Conserved Protein Domain Family
DNA_pol_A_Aquificae_like

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cd08639: DNA_pol_A_Aquificae_like 
Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences
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 for phylogenetic anaylsis of bacteria. Species of the phylum Aquificae grow in extreme thermophilic environments. The Aquificae are non-spore-forming, Gram-negative rods and strictly thermophilic. Phylum Aquificae Pol A is different from E. coli Pol I by three signature sequences consisting of a 2 amino acids (aa) insert, a 5-6 aa insert and a 6 aa deletion. These signature sequences may provide a molecular marker for the family Aquificaceae and related species.
Statistics
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PSSM-Id: 176476
View PSSM: cd08639
Aligned: 17 rows
Threshold Bit Score: 412.444
Threshold Setting Gi: 119493749
Created: 23-Feb-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                                                                                         
O67779        208 VDVEELTNKLKAVERETQKRIQEFYIkyrvdplspkqlaslltkkfk--------------lnlpktpkgnvstddkalt 273  Aquifex aeolicus
ZP_02730163  1092 FDRPAWDAVAADTEACAARAREHLDEllpnagnlfgvtnwnsvdevt---------------aafaaagvaltstgddal 1156 Gemmata obscu...
ZP_04036592   322 FNPERWLATAKEAELSAQEALKRLDWrtnwdspkqvlealrr------------------------agielsdtreetls 377  Meiothermus s...
ZP_03156829    77 LDLEQWHSLGIELQQQQTLLSETISLqlelepkpvqlslleeyapqqttsinlrspqqviaalkkigisvnstdaselil 156  Cyanothece sp...
YP_001806245  283 LDLDRWGELAKEIETRREDAAKIACQvlkpdhaqlnlfggeasinldsneq-------viaalarlgihtdstskdtldk 355  Cyanothece sp...
YP_002121207  209 IDTKEIETMKKQLQKKTQELAMNFYIkyridisspkkvgeflenhlnisl--------prtdkdniitddsvliehldye 280  Hydrogenobacu...
YP_001930793  223 IDEEEAKKLLKQKESEFQSDYMKFKIktgadpfspqqvvnyltnklk--------------iklpktekgsfssqdvflk 288  Sulfurihydrog...
ZP_02179064     3 VDKNLLKNMLTDIQSKYQRMYIEFVRnygvdpfspakvsnwlvnkvg--------------itlpktqkgalssqdkalk 68   Hydrogenivirg...
ZP_05130182   186 LDDDRRLAVELEIRIKDLLNRKELNLnspkqlveaiveygi---------------------------klhstsddelak 238  Clostridium s...
YP_645884     205 LDVRRWRELERVVRRRRDEAARRLEShfpqpegvlpleglgprlnlnspq---------qimeafrsigielpdtrmwtl 275  Rubrobacter x...
Feature 1                       #   #  ##                             ### # ####                  
O67779        274 syQDVEPVKLVLEIRKLKKIADKLKELKEHl-------KNGRVYPEFKQIg-AVTGRMSSAHPNIQNIH--RDMRGIFKA 343  Aquifex aeolicus
ZP_02730163  1157 aaVAHPAAALLREHRAASKLSGTYGRGWLRhv-----aDDGRVYAAWKQVgaGASGRMSCKDPNLQQLPrdPRFRRCFVT 1231 Gemmata obscu...
ZP_04036592   378 rhREHPTVAALLAYREHRKRQSTYGAAWLEnl----hpLTGRIHPSWQQIg-AESGRMSCSRPNLQQVPrePAYRACFQA 452  Meiothermus s...
ZP_03156829   157 raEKHPIIRNLLDYRSITTLMSTFIEGFPKyi----haISGRVHGHWFQMg-TKSGRFSCHRANLTNIPkdTRFRRCFVA 231  Cyanothece sp...
YP_001806245  356 lsENHPEVFTIIEYRHWSKAHSSFGEKLPTfv----npVTHRIHPNVNQMr-AASGRFSFSNPNLQQIPreRQYRSCFVP 430  Cyanothece sp...
YP_002121207  281 neKAKDVISSVLEFRKLHKLQEKLSEILEYn-------ENNRIHPEFWQIg-AVTGRMSSSRPNVQNIP--RELRSILKA 350  Hydrogenobacu...
