1TAQ,2KTQ,1QTM,1BGX,5KTQ,3KTQ,4BDP,3BDP,1L3S,1U45,1LV5,2HVH,2HHW,1L3V


Conserved Protein Domain Family
DNA_pol_A_pol_I_C

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cd08637: DNA_pol_A_pol_I_C 
Click on image for an interactive view with Cn3D
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication
Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.
Statistics
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PSSM-Id: 176474
View PSSM: cd08637
Aligned: 180 rows
Threshold Bit Score: 479.225
Threshold Setting Gi: 116515191
Created: 23-Feb-2010
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 22 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:The Pol A domain has a shape of a right hand in which the palm, fingers and thumb form the DNA-binding crevice; the active site, composed of three acidic residues, is located at the palm which forms the base of the crevice.
  • Structure:3KTQ; Thermus aquaticus DNA polymerase I binds DNA, two Mg ions, and ddCTP; contacts at 4.0A
    View structure with Cn3D
  • Citation:PMID 9857206

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
1TAQ_A       452 DVAYLRALSLEVAEEIARLEAEVFRlaGHPFNLNSrDQLERVLFDELgLPAIGKTEktgkrstsaavlealreaHPIVEK 531  Thermus aquaticus
3KTQ_A       160 DVAYLRALSLEVAEEIARLEAEVFRlaGHPFNLNSrDQLERVLFDELgLPAIGKTEktgkrstsaavlealreaHPIVEK 239  Thermus aquaticus
YP_003308805 505 DPDYFGKYGNELKNNLAEIEKNIYGlaGEEFNINSpKQLSEILFEKMmLDPVKKTKtgystdvev-levlaaqgVEVAEK 583  Sebaldella ter...
NP_603602    531 DVQYFKNYSLELEKELLKVEKAIYEeaGEEFNINSpKQLGDILFVKLnLPSGKKTKtgystdvmv-ledlesygYNIARL 609  Fusobacterium ...
YP_003306441 485 NQNYFEKYNLELEKKIKDIENKIYIesGESFNISSpKQLGEVLFETMgIEGVKKNKrgystdaev-lellrdrgIKIAEL 563  Streptobacillu...
YP_802820    503 KKKILKKQKKNHEKTLKKLKKKIFKitKEKFNINSsKQLQNILFKKFnLPKIYKTKlgnistnei-vlkklskiHILPKI 581  Buchnera aphid...
AAG43104     540 SSERMKALSDEYSSLLEKTKEKIYAeaGEEFNLQSpKQLEYILFDKMgIPPTKKTKtgfstdee--vltelsqkYKIAEY 617  Brachyspira hy...
YP_002249284 462 NIEKLETLTKHISMELDKIKEKIYTiaGTEFNINSpKQLAEVLYDRLgLKTRKRGKkarsteme--vleelaiqHELPHE 539  Thermodesulfov...
AAR11877     477 DKEYLKQLSDEFCERIKKLEEEIYElaGTRFNLNSpKQLSEVLFERLkLPSGKKGKtgystsss--vlqnlinaHPIVRK 554  Dictyoglomus t...
YP_007222    512 DTAYLKHLSQFIGQEIHCLEQNIYAlaGEIFNLNSpKQLSQILFHKLgIKPPKKIAtghstnae--vleilkhvYPIAEK 589  Candidatus Pro...
Feature 1            #   #  ##                        ### # ####                                #
1TAQ_A       532 ILQYRELTKLKSTYIDPLPDLIhprtGRLHTRFNQTATATGRLCCCDPNLQNIPVrtplGQRIRRGFIAEe-gWLLVALD 610  Thermus aquaticus
3KTQ_A       240 ILQYRELTKLKSTYIDPLPDLIhprtGRLHTRFNQTATATGRLSSSDPNLQNIPVrtplGQRIRRAFIAEe-gWLLVALD 318  Thermus aquaticus
YP_003308805 584 ILEYRGYTKLLTTYVEPLPKLAds-eNRIHTTFHQNGTATGRLSSSNPNIQNIPVktdeGIKIRRGFVSEe-gWSFISFD 661  Sebaldella ter...
