Conserved Protein Domain Family
POLBc_epsilon

?
cd05535: POLBc_epsilon 
DNA polymerase type-B epsilon 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. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Statistics
?
PSSM-Id: 99918
View PSSM: cd05535
Aligned: 22 rows
Threshold Bit Score: 956.742
Threshold Setting Gi: 19074730
Created: 23-May-2007
Updated: 17-Jan-2013
Structure
?
Aligned Rows:
 
active sitemetal-binding
Feature 1:active site [active site]
Evidence:
  • Comment:Based on similarity to bacteriophage RB69 POLBc (1Q9Y)

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 118841     545 GHLLESETYVGGHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFsvevenkssvdkvTNFEEIKNQITQKLLEL 624
gi 3885342    495 GKLLESETYIGGHVECLQSGVFRSDIPTSFKLDASAYQQLIDNLGRDLEYaitvegkmrmdsvSNFDEVKEVIREKLEKL 574
gi 66359706   549 NRPILNSTYVGGTVESLCSGVFRADIPEKFCLNTDTLKHLIKILDTTLNFgikdsg-ttidniENYEQVRNEILEKLQSL 627
gi 66811008   527 GHLLESETYVGGHVECLESGVFRSDIPTNFSLDPASIEKHMGNIDQVLKFalkegg-ipldtvSNYQEVKEDVLKKFTLL 605
gi 74682669   573 GHLLASETYVGGHVEALEAGVFRSDIPTHFKIVPSAIQELIDDLDAALRFslieegqvkledvENYDEVKQQIQTALETM 652
gi 116060470  551 GHLLNSETYIGGHVECLQAGVYRSDIPCDFNLTPDGYQKLLDTLDDDLKYalevegkmkqsdvSNYDEIRAAIVEKLEFL 630
gi 134065872  491 GHLIDTETYIGGRVEALRSGVYRSDIPMTFDMNPDTYQSLMDDVDEALRFalevengvkveevTNLEEVRAAVLAKLTNL 570
gi 145490728  482 GHLIDSETYIGGKVECLRSGIYRSDIDVEFKIDKECMQSMWSTVDSLIRFvgkien--etfseEEIEKCSEQIRSKLDVL 559
gi 19074730   468 GHIAESITYVGGHVECLKSGIFRSDFEYEFDVDKEFIDTVALKIDEMLSEyr---------geEGFEDMRGKVLRNLQEN 538
gi 50554027   515 GHLVDNETYTGGHVESLAAGVFRSDIMVDFDIDTNSIDELLVNLDETLEFcvtveagkkssdfENLDEVRDQIIEQLQEL 594
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                         #  ###                                                          
gi 118841     625 KENn-iRNELPLIYHVDVASMYPNIMTTNRLQPDSIKAERDCASCDFNRPGK--TCARKLKWAWRGEFFPSKMDEYnmik 701
gi 3885342    575 RDDp-iREEGPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNGPEK--TCLRKLEWVWRGVTFKGNKSEYyhlk 651
gi 66359706   628 LESp-rIKIEPLIYHLDVAAMYPNIILTNRLQPTAVIEETTCMKCPFNSESK--LCQRRMNWRWKGDVFPISKGEMermi 704
gi 66811008   606 KENp-kQQSHPLIYHLDVSAMYPNIILTNKLQPTAVVNDEVCATCVYNKPES--QCQRTLDWQWRGDYSPSNQSEYrlil 682
gi 74682669   653 RDEp-nRFDNPLIYHLDVAAMYPNIMLSNRLQPDSVKEEADCAVCDYNRPDK--KCDRRMEWAWRGEYFPAKRDEVnmvr 729
gi 116060470  631 RDNp-rIKSKPLIYHLDVAAMYPNIILTNRLQPAAMVTEDVCAACDYNRPGK--KCLRELEWVWRGEHFASTSSEYaqik 707
gi 134065872  571 RNRp-hQQEKPFIYHLDVGAMYPNIILTNRLQPYAIARPDVCAGCCFNSPNNeaQCKRVMSWKWRAELFTAGRYEFqrvk 649
gi 145490728  560 INRgevFKEKPLIYHLDVAAMYPNIILTNRLQPVSIVGDQICSQCYFNQPQN--RCQRQLEWQWKGDFFPLKRTEYefvk 637
gi 19074730   539 RGG---FRREGLIYHLDVGAMYPNIILTNKLQPIAIVDEDACIRCDFSDESN--GCKKRMEWTLKVEYIPAGREETerir 613
gi 50554027   595 KSNp-kRSDYPLIYHVDVASMYPNIMTTNRLQPDSMVDEKDCAVCDYNRPDK--TCARELEWARRVDYYPVSKGDVnnlk 671
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 118841     702 ralqnetfpnkn-------------------------------------------------------------------- 713
