Conserved Protein Domain Family
DNA_pol_A_pol_I_A

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cd08642: DNA_pol_A_pol_I_A 
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 ,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: 176479
View PSSM: cd08642
Aligned: 28 rows
Threshold Bit Score: 584.587
Threshold Setting Gi: 255994008
Created: 4-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                                                                                        
YP_002804824 214 LIKQAIECDTNYTERLTKAAIKLTGLENPNSPTQIKKWIGERLGrevksltktsip-----glieeakdlnkSEVIKMLE 288 Clostridium bot...
ZP_05733890  212 LVRGALAIDDQHKTELVEKAIQITGLTNPNSRNQLLTWINDNSDlklekltket---------vaeslqiaeDQVAEVLH 282 Dialister invis...
ZP_06405264  292 LANNAIRMNDEAQDELFAEMQEITNLENPNSPVQLKQWLSSKLGrpiqslaked---------akelatgasEDVKRVLY 362 Prevotella sp. ...
ZP_02085015  216 LADKIIQYDGIYQERLKQEARKLTGLNNPNSLPQLKMWFFMTYGldvpsitkdsipvi-eaqlkelktthdvLPGLRMLQ 294 Clostridium bol...
YP_002351535 113 LVKHAIACQERYQASLSKKAKGLTGLENPNSVQQLKDWLADMGYpvsslnkdsv--------selladedldEDVREMLL 184 Listeria monocy...
ZP_04599267  206 LVDAALACNDEIVEEATESSKILTGLENPNSTMQLKEWLTARLGydletmrkdd--------vsnllaqdipSDVRKVLQ 277 Veillonella dis...
ZP_06334079  216 LMLGANVLDKQSKEELLNQAKHITGLENPNSPTQLLAWLKDDQGldipnlqkkt---------vqeylkeatGKAKKMLE 286 Staphylococcus ...
ZP_03761012  215 LIAGALYVDEVSTEKLTAEAVELTGLDNPNSGAQLVPWINAHNKehpddpdlladlrketveealkdrdnlpEDVARMLE 294 Clostridium asp...
ZP_04569109  212 LVNGALYIDALSRANLLEEARDITKLDNPNSTSQLLNWLEEAGEevenlqkatv---------gkmidtlddGKAKRVLE 282 Fusobacterium s...
ZP_04858949  212 LVKGALSINDIVTAELTEEAIQVTGLDNPNSAAQLGKWLKEKTGqdienlqkgt--------vseligsledKEAVRVLE 283 Fusobacterium v...
Feature 1               #   #  ##                   ### # ####                                   
YP_002804824 289 LRQLMAKTSIKKYDTMQNARCKDGRVRGLLQFYGaNRTGRWAGRLVQVQNLPQNHlpdldnarnfvregkf---eevefl 365 Clostridium bot...
ZP_05733890  283 IRRALAKSSISKYESMKNAVCADGRIRGVLQFYGaNRTGRWAGRLVQVQNLPHDVpvamdtairlvkngna---rgvklm 359 Dialister invis...
ZP_06405264  363 LRSMSSKTSVKKYEAMTLAKCSDNKLHDLLQFYG-AKTGRWAGRIVQVHNLPRNSskdlalarelvkkndf---ellelt 438 Prevotella sp. ...
ZP_02085015  295 IRKELGKTSVKKYQAMRHAVCPDGYLRGILQFYGaNRTGRWAGRIVQVHNLPQNKipdldlardlvkqedf---dtlell 371 Clostridium bol...
YP_002351535 185 LRQEMSKTSIKKYEKMQHARCHDGRVRGLLQFNGaNRTGRWAGRLVQVQNLPRNYikdiaevrkdlkagdy---eafemm 261 Listeria monocy...
ZP_04599267  278 NRQVLGNSSIKKYLAMKNAVCSDGRIHGMLQFYGaMRSGRWAGRVVQLQNLPRNYledldtardvlksrdv---emldll 354 Veillonella dis...
ZP_06334079  287 IRLQMSKTSVKKYNKMHDMMCSDERVRGLFQFYG-AGTGRWAGRGVQLQNLTKHYisdteleiardlikeqrfddldlll 365 Staphylococcus ...
ZP_03761012  295 IRQQLGKTSVKKYVAMDVARGEGDRVRGLTQYYGaNRTGRWAGRLVQLQNLPRNYlktldyarelvkakny---dglril 371 Clostridium asp...
ZP_04569109  283 IRQELSKTSVKKYKAMDEAMCKDERVRGLLQFYGaNRTGRYAGRLVQVQNLPRNYietldvardvikkgdg---elleml 359 Fusobacterium s...