YP_001930793  289 dyEDIEEVRLLLKLRADKKIIDKIKEILQFt-------RNERVYGEFKQIg-AATGRMSSLRPNLQNIP--KNLKYLFKP 358  Sulfurihydrog...
ZP_02179064    69 kyEHLKEVRQLMEIRTTKKLLDKLKELNEHtrndpsdsDTVRIHSQFRQIg-APTGRMSSSKPNLQNIP--PELRVLFRP 145  Hydrogenivirg...
ZP_05130182   239 ysDEHEVIKLIRKYRRLQAKIKTYGEKLKKfi-----dNDGRIRAHWRLIg-SRSGRMSCNNPPLQAMP--GNSREFFVA 310  Clostridium s...
YP_645884     276 ltVDHPAARDLLEYRELQKKLGTYLETYEGfv----hpKTGRIHASFLQCr-VPTGRLACTNPNVQQIPheDEFRRCFVA 350  Rubrobacter x...
Feature 1                  ##                           #                   #   #                 
O67779        344 EegNTFVISDFSQIELRIAAEYVKDPLMLDAFKKGKDMHRYTASVVLGKKeeEITKEERQLAKAINFGLIYGISAKGLAE 423  Aquifex aeolicus
ZP_02730163  1232 PpgRVLVKADYSQIELRIAAKITGDKRMLDAYQKGEDLHTTTARAVLGKT--DVTKADRQLSKSLNFGLLYGMGAKALAA 1309 Gemmata obscu...
ZP_04036592   453 PggRVLIKADYSQIELRLAAQIAGEKRMLEAFEQGEDLHTLTARLVTGKA--EPSREDRQLAKALNFGLLYGMGSEGLRT 530  Meiothermus s...
ZP_03156829   232 TegNVLIKADYSQIELRLMAKASGDLLMQLAYQKGEDLHKLTAAQLFNKPvaQITDSERYLGKIVNFGFIYGMGVKKFLV 311  Cyanothece sp...
YP_001806245  431 ApgYKLIIADYSQIELRIAAEIANDSVMIDAYCNEKDLHRLTAALVSGKDidEVTKQERQLGKAVNFGLIYGMGATKLRI 510  Cyanothece sp...
YP_002121207  351 KdgYVFVIADFSQIELRIAAEYVKDEVMIDIINKGEDLHKFTASLITGKSleDITKEERQRAKAANFGLIYGISEKSLSL 430  Hydrogenobacu...
YP_001930793  359 KegYKFIVADYSQIELRIAAQYTKDENMITAFNEGKDLHKLTASIITGKSydEITKEERQLAKAINFGLIYGMSPKSLVE 438  Sulfurihydrog...
ZP_02179064   146 SkgYSMIVADYSQIELRIAAEYTNDEVMINAFKEGKDLHRFTASLITGKSyeEITKEERQLAKAINFGLIYGISPRSLME 225  Hydrogenivirg...
ZP_05130182   311 DegYKLIGSDYSQIELRVLASISKDETLISYFNNGIDLHLGTASLIFKKPidEISKEERQVAKSLNFGIVYGITAYGIQK 390  Clostridium s...
YP_645884     351 GegNVLVIADYSQIELRILAEVSGDPGFVEAFRRGEDLHRVTAATMFGVPkeEVTKEQRSAAKRINFGLAYGRGPRSLAA 430  Rubrobacter x...
Feature 1                                                                                   #     
O67779        424 YAKlGYGVEISLEEAQVLrerffknfKAFKEWHDRVKKELKEKGEVKGHTLLGRrfs------------antFNDAVNYP 491  Aquifex aeolicus
ZP_02730163  1310 YAAsNFGVALTEGEAADHrd-----aFFRTYPGLRAWHRKVPDGIIQTRTLAGRrrvg-----------vgaFTEKLNTP 1373 Gemmata obscu...
ZP_04036592   531 YARaNYGLELSPQEAEALre-----aFFRAYPGLRAWHRHQPEGEVEVRTLAGRrrv------------tgrYTEKLNTP 593  Meiothermus s...
ZP_03156829   312 CTAfNYGIYLSAAEASRFrktf-fktYTGIAAYHKKKRKRWQQGTRVSRTLDGRrriwsl-------tsgptLNELLNNP 383  Cyanothece sp...
YP_001806245  511 YAEtNYGVSMTFDEAQRFrdnffkgyPGLHQWHQDTACKLRTTKVKDIRTLSGRlrrwk---------deppLTSLLNTP 581  Cyanothece sp...