gi 3885342    652 kqiesesvdag--------------------------------------------------------------------- 662
gi 66359706   705 nhiqietfenvkneigavnkkkkfedhe---------------------------------------------------- 732
gi 66811008   683 qqlesekfgd---------------------------------------------------------------------- 692
gi 74682669   730 yaleqetfppk--------------------------------------------------------------------- 740
gi 116060470  708 aqlqvdtfpaa--------------------------------------------------------------------- 718
gi 134065872  650 aqlenesfaagvieqanlaavqkkaygnrkgnvlegtlyerkddwrknqrnrnsssssggggyrqesrrqqreaadallq 729
gi 145490728  638 qqleqeqtekerkeneekkk------------------------------------------------------------ 657
gi 19074730   614 kqir---------------------------------------------------------------------------- 617
gi 50554027   672 qglveeysggrfgngssvei------------------------------------------------------------ 691
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 118841     714 ----------------kfskkkvltfdelsyaDQVIHIKKRLTEYSRKVYHRVKVSEIv-EREAIVCQRENPFYVDTVKS 776
gi 3885342    663 -----------------anmqsskpfldlpkvEQQSKLKERLKKYCQKAYSRVLDKPIteVREAGICMRENPFYVDTVRS 725
gi 66359706   733 sdsenddkmeftgenvninnkekikwssltprQQSEILIQRMKAYCNKIYRKQTENIEe-TRSSIVCQRENPFYIDTVRR 811
gi 66811008   693 -------------------gderksflslseeKRNELLRKRLKEYSRKVYRKTHQITQe-IRSDTICMRENSFYVDTVRL 752
gi 74682669   741 -----------------rpydpkrrfvdltptEQSALLHKRLGDYSRKVYKKTHDTKIv-TKTTIICQRENSFYIDTVRA 802
gi 116060470  719 -----------------dpggssrtwyelsyeEQQEQKKNRLKMYTQKVYRKVMEKPVtaTKTAGICQRENAFYIDTVRA 781
gi 134065872  730 refgadrngvsgdsdsdddvdgpkayhkltenTQFNMLKRRLSEYSRKAYGKIHETREv-MQSNVVCQRENSFYVDTVRL 808
gi 145490728  658 ---------qmlkegldtrrlqlkgfsdlapdEQIKRIKQRVIEHCKKTYKTIHHHSVe-LKKDTVCMRENDFYVQTVRD 727
gi 19074730   618 -------------------------rekgfagDENEELRQRARRYSKDTYRRAKVRESc-IRSSTVCQREIPFYVETVRK 671
gi 50554027   692 --------sydegmterekfqkrkgwaglsgqEQANKLKERVAAFSLKTKARKTDSETt-VQKTIVCQRENPFYVDVVQE 762
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1          #                                                 #   #                        
gi 118841     777 FRDRRYEFKGLAKTWKGNLSKIDPSDKHARDea----kKMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCL 852
gi 3885342    726 FRDRRYEYKTLNKVWKGKLSEAKASGNLIKIqe---ahDMVVVYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTY 802
gi 66359706   812 FRDRRYVYKGKKKEAEEKLKRAELLGDLLAVqe---aqNEELLYESLQLAHKCILNSFYGYVMRKGSRWFSMEMAAIVTW 888
gi 66811008   753 FRDRRYVFKNHHRDWKIKYDQAMQESGGTNSvavvaaqGMVVLYESLQLAHKCILNSFYGYVMRKGARWYSMQMAGIVTH 832
gi 74682669   803 FRDRRYEYKGLHKTWKKNLDKAFEEGGAVATvde--akKMIVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGITCL 880
gi 116060470  782 FRDRRYVYKGKNKEAGKQLEAAKQAGSIADIqq---aaNNVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTN 858
