Conserved Protein Domain Family
DNA_pol_A_pol_I_B

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cd08643: DNA_pol_A_pol_I_B 
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication
Family A polymerase 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 ,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: 176480
View PSSM: cd08643
Aligned: 8 rows
Threshold Bit Score: 593.256
Threshold Setting Gi: 254502983
Created: 16-Mar-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
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.
  • Citation:PMID 9857206

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
NP_744422    222 FNREKAALLYAKLAQRRGDLERELKEFFKFWhapagevltkktrrvfiedprgnt-------------errvklkgqpaf 288 Pseudomonas put...
YP_001526513 199 FDQAKAASLYADLVQRKTELEAELQSAFPPWevesvfvpkv--------------------------------------- 239 Azorhizobium ca...
ZP_05115134  173 LNTGKARGLEAELRQEASDIERELQEVFPPRliadkrkgtaev------------------------------------- 215 Labrenzia alexa...
ZP_05891117  225 FDEEKAIKLLGRLAGRREYLYNKLIETFGGWwvsdgvsvparti-----------------------------------n 269 Vibrio parahaem...
ZP_06361333  189 FDQEAAQKLHVALLGKQEHIANDLIAEFGSWyepekkgmgpdgfaqtwtpkkadpkrgywghyeqvevpvttfdpfegtp 268 Rhodopseudomona...
ZP_02357916  186 LNMREAMTLAAQLWERRDGYLAEMQRVFPPIyvsagavtpkr-------------------------------------- 227 Burkholderia ok...
ZP_06266926  202 FNQEKAVLYYSQLAKRREELTQELQRIFPPEdkgdwfvpkv--------------------------------------- 242 Synergistetes b...
YP_003550718 194 FNVEKAGILYGQLAGEKAQLESELKELFPPWtkeeifipkr--------------------------------------- 234 alpha proteobac...
Feature 1                                                                                   #   #
NP_744422    289 nqvgwfekyteGVRYTKVKIVEFNPSSRDHIADRLtalYGWVPEKFTKGGKPQVDDEVMSKLS--YPPCKLLTEYLLVAK 366 Pseudomonas put...
YP_001526513 240 --nnrvrgyvkGVPFTKRRTIHFKPSSRDHIAGRLkakYGWEPSEFTDEGKPKVDEDVLSHLP--YPEAKLLSEYLMVEK 315 Azorhizobium ca...
ZP_05115134  216 mpkanrkairkGQPYSRLKLEIFNPGSRPQAADRLikkYKWKPKKFTDKGSPAIDESVLAKLK--YPEAKVLNRYLRITK 293 Labrenzia alexa...
ZP_05891117  270 ykdptkpsrvqGAPFTKVKWVDFNPSSRRHIIKVLt-dRGWTPQEFTPSGEAKVDESILKELD--FPEARLMAEWFLVQK 346 Vibrio parahaem...
ZP_06361333  269 ttitsvkrvfkGYPLTKIERVTFNPSSRKHIIKKLk-eMGWEPQEFTESGEAKVDDDVLEGLTdtFPQASKLVEYLLLDK 347 Rhodopseudomona...
ZP_02357916  228 tmkregreytaGAPYTKIVLQEFNPGSEYHVANRLk-rKYGWRAPLTEKGNPNITEAVLKKLD--FPEVQPLLHFARVDK 304 Burkholderia ok...
ZP_06266926  243 --nnakrgyvkGERVWRARITAFNPGSRKDIAERLretRGWEPQEYTERGTPKVDEEVLSALD--WPEAKALSEYFLVQK 318 Synergistetes b...
YP_003550718 235 --nnktlgyvaDEPFIKCKEITFNPNSRKHIQRCLmdkYDWKPRQFTYSGDAKIDEGVLSRLP--YPEAKKLARSFLLQK 310 alpha proteobac...
Feature 1          ##                                ### # ####                                  
NP_744422    367 RISQLAEGKQAWml-------veKQGRIHGSVNPNGAATGRATHAYPNVAQVPasgspygKDCRELFTVPl--------- 430 Pseudomonas put...
YP_001526513 316 RLGQIATGKEAWlkh------vkADGRIHGDVTTNGAVTGRMTHSKPNIAQVPgngspygHRCRELFVAAk--------- 380 Azorhizobium ca...
ZP_05115134  294 LLGQVVDGENGWlkl-----vneETSRVHGAVNTIGAATGRCSHFKPNMAQVDkk----dLRMRECWEARp--------- 355 Labrenzia alexa...
ZP_05891117  347 RLGQLADGNQAWlnt------vhPDGFIRGSVNPNGAVTGRATHSFPNVAQVPscsaeygAECRELFTVPd--------- 411 Vibrio parahaem...
ZP_06361333  348 RLGQLADGDNAWlkk------vhDDGKMHGAMDTMGTVHSRASHFSPNMGQVPaakspygAECRALFGPNgidthtagwg 421 Rhodopseudomona...
ZP_02357916  305 QWTQLASPPKKNgtgggwihhadENHRVHGYVNSNGAVTGRMTHSRPNSANID-------KEMRHIWIPSm--------- 368 Burkholderia ok...
ZP_06266926  319 RIGQLAEGNNAWlkl------vgRDGRIHGHVITNGAVTGRCTHVSPNMAQVPavgvpwgAEFRSLFYAPp--------- 383 Synergistetes b...
YP_003550718 311 RIGMLAEGNNAWlr-------lvEGNTLCHVINPNGAVTGRATHFNFNTAQVPsvrapygKECRELFGVPe--------- 374 alpha proteobac...
Feature 1                   ##                                   #                           #   
NP_744422    431 ----gWLLVGADASGLELRCLAHFMARYDGGkyvd------illnGDIHWANVQAMgitsekrd---dhntlhklYRDGA 497 Pseudomonas put...
YP_001526513 381 ----rKLLVGCDADALELRCLAGYMARYDGGayvrtvlegkkelgTDMHTLNAKALg-----------------cSRDVA 439 Azorhizobium ca...
ZP_05115134  356 ----gWDLVGVDAEGLELRMLAHYLGKFDGGaltrallegskeagTDAHTINQKAVgl----------------hKRDNA 415 Labrenzia alexa...
ZP_05891117  412 ----gWYLLGSDASGLELRCLANFMARYDDGkyid------vvlnGDIHWSNAQAAgfipkgtir-dphnpiheeARRKA 480 Vibrio parahaem...
ZP_06361333  422 gekeeIVQVGADMSGLQLRALAHLLHPLDGGaysd------ivtsGDVHWSHTQAMglvgpeeprdkhselhnilREKGA 495 Rhodopseudomona...
ZP_02357916  369 ----gMKQVGCDAEGLELRVLAHYLARYDGGrltrqlldgdkalgTDAHSVNRDNTdl----------------fSRDGA 428 Burkholderia ok...
ZP_06266926  384 ----gWSVLGADASGLELRCLAHFMARYDGGayar------kileGDIHWANAQALglvaegekkdpenpyhmwaRNKVA 453 Synergistetes b...
YP_003550718 375 ----gYSLVGSDLSGVELRCLANVLQDQGKYani--------ilnADIHLANMHSMgl----------------tSRDQA 426 alpha proteobac...
Feature 1        #                                                                               
NP_744422    498 KTFIYAFLYGAGDEKVGTIVfgmvakakalgldyqhll---------dvffngqdnpdeealkaAGKKLKATFLRKTPaL 568 Pseudomonas put...
YP_001526513 440 KVWFYAFIYGAGDFKLGTILgapkg-----------------------------------eeqkWGRRSRARFLKALPaL 484 Azorhizobium ca...
ZP_05115134  416 KRLLYALMYGAGDVKLGQIIvddareagi---------------------------nlkgnkkaLGAKARKDLAKGMKgL 468 Labrenzia alexa...
ZP_05891117  481 KTFIYAFLYGCGAELTGQQVgwteeeylnwkakgahkpii-----nrfkrqgkpwtrekicnilKGEEVQKNFMKGLPaL 555 Vibrio parahaem...
ZP_06361333  496 KTFGYSYLFGCFPPKSGRVVrdclttaknknpewgylfd------rffkamttkgairirsdkeVGTVVRKSFDERLK-L 568 Rhodopseudomona...
