Conserved Protein Domain Family
POLBc_B3

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cd05536: POLBc_B3 
Click on image for an interactive view with Cn3D
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Statistics
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PSSM-Id: 99919
View PSSM: cd05536
Aligned: 18 rows
Threshold Bit Score: 518.032
Threshold Setting Gi: 495654
Created: 20-Jul-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                               #  ###                                                   
1D5A_A       381 TESYAGGYVKEPEKGLWENIVYLDYKSLYPSIIITHNVSPDTLNRegcreydvapq-----------vghrfckdfpGFI 449
gi 495654    427 KFSYEGGYVREPLKGIQEDIVSLDFMSLYPSILISHNISPETVIYeeker----------------------enmelGII 484
gi 807830    416 GESYKGAVVLKPLKGVHENVVVLDFSSMYPSIMIKYNVGPDTIVDdpsecpkyggcyv------apevghrfrrsppGFF 489
gi 3122019   388 AESYEGAFVLEPERGLHENVACLDFASMYPSIMIAFNISPDTYGCrddcyeapev-------------ghkfrkspdGFF 454
gi 4519584   386 EGRYAGAIVLRPKPGVHEDIAVLDFASMYPNIMVKYNVGPDTLVRpgeeygeeevyta-------pevghkfrksppGFF 458
gi 15922397  406 YESYEGGLVISPLPGIHEDVYVLDFSSMYPSIMIKYNIGPDTLVKgecencwisp------------aghkfrkdppGLY 473
gi 20094475  428 RKAYKGAIVFEPEIGLHENVVCVDFASLYPNVMVAHNISPDTFDCdccprvtveevddptdatvapdvghkfckrrkGFF 507
gi 70605924  407 TEASDEGIIVPPVSGLHNNVYMLDFSTIYPSIILKYNISPDTLVRgdcsdcwtsln-----------gnykfrkdikGLY 475
gi 119719310 412 EETYKGAIVLKPKPGVHKKIAVLDFSSMYPNIMIKYNISPDTYVPpeehvdpsevwva-------pevghrfrkhppGFY 484
gi 147918852 403 VETYAGGFVFEPVKGLHKNVAALDFSAMYPSIMIAYNISPDTVCEagdqdcsepap----------evgyrfkkqpeGFF 472
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                  #                              #   #                                  
1D5A_A       450 PSLLGDLLEERQKVKkkmkatvdp----ierklldyrQRAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTM 525
gi 495654    485 PKTLNELLSRRKHIKmllkdkiqknefdeeysrleheQKSIKVLANSHYGYLAFPMARWYSDKCAEMVTGLGRKYIQETI 564
gi 807830    490 KTVLENLLKLRRQVKekmkefppds---peyrlyderQKALKVLANASYGYMGWSHARWYCKRCAEAVTAWGRNLILTAI 566
gi 3122019   455 KRILRMLIEKRRELKvelknlspes---seyklldikQQTLKVLTNSFYGYMGWNLARWYCHPCAEATTAWGRHFIRTSA 531
gi 4519584   459 KKILERFLSWRRQIRsemkkhppds---peykllderQKAIKLLANASYGYMGWPHARWYCRECAEAVTAWGRSIIRTAI 535
gi 15922397  474 KNVLEKLIQERKEVKklmektmde----ydkrvldarQRALKVMANAFYGYMGWLGARWYSKEGAEAVTAWGRQIISESA 549
gi 20094475  508 PRLVEGLIERRRELKrrlrkldtesh-pheakildvrQQAYKVLANSYYGYMGWANARWFCRECAESVTAWGRYYISEVR 586
gi 70605924  476 QNVLLNLSAEIERREeiiktldpe-----krrrleeeLRALRSILNSFYDYIRWTNARWYVKECAEGLFEWGRELILQIL 550
gi 119719310 485 RKVLESLLEARRRLRekmktldprs---eeyriyderQKAIKVITNATYGYSGWSMARWYKREVAEATTAWGRELIKATI 561
gi 147918852 473 TTILKNLVTHRSTLKkrlaqldrks---neyrmldlrQKSIKILTNAFYGYTGWAQAKWYRRECAEATSAWGRYFIKKAN 549
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                        #                                                               
1D5A_A       526 REIEEKfGFKVLYADTDGFFATIPgadae----------------------tvknkAKEFLNYINPRLPglLELEYEGFY 583
gi 495654    565 EKAEEF-GFKVIYADTDGFYAKWDydklqkgkkeendksdklsnlpklskeeliilTKKFLKGINEELPegMELEFEGHF 643
gi 807830    567 EYARKL-GLKVIYGDTDSLFVVYDke-----------------------------kVEKLIEFVEKELG--FEIKIDKIY 614
gi 3122019   532 KIAESM-GFKVLYGDTDSIFVTKAgmt--------------------------kedVDRLIDKLHEELP--IQIEVDEYY 582
gi 4519584   536 RKAGEL-GLEVIYGDTDSLFVKNDpe-----------------------------kVERLIRFVEEELG--FDIKVDKVY 583