gi 134065872  809 FRDRRYEYKAALKIWKKKLDAAKDADERKLCq------SRCVQMESLQLAHKCILNSFYGYVMRKGSRWSSMEMAGIVTY 882
gi 145490728  728 FRDRRYEFKELVKVYKNKLEQAKKEGVGVKEc-----hDFMALYESLQLAHKIILNSFYGYVMRKGARWYSMPMAGIVTH 802
gi 19074730   672 FRDQRYVYKKLHSQAQKAFESASSDEERKHAm------KSVVVYSSLQIAHKCVLNSFYGYVMRKSSRWYSMEMAAIVCN 745
gi 50554027   763 FKQRRIDYKTKAKRWNKEAASASDPASREEAk------KMAITNDSMQLAHKVILNSFYGYVMRKGSRWYSMEMAGVTCY 836
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                 #                                                       
gi 118841     853 TGATIIQMARALVERVGRPLELDTDGIWCILPKSFPETYFFtlen--gkkLYLSYPCSMLNYRVHQKFTNHQYqelKDPL 930
gi 3885342    803 TGAKIIQNARLLIERIGKPLELDTDGIWCALPGSFPENFTFktid--mkkFTISYPCVILNVDVAKNNSNDQYqtlVDPV 880
gi 66359706   889 VGGNVIREARSLMEGIGRPLELDTDGIWAILPKGFPEEITFrlkd--ggkKKIHYICTLLNQQVHKSWTNDQYl-eYDAD 965
gi 66811008   833 TGSNIIKEAREVVEQMGRPLEIDTDGIWCILPSHFPENYTLksas-tgkkVTFSYICEMLNEKVAKSFTNHQYq-dYNAE 910
gi 74682669   881 TGATIIQMARQLVEQIGRPLELDTDGIWCMLPGVFPEDFNFklkn--gkkFGISYPCTMLNHLVHAQFTNDQYhelVNND 958
gi 116060470  859 TGAKIIQMAKQLVDDIGMPLELDTDGIWCCLPCEFPEDYTFtmkgegkkpYQISYPCVVLNRMTAVRNTNDQYl-tFDEK 937
gi 134065872  883 LGATLIQMARSLVQQIGVTLELDTDGIWCCLPNTFPENFTFtttnaskpqISISYPCVVLNKMVHDRYTNHQYq--NLLS 960
gi 145490728  803 MGSQIISTAKQRVDQIGLPLELDTDGIWCLLPSGFPEDFLIksqt--grnLKFSYPCYILNELVYEKYKNNQYqwlKDPN 880
gi 19074730   746 VGGNIIKRAKEVVEKIGISLELDTDGIWCIVPSSLISSYTLps------gRRFSFLSSLLNHFVCKEFTNWQY---QERV 816
gi 50554027   837 TGAKIIKIARQTMEGLGIPLELDTDGIWCMLPKTFPEKFKCkfkd--gssYELEYPCSIMNYLVHRDFTNHQYq-kLNPE 913
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 118841     931 NYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEdGSLAELKGFELKRRgeLQLIKNFQSDIFKVFLEGD 1010
gi 3885342    881 RKTYNSRSECSIEFEVDGPYKAMIIPASKEEGILIKKRYAVFNHdGTIAELKGFEMKRRgeLKLIKVFQAELFDKFLHGS 960
gi 66359706   966 LGKYNIKVENSIYFEVDGPYKCFFIPASDKQNKLLKKRYAVFDFeNRLKELKGFELKRRgeLQLIKILQEELFPAFLKGN 1045
gi 66811008   911 TNTYTIRDECSILFECDGPYRCMLIPTSKEKDVKLKKRYAVFNReGRICELKGFEIKRRgeLKLIKLFQSEVFKEFLGGD 990
gi 74682669   959 SGTYNVKKENSIFFELDGPYKAMILPSSKEEDKLLKKRYAVFNPdGSLAELKGFEVKRRgeLQMIKIFQSQIFDKFLLGK 1038
gi 116060470  938 TGTYKQSSEMSIEFEVDGPYKAMILPASKEEGVLIKKRYAVFDEaGKLVELKGFELKRRgeLKLIKVFQSEVFDYFLKGE 1017
gi 134065872  961 TGVYRTHSECSIYFEVDGPYLAMLLPASREEGKSIKKRYAVFNPdGQLGRAQRVELKRRgeLMLVKDFQSQVFRRFLDGS 1040
gi 145490728  881 SFEYGIRSEMSIFFEVDGPYRCMIIPAAREENKQLKKRYVVYNKnGSIAEVKGFEIKRRgeLQIIKQFQQELFSEFLKGT 960
gi 19074730   817 DGKYVMRAENSIFFEIDGPYRAMLLPSSTEESKLLKKRYAIIDSnNRIAELKGFEIKRRgeLEIVKKFQEELFLHFLDGS 896
gi 50554027   914 TGKYDTHSENSIFFELDGPYKCMMMPTSTDKGKGLKKRYVVFDDrNKIVELKGFEVKRRgeLSLIKKFQSQLWDTFLEGS 993
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 118841    1011 TLEGCYSAVASVCNRWLDVLDSHGLMl-EDEDLVSLICENRSMSKTLKEYE-GQKSTSITTARRLGDFL-GEDMVKDkgL 1087
gi 3885342    961 TLEECYSAVAAVANRWLDLLEGQGKDi-ADSELLDYISESSTMSKSLADYG-QQKSCAVTTAKRLADFL-GDTMVKDkgL 1037