YP_002121207  431 YARnSYGIDMSIEEAKRFrevffstfQGIKAWHERIKKELKAKGEIRLKTIGGKpmi------------aytFTDAANYP 498  Hydrogenobacu...
YP_001930793  439 YAKaNYGVSISLQEAKKFhenyfkfyKSFKDWHDKVKEHLDKHRSIELETLLGRkli------------aykFTDAVNYP 506  Sulfurihydrog...
ZP_02179064   226 YARnNYGVDISLKEAQDFhdkffqhyRGFKKWHEETKEKLNKHRQITVQSLLGRrmk------------vsrFTDAVNYP 293  Hydrogenivirg...
ZP_05130182   391 NLR-KSGVDTSLEEAEKYr------iEFLNVYPKVKELQDSLLKADYIKTLGGRrwqg----------gsltMTQRLNLP 453  Clostridium s...
YP_645884     431 QLGtDEERARRLIDEYFA--------TYGRVQRYLNETANRALKEGALRTLSGRlrkfgrtrglssaergalKREAMNYP 502  Rubrobacter x...
Feature 1          #                                   ###                                        
O67779        492 IQGTGADLLKLAVLLFDANlqkk-----gidaKLVNLVHDEIVVECEKekAEEVKEILEKSMKTAGkiILKEVPVEVESV 566  Aquifex aeolicus
ZP_02730163  1374 VQGTGADGLKRALALLWARrnsc------pdaFPVLLVHDEIVVECSEerRDEAIAWVRDAMRDGMapLIDPVPVEVEVS 1447 Gemmata obscu...
ZP_04036592   594 VQGSGADGLKLTLALLYESrqka------pgcFPVLAVHDEIVIEAPAdgVSAAYAWLTRSMREGMeaILTKVPVLVEVG 667  Meiothermus s...
ZP_03156829   384 IQGTNAGILKRAIALLGGNllev-----ypsiLLVAVIHDEIVLECPRdlAQNAAKILVRCMKQAAkpVLSPIPVQVDVK 458  Cyanothece sp...
YP_001806245  582 VQGTSADITKLALHKLNSDlde-------iggFPIVVVHDEIVLEVPEdhVAEGSAMLEEAMVSAGkrFLKSVPVVVEAA 654  Cyanothece sp...
YP_002121207  499 IQGTGAELLKLSVLIFSQElkrafpsifhevaNVVNLVHDEIVVEAKEdyKEEVSKLLEKSMKKAGsiLLNNVKIETEIV 578  Hydrogenobacu...
YP_001930793  507 IQGSGSDLLKMAVVFFFKErnd-------ldaKVVNLVHDEILVEVAAkdIEKAKEVLSSSMEKAGklILKDVPVAFEMV 579  Sulfurihydrog...
ZP_02179064   294 IQASGSDMLKMAVNFFGILkkd-------lnaYIVNLVHDEIIVEAKEdiTVQAKNILEESMKKAGkiLLKKVPVEYEAN 366  Hydrogenivirg...
ZP_05130182   454 IQGSAAEGLKEALALLVERmke--------swRLVAVIHDEILLEVPEdeAEEAKNILESCMVEGMktIVKDIPIIVDSS 525  Clostridium s...
YP_645884     503 IQGTSADIAKLALIFIHSElrd-------ldaRLINCIHDEFVVECAEeqAEEAASRVRSAMVRAGerLLKRVPVEVEVA 575  Rubrobacter x...
Feature 1               
O67779        567 INERWT 572  Aquifex aeolicus
ZP_02730163  1448 AGRTWG 1453 Gemmata obscuriglobus UQM 2246
ZP_04036592   668 VCEDWG 673  Meiothermus silvanus DSM 9946
ZP_03156829   459 ICKHWS 464  Cyanothece sp. PCC 7822
YP_001806245  655 IADSWA 660  Cyanothece sp. ATCC 51142
YP_002121207  579 INHRWT 584  Hydrogenobaculum sp. Y04AAS1
YP_001930793  580 VSDSWN 585  Sulfurihydrogenibium sp. YO3AOP1
ZP_02179064   367 IVKSWA 372  Hydrogenivirga sp. 128-5-R1-1
ZP_05130182   526 VSNNWC 531  Clostridium sp. 7_2_43FAA
YP_645884     576 VSREWR 581  Rubrobacter xylanophilus DSM 9941

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