|
Name |
Accession |
Description |
Interval |
E-value |
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
1-790 |
0e+00 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 721.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 1 MKISLRIISSSYRTSD--TVLEIFGRTIDGTSVTVLCGGFDPYFDVIEPNEQEIEGIKKNQ-EFKRMENLELW-VKGETR 76
Cdd:COG0417 1 MKIPGFLLDRSYRDEDgkPVIELWGRTEDGPSVLLDVTGFRPYFYVPLPDEEKLEELLRDIkEITEVEPVKLKsFFGEPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 77 KAIRIYVNHPYKVPELRSLF---VSTVMAADIPFHHRFIYDLDLGACIEVEGEEviDRNRYHTDMVLKADIKGIrtTDDF 153
Cdd:COG0417 81 PVLKIYTRDPRDVRELRDRLkegGIDVYEADIRFHDRYLIDRFLTPGVWYEGEV--EEDGGKLDYEVKENPRLK--PEDY 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 154 TPDVRVLSFDIE----NAFPPDEGDtyGKIIVIGYSirSKKGIET----------EKGAITGEEKEILSNFNKLILEKDP 219
Cdd:COG0417 157 RPKLKVLSFDIEvstpRGFPDPERD--GPIISIGLA--GSDGEKKvlmlgregvdFEVEYFDDEKALLEAFFEIIREYDP 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 220 DIIIGYNIDGYDLPVIEYRMERYRLTLDIGRDGSKARRMNG---QFWRVKGRIISDVWWNVK-KILKPKHETLNYVAMEL 295
Cdd:COG0417 233 DIIIGWNVDNFDLPYLQKRAERLGIPLDLGRDGSEPSWREHggqGFASIPGRVVIDLYDALKsATYKFKSYSLDAVAEEL 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 296 LNEGKDDVDRLNIMEEYKNRPKEVIDYCIKDADLTLRIMEKMRVVDRNMFMSTVTKLPLEDTTNGGTSNYVDSLLIRLAT 375
Cdd:COG0417 313 LGEGKLIVDGGEIERLWDDDKPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAH 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 376 QRNIAVPMTASQalKDRAIEGGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICFTTLSEKG------TIISPT-GARFL 448
Cdd:COG0417 393 RRGYLAPNKGEI--KGEAYPGGYVLDPKPGLYENVLVLDFKSLYPSIIRTFNISPETLVEGGeepcgdEDVAPGfGHRFC 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 449 DPsvRKGLIPELLQTLMARRDQVKKQMKQA--TGDEKDYLDGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARN 526
Cdd:COG0417 471 RE--PKGILPSILEELWDERDEAKKKMKKAkpDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGRE 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 527 TIMGLIDKLKKKDLKVIYGDTDSVFIESGKKELTDAIKMGNDLSKEISDDL--HILIEFEKIMDPFFSHGAKKRYVGkiv 604
Cdd:COG0417 549 IIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWpsGLELEFEKHYRRFFFPGSKKRYAG--- 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 605 ypMDSAGEMLVRGYEVRRTDSFDMQSELLESVFDSLMK-KDVSGARKNAVDVIERMISGDrsIDISKLVISRSV-KDSAS 682
Cdd:COG0417 626 --LTEDGKIDIKGLEAVRSDWTELAKEFQQEVYERILKeEDVEKAVEYVRDVIEKLRAGE--VDLDDLVIRKRLrKPLSE 701
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 683 YANaDSMANVRAARKLQERGERFIPGMKVSWIVTNSRVtpqEVEPYIDGEKFEDEPDWLYYA-KRVEETVNRVFESLDEP 761
Cdd:COG0417 702 YEK-NVPPHVRAARKLDERGRPYQRGDKISYVITKGGG---RVEPVELAKERESEIDYDYYIeKQLKPTADRILEAFGVS 777
|
810 820
....*....|....*....|....*....
gi 1143084521 762 IHLVeqgsKSGKRQqavhnsknTTLDSFM 790
Cdd:COG0417 778 FDEL----KGGSKQ--------LGLFDFF 794
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
1-756 |
0e+00 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 587.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 1 MKISLRIISSSYRTSD--TVLEIFGRTIDGTSVTVLCGGFDPYFDVIEPNEQEIEGIKKNQEFkRMENLEL------WVK 72
Cdd:PRK05762 2 MLQQGFILTRHYRDTPggPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERAESLLAGEIGV-RLSPLALkdfhrrPVL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 73 GETRKAIRIYVNHPYKVPELrslfVSTVMAADIPFHHRFIYDLDLGACIEVEGEEVIDrnryHTDMVLKAdiKGIRTTDD 152
Cdd:PRK05762 81 GLYCRQHRQLTRLPKRLREG----GVDVYEADIRFPERYLMERFITPCVWFSGEVEQY----TTDGVLRN--ARLKPAPD 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 153 FTPDVRVLSFDIENAFPPD------EGDTYGKIIVIGysirSKKGIETEKGAITGEEKEILSNFNKLILEKDPDIIIGYN 226
Cdd:PRK05762 151 YRPPLKVVSLDIETSNKGElysiglEGCGQRPVIMLG----PPNGEALDFLEYVADEKALLEKFNAWFAEHDPDVIIGWN 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 227 IDGYDLPVIEYRMERYRLTLDIGRDGSKA------RRMNGQFWRVKGRIISDVWWNVKKILKP-KHETLNYVAMELLNEG 299
Cdd:PRK05762 227 VVQFDLRLLQERAERYGIPLRLGRDGSELewrehpFRSGYGFASVPGRLVLDGIDALKSATWVfDSFSLEYVSQRLLGEG 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 300 K---DDVDRLN-IMEEYKNRPKEVIDYCIKDADLTLRIMEKMRVVDRNMFMSTVTKLPLEDTtnGGTSNYVDSLLIRLAT 375
Cdd:PRK05762 307 KaidDPYDRMDeIDRRFAEDKPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRV--GGSVAAFEHLYLPRAH 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 376 QRNIAVPMtaSQALKDRAIEGGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICFTTLSE------KGTIISPTGARFld 449
Cdd:PRK05762 385 RAGYVAPN--LGERPGEASPGGYVMDSKPGLYDSVLVLDFKSLYPSIIRTFNIDPDGLVEglaqppEESVAGFLGARF-- 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 450 pSVRKGLIPELLQTLMARRDQVKKQMKQAtgdekdyldgVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIM 529
Cdd:PRK05762 461 -SREKHFLPEIVERLWEGRDEAKREMNKP----------LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMK 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 530 GLIDKLKKKDLKVIYGDTDSVFIESG-KKELTDAIKMGNDLSKEISD------------DLHILIEFEKIMDPFFSH--- 593
Cdd:PRK05762 530 QTRELIEAQGYQVIYGDTDSTFVWLGgAHDEEDAAKIGRALVQEINQwwqehlqqefglESALELEFEKHYRRFFMPtir 609
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 594 ----GAKKRYVGKIVyPMDSAGEMLVRGYEVRRTDSFDM----QSELLESVFDSlmKKDVSGARknavDVIERMISGDrs 665
Cdd:PRK05762 610 gaeeGSKKRYAGLIQ-EGDGDGRIVFKGLETVRTDWTPLakefQQELYERIFRG--EPYVDYVR----EVIDKLRAGE-- 680
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 666 IDiSKLVISRSVKDSASYANADSMANVRAARKLQERGERFI------PGMKVSWIVTNSRVTPQEVEPyidgekfeDEPD 739
Cdd:PRK05762 681 LD-EKLVYRKRLRRPLDEYQRNVPPHVRAARLADEMGYKVGrplqyqNGGKIGYVITVNGPEPLEYRK--------SPID 751
|
810
....*....|....*...
gi 1143084521 740 WLYY-AKRVEETVNRVFE 756
Cdd:PRK05762 752 YDYYiEKQLQPVADRILP 769
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
393-756 |
1.66e-89 |
|
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.