gi 66359706  1046 SKKEAYDHVAAISKKWLSLIDTKGRGilDDEQLFFLISESKNMSKSVQQMG-NAKSMSITTAKRLFEFLqNPSYIQDknI 1124
gi 66811008   991 SLEGCYQSVGAVANRWLDILDSHAENy-EEKDLIELITESSNMSRKLEEYG-TQKSSAISTAKKLAEFL-GDDMIKDkgL 1067
gi 74682669  1039 TTEECYAAVATVADQWLDILQSKASSl-HDDELVDLIAENRSMSKTLAEYA-GQKSTSISTARRLAEFL-GEQMVKDkgL 1115
gi 116060470 1018 TLDGVYQAVGAIANRWFDMLKTRGAKf-DDEELMEYISESSVMSKPAIDYG-DRKSTSLTTARRLAQFL-GADLVKDkgL 1094
gi 134065872 1041 TLADAYASAAVVANAALDMLESKGEGy-DTEEILEKITESSNMTRRLSEYPeSQKSLAITTARRIAEFL-GPQMVKDkgL 1118
gi 145490728  961 NLTECYQACAEVGKKLLRILMTGGEGi-SQQELLDLIGESRVLSKEISEYD-NKKGVAITAGKRIAEYL-GSDQVRGgsL 1037
gi 19074730   897 NLEECYESLAGVCRYWLDILKSRGEYl-DDDTILELLSESRSMSKGFGEYR-GRKSNLTVTALRMSELL-GEGILEEk-L 972
gi 50554027   994 NLVECYAAQARVAEAWLAVIDSRGKNl-SDEELIDLVCENKSMSKPVHEYG-SQKSTALTTARRLAEIM-GDSILTGgkL 1070
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 118841    1088 QCKYIISSKPf--------------NAPVTERAIPVAIFSADIpik-rsfLRRWtldp---------------------- 1130
gi 3885342   1038 RCQYIVAREPe--------------GTPVSERAVPVAIFQTDDpek-kfyLQKWcki----------------------- 1079
gi 66359706  1125 VCKFIVSEFPk--------------GEDKSQRAVPLSIFSTPLetr-vswLSKWlrisksggrrekdelvehrrkadvdi 1189
gi 66811008  1068 SCQYIISNKPa--------------GSPITERALPVAIFDADFetr-chyLRRWtksp---------------------- 1110
gi 74682669  1116 SCRFIISAKPn--------------GAPVTERAVPVAIFTAEEpvk-rhyLRKWlkdn---------------------- 1158
gi 116060470 1095 VCKYIISKKPl--------------GAPTSQRAIPVSIFNAEVsva-rsfLKEWtkdndls------------------- 1140
gi 134065872 1119 ACHFIISRMPa--------------GRPVTERAIPVTIFRADQair-thfLRKWtadtt--------------------- 1162
gi 145490728 1038 NCQYIITKLPh--------------NTPVNERSIPLLIFESSFetr-kkyLRKWlkepq--------------------- 1081
gi 19074730   973 KCEYIVAVYPe--------------NGSVAERAIPVVVFRSEQke---efLRRWmgr----------------------- 1012
gi 50554027  1071 STKYIIAVRTknsmpvpeakkgsdeDSSTADRAIPTLVFETESldeklrfLKRWmgpr---------------------- 1128
                         730       740       750       760       770
                  ....*....|....*....|....*....|....*....|....*....|.
Feature 1                                                            
gi 118841    1131 ---------------sledLDIRTIIDWGYYRERLGSAIQKIITIPAALQG 1166
gi 3885342   1080 ----------------ssyTGIRSIIDWMYYKQRLHSAIQKVITIPAAMQK 1114
gi 66359706  1190 tsgsgggsgilnkenennkWNVRNILDWEYYKNRLTNTILKIVIIPAINQG 1240
gi 66811008  1111 ----------------sgdLDIRELIDWDYYRQRLSGVIQKIITIPAALQN 1145
gi 74682669  1159 ---------------sltdFDLRTILDWDYYTERLGSVIQKLITIPAALQK 1194
gi 116060470 1141 -------------geddemPDMRDLVDWEYYKTRLAGAIQKIISIPAALQG 1178
gi 134065872 1163 ---------------vpseLNLKALLDWDYYIARFSACVQKIVSIPAALQS 1198
gi 145490728 1082 --------------lqdedLTLSKIVDWDYYIERLKNTILKLLVIPAALQN 1118
gi 19074730  1013 ----------------dylGDIRAIIDWDYYRQRLECVVQRMVILPALSQG 1047
gi 50554027  1129 ----------------wesTDPRDVIDWMYYRERLATTINKLVVIPAILLG 1163

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap