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: 2-Oct-2020
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:
Feature 1                              #  ###                             #                      
YP_386125    389 GTFEGGYAAVfETGVLGPIVHCDVASLYPSIMLAYGLDPRREHLGLFLPLLAQLRQFRLaakerareaal---pherdyf 465 Unknown
NP_663155    413 QQQTGGFTEVfIKGILGPIVYADVESLYPSIMLTFDVCPKSDSLKVFPTILKDLKELRFaakkraeeekergnaslsynf 492 Chlorobium tepi...
YP_828600    403 TEHSGAALHLfATGVAHRIVKADVASLYPSLMRAFRIGPARDRLGAMLALVDRLVEWRLaakasaraapr--gsaerfah 480 Solibacter usit...
NP_478219    289 YKFQGGMAYS-IPGLYRRVGYADISSMHPWAMLDKGICSIKDTERIGLSILQYLVNEKFrleqlasa--------gdvaa 359 Nostoc sp. PCC ...
YP_001229085 388 GSFEGGYTDVlEYGVVGPIVHCDVASLYPSILISYQLTPAHDSLSLFLPLLKELREFRLtakrlartgad---pfrrdyy 464 Unknown
ZP_01594687  362 MAAESNGSLVlRRGRLGPVVHCELSSLAAAIMLAYRIAPHGDELGIFPAALHAVLRLCSeqaesv-------------fg 428 Geobacter lovle...
Feature 1               #   #                                                   #                
YP_386125    466 nalQQTFKVLINSFYGYL--GTTIHTFSDPGVAAEVTRRGRELIQDMIEWLRRHGARPVEVDTDGIYFIPPqgietigqE 543 Unknown
NP_663155    493 damQSSFKIIINAMYGYL--GFGNGMFNDFEEADRVTTKGQEIAKKMIREFESRGAKVIEVDTDGIFLVPPpyvvteeeE 570 Chlorobium tepi...
YP_828600    481 earSAAMKLVVNSAYGYLaaGGGLTRFADVHAANKVTRRGRETLDLMCRELAARGVTLLEADTDGVYFAVPegws-edeE 559 Solibacter usit...
NP_478219    360 kekRESVKVLANSEFGFL--GTSELAFNDMEAAALVTAYSRKVLKLMIEIITRYGGTPVEVDTDGVFFTHPn-------P 430 Nostoc sp. PCC ...
YP_001229085 465 qalQQAFKVLINSFYGYL--GSPLHNFSDVALAAEVTRLGRETIKTMLAWLLERGAQPVEVDTDGIYFIPPsvvataekE 542 Unknown
ZP_01594687  429 rqkQAACRLLLPAWSELL--ARGQYPFSDPAAAGELERLRNVLVRDLLDWLREEGAEPVVADLQGIYFMPPaghdgtdeI 506 Geobacter lovle...
Feature 1                                                                                        
YP_386125    544 EALVRELSATLPEGIAVEMDGRYRAIFS--YKIKNYALLDHDGKVIVRGSaLRSRGIERYLRDFMAAAVRLLLQGDGakI 621 Unknown
NP_663155    571 RQLVCEVSSTMPQGIRIGFDGRFKKMIS--YMKKNYALLDYNEKLKLKGSaFVSRSGEKFGRDFVREGFILLLNDDIqgL 648 Chlorobium tepi...
YP_828600    560 RGVVAEVASLLPPLVQLEFDGRYAAMLS--HEPKNYALLSYDDKLLLRGVaFRSSRAEPFGENFLRRAIGRLLKGDVpgV 637 Solibacter usit...
NP_478219    431 EEVRSLLQSQLPKGITVKLEFIADAMFIpeRGTKNYLLWLPDGKIITKGN-WRNRDRSQLEKEFSIEYLTLLIQNVSa-A 508 Nostoc sp. PCC ...
YP_001229085 543 ELLVRELSQSLPGGIEVELDGRYRAMFS--YKIKNYALLGYDGKMTVKGSgLRSRGIEKYLRAFMEEIIRLLLAGEGakV 620 Unknown
ZP_01594687  507 KMLARRLDRILPRGADLYCSGRYQAMLV--YKQNNYALLEQGGELVVRGSsFVSRAMEPFLREFLVEAVRLLLAGQGeqV 584 Geobacter lovle...
Feature 1                                                                                        
YP_386125    622 PAFHEDCIRRLRNHLIPIESLARTETLGEAPPTYlqkVRQGkrnpsaafeialraerpfraGDQISYYVtghgkGVTVYE 701 Unknown
NP_663155    649 HDLYVKYRNDLINHRLHISDFSRTESMKTTLDQYvsdVRAGkrsksityeialrqgleiakGDRITYYVagtgnPASFVE 728 Chlorobium tepi...
YP_828600    638 RDAYLVTLDALRRRELPTRDVSSLVRLTKSPEHYletREARrelpyeaml--aagrrqwsaGERVRVYRtrtsaGVVEET 715 Solibacter usit...
NP_478219    509 EDYYAHIKSQILSREYPKEKLAITRKIKEGEKEI---LKLGk------------------pGDVVTYYY-----GISGIT 562 Nostoc sp. PCC ...
YP_001229085 621 EAVYRDYTQKLRDHEFGISWLAKSETLGESLAVYrekVRAGkrnpaaayeiatksprefraGDQISYYIsgrrkGVTAYE 700 Unknown
ZP_01594687  585 HQLYEMFLRRLTSHACPVSWVMRSETVLDSRENYlqgIQSGrrnraavyelalarpetwrvGDRVEYYVsghakNVVVHE 664 Geobacter lovle...
Feature 1                                          
YP_386125    702 NCKPVSQYDPTRPDENTEFYLDKLNQLVKRLAAY 735 Unknown
NP_663155    729 NGRLAEEWNKEQPDENTGFYLKRLDEYAQKFLPF 762 Chlorobium tepidum TLS
YP_828600    716 DDDEDAIAGEDPRDYDVGHYARVLREIFASRLER 749 Solibacter usitatus Ellin6076
NP_478219    563 NISSNENYSRQYYLHLIEKRREEILKIAAPTTLE 596 Nostoc sp. PCC 7120
YP_001229085 701 NCRPIADYDPAHPDENTDYYMDKLKQLHKKFARF 734 Unknown
ZP_01594687  665 SCRLVADFDPAHPDLNIPWYAERLHQLFRRLEPL 698 Geobacter lovleyi SZ

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