Pssm-ID: 99912 [Multi-domain] Cd Length: 323 Bit Score: 285.03 E-value: 1.66e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 393 AIEGGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICFTTLSEKGTIISP---TGARFLDPSVRKGLIPELLQTLMARRD 469
Cdd:cd00145 2 PYEGGYVFDPIPGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPedyIGVGFRSPKDRKGLLPRILEELLNFRD 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 470 QVKKQMKQA--TGDEKDYLDGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGLIDKLKKKDLKVIYGDT 547
Cdd:cd00145 82 EAKKRMKAAklAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYGDT 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 548 DSVFIESGKKE-LTDAIKMGNDLSKEISDDLHILIEFEKIMDPFFSHgAKKRYVGKIVYPMDSAGEMLVRGYEVRRTDSF 626
Cdd:cd00145 162 DSIFVSLPKMGtKEDAIKEGREILQELADEHLLELEFEKVYLPFFLG-KKKRYAGLDIWKGQDEGKIDIKGLETRRRDSP 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 627 DMQSELLEsvfdslmkkdvsgarknavDVIERMISGDRSIDISKlvisrsvkdsasyanadsmanvRAARKLqergerfi 706
Cdd:cd00145 241 PLVKKFQK-------------------EVLELILEEERKVEAVK----------------------EYIDEL-------- 271
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 1143084521 707 pgMKVSWIVTNSRVTPQEVEPYIDGEKFED---EPDWLYYA-KRVEETVNRVFE 756
Cdd:cd00145 272 --DKVKYVVTRGGKGVPDYERADPPLEDLDkrhRIDYEYYLeRLLQPPLERIFE 323
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
155-553 |
1.94e-74 |
|
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Pssm-ID: 214691 [Multi-domain] Cd Length: 474 Bit Score: 250.14 E-value: 1.94e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 155 PDVRVLSFDIE----NAFPPDEGDTYGKIIVIGYSIRSKKGIETEKGAITGE----------------EKEILSNFNKLI 214
Cdd:smart00486 1 PPLKILSFDIEtytdGGNFPDAEIFDDEIIQISLVINDGDKKGANRRILFTLgtckeidgievyefnnEKELLLAFFEFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 215 LEKDPDIIIGYNIDGYDLPVIEYRMERYRLT--LDIGRDGSKARRMN-------------GQFWRVKGRIISDVWWNVKK 279
Cdd:smart00486 81 KKYDPDIIYGHNISNFDLPYIISRLEKLKIDplSKIGRLKIGLRIPNkkplfgsksfglsDIKVYIKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 280 ILKPKHETLNYVAMELLNEGKDDVDRLNIMEEYKNRPK---EVIDYCIKDADLTLRIMEKMRVVDRNMFMSTVTKLPLED 356
Cdd:smart00486 161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEerdELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 357 TTNGGTSNYVDSLLIRLATQRNIAVPMTASQAL--------KDRAIEGGHVESIGAGLYDM-VIVLDFKSMYPSIIMKYN 427
Cdd:smart00486 241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkKKVKYEGGKVLEPKKGFYDNpVLVLDFNSLYPSIIIAHN 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 428 ICFTTL-----------------SEKGTIISPTGARFLDPSVRKGLIPELLQTLMARRDQVKKQMKQATGD---EKDYLD 487
Cdd:smart00486 321 LCYSTLvgvgevvikgdliipedLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDEseeLKKLLD 400
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1143084521 488 GVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGLI-----DKLKKKDLKVIYGDTDSVFIE 553
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKelieeNGYPKPGFKVIYGDTDSIFVT 471
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
352-704 |
1.26e-64 |
|
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.
Pssm-ID: 395085 Cd Length: 439 Bit Score: 222.49 E-value: 1.26e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 352 LPLEDTTNGGTSNYVDSLLIRLATQRNIAVPMTASQALKDRAIEGGHVESIGAGLYDM-VIVLDFKSMYPSIIMKYNICF 430
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGDEDGYQGATVIEPKKGFYDKpVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 431 TTL-------------SEKGTI-ISPTGARFLDPSVRKGLIPELLQTLMARRDQVKKQMKQATGD-EKDYLDGVQNAIKI 495
Cdd:pfam00136 81 TTLvrsvdeannlppeDNLITVeCTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPfERAILDKQQLALKI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 496 LMNTFYGVLASSFYRFTNPELGSSVTSFARNTIM---GLIDKLKKKDLKVIYGDTDSVFIESGKKELTDAIKMGNDLSKE 572
Cdd:pfam00136 161 TANSVYGFTGFANGRLPCLPIAASVTAIGREMLEntkDLVEGMYTYNFRVIYGDTDSVFIEFGGKDVEEAMKIGDELAEH 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 573 ISDDL---HILIEFEKIMDPFFSHgAKKRYVGKIVYPMDSAGEMLVRGYEVRRTDSFDMQSELLESVFDSLMK-KDVSGA 648
Cdd:pfam00136 241 VNQDLfksPIKLEFEKVYKPLLLI-SKKKYAGLKYTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSdRGLPVG 319
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 1143084521 649 RKNAVDVIERMISG--DRSIDISKLVISRSV-KDSASYANADsMANVRAARKLQERGER 704
Cdd:pfam00136 320 LEFVISILNDARSDlrNNKVPLEKFVISKELsKPPDNYKSKN-LPHVEVALRMNKRNGE 377
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
203-756 |
1.27e-54 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 204.52 E-value: 1.27e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 203 EKEILSNFNKLILEKDPDIIIGYNIDGYDLPVIEYRMERYRLTL--DIGRDGSKARRMNGQFWRVKGRIISDVWWNVKKI 280
Cdd:TIGR00592 584 ERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTwsKIGRLRRSPKFGRRFGERTCGRMICDVEISAKEL 663
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 281 LKPKHETLNYVAMELLNEGKDDVDRLNIMEEYK--NRPKEVIDYCIKDADLTLRIMEKMRVVDRNMFMSTVTKLPLEDTT 358
Cdd:TIGR00592 664 IRCKSYDLSELVQQILKTERKVIPIDNINNMYSesSSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTL 743
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 359 NGGTSNYVDSLLIRLATQRNIAVP-----------------MTASQALKDRAIEGGHVESIGAGLYD-MVIVLDFKSMYP 420
Cdd:TIGR00592 744 MGGRSERNEFLLLHAFYENNYIVPdkqifrkqqklgdedeeIDGYKKGKKAAYAGGLVLEPKVGLYDkYVLLMDFNSLYP 823
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 421 SIIMKYNICFTTLSEKGTIisPTGARFLDPSVRKGLIPELLQTLMARRDQVKKQMKQATGDEKDY-LDGVQNAIKILMNT 499
Cdd:TIGR00592 824 SIIQEFNICFTTVQQKVDE--DELPELPDSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLqYDIRQKALKLTANS 901
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 500 FYGVLASSFYRFTNPELGSSVTSFARNTIMGLIDKLKKKDLKVIYGDTDSVFIESGKKELTDAIKMGNDLSKEISDDLHI 579
Cdd:TIGR00592 902 MYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKL 981
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 580 L-IEFEKIMDPFFSHgAKKRYVGKIVYPMDSAG---EMLVRGYEVRRTDSFDMQSELLESVFDS-LMKKDVSGARKNAVD 654
Cdd:TIGR00592 982 LeLDIDGVFKRLLLL-KKKKYAAIKVEGDSDGNyttKQEVKGLDIVRRDWSPLAKETGKKVLDTiLSDKDVEEAVEEVQE 1060
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 655 VIE--RMISGDRSIDISKLVISRSV-KDSASYANADSMANVRAARKLQERGERFI-PGMKVSWIVT--NSRVTPQEVEPY 728
Cdd:TIGR00592 1061 VLEkiGKNVLNGEVPLEKFVINKQLtRDPKDYPDGASLPHVHVALRINARGGRKVkAGDVVSYVICkdGGNLSARQRAYA 1140
|
570 580 590
....*....|....*....|....*....|..
gi 1143084521 729 IDGEKFEDE---PDWLYY-AKRVEETVNRVFE 756
Cdd:TIGR00592 1141 LEELQRKHNnliYDTQYYlEHQIHPVVLRILE 1172
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
1-790 |
0e+00 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 721.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 1 MKISLRIISSSYRTSD--TVLEIFGRTIDGTSVTVLCGGFDPYFDVIEPNEQEIEGIKKNQ-EFKRMENLELW-VKGETR 76
Cdd:COG0417 1 MKIPGFLLDRSYRDEDgkPVIELWGRTEDGPSVLLDVTGFRPYFYVPLPDEEKLEELLRDIkEITEVEPVKLKsFFGEPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 77 KAIRIYVNHPYKVPELRSLF---VSTVMAADIPFHHRFIYDLDLGACIEVEGEEviDRNRYHTDMVLKADIKGIrtTDDF 153
Cdd:COG0417 81 PVLKIYTRDPRDVRELRDRLkegGIDVYEADIRFHDRYLIDRFLTPGVWYEGEV--EEDGGKLDYEVKENPRLK--PEDY 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 154 TPDVRVLSFDIE----NAFPPDEGDtyGKIIVIGYSirSKKGIET----------EKGAITGEEKEILSNFNKLILEKDP 219
Cdd:COG0417 157 RPKLKVLSFDIEvstpRGFPDPERD--GPIISIGLA--GSDGEKKvlmlgregvdFEVEYFDDEKALLEAFFEIIREYDP 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 220 DIIIGYNIDGYDLPVIEYRMERYRLTLDIGRDGSKARRMNG---QFWRVKGRIISDVWWNVK-KILKPKHETLNYVAMEL 295
Cdd:COG0417 233 DIIIGWNVDNFDLPYLQKRAERLGIPLDLGRDGSEPSWREHggqGFASIPGRVVIDLYDALKsATYKFKSYSLDAVAEEL 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 296 LNEGKDDVDRLNIMEEYKNRPKEVIDYCIKDADLTLRIMEKMRVVDRNMFMSTVTKLPLEDTTNGGTSNYVDSLLIRLAT 375
Cdd:COG0417 313 LGEGKLIVDGGEIERLWDDDKPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAH 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 376 QRNIAVPMTASQalKDRAIEGGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICFTTLSEKG------TIISPT-GARFL 448
Cdd:COG0417 393 RRGYLAPNKGEI--KGEAYPGGYVLDPKPGLYENVLVLDFKSLYPSIIRTFNISPETLVEGGeepcgdEDVAPGfGHRFC 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 449 DPsvRKGLIPELLQTLMARRDQVKKQMKQA--TGDEKDYLDGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARN 526
Cdd:COG0417 471 RE--PKGILPSILEELWDERDEAKKKMKKAkpDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGRE 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 527 TIMGLIDKLKKKDLKVIYGDTDSVFIESGKKELTDAIKMGNDLSKEISDDL--HILIEFEKIMDPFFSHGAKKRYVGkiv 604
Cdd:COG0417 549 IIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWpsGLELEFEKHYRRFFFPGSKKRYAG--- 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 605 ypMDSAGEMLVRGYEVRRTDSFDMQSELLESVFDSLMK-KDVSGARKNAVDVIERMISGDrsIDISKLVISRSV-KDSAS 682
Cdd:COG0417 626 --LTEDGKIDIKGLEAVRSDWTELAKEFQQEVYERILKeEDVEKAVEYVRDVIEKLRAGE--VDLDDLVIRKRLrKPLSE 701
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 683 YANaDSMANVRAARKLQERGERFIPGMKVSWIVTNSRVtpqEVEPYIDGEKFEDEPDWLYYA-KRVEETVNRVFESLDEP 761
Cdd:COG0417 702 YEK-NVPPHVRAARKLDERGRPYQRGDKISYVITKGGG---RVEPVELAKERESEIDYDYYIeKQLKPTADRILEAFGVS 777
|
810 820
....*....|....*....|....*....
gi 1143084521 762 IHLVeqgsKSGKRQqavhnsknTTLDSFM 790
Cdd:COG0417 778 FDEL----KGGSKQ--------LGLFDFF 794
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
1-756 |
0e+00 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 587.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 1 MKISLRIISSSYRTSD--TVLEIFGRTIDGTSVTVLCGGFDPYFDVIEPNEQEIEGIKKNQEFkRMENLEL------WVK 72
Cdd:PRK05762 2 MLQQGFILTRHYRDTPggPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERAESLLAGEIGV-RLSPLALkdfhrrPVL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 73 GETRKAIRIYVNHPYKVPELrslfVSTVMAADIPFHHRFIYDLDLGACIEVEGEEVIDrnryHTDMVLKAdiKGIRTTDD 152
Cdd:PRK05762 81 GLYCRQHRQLTRLPKRLREG----GVDVYEADIRFPERYLMERFITPCVWFSGEVEQY----TTDGVLRN--ARLKPAPD 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 153 FTPDVRVLSFDIENAFPPD------EGDTYGKIIVIGysirSKKGIETEKGAITGEEKEILSNFNKLILEKDPDIIIGYN 226
Cdd:PRK05762 151 YRPPLKVVSLDIETSNKGElysiglEGCGQRPVIMLG----PPNGEALDFLEYVADEKALLEKFNAWFAEHDPDVIIGWN 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 227 IDGYDLPVIEYRMERYRLTLDIGRDGSKA------RRMNGQFWRVKGRIISDVWWNVKKILKP-KHETLNYVAMELLNEG 299
Cdd:PRK05762 227 VVQFDLRLLQERAERYGIPLRLGRDGSELewrehpFRSGYGFASVPGRLVLDGIDALKSATWVfDSFSLEYVSQRLLGEG 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 300 K---DDVDRLN-IMEEYKNRPKEVIDYCIKDADLTLRIMEKMRVVDRNMFMSTVTKLPLEDTtnGGTSNYVDSLLIRLAT 375
Cdd:PRK05762 307 KaidDPYDRMDeIDRRFAEDKPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRV--GGSVAAFEHLYLPRAH 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 376 QRNIAVPMtaSQALKDRAIEGGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICFTTLSE------KGTIISPTGARFld 449
Cdd:PRK05762 385 RAGYVAPN--LGERPGEASPGGYVMDSKPGLYDSVLVLDFKSLYPSIIRTFNIDPDGLVEglaqppEESVAGFLGARF-- 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 450 pSVRKGLIPELLQTLMARRDQVKKQMKQAtgdekdyldgVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIM 529
Cdd:PRK05762 461 -SREKHFLPEIVERLWEGRDEAKREMNKP----------LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMK 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 530 GLIDKLKKKDLKVIYGDTDSVFIESG-KKELTDAIKMGNDLSKEISD------------DLHILIEFEKIMDPFFSH--- 593
Cdd:PRK05762 530 QTRELIEAQGYQVIYGDTDSTFVWLGgAHDEEDAAKIGRALVQEINQwwqehlqqefglESALELEFEKHYRRFFMPtir 609
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 594 ----GAKKRYVGKIVyPMDSAGEMLVRGYEVRRTDSFDM----QSELLESVFDSlmKKDVSGARknavDVIERMISGDrs 665
Cdd:PRK05762 610 gaeeGSKKRYAGLIQ-EGDGDGRIVFKGLETVRTDWTPLakefQQELYERIFRG--EPYVDYVR----EVIDKLRAGE-- 680
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 666 IDiSKLVISRSVKDSASYANADSMANVRAARKLQERGERFI------PGMKVSWIVTNSRVTPQEVEPyidgekfeDEPD 739
Cdd:PRK05762 681 LD-EKLVYRKRLRRPLDEYQRNVPPHVRAARLADEMGYKVGrplqyqNGGKIGYVITVNGPEPLEYRK--------SPID 751
|
810
....*....|....*...
gi 1143084521 740 WLYY-AKRVEETVNRVFE 756
Cdd:PRK05762 752 YDYYiEKQLQPVADRILP 769
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
393-756 |
1.66e-89 |
|
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.
Pssm-ID: 99912 [Multi-domain] Cd Length: 323 Bit Score: 285.03 E-value: 1.66e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 393 AIEGGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICFTTLSEKGTIISP---TGARFLDPSVRKGLIPELLQTLMARRD 469
Cdd:cd00145 2 PYEGGYVFDPIPGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPedyIGVGFRSPKDRKGLLPRILEELLNFRD 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 470 QVKKQMKQA--TGDEKDYLDGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGLIDKLKKKDLKVIYGDT 547
Cdd:cd00145 82 EAKKRMKAAklAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYGDT 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 548 DSVFIESGKKE-LTDAIKMGNDLSKEISDDLHILIEFEKIMDPFFSHgAKKRYVGKIVYPMDSAGEMLVRGYEVRRTDSF 626
Cdd:cd00145 162 DSIFVSLPKMGtKEDAIKEGREILQELADEHLLELEFEKVYLPFFLG-KKKRYAGLDIWKGQDEGKIDIKGLETRRRDSP 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 627 DMQSELLEsvfdslmkkdvsgarknavDVIERMISGDRSIDISKlvisrsvkdsasyanadsmanvRAARKLqergerfi 706
Cdd:cd00145 241 PLVKKFQK-------------------EVLELILEEERKVEAVK----------------------EYIDEL-------- 271
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 1143084521 707 pgMKVSWIVTNSRVTPQEVEPYIDGEKFED---EPDWLYYA-KRVEETVNRVFE 756
Cdd:cd00145 272 --DKVKYVVTRGGKGVPDYERADPPLEDLDkrhRIDYEYYLeRLLQPPLERIFE 323
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
18-790 |
1.51e-85 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 293.47 E-value: 1.51e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 18 VLEIFGRTIDGTSVTVLCGGFDPYFDVIEPN----------EQEI-EGIKKNQEFKRMENLELWVKGETRKAI------- 79
Cdd:PTZ00166 76 IIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPnflpedsqklKRELnAQLSEQSQFKKYQNTVLDIEIVKKESLmyykgng 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 80 -----RIYVNHPYKVPELRSLFVSTVMA---------------ADIPFHHRFIYDLDLGACIEVEgeevIDRNRYHTDMV 139
Cdd:PTZ00166 156 ekdflKITVQLPKMVPRLRSLIESGVVVcgggwdgirlfqtyeSNVPFVLRFLIDNNITGGSWLT----LPKGKYKIRPP 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 140 LK-------------ADIKGIRTTDDFT--PDVRVLSFDIE------NAFPPDEGDTygkIIVI-------GYSIRS-KK 190
Cdd:PTZ00166 232 KKktstcqievdcsyEDLIPLPPEGEYLtiAPLRILSFDIEciklkgLGFPEAENDP---VIQIssvvtnqGDEEEPlTK 308
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 191 GIETEK--GAITG-------EEKEILSNFNKLILEKDPDIIIGYNIDGYDLPVIEYR-----------MERYRLTLDIGR 250
Cdd:PTZ00166 309 FIFTLKecASIAGanvlsfeTEKELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRakalklndfkyLGRIKSTRSVIK 388
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 251 DGSKARRMNGQF----WRVKGRIISDVWWNVKKILKPKHETLNYVAMELLNEGKDDVdRLNIM----EEYKNRPKEVIDY 322
Cdd:PTZ00166 389 DSKFSSKQMGTReskeINIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDV-HYSIIsdlqNGSPETRRRIAVY 467
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 323 CIKDADLTLRIMEKMRVVDRNMFMSTVTKLPLEDTTNGGTSNYVDSLLIRLATQRNIAVPMT-ASQALKDRAIEGGHVES 401
Cdd:PTZ00166 468 CLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVkYSGGGSEEKYEGATVLE 547
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 402 IGAGLYDMVI-VLDFKSMYPSIIMKYNICFTTL---------SEKGTIISPTGARFLDPSVRKGLIPELLQTLMARRDQV 471
Cdd:PTZ00166 548 PKKGFYDEPIaTLDFASLYPSIMIAHNLCYSTLvppndannyPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKA 627
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 472 KKQMKQATGD-EKDYLDGVQNAIKILMNTFYGVL-ASSFYRFTNPELGSSVTSFARNTI---------MGLIDKLKKKDL 540
Cdd:PTZ00166 628 KKEMKDEKDPlLKKVLNGRQLALKISANSVYGYTgAQVGGQLPCLEVSTSITSFGRQMIdktkelvekHYTKANGYKHDA 707
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 541 KVIYGDTDSVFIESGKKELTDAIKMGNDLSKEISDD-LH-ILIEFEKIMDPFFSHgAKKRYVGKIVYPMDSAGEMLVRGY 618
Cdd:PTZ00166 708 TVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKfLKpIKLEFEKVYCPYLLM-NKKRYAGLLYTNPEKYDKIDCKGI 786
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 619 EVRRTDSFDMQSELLESVFDS-LMKKDVSGARKNAVDVIERMISGDrsIDISKLVISRS-VKDsaSYANAdsMANVRAAR 696
Cdd:PTZ00166 787 ETVRRDNCLLVQQMVETVLNKiLIEKDVESAIEFTKGKISDLLQNR--IDISLLVITKSlGKD--DYEGR--LAHVELAK 860
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 697 KLQERGERFIP--GMKVSW-IVTNSRVTPQevepYidgEKFEDeP----------DWLYYAKRVEETVNRVFES-LDEPI 762
Cdd:PTZ00166 861 KLRQRDPGSAPnvGDRVSYvIVKGAKGAPQ----Y---ERAED-PlyvlennipiDTQYYLDQIKNPLLRIFEGvMDNPD 932
|
890 900
....*....|....*....|....*...
gi 1143084521 763 HLVeqgSKSGKRQQAVHNSKNTTLDSFM 790
Cdd:PTZ00166 933 SLF---SGEHTRHITISSSSKGGLSKFV 957
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
155-553 |
1.94e-74 |
|
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Pssm-ID: 214691 [Multi-domain] Cd Length: 474 Bit Score: 250.14 E-value: 1.94e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 155 PDVRVLSFDIE----NAFPPDEGDTYGKIIVIGYSIRSKKGIETEKGAITGE----------------EKEILSNFNKLI 214
Cdd:smart00486 1 PPLKILSFDIEtytdGGNFPDAEIFDDEIIQISLVINDGDKKGANRRILFTLgtckeidgievyefnnEKELLLAFFEFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 215 LEKDPDIIIGYNIDGYDLPVIEYRMERYRLT--LDIGRDGSKARRMN-------------GQFWRVKGRIISDVWWNVKK 279
Cdd:smart00486 81 KKYDPDIIYGHNISNFDLPYIISRLEKLKIDplSKIGRLKIGLRIPNkkplfgsksfglsDIKVYIKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 280 ILKPKHETLNYVAMELLNEGKDDVDRLNIMEEYKNRPK---EVIDYCIKDADLTLRIMEKMRVVDRNMFMSTVTKLPLED 356
Cdd:smart00486 161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEerdELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 357 TTNGGTSNYVDSLLIRLATQRNIAVPMTASQAL--------KDRAIEGGHVESIGAGLYDM-VIVLDFKSMYPSIIMKYN 427
Cdd:smart00486 241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkKKVKYEGGKVLEPKKGFYDNpVLVLDFNSLYPSIIIAHN 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 428 ICFTTL-----------------SEKGTIISPTGARFLDPSVRKGLIPELLQTLMARRDQVKKQMKQATGD---EKDYLD 487
Cdd:smart00486 321 LCYSTLvgvgevvikgdliipedLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDEseeLKKLLD 400
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1143084521 488 GVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGLI-----DKLKKKDLKVIYGDTDSVFIE 553
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKelieeNGYPKPGFKVIYGDTDSIFVT 471
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
352-704 |
1.26e-64 |
|
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.