NP_603602    610 LLDYRKLNKLKTTYVDTLPLLVde-nSRIHTSFNQIGTATGRLSSSEPNLQNIPVktddGIKIREGFIAGe-gKVLMSID 687  Fusobacterium ...
YP_003306441 564 LLEYRELVKLKSTYVEPLLKLSi--nGRIHTTYNQTGTATGRLSSSNPNLQNIPTrtyeGTKIREGFIASk-gMKLVSFD 640  Streptobacillu...
YP_802820    582 ILQFRLIKKIINTYLRNLIKSInnktNRIHTTYNQINTSTGRLSSKNPNLQNIPIktkiGRKLRIAFITKk-kWLLLTAD 660  Buchnera aphid...
AAG43104     618 MLTYRKYAKLKNTYLDVFPTLInektGRIHASFNQTVTATGRLSSSEPNLQNIPVrgeeGREIRNTFIPEk-gNLLIAAD 696  Brachyspira hy...
YP_002249284 540 VINYRTLNKLLTGYLIPLRDYInpetKRIHTKWSQTVAGTGRIVSSEPNLQNIPVkgewAEFLREVFIPEn-gYMFLSAD 618  Thermodesulfov...
AAR11877     555 ILQYRELYKLKSTYVDAIPNLVnpqtGRVHTKFNPTGTATGRISSSEPNLQNIPIkseeGRKIRRAFVSEd-gYFLVSLD 633  Dictyoglomus t...
YP_007222    590 LLEYRTLEKLRSTYVNSLPLQVnaktGRIHCNFNQSMAATGRLSCQDPNLQNIPVrtevGRQIREAFRPEkedWSYLSAD 669  Candidatus Pro...
Feature 1        #                           #                    #   #                          
1TAQ_A       611 YSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFgvpr-eavdPLMRRAAKTINFGVLYGMSAHRLSQELaipyeEA 689  Thermus aquaticus
3KTQ_A       319 YSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFgvpr-eavdPLMRRAAKTINFGVLYGMSAHRLSQELaipyeEA 397  Thermus aquaticus
YP_003308805 662 YSQIELRVLAELSEDETLILAYQKDKDLHDLTARKLFfktdeepvsREERSIAKVINFSILYGKTPFGLSKELkipmgDA 741  Sebaldella ter...
NP_603602    688 YSQVELRVLTSMSKDENLIEAYREEKDLHDLTARRIFnlpdsetvsREQRTIAKIINFSIIYGKTPFGLAKELkipvkDA 767  Fusobacterium ...
YP_003306441 641 YSQIELRVLAEISKDENLINAYKHNLDLHELTARKIFmlkddekvsKTQRNIAKVINFSVLYGKTPFGLSKELkitvsDA 720  Streptobacillu...
YP_802820    661 YSHIELRIIAHYSKDKNLIKDLLKNKDIHISTASHIFnkpl-ekikKYHRNIAKTINFSILYGISPFGLSKKLnisikKS 739  Buchnera aphid...
AAG43104     697 YSQIELRLLAHFSNDPALVEAFKNNDDIHRKTAMKIYsvsk-ehvtASMRNIAKIINFSIIYGKTAFGLSKELgikkkEA 775  Brachyspira hy...
YP_002249284 619 YSQIELRLLAHMSEDPALIKAFLDGKDIHTATASEIFsipe-navtDEHRRIAKTVNFGISYGISPFGLSESIkipyeKA 697  Thermodesulfov...
AAR11877     634 YSQIELRIMAHLSQEPKLISAFQKGEDIHRRTASEIFgvpe-eevdDLLRSRAKAVNFGIIYGISSFGLSETVsitpeEA 712  Dictyoglomus t...
YP_007222    670 YSQIELRLLAHLSEDPVLIKAFLSNEDIHKYTASLIFdvpl-qqvsSEQRYQAKAVNFGLIYGQQAFGLAHELgidtkTA 748  Candidatus Pro...
Feature 1                                                                  #      #              
1TAQ_A       690 QAFIERYFqsFPKVRAWIEKTLEEGRRrGYVETLFGR-RRYVPDLEArvksvREAAERMAFNMPVQGTAADLMKLAMVKL 768  Thermus aquaticus
3KTQ_A       398 QAFIERYFqsFPKVRAWIEKTLEEGRRrGYVETLFGR-RRYVPDLEArvksvREAAERMAFNMPVQGTAADLMKLAMVKL 476  Thermus aquaticus
YP_003308805 742 KLYINKYFeeYPRVRTFLNSVLQEAKLnGFVETLYGT-RRYITGINSsnkniEAQADRMAVNTVVQGTAANIIKIVMVKL 820  Sebaldella ter...