ZP_04858949  284 IRQELAKTSIKKYVAMEEAICPDGRIRGLLQFYGaNRTGRWAGRLVQVQNLPRNYletldyareivksqda---dflklv 360 Fusobacterium v...
Feature 1                                   ##                           #                       
YP_002804824 366 fdsvpdtlsQLIRTAFIPRegNRFIVSDFSAIEARVIAWFAGEqwrldvfstHGKIYEASASQMFkvpies---ikkgse 442 Clostridium bot...
ZP_05733890  360 yghistslsHLIRAAFVAPegSLLCVSDFSAIEARVLSWLADEkwrqdvfakGGDIYCASASSMFgvpvek---hgingh 436 Dialister invis...
ZP_06405264  439 fgnvcdilsQLIRTAFIAKenYTLCVCDFSAIEARVIAWLAGEewrlkvfrgSGRIYEASAARMFgvdekt---ithdsp 515 Prevotella sp. ...
ZP_02085015  372 fegipfvfsQLIRTAFIPSegYRFVVSDFSAIEARVIAWLADEkwrlnvfrtHGKIYEASAAQMFhvpien---ikkgsr 448 Clostridium bol...
YP_002351535 262 ysnvpdvlsQLIRTAFIAEdgYTFDITDFSAIEARVIAWLAGEqwrldvfnsHGKIYEASASQMFhipie-----evdkn 336 Listeria monocy...
ZP_04599267  355 ygnpgdvikQLIRTALVAEdgHRFIVADFSAIEARVIAWLAHEkwrqdvfaqGGDIYCASASSMFhvpvek---hgvngh 431 Veillonella dis...
ZP_06334079  366 nvhpqdllsQLVRTTFTAEegNELAVSDFSAIEARVIAWYAKEqwrldvfntHGKIYEASASQMFnvpves---itkgdp 442 Staphylococcus ...
ZP_03761012  372 ygnvpdtlsQLIRTAFIPSegHKFVVADFSAIEARAIAWLAGEqwvnevfatHGKIYEATAAQMFgvpveritkgnpeys 451 Clostridium asp...
ZP_04569109  360 ygnipdtlsQLIRTAFIPSegNHFVVSDFSAIEARVIAWLAGEewrmevfktHGKIYEASASQMFgvpintiakgeenyh 439 Fusobacterium s...
ZP_04858949  361 ygnvsdtlsQLIRTAFVPSegHKFVVADFSAIEARVIAWLAGEqwrqevfatHGKIYEASASQMFgvpielikkgnpeya 440 Fusobacterium v...
Feature 1         #   #                                                                          
YP_002804824 443 LRQKGKIAELALGYGGSVGALSSMDrk-ksIPEEELPGLVKSwrnaNPNITKFWWDVDKAAKKAIRERTTVNLqyglkfi 521 Clostridium bot...
ZP_05733890  437 LRQKGKVAELALGYQGGPPALITMGalkqgLTEDELPDIVHRwrgaNPRICGFWYDVDGAALSVMSDARPVGLphgilis 516 Dialister invis...
ZP_06405264  516 LRQKGKIAELALGYEGGANALKIMGadkmgLSDPEIAQIVSGwrnsSPNIVKLWRDVERAAKEAILSDRIIKLkqgglif 595 Prevotella sp. ...
ZP_02085015  449 LRQQGKVAELALGYGGGFGAMKAMDka-gtIPDDEIPMIIANwrkaSPNICKLWRNAEAAARAAIEERRTIKLkhglsfs 527 Clostridium bol...
YP_002351535 337 LRQKGKVSELALGYNGGVNALIAMGalemgLKENELQGIVDAwrkaSPAITSLWRGVEKHAKLAISTRKSQKYkgltfyy 416 Listeria monocy...
ZP_04599267  432 LRQKGKVAELALGYGGGVGAMKAMDsk-geIPEKELPGIIEAwrqaSPRITKFWKDADSAAKQVVRTGEPVRIiqgnikf 510 Veillonella dis...
ZP_06334079  443 LRQKGKVSELALGYQGGAGALKAMGalemgIEENELQGLVDSwrnaNPNIVNFWKACQEAAINTVKSRKTHHThglrfym 522 Staphylococcus ...
ZP_03761012  452 LRQKGKVATLALGYQGSTAALIAMGalkmgLTEDELPDIVTRwrnaNKRICGLWYAVENTALRVMQTAQPQGLnglifal 531 Clostridium asp...
ZP_04569109  440 LRAKGKVAELALGYQGSVGALTAMGaadmgLTDEEMKDIVDRwrksSKRIVELWYALENAAVEVLETGEPQIVkcvklak 519 Fusobacterium s...
ZP_04858949  441 LRQKGKVAELALGYGGSSGALIAMGaldmgLEEKELPDVVRRwrnaNKRITDLWYGIENAVIKLMETGETQGLkgiifsr 520 Fusobacterium v...
Feature 1                                                                  #      #              
YP_002804824 522 ydpgvlfiqlpsgrklsyirpki----ephetfsgdkityegmeqtskqwkridtyGPKLVENIVQATSRDCLREAMFRV 597 Clostridium bot...
ZP_05733890  517 recnllygydyltirlpsgrklyy-pqpyinenqfgkpalhyrvqagikwshtstyGGKLVENITQAIARDCLALAINRL 595 Dialister invis...
ZP_06405264  596 rktsnilqiklpsgrllsyp---------lakivdnkicymsqnqttrqwvdtetyGGKLVENIVQAIARDCLGETILRV 666 Prevotella sp. ...
ZP_02085015  528 yinrilfiglpsgrklayydtr-----ieddekgksvityagvdqetkkwgrlktwGGKLVENIVQATARDCLAVTMERV 602 Clostridium bol...
YP_002351535 417 eagilfiklpsgrnlayfra---------klvpgkygpqicyegvtdkgwrkqytyGGKLVENIVQAIARDCLAISLRRI 487 Listeria monocy...
ZP_04599267  511 fkskgflfielpsgrrlayarpr----lglnqfgsesieydgmdqvkntwgrvetyGGKLVENIVQAVARDCLAASMLRL 586 Veillonella dis...
ZP_06334079  523 kkgflmielpsgralaypkas-------vgenswgsqvvefmgldlnrkwsklktyGGKLVENIVQATARDLLAISIARL 595 Staphylococcus ...
ZP_03761012  532 egdliygqsfltvrlpsgrklyypkpflqenrfgkqaihyyavgqqtrkweidstyGGKMTENIVQAIARDCLAVTLRRI 611 Clostridium asp...
ZP_04569109  520 eydfiygqdfftielpsgrklfypkpflkenqfgqmqmhymginqttkkweviptyGGKLTENIVQAIARDCLAETLLRV 599 Fusobacterium s...
ZP_04858949  521 eidliydqdfltiklpsgrklyypkphlkenrfgsnalhyfgvnqttkkwevqetyGGKLVENIVQAISRDCLAVTLKRL 600 Fusobacterium v...
Feature 1                  ###                                              
YP_002804824 598 NKEgyDIVMHVHDEVVLDIPk---dRATVKEINELMGqpikWAPGLPLKADGYECNYYM 653 Clostridium botulinum A2 str. Kyoto-F
ZP_05733890  596 VKAgyKPLMHIHDEVVLEVPkdkihEDEIDRINQIMCapipWAPGLLLNADGFISPYYT 654 Dialister invisus DSM 15470
ZP_06405264  667 DKKgyNICFHVHDEIIAEVPtd-esAKALQDIKNIFAtpitFAPDLPLKGEGYITPYYL 724 Prevotella sp. oral taxon 299 str. F...
ZP_02085015  603 SGAgyQIVMHVHDEIIVDVPet--dIDALEKITAIMAqpvpWAQELPLRGDGYETPFYK 659 Clostridium bolteae ATCC BAA-613
YP_002351535 488 EDTgiDTVMHVHDEAITEVQe---sESSVDKLNAILAepisWAPGLPLQGDGFSSDFYM 543 Listeria monocytogenes HCC23
ZP_04599267  587 SKAgyKIVAHIHDEVVIEAPi---gVGSLEEVIDIMCepepWNEGLILNAAGFENPYYM 642 Veillonella dispar ATCC 17748
ZP_06334079  596 EASgfKIVGHVHDEVIVEIPr---gSNGLKEIETIMNkpveWAEGLNLNSDGFTSPFYM 651 Staphylococcus aureus A10102
ZP_03761012  612 AQKglQTVFHVHDEVIIDAPm----ETTVDEICDLMAepipWAPGLILKGAGFESSYYM 666 Clostridium asparagiforme DSM 15981
ZP_04569109  600 KAKgwPIVFHVHDEIILDVPk----SVELEEVIKTMTeeisWAKGLILNAAGFTGSYYM 654 Fusobacterium sp. 2_1_31
ZP_04858949  601 ETEglQTVMHIHDEAVIDADp----NVDLNKVCELMGqpieWAPGLLLKAAGFESGYYM 655 Fusobacterium varium ATCC 27725

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