Pssm-ID: 395085 Cd Length: 439 Bit Score: 222.49 E-value: 1.26e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 352 LPLEDTTNGGTSNYVDSLLIRLATQRNIAVPMTASQALKDRAIEGGHVESIGAGLYDM-VIVLDFKSMYPSIIMKYNICF 430
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGDEDGYQGATVIEPKKGFYDKpVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 431 TTL-------------SEKGTI-ISPTGARFLDPSVRKGLIPELLQTLMARRDQVKKQMKQATGD-EKDYLDGVQNAIKI 495
Cdd:pfam00136 81 TTLvrsvdeannlppeDNLITVeCTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPfERAILDKQQLALKI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 496 LMNTFYGVLASSFYRFTNPELGSSVTSFARNTIM---GLIDKLKKKDLKVIYGDTDSVFIESGKKELTDAIKMGNDLSKE 572
Cdd:pfam00136 161 TANSVYGFTGFANGRLPCLPIAASVTAIGREMLEntkDLVEGMYTYNFRVIYGDTDSVFIEFGGKDVEEAMKIGDELAEH 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 573 ISDDL---HILIEFEKIMDPFFSHgAKKRYVGKIVYPMDSAGEMLVRGYEVRRTDSFDMQSELLESVFDSLMK-KDVSGA 648
Cdd:pfam00136 241 VNQDLfksPIKLEFEKVYKPLLLI-SKKKYAGLKYTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSdRGLPVG 319
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 1143084521 649 RKNAVDVIERMISG--DRSIDISKLVISRSV-KDSASYANADsMANVRAARKLQERGER 704
Cdd:pfam00136 320 LEFVISILNDARSDlrNNKVPLEKFVISKELsKPPDNYKSKN-LPHVEVALRMNKRNGE 377
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
37-762 |
1.99e-60 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 218.79 E-value: 1.99e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 37 GFDPYF-DVIEPNE-QEIEGIKKNQEFKRMEnLELWVKGETRKAIR---IYVNHPYKVPELRSLFVSTVMA--ADIPFHH 109
Cdd:PRK05761 53 GHKPYFlTDLDPDEiDKIPKILRHPSFDHLE-IVEKYDGLRDKKVKvtkIVVKDPLAVRRLRLSVRDIPRAweADIKYEF 131
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 110 RFIYDLDL---------GACIEVEGEEVIDRNRYHTDMVLKADIKGIRTTDDFTPDVRVLSFDIEnAFPPDEGdtygKII 180
Cdd:PRK05761 132 RYIYDNGLipgmpydvkNGLESVEPEILVEEIKKAFKDERKLAEDWLPIFEAPIPKIKRIAIDIE-VYTPAKG----RIP 206
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 181 VigysirskkgietekgaitGEEKEILSNFNKLILEKDPDIIigYNIDGYDLPVIEYRMERY-----RLTLDIGRDGSKA 255
Cdd:PRK05761 207 D-------------------DSEKELLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKLgipkeEIPIEPGRAGIHI 265
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 256 RRMngQFWRVKGRiisDVWWNVKKIlKPKHETLNYVAMELLNEGKDDVDRlnimEEYKNRPKEVIDYCIKDADLTLR--I 333
Cdd:PRK05761 266 DLY--KFFQNKAV---RSYAFYGKY-RHREARLDAVGRALLGISKVELET----NISELDLEELAEYNFRDAEITLKltF 335
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 334 MEKMRVVDRNMFMSTVTKLPLEDTTNGGTSNYVDSLLIRLATQRNIAVPMTASQALKD-----RAIE------GGHVESI 402
Cdd:PRK05761 336 FNNELVLKLILLLSRISKLPIEELSRATISTWISNLEYWEHRKRGWLIPWKEDILRLDhevykKAIIkgkkyrGGLVFQP 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 403 GAGLYDMVIVLDFKSMYPSIIMKYNICFTTLS----EKGTIISPTGARFLDPSVRKGLIPELLQTLMARRDQVKKQMKQ- 477
Cdd:PRK05761 416 PPGIFFNVYVLDFASLYPSIIVKWNLSPETVRipecKCHYDDEVPELGHSVCDDRPGLTSVLVGLLRDFRVKIYKKKAKd 495
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 478 --ATGDEKDYLDGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGLIDKLKKKDLKVIYGDTDSVFIESG 555
Cdd:PRK05761 496 pnLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAEELGLKVLYGDTDSLFVWGP 575
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 556 KKELTDAIKmgndlsKEISDDLHILIEFEKIMD-PFFShGAKKRYVGKivypmDSAGEMLVRGYEVRRTDS--F--DMQS 630
Cdd:PRK05761 576 TKESLEELI------KEIEERTGIDLEVDKTYDwVAFS-GLKKNYFGV-----LKDGKVKIKGIVAKKRNTpeFvkELQR 643
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 631 ELLEsVFDSLMK-KDVSGARKNAVDVIERMISGDRS--IDISKLVISRSV-KDSASYaNADSMANVRAARKLQERGERFI 706
Cdd:PRK05761 644 EVLE-VLKSIRSpEDVEKVKDEIEDVLKRYYEKLRAkdYPLDELAIRVRLsKPLDEY-TKNTPQHVKAALQLRDYGVEVS 721
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....*.
gi 1143084521 707 PGMKVSWIVTNSRVTpqeVEPyIDGEKfEDEPDWLYYakrvEETVNRVFESLDEPI 762
Cdd:PRK05761 722 PGDIISYVKVDDKRG---VKP-VQLAK-LSEIDVEKY----IELLRSALEQILSAL 768
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
203-756 |
1.27e-54 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 204.52 E-value: 1.27e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 203 EKEILSNFNKLILEKDPDIIIGYNIDGYDLPVIEYRMERYRLTL--DIGRDGSKARRMNGQFWRVKGRIISDVWWNVKKI 280
Cdd:TIGR00592 584 ERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTwsKIGRLRRSPKFGRRFGERTCGRMICDVEISAKEL 663
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 281 LKPKHETLNYVAMELLNEGKDDVDRLNIMEEYK--NRPKEVIDYCIKDADLTLRIMEKMRVVDRNMFMSTVTKLPLEDTT 358
Cdd:TIGR00592 664 IRCKSYDLSELVQQILKTERKVIPIDNINNMYSesSSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTL 743
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 359 NGGTSNYVDSLLIRLATQRNIAVP-----------------MTASQALKDRAIEGGHVESIGAGLYD-MVIVLDFKSMYP 420
Cdd:TIGR00592 744 MGGRSERNEFLLLHAFYENNYIVPdkqifrkqqklgdedeeIDGYKKGKKAAYAGGLVLEPKVGLYDkYVLLMDFNSLYP 823
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 421 SIIMKYNICFTTLSEKGTIisPTGARFLDPSVRKGLIPELLQTLMARRDQVKKQMKQATGDEKDY-LDGVQNAIKILMNT 499
Cdd:TIGR00592 824 SIIQEFNICFTTVQQKVDE--DELPELPDSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLqYDIRQKALKLTANS 901
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 500 FYGVLASSFYRFTNPELGSSVTSFARNTIMGLIDKLKKKDLKVIYGDTDSVFIESGKKELTDAIKMGNDLSKEISDDLHI 579
Cdd:TIGR00592 902 MYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKL 981
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 580 L-IEFEKIMDPFFSHgAKKRYVGKIVYPMDSAG---EMLVRGYEVRRTDSFDMQSELLESVFDS-LMKKDVSGARKNAVD 654
Cdd:TIGR00592 982 LeLDIDGVFKRLLLL-KKKKYAAIKVEGDSDGNyttKQEVKGLDIVRRDWSPLAKETGKKVLDTiLSDKDVEEAVEEVQE 1060
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 655 VIE--RMISGDRSIDISKLVISRSV-KDSASYANADSMANVRAARKLQERGERFI-PGMKVSWIVT--NSRVTPQEVEPY 728
Cdd:TIGR00592 1061 VLEkiGKNVLNGEVPLEKFVINKQLtRDPKDYPDGASLPHVHVALRINARGGRKVkAGDVVSYVICkdGGNLSARQRAYA 1140
|
570 580 590
....*....|....*....|....*....|..
gi 1143084521 729 IDGEKFEDE---PDWLYY-AKRVEETVNRVFE 756
Cdd:TIGR00592 1141 LEELQRKHNnliYDTQYYlEHQIHPVVLRILE 1172
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
395-715 |
1.11e-51 |
|
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Pssm-ID: 99916 Cd Length: 393 Bit Score: 185.16 E-value: 1.11e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 395 EGGHVESIGAGLYDMVI-VLDFKSMYPSIIMKYNICFTTLSEKGT---------IISPTGARFLDPSVRKGLIPELLQTL 464
Cdd:cd05533 4 EGATVIEPIKGYYDVPIaTLDFASLYPSIMMAHNLCYTTLLNKNTakklppedyIKTPNGDYFVKSSVRKGLLPEILEEL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 465 MARRDQVKKQMKQATGD-EKDYLDGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGL---------IDK 534
Cdd:cd05533 84 LAARKRAKKDLKEETDPfKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTkklveekytKAN 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 535 LKKKDLKVIYGDTDSVFIESGKKELTDAIKMGNDLSKEISDDL--HILIEFEKIMDPFFSHgAKKRYVGKIVYPMDSAGE 612
Cdd:cd05533 164 GYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFikPIKLEFEKVYFPYLLI-NKKRYAGLLWTNPDKHDK 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 613 MLVRGYEVRRTDSFDMQSELLESVFDS-LMKKDVSGARKNAVDVIERMISGDrsIDISKLVISRSV-KDSASYANAdsMA 690
Cdd:cd05533 243 MDTKGIETVRRDNCLLVQNVVETCLNKiLIERDVEGAIEFVKGVISDLLQNK--IDISLLVITKALtKTADDYAGK--QA 318
|
330 340
....*....|....*....|....*..