ZP_02357916  429 KTLLYGSLYGAGDEKAGNIWiadwrtsgkpvsewp---------------vwchvrgklktakaIGRVVKAKLLDGIVgF 493 Burkholderia ok...
ZP_06266926  454 KRFIYALNYGAGDHKLGELVeltddqakallaaapkskidqtsarlakqfqyktitfkdiaqslKGAELRATFMKNLPaL 533 Synergistetes b...
YP_003550718 427 KTAIYCMIYGGGDARLGEVVgkg---------------------------------------aaEGRTLRNNFMKANPaF 467 alpha proteobac...
Feature 1                                        #      #                                    ### 
NP_744422    569 KKLVKAVKEAAKR--GHLVGLDGRHVhvKSAHAALNYLLQGAGALACKQWLVFLDDElqarglkhgwdgdyAFCAWVHDE 646 Pseudomonas put...
YP_001526513 485 GTIIKKVQEKVQKk-GFLRGLDGRELrvRSAHSAFNTLLQSAGAVLMKMALVLLDEDlqaagy--vpgqhyEFVANVHDE 561 Azorhizobium ca...
ZP_05115134  469 DKLVDKVKDKAGKk-KYIQGLDGRRIyvRSEHSAFNFLLQGGGAIVMKQALILFHFNhshkfg--pygerwAYCANVHDE 545 Labrenzia alexa...
ZP_05891117  556 KNLIDECKELHKEq-GYIEGIDGRRIytRSAHASLNTLLQGAGALVCKAWIVEIEKLaiaeglkhgidgdfMYCAWVHDE 634 Vibrio parahaem...
ZP_06361333  569 GRLHAKLKACLKHykNHLPGLDDRLVpcRSEHSALNFACSSIEAILCKQWLCDSVSAleakgy--vwgrdfVLMLWVHDE 646 Rhodopseudomona...
ZP_02357916  494 RKLIKDIETAAKSr-GWLKGIDGRRIrvRHAHAALNTLLQGTGAIIMKKALAIYHAEiteihgl-vhgvhfGYLANVHDE 571 Burkholderia ok...
ZP_06266926  534 ASLIEDVKRVAKKr-GYLIGLDKRRLnvRSIHSAFNTLLQSAGAIAVKKATCVLWDDlttag----ladkvQQVAHVHDE 608 Synergistetes b...
YP_003550718 468 ADLVRQLKQVVTKr-GHLVGLDGRKLa-VRGHAQLNVLLQSAAALLSKKWVELIDTEiatq------gidaEIIAWVHDE 539 alpha proteobac...
Feature 1                                                                
NP_744422    647 VQIACRn-------EAIAVIVREAAEacvakageaFNFRCPLAGESKMGLNWAETH 695 Pseudomonas putida KT2440
YP_001526513 562 WQIEVNee----iaEDVGKRAVTAIVrag----ehFGFGCPLSGNFAVGRSWAETH 609 Azorhizobium caulinodans ORS 571
ZP_05115134  546 VQSETHpdiskayaETLADCIREAGEh--------FDMRCPLAGAYDIGKNWKDTH 593 Labrenzia alexandrii DFL-11
ZP_05891117  635 VQIACRtke---iaERIGQLCQVAMTnve----keFNFVCRLDADFDIGKSWKETH 683 Vibrio parahaemolyticus AN-5034
ZP_06361333  647 QQIACRks----iaEEVGKTLVECAKqag----vkLGFRVPLASEYKIGRNWLDCH 694 Rhodopseudomonas palustris DX-1
ZP_02357916  572 VQQECLpq----yaELIGTTFKNAITkag----ehWNFRCRLDGAFDIGNNWHETH 619 Burkholderia oklahomensis EO147
ZP_06266926  609 YQLLVKeg----eeEHVGQIATAAFGkag----lfFEFRIPLAGEFKFGRNWAETH 656 Synergistetes bacterium W5455
YP_003550718 540 VQIKVRkg----deENVGHITGRMAEeag----kfFKFKIPIESEFNIGRNWAETH 587 alpha proteobacterium IMCC1322

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