NP_603602    768 SEYIKKYFeqYPRVTTFEKEVIEFGEEhGYVKTLFGR-KRYISGIDSknktiKSQAERMAVNTVIQGTAAEVLKKVMVKV 846  Fusobacterium ...
YP_003306441 721 KLYINTYFkeYPKVRILLDDIIEKAKKdGYVETKFGT-RRYVYDINSsniniKEQAKRMAVNTVIQGTAANIIKKVMKEI 799  Streptobacillu...
YP_802820    740 KNLIYRYFlkYNKIKRFIKNTYKTAKKrGYIKTLFKR-KLYIPNINSkniylKNSAKRFCINLMIQNTASDIIKKSMITL 818  Buchnera aphid...
AAG43104     776 EDFIKGYSstYSRVKPFCDEVVEEVRNkGFVRTMCGRiRDLSKTINSsnamaRNEAERMALNTLIQGSAADMIKVAMVAI 855  Brachyspira hy...
YP_002249284 698 EELIELYFlrYPMVRKFIEETISFAQKnGYVRTLFGR-IRPLPEINSpnqflRMQSERMAVNARVQGTAADIIKIAMIRI 776  Thermodesulfov...
AAR11877     713 EKFIDSYFkhYPRVKLFIDKTIHEAREkLYVKTLFGR-KRYIPEIKSinkqvRNAYERIAINAPIQGTAADIIKLAMIEI 791  Dictyoglomus t...
YP_007222    749 AAFIQRYFerYGKVKEFLEACKQSAREtGKAVTMYGR-ERLLPEIRSqnamiRATADRFAVNTPIQGTQADLIKMAMLKI 827  Candidatus Pro...
Feature 1                         ###                                              
1TAQ_A       769 FPRLEem---gARMLLQVHDELVLEAPke--rAEAVARLAKEVMEgv-ypLAVPLEVEVGIGEDWL 828  Thermus aquaticus
3KTQ_A       477 FPRLEem---gARMLLQVHDELVLEAPke--rAEAVARLAKEVMEgv-ypLAVPLEVEVGIGEDWL 536  Thermus aquaticus
YP_003308805 821 YEEFKdk--edINMLLQVHDELIFEVKne--sVDKYLKEIDNIMEntiklKNVRLAANGNVGKNWG 882  Sebaldella termitidis ATCC 3...
NP_603602    847 YDILKdk--edIALLLQVHDELIFEVEkn--sVEKYSGILADIMKntvqlEDVKLNININIGKNWA 908  Fusobacterium nucleatum subs...
YP_003306441 800 YDKLCnd---nVKMLLQVHDELIFEVRediniFEEIRDIMQNTIVf----DDVVLKVNGSEGDNWA 858  Streptobacillus moniliformis...
YP_802820    819 HHLFKkkfpkdIKIIMQIHDELIFEIKek--kKDKIIDVIKKIMEnn-tkLIIPLYITTKIGKNWK 881  Buchnera aphidicola str. Cc ...
AAG43104     856 HKEFKnhl-ktAKIVMQVHDELVVEVSea--eADKAMTIMKEIMEhs-vkANVPIIVDIHKGNSWG 917  Brachyspira hyodysenteriae
YP_002249284 777 YNRLKkek-lnAKIILQIHDEIVLEVEqk--vIEKVSEIVQNEMKdf--sLSVPLEVNVFSGNSLN 837  Thermodesulfovibrio yellowst...
AAR11877     792 YKEIEnkn-lkSRILLQIHDELILEVPee--eMEFTPLMAKEKMEkv-veLSVPLVVEISVGKNLA 853  Dictyoglomus thermophilum
YP_007222    828 NKLLIqek-kkGFMILQIHDELIFEVPnq--eLESISHLVKNTMEni-inLKVPLIVNIHIGKNWK 889  Candidatus Protochlamydia am...

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