gi 1143084521 691 NVRAARKLQERGERFIPGM--KVSWIV 715
Cdd:cd05533 319 HVELAERMRKRDPGSAPNVgdRVPYVI 345
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
361-759 |
4.71e-50 |
|
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Pssm-ID: 99917 Cd Length: 451 Bit Score: 182.41 E-value: 4.71e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 361 GTSNYVDSLLIRLATQRNIaVPMTAS--QALKDRAIEgghveSIG------AGLY-DMVIVLDFKSMYPSIIMKYNICFT 431
Cdd:cd05534 1 GSQFRVESMLLRLAKPENY-ILPSPSrqQVAQQRALE-----CLPlvmepeSGFYsDPVIVLDFQSLYPSIMIAYNYCYS 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 432 T-------------------------------LSEKGTIISPTGARFLDPSVRKGLIPELLQTLMARRDQVKKQMKQATG 480
Cdd:cd05534 75 TclgrveelngggkfgflgvklylppppldllLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKD 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 481 DEKDY--LDGVQNAIKILMNTFYGVLASSFY-RFTNPELGSSVTSFARNTI---MGLIDKLKKKDLKVIYGDTDSVFIES 554
Cdd:cd05534 155 DKKLQriLDARQLALKLLANVTYGYTAASFSgRMPCVEIADSIVQTGRETLeraIELIESTPKWGAKVVYGDTDSLFVLL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 555 GKKELTDAIKMGNDLSKEISDDL--HILIEFEKIMDPFFSHgAKKRYVG-KIVYPMDSAGEMLVRGYEVRRTDSFDMQSE 631
Cdd:cd05534 235 PGRTKEEAFKIGKEIAEAVTAANpsPIKLKFEKVYHPCVLV-TKKRYVGyKYESPDQTEPTFDAKGIETVRRDGCPAVQK 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 632 LLESVFDSLMK-KDVSGARKNAVDVIERMISGDrsIDISKLVISRSVKDSASYANADSMANVRAARKLQERGERFIP--G 708
Cdd:cd05534 314 ILEKSLRILFEtKDLSTVKSYLQRQWSKLLQGR--VSIQDFIFAKEVRLGTYKEGATLPAGAIVALRRMEKDPRAEPqyG 391
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 709 MKVSWIV----TNSRVTPQEVEPyidgEKFEDEP----DWLYYAKR-VEETVNRVFESLD 759
Cdd:cd05534 392 ERVPYVVvrgePGSRLIDLVVSP----EEFLADPslrlDAEYYITKqIIPALDRLFNLVG 447
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
395-758 |
8.92e-50 |
|
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Pssm-ID: 99919 Cd Length: 371 Bit Score: 179.44 E-value: 8.92e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 395 EGGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICFTTLSEKG----TIISPTGARFL-DPsvrKGLIPELLQTLMARRD 469
Cdd:cd05536 5 EGGIVLEPEKGLHENIVVLDFSSLYPSIMIKYNISPDTLVREGcedcDVEPQVGHKFRkDP---PGFIPSVLEDLLEERR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 470 QVKKQMKQATGDEKDY--LDGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGLIDKLKKKDLKVIYGDT 547
Cdd:cd05536 82 RIKEKMKKLDPESEEYklLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEKGFKVIYGDT 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 548 DSVF--IESGKKELTDAIKmgndLSKEISDDLHILIEFEKimdpFFSHG---AKKRYVGkivypMDSAGEMLVRGYEVRR 622
Cdd:cd05536 162 DSLFvkIDGADAVKKKVKK----LLKYINEELPLELEIEK----FYKRGffvTKKRYAG-----LTEDGKIDVVGLEVVR 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 623 TDSFDMQSELLESVFDSLMK-KDVSGARKNAVDVIERMISGDrsIDISKLVISRSV-KDSASYANAdsMANVRAARKLQE 700
Cdd:cd05536 229 RDWSEIAKETQARVLEAILKeGDVEEAVKIVKEVIEKLKRGE--VPPEKLVIWKQLtKDLSEYKAT--GPHVAAAKKLAK 304
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 701 RGERFIPGMKVSWIVTN-SRVTPQEVEPYIDGEKfEDEPDWLYYA-KRVEETVNRVFESL 758
Cdd:cd05536 305 RGYKVRPGTKIGYVIVKgSGKISDRAYPYDMVDE-KHKYDAEYYIdNQVLPAVLRILEAF 363
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
390-756 |
5.99e-49 |
|
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Pssm-ID: 99915 Cd Length: 400 Bit Score: 177.77 E-value: 5.99e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 390 KDRAIEGGHVESIGAGLYD-MVIVLDFKSMYPSIIMKYNICFTTLSEKGT-IISPTGARFLDPSVRKGLIPELLQTLMAR 467
Cdd:cd05532 4 KKAKYAGGLVLEPKKGLYDkFILLLDFNSLYPSIIQEYNICFTTVDRADPdDEDDEEPPLPPSDQEKGILPRIIRKLVER 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 468 RDQVKKQMKQ-ATGDEKDYLDGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGLIDKLKKKDLKVIYGD 546
Cdd:cd05532 84 RRQVKKLMKSeKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMNLEVIYGD 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 547 TDSVFIESGKKELTDAIKMGNDLSKEIsDDLHILIEFEkiMDPFFSH---GAKKRYVGKIVYPMDSA-GEMLVRGYEVRR 622
Cdd:cd05532 164 TDSIMINTGTTDYEEAKKLGNKIKKEV-NKSYKKLEID--IDGVFKRlllLKKKKYAALKVVDDDKGkLKKEVKGLDIVR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 623 TD----SFDMQSELLESVFDSLMKKDVSGA-RKNAVDVIERMISGdrSIDISKLVISRSV-KDSASYANADSMANVRAAR 696
Cdd:cd05532 241 RDwcplSKEIGNYVLDQILSDKSREDIVENiHEYLRKINEDLRNG--KIPLEKFIITKQLtKNPEEYPDKKSLPHVQVAL 318
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 697 KLQERGERFIPGMKVSWIVTNSRVT---------PQEVEpyiDGEKFedEPDWLYY-AKRVEETVNRVFE 756
Cdd:cd05532 319 RMNKRGRKVKAGDTIPYIICKDGSSksladrayhPDEVK---KNENL--KIDIEYYlSQQILPPISRLCE 383
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
396-728 |
8.07e-46 |
|
DNA polymerase type-II 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 proven 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.
Pssm-ID: 99920 Cd Length: 371 Bit Score: 168.21 E-value: 8.07e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 396 GGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICFTTLSE-------KGTIISPTGARFldpSVRKGLIPELLQTLMARR 468
Cdd:cd05537 5 GGYVMDSKPGLYKNVLVLDFKSLYPSIIRTFLIDPLGLIEglkapdpEDLIPGFLGARF---SREKHILPDLIARLWAAR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 469 DQVKKQMKQAtgdekdyldgVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTsFARNTIMGLIDKLKKKD-LKVIYGDT 547
Cdd:cd05537 82 DEAKREKNAP----------LSQAIKIIMNSFYGVLGSTGCRFFDPRLASSIT-LRGHEIMKQTRAWIEQQgYQVIYGDT 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 548 DSVFIESG-KKELTDAIKMGNDLSKEISD------------DLHILIEFEKIMDPFF------SH-GAKKRYVGKIVypM 607
Cdd:cd05537 151 DSTFVWLGeELDAAEAQAIGKELASQINQwwaqklkeefglESFLEIEFETHYSRFFmptirgSDeGSKKRYAGLKS--T 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 608 DSAGEMLVRGYEVRRTD----SFDMQSELLESVFDslmKKDVSGARKnavDVIERMISGDRSidiSKLVISRSVKDSASY 683
Cdd:cd05537 229 DGGDELVFKGLETVRSDwtplARQFQKELYERVFN---DEPYEGFIK---ETVEELLAGELD---ELLVYRKRLRRPLSE 299
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 1143084521 684 ANADSMANVRAARKLQERGERFIPGMKVSWIvtNSRVTPQEVEPY 728
Cdd:cd05537 300 YTKNVPPHVQAARLADQINRELGRPRQYQWI--EYVITVNGPEPL 342
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
159-335 |
1.60e-45 |
|
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 176646 [Multi-domain] Cd Length: 199 Bit Score: 161.75 E-value: 1.60e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 159 VLSFDIENAFPPDEG-DTYGKIIVIGYSI------------RSKKGIETEKGA-----ITGEEKEILSNFNKLILEKDPD 220
Cdd:cd05160 1 VLSFDIETTPPVGGPePDRDPIICITYADsfdgvkvvfllkTSTVGDDIEFIDgieveYFADEKELLKRFFDIIREYDPD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 221 IIIGYNIDGYDLPVIEYRMERYRLTLDIGRD---GSKARRMNGQFWRVKGRIISDVWWNVKKILKPKHETLNYVAMELLN 297
Cdd:cd05160 81 ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYrrsGGEKSSGSTERIAVKGRVVFDLLAAYKRDFKLKSYTLDAVAEELLG 160
|
170 180 190
....*....|....*....|....*....|....*....