gi 15922397  550 KIAKEK-GFTVIYGDTDSIFVKGGg------------------------------dINSLITEISSKFG--LEIKIDKIY 596
gi 20094475  587 RIAEEKyGLKVVYGDTDSLFVKLPdadle----------------------etierVKEFLKEVNGRLP--VELELEDAY 642
gi 70605924  551 KIVKES-GFQVIYADTDLMFFKGEn------------------------------dPKKLEEDIANRLS--LNLKFNKFY 597
gi 119719310 562 KKAQSL-GLSIIYGDTDSIFVQFDee-----------------------------kIGRLVEYVEKELG--FEIKLDKVY 609
gi 147918852 550 DIAIEM-GLQVLYGDTDSLFVEMEdnkr------------------------lmdvVRQYIQRVKAELP--LDMDIDNVY 602
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1D5A_A       584 RRGFFV-TKKKYAVIDEEDKITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEeAVRIVKEVTEKLSRHEVPPEKLVI 662
gi 495654    644 KRGLFV-TKKKYALIEDDGHIVVKGLEVVRRDWSNIAKDTQQAVIRALLEDGDVNlAKKIIKNTIDNLKKGNIDKNDLLI 722
gi 807830    615 KKVFFTeAKKRYVGLLEDGRIDIVGFEAVRGDWCELAKEVQEKAAEIVLNTGNVDkAISYIREVIKQLREGKVPITKLII 694
gi 3122019   583 SAIFFV-EKKRYAGLTEDGRLVVKGLEVRRGDWCELAKKVQREVIEVILKEKNPEkALSLVKDVILRIKEGKVSLEEVVI 661
gi 4519584   584 RRVFFTeAKKRYVGLTVDGKIDVVGFEAVRGDWSELAKETQFKVAEIVLKTGSVDeAVDYVRNIIEKLRRGQVDMRKLVI 663
gi 15922397  597 KRVFFTeNKKRYAGLTEDGKIDIVGFEAVRGDWCDLAKQVQTNVIELILKSGKVEdAIKYVKTVIFDLRRYNFRIEDLII 676
gi 20094475  643 KRILFV-TKKKYAGYTEDGKIVTKGLEVVRRDWAPIARETQRRVLKRILADNDPEaALKEIHEVLERLKSGDVDIDELAV 721
gi 70605924  598 TKLILLeGKKQYAALTKDNKVDMVGIEDYRNNWCDLAKEVLQNVVDQVLRSDKINeAVRYVKSVIYSLRRGEFKIEDLVT 677
gi 119719310 610 EKVFFTeSKKKYCGLLADGRVDLVGFEAVRGDWAEISKEIQERVVEIVLKEEDPWkAVDFVRKTITELSEGRIPLEKLVI 689
gi 147918852 603 RIIFFTeSKKRYAGLTDRGEIVVRGLEVRRGDWCEIAKELQSEVIRIILEEENPDkAAKFVKDTVQKVKSGKVPLDALVI 682
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1D5A_A       663 Ye-----------aGPHVAAA-------------ATVISYIVLKGPGRVGDRAIPFDEfd--------------paKHRY 704
gi 495654    723 HtqltknieeykstAPHIEVAkkikqr-gdsvrvGDVISYIIVKGSRSISERAELLEY------------------AGDY 783
gi 807830    695 WktlskrieeyehdAPHVMAArrmkea-gyevspGDKVGYVIVKGSGSVSSRAYPYFMv----------------dPSTI 757
gi 3122019   662 YkgltkkpskyesmQAHVKAAlkarem-giiypvSSKIGYVIVKGSGNIGDRAYPIDLiedfdgenlriktksgieIKKL 740
gi 4519584   664 WktltrppsmyearQPHVTAAllmera-gikvepGAKIGYVVTKGSGPLYTRAKPYFMa----------------sKEEV 726
gi 15922397  677 WktidknldeydvtAPHVVAAkkaaka-gylvskGVKIGYVIVKGSGKISDKAEPYFLik---------------eKNKI 740
gi 20094475  722 TsqltkkpseyvqkGPHVRAAlrlarhlgvepepGTIVRYVIVRGPGSVSDKAYPVELvr--------------eeGKEP 787
gi 70605924  678 WniidkdieeykfdLPHIVAArkamks-ghlvtrGSKIGYVIVKGSGKLSNRAEPYFMvk---------------eKSKV 741
gi 119719310 690 WktlskdldeyevdAPHVVVArelkrl-gyrvgkGAKIGYIVVKGAGKVSEKAKPLISvk---------------sPDEV 753
gi 147918852 683 HktltksvtryesaQAHVKAAeramer-dmaaeiGNKISYVIVKGTGTLSDRAYPVDMfhkfkds----klyakdkTYEI 757
                        410       420       430
                 ....*....|....*....|....*....|
Feature 1                                      
1D5A_A       705 DAEYYIEnQVLPAVERILR-AFGYRKEDLR 733
gi 495654    784 DINYYIDnQVLPPVIRIME-SLGISEDELK 812
gi 807830    758 DVNYYIDhQIVPAALRILS-YFGVTEKQLK 786
gi 3122019   741 DKDYYIDnQIIPSVLRILE-RFGYTEASLK 769
gi 4519584   727 DVEYYVDkQVVPAASAHTSsNFGVIEKRLK 756
gi 15922397  741 DVEYYIDkQIIPVAMRILE-GFGVKESSLK 769
gi 20094475  788 DVDYYIEhQILPAVERIMR-AIGYSRGQIV 816
gi 70605924  742 DIEYYIDkQIIPSALKVLG-LFGVKENTFK 770
gi 119719310 754 DTDYYVKrQIVPAALRILE-YFGVKEEHFS 782
gi 147918852 758 DADYYVDkQLIPTALRILG-YFGYTEDALK 786

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