFVKQKVSELLKNDIDVSLLVITKTLGKv--------------------------------DYEQRLPHVE 891
gi 66809121   859 DLK---SAEEYTKSVISDLLQNRLDLSMLVITKALSKt--------------------------------QYKGKVIHNE 903
gi 67478112   834 DVE---GAISFVKNMISDLLQNKLDLSMLIISKTLSKe--------------------------------DYAGKQAHVE 878
gi 134065298  785 SVE---SAIDFVKGTISDLLLNRLDISNLVITKAFSKae------------------------------dEYAGAQAHIA 831
gi 123496446  787 DPG---SAKVFVKKIVSDLVSDHIDLSFLVISKGLSKka------------------------------dQYKGKQAHVE 833
gi 145514650  704 DEK---SAVQYTKEQIRNLYLNKVDISELVITKSLNSkkedkdnnnnnnnnnnkekkknqneddgnkltkNYKQKQAHVV 780
gi 85014201   733 NVE---KAKQFVKDAVRDLYLGRTDLSLLVISKSLTKag------------------------------dKYESKQAHVQ 779
gi 118400060  848 KQDgvqRSIQFIKGCISDLYQNKVDISKLVITKSLTKksadddegeedgkk-----gsshnnkakepsanQYKGKQAHVE 922
                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
Feature 1                                                                                 
gi 13124199   873 LAARMKKRDaGSAPRLGDRVPYVFVAAakNVPAYERAEDPTFVLQNNIPLDTKHYLTNqlAKPLARIFEPIL 944
gi 232011     898 LAKKLKQRDsATAPNVGDRVSYIIVKGvkGQAQYERAEDPLYVLDNNLAIDYNHYLDAi-KSPLSRIFEVIM 968
gi 71033557   892 LAKKLRKRDpGKAPGVGDRISYIIVKGtkGEPLFDRAEEPLYVTENNLPIDTNYYLDSl-KNVLLRIFEVVM 962
gi 66809121   904 LARKMRARDpATAPNLGDRVPYVVIQGskGAPIYEKAEDPLYALEHNILLDCQYYLDKqlKAPLIRIFKPIM 975
gi 67478112   879 LVKRIRERDkTTTINTGDRIPYVIIKStkDAKAYEKAEDPLYVLENNIPIDFDYYIENqlKKPLTRIFKPIL 950
gi 134065298  832 LVERMRQRDpASAPTIGDRVAYVIIKAakGAKAYERSEDPIYVLDNNIPIDTQYYLEHqlAPPILRVFEGVL 903
gi 123496446  834 LADRMMKRDpGSAPRMGDRIPFVMCDVgnGAKGYEKSEDPIWALEHSIPIDTKYYLENqlSGPLNRLFGPII 905
gi 145514650  781 VAEKMQNRDaSNAPSAGDRIAYIIIQGakGTKTYENAEDPVEVLEKDFPIDFDYYVNNqiKKPIMRLFEFVI 852
gi 85014201   780 LAEKLRKRDeSTAPVLGDRVPYVIVRKekGAAAHEKSEDPVYVLENNLPIDTEYYISQqiSKPLSRIFEPIM 851
gi 118400060  923 LAKKMAKRDpGSAPCIGDRIPYVIVAGakSAKNYEKVEDPIYVLENDIPLDYDYYIEKqiKNPITRIYSHII 994

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