gi 1143084521 298 EGKDDVDRLNIMEEY-KNRPKEVIDYCIKDADLTLRIME 335
Cdd:cd05160 161 EGKEKVDGEIIEDAEwEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
389-762 |
1.47e-35 |
|
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99914 Cd Length: 352 Bit Score: 138.25 E-value: 1.47e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 389 LKDRaieGGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICFTTLSEKGTIISPTG-ARFLDPSVRKGLIPELLQTLMAR 467
Cdd:cd05531 3 LADR---GGLVFQPEPGLYENVAQIDFSSMYPSIIVKYNISPETINCRCCECRDHVyLGHRICLKRRGFLPEVLEPLLER 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 468 RDQVKKQMKqatgdEKDYLDGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGLIDKLKKKDLKVIYGDT 547
Cdd:cd05531 80 RLEYKRLKK-----EEDPYAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEMGFRVLHGIV 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 548 DSVFIesgkKELTDAIKmgndLSKEISDDLHILIEFEKIMD--PFF----SHGAKKRYVGKivypmDSAGEMLVRGYEVR 621
Cdd:cd05531 155 DSLWI----QGRGDIEE----LAREIEERTGIPLKLEGHYDwiVFLperdGLGAPNRYFGR-----LSDGEMKVRGIELR 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 622 RTDSFDMQSELLESVFDSLMK----KDVSGARKNAVDVIERMISGDRSIDISKLVISRSV-KDSASYANadsmANVRAAR 696
Cdd:cd05531 222 RRDTPPFVKKFQEEALDILASaktpEELLKLREEALDLFRRYLQRLREGDLEDLIIEKKIsKRSSEYKV----LASTALK 297
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1143084521 697 KLQERGERFIPGMKVSWIVTNSRvtpqEVEPYIDGEKFEDEpdwLYYakrvEETVNRVFESLDEPI 762
Cdd:cd05531 298 ALRAKGVSVVPGMKIEYIVRDGK----RPVPDLGNDEGYDT---KYY----RELLERAAEELLFPL 352
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
384-734 |
2.71e-28 |
|
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99913 Cd Length: 372 Bit Score: 117.45 E-value: 2.71e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 384 TASQAL-KDRAIEGGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICFTTLS----EKGTIISP-TGARFLDPsvRKGLI 457
Cdd:cd05530 2 TSTQAIiKGKKYRGAIVLEPPPGIFFNVVVLDFASLYPSIIKVWNLSYETVNcphcECKTNEVPeVGHWVCKK--RPGIT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 458 PELLQTLMARRDQV-KKQMKQATGDEKDYL--DGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGLIDK 534
Cdd:cd05530 80 SQIIGLLRDLRVKIyKKKAKDKSLDEEMRQwyDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 535 LKKKDLKVIYGDTDSVFIESGKKELTdaikmgNDLSKEISDDLHILIEFEKIMDPFFSHGAKKRYVGkiVYPmdsAGEML 614
Cdd:cd05530 160 ARELGLKVLYGDTDSLFLWNPPQEQL------EDLVEWVEKELGLDLELDKEYRYVVFSGLKKNYLG--VTK---DGSVD 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 615 VRGYEVRRTDSFDMQSELLESVFDSLMKKDVSGARKNAVDVIERMISG------DRSIDISKLVISRSVKDSASYANADS 688
Cdd:cd05530 229 IKGLLGKKRNTPEFVKELFYEVIEILSAVNSPEDFEKAREKIRDIVKGvykrlkKKEYTLDQLAFKVMLSKPPEEYTKNT 308
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|
gi 1143084521 689 MANVRAARKLQERGERFIPGMKVSWIVTNSRVTPQEVE----PYIDGEKF 734
Cdd:cd05530 309 PQHVKAARQLEKYGRNVEAGDIISYVKVKGKEGVKPVQlarlDEVDVEKY 358
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
155-336 |
4.94e-25 |
|
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family-B DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99823 [Multi-domain] Cd Length: 195 Bit Score: 103.20 E-value: 4.94e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 155 PDVRVLSFDIENAFPPDEGDT-YGKIIVIGYS------IRSKKGIETEKGAITGEEKEILSNFNKLILEKDPDIIIGYNI 227
Cdd:cd05780 1 EDLKILSFDIEVLNHEGEPNPeKDPIIMISFAdeggnkVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 228 DGYDLPVIEYRMERYRLTLDIGRDGSKARRMNGQFWR---VKGRIISDVWWNVKKILKPKHETLNYVAMELLNEGKDDVD 304
Cdd:cd05780 81 DNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNaseIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVP 160
|
170 180 190
....*....|....*....|....*....|....
gi 1143084521 305 RLNIMEEYKNRP--KEVIDYCIKDADLTLRIMEK 336
Cdd:cd05780 161 GEEIAEAWDSGEnlERLFRYSMEDAKYTYEIGKE 194
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
395-753 |
3.69e-24 |
|
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.
Pssm-ID: 99921 Cd Length: 347 Bit Score: 104.49 E-value: 3.69e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 395 EGGHVESIGAGLYDMVIVLDFKSMYPSIIMKYNICfttlsekgtiisPTGARFldpsvrkGLIPELLQTLMARRDQVKKQ 474
Cdd:cd05538 4 EGGYAYVFITGVLGPIVHADVASLYPSIMLAYRIC------------PARDSL-------GIFLALLKYLVELRLAAKES 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 475 MKQAT-GDEKDYLDGVQNAIKILMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGLIDKLKKKDLKVIYGDTDSV-FI 552
Cdd:cd05538 65 ARAAArPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIyFI 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 553 ESGKKELTDAIKMgndLSKEISDDL--HILIEFEKIMDPFFSHGaKKRYVgkivyPMDSAGEMLVRGYEVRRTDSFDMQS 630
Cdd:cd05538 145 PPNGVDTEDEEEE---LVRELSSTLpkGITVEFDGRYRAMFSYK-IKNYA-----LLDYDGKLIVKGSAFRSRGIEPFLR 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 631 ELLESVFDSLMKKDVSGARKNAVDVIERMISgdRSIDISKLVISRSVKDSAsyanADSMANVRAARKLQ--------ERG 702
Cdd:cd05538 216 EFLREAVRLLLQGDGAGVHDLYEDYLRRLRS--HELPISDLARTETLKESP----EEYLQKVRAGKRNPaaayeialARP 289
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 1143084521 703 ERFIPGMKVSWIVTNSRVTPQEVEPYIDGEKF-EDEPDWL--YYAKRVEETVNR 753
Cdd:cd05538 290 REWRAGDRVTYYVSGTGKGVSVYENCRLVADYdPAHPDENtgFYAERLLQLAAR 343
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
158-340 |
1.79e-23 |
|
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues necessary for metal binding and catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation.
Pssm-ID: 99820 [Multi-domain] Cd Length: 230 Bit Score: 99.57 E-value: 1.79e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 158 RVLSFDIE-----NAFPPDEGDtygKIIVIGYSIR-------SKKGIETEKG--AITG-------EEKEILSNFNKLILE 216
Cdd:cd05777 8 RILSFDIEcagrkGVFPEPEKD---PVIQIANVVTrqgegepFIRNIFTLKTcaPIVGaqvfsfeTEEELLLAWRDFVQE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 217 KDPDIIIGYNIDGYDLPVI----------EY----RMERYRLTLdigRDGSKARRMNGQFWR----VKGRIISDVWWNVK 278
Cdd:cd05777 85 VDPDIITGYNICNFDLPYLlerakalklnTFpflgRIKNIKSTI---KDTTFSSKQMGTRETkeinIEGRIQFDLLQVIQ 161
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1143084521 279 KILKPKHETLNYVAMELLNEGKDDVDrLNIMEEYKNRPKE----VIDYCIKDADLTLRIMEKMRVV 340
Cdd:cd05777 162 RDYKLRSYSLNSVSAHFLGEQKEDVH-YSIITDLQNGNPEtrrrLAVYCLKDAYLPLRLLDKLMCL 226
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
24-291 |
2.75e-23 |
|
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.
