Conserved Protein Domain Family
POLBc_Pol_II_B

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cd05538: POLBc_Pol_II_B 
DNA polymerase type-II B 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 proved 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: 99921
View PSSM: cd05538
Aligned: 6 rows
Threshold Bit Score: 413.035
Threshold Setting Gi: 17158708
Created: 13-Sep-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 78224378  389 GTFEGGYAAVfETGVLGPIVHCDVASLYPSIMLAYGLDPRREHLGLFLPLLAQLRQFRLaakerareaal---pherdyf 465
gi 21675090  413 QQQTGGFTEVfIKGILGPIVYADVESLYPSIMLTFDVCPKSDSLKVFPTILKDLKELRFaakkraeeekergnaslsynf 492
gi 116626444 403 TEHSGAALHLfATGVAHRIVKADVASLYPSLMRAFRIGPARDRLGAMLALVDRLVEWRLaakasaraapr--gsaerfah 480
gi 17158708  289 YKFQGGMAYS-IPGLYRRVGYADISSMHPWAMLDKGICSIKDTERIGLSILQYLVNEKFrleqlasa--------gdvaa 359
gi 148262379 388 GSFEGGYTDVlEYGVVGPIVHCDVASLYPSILISYQLTPAHDSLSLFLPLLKELREFRLtakrlartgad---pfrrdyy 464
gi 118746768 362 MAAESNGSLVlRRGRLGPVVHCELSSLAAAIMLAYRIAPHGDELGIFPAALHAVLRLCSeqaesv-------------fg 428
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1               #   #                                                   #                
gi 78224378  466 nalQQTFKVLINSFYGYL--GTTIHTFSDPGVAAEVTRRGRELIQDMIEWLRRHGARPVEVDTDGIYFIPPqgietigqE 543
gi 21675090  493 damQSSFKIIINAMYGYL--GFGNGMFNDFEEADRVTTKGQEIAKKMIREFESRGAKVIEVDTDGIFLVPPpyvvteeeE 570
gi 116626444 481 earSAAMKLVVNSAYGYLaaGGGLTRFADVHAANKVTRRGRETLDLMCRELAARGVTLLEADTDGVYFAVPegws-edeE 559
gi 17158708  360 kekRESVKVLANSEFGFL--GTSELAFNDMEAAALVTAYSRKVLKLMIEIITRYGGTPVEVDTDGVFFTHPn-------P 430
gi 148262379 465 qalQQAFKVLINSFYGYL--GSPLHNFSDVALAAEVTRLGRETIKTMLAWLLERGAQPVEVDTDGIYFIPPsvvataekE 542
gi 118746768 429 rqkQAACRLLLPAWSELL--ARGQYPFSDPAAAGELERLRNVLVRDLLDWLREEGAEPVVADLQGIYFMPPaghdgtdeI 506
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 78224378  544 EALVRELSATLPEGIAVEMDGRYRAIFS--YKIKNYALLDHDGKVIVRGSaLRSRGIERYLRDFMAAAVRLLLQGDGakI 621
gi 21675090  571 RQLVCEVSSTMPQGIRIGFDGRFKKMIS--YMKKNYALLDYNEKLKLKGSaFVSRSGEKFGRDFVREGFILLLNDDIqgL 648
gi 116626444 560 RGVVAEVASLLPPLVQLEFDGRYAAMLS--HEPKNYALLSYDDKLLLRGVaFRSSRAEPFGENFLRRAIGRLLKGDVpgV 637
gi 17158708  431 EEVRSLLQSQLPKGITVKLEFIADAMFIpeRGTKNYLLWLPDGKIITKGN-WRNRDRSQLEKEFSIEYLTLLIQNVSa-A 508
gi 148262379 543 ELLVRELSQSLPGGIEVELDGRYRAMFS--YKIKNYALLGYDGKMTVKGSgLRSRGIEKYLRAFMEEIIRLLLAGEGakV 620
gi 118746768 507 KMLARRLDRILPRGADLYCSGRYQAMLV--YKQNNYALLEQGGELVVRGSsFVSRAMEPFLREFLVEAVRLLLAGQGeqV 584
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 78224378  622 PAFHEDCIRRLRNHLIPIESLARTETLGEAPPTYlqkVRQGkrnpsaafeialraerpfraGDQISYYVtghgkGVTVYE 701
gi 21675090  649 HDLYVKYRNDLINHRLHISDFSRTESMKTTLDQYvsdVRAGkrsksityeialrqgleiakGDRITYYVagtgnPASFVE 728
gi 116626444 638 RDAYLVTLDALRRRELPTRDVSSLVRLTKSPEHYletREARrelpyeaml--aagrrqwsaGERVRVYRtrtsaGVVEET 715
gi 17158708  509 EDYYAHIKSQILSREYPKEKLAITRKIKEGEKEI---LKLGk------------------pGDVVTYYY-----GISGIT 562
gi 148262379 621 EAVYRDYTQKLRDHEFGISWLAKSETLGESLAVYrekVRAGkrnpaaayeiatksprefraGDQISYYIsgrrkGVTAYE 700
gi 118746768 585 HQLYEMFLRRLTSHACPVSWVMRSETVLDSRENYlqgIQSGrrnraavyelalarpetwrvGDRVEYYVsghakNVVVHE 664
                        330       340       350
                 ....*....|....*....|....*....|....
Feature 1                                          
gi 78224378  702 NCKPVSQYDPTRPDENTEFYLDKLNQLVKRLAAY 735
gi 21675090  729 NGRLAEEWNKEQPDENTGFYLKRLDEYAQKFLPF 762
gi 116626444 716 DDDEDAIAGEDPRDYDVGHYARVLREIFASRLER 749
gi 17158708  563 NISSNENYSRQYYLHLIEKRREEILKIAAPTTLE 596
gi 148262379 701 NCRPIADYDPAHPDENTDYYMDKLKQLHKKFARF 734
gi 118746768 665 SCRLVADFDPAHPDLNIPWYAERLHQLFRRLEPL 698

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