Pssm-ID: 397292 Cd Length: 333 Bit Score: 101.72 E-value: 2.75e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 24 RTIDGTSVTVLCGGFDPYF-----DVIEPNEQEIEGIKKNQEFKRMENLELWVK-------GETRKAIRIYVNHPYKVPE 91
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFyclapDGKELEEVIEEIKELYEGLDKIEKIELKLKkslygyeEDPVPYLKVSFANPRPLLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 92 LRSLF----VSTVMAADIPFHHRFIYDLDL--GACIEVEGEEVIDRNRYHTD----MVLKADIKGIRTTDDFtPDVRVLS 161
Cdd:pfam03104 81 IRKYLspenISDVYEYDVDYLERFLIDNDIvgFGWYKVKVYPFRAEGRISNCdveiDCDSPDLISVPFEKEW-PPLRVLS 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 162 FDIENAFP----PDEGDTYGKIIVIGYSIRSKKGIETE----------------------KGAITG-------EEKEILS 208
Cdd:pfam03104 160 FDIECTSLpgkfPDAENVKDPIIQISCMLDGQGEPEPEprflftlrecdsediedfeytpKPIYPGvkvfefpSEKELLR 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 209 NFNKLILEKDPDIIIGYNIDGYDLPVIEYRMERYRL--TLDIGRDGSKARRM---NGQFWR------VKGRIISDVWWNV 277
Cdd:pfam03104 240 RFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIvkLSSIGRLNRGGRSKvreIGFGTRsyekvkISGRLHLDLYRVI 319
|
330
....*....|....
gi 1143084521 278 KKILKPKHETLNYV 291
Cdd:pfam03104 320 KRDYKLPSYKLNAV 333
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
203-590 |
5.12e-22 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 102.08 E-value: 5.12e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 203 EKEILSNFNKLILEKDPDIIIGYNIDGYDLPvieYRMERYRLTLdigrdGSKARRMNGQFWRVKGRIISDVWWN------ 276
Cdd:PHA02528 178 EREMLLEYINFWEENTPVIFTGWNVELFDVP---YIINRIKNIL-----GEKTAKRLSPWGKVKERTIENMYGReeiayd 249
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 277 ------------VKKILKPKHET--LNYVAMELLNEGKDDVDRLNIMEEYKNRPKEVIDYCIKDADLTLRIMEKMRVVDR 342
Cdd:PHA02528 250 isgisildyldlYKKFTFTNQPSyrLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDKRKLIEL 329
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 343 NMFMSTVTKLPLEDTTNggTSNYVDSLLIRLATQRNIAVPMTASQalKDRAIEGGHVESIGAGLYDMVIVLDFKSMYPSI 422
Cdd:PHA02528 330 VLSMAYYAKINFEDVFS--PIKTWDAIIFNSLKEEKIVIPENKSH--KKQKYAGAFVKEPVPGAYRWVVSFDLTSLYPSI 405
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 423 IMKYNICFTTLSE-----------KGTI--------ISPTGARFLDPsvRKGLIPELLQTLMARRDQVKKQMKQA----- 478
Cdd:PHA02528 406 IRQVNISPETIAGtfhvapvheyiNKTAprpsdeysCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIYKKKMLAAernae 483
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 479 ------------------------TGDE---------KDYLDGV--------------QNAIKILMNTFYGVLASSFYRF 511
Cdd:PHA02528 484 liktiledlndsvdtpidvdyyfdFSDEfkaelktltKSSLKALleecekeialcntiQMARKILINSLYGALGNEHFRY 563
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 512 TNPELGSSVTSFAR--------------NTIMGlidklKKKDLKVIYGDTDSVFIESGKkeLTDaiKMGNDLSKEISDDL 577
Cdd:PHA02528 564 YDLRNAEAITLFGQlaiqwierkmneylNKLCK-----TEDEDYVIYGDTDSIYVNLDP--LVE--KVGEDKFKDTNHWV 634
|
490
....*....|....
gi 1143084521 578 HILIEF-EKIMDPF 590
Cdd:PHA02528 635 DFLDKFcKERMEPY 648
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
155-335 |
7.75e-18 |
|
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Pol II is also involved in lagging strand synthesis.
Pssm-ID: 99827 [Multi-domain] Cd Length: 193 Bit Score: 82.23 E-value: 7.75e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 155 PDVRVLSFDIENAFPPD------EGDTYGKIIVIGYSIrSKKGIETEKGAitgEEKEILSNFNKLILEKDPDIIIGYNID 228
Cdd:cd05784 1 PKLKVVSLDIETSMDGElysiglYGEGQERVLMVGDPE-DDAPDNIEWFA---DEKSLLLALIAWFAQYDPDIIIGWNVI 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 229 GYDLPVIEYRMERYRLTLDIGRDGS----KARRMNGQ-FWRVKGRIISD-------VWWNVKKIlkpkheTLNYVAMELL 296
Cdd:cd05784 77 NFDLRLLQRRAEAHGLPLRLGRGGSplnwRQSGKPGQgFLSLPGRVVLDgidalktATYHFESF------SLENVAQELL 150
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1143084521 297 NEGK---DDVDRLN-IMEEYKNRPKEVIDYCIKDADLTLRIME 335
Cdd:cd05784 151 GEGKlihDVDDRGAeIERLFREDKLALARYNLQDCELVWRIFE 193
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
155-337 |
3.65e-17 |
|
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99824 [Multi-domain] Cd Length: 188 Bit Score: 80.06 E-value: 3.65e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 155 PDVRVLSFDIE----NAFPPDEGDtygKIIVIGYSirSKKGIETEKGAITGEEKEILSNFNKLILEKDPDIIIGYNIDGY 230
Cdd:cd05781 1 PDLKTLAFDIEvyskYGTPNPRRD---PIIVISLA--TSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDIIVGYNSNAF 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 231 DLPVIEYRMERYRLTLDIGRDGSKA--RRMNGQfWRVKGRIISDVWWNVKKILKPKHETLNYVAmELLNEGKDDvDRLNI 308
Cdd:cd05781 76 DWPYLVERARVLGVKLDVGRRGGSEpsTGVYGH-YSITGRLNVDLYDFAEEIPEVKVKTLENVA-EYLGVMKKS-ERVLI 152
|
170 180 190
....*....|....*....|....*....|....*..
gi 1143084521 309 ----MEEY----KNRPKeVIDYCIKDADLTLRIMEKM 337
Cdd:cd05781 153 ewyrIYEYwddeKKRDI-LLKYNRDDARSTYGLAEKL 188
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
156-333 |
1.05e-16 |
|
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 99828 [Multi-domain] Cd Length: 207 Bit Score: 79.38 E-value: 1.05e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 156 DVRVLSFDIENAFPPD--------EGDtygKIIVIgySIRSKKGIETEKGAITGEEKEILSNFNKLILEKDPDIIIGYNI 227
Cdd:cd05785 8 DLRRLQLDIETYSLPGfffsnpdrGDD---RIIIV--ALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPDVIEGHNI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 228 DGYDLPVIEYRMERYRLTLDIGRDGSKARRMNG-----------QFWRVKGRIISDVWWNVKKILKPKHE----TLNYVA 292
Cdd:cd05785 83 FRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSrfrfaerlidyPRYDIPGRHVIDTYFLVQLFDVSSRDlpsyGLKAVA 162
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1143084521 293 --MELLNEGKDDVDRLNIMEEYKNRPKEVIDYCIKDADLTLRI 333
Cdd:cd05785 163 khFGLASPDRTYIDGRQIAEVWRSDPARLLAYALDDVRETEGL 205
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
299-679 |
2.90e-16 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 83.53 E-value: 2.90e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 299 GKDDVDrlnIMEEYKNRPKEVID----YCIKDADLTLRIMEKMRVVDRNMFMSTVTKLPLEDTTNGGTSNYVDSLLIRLA 374
Cdd:PHA03036 436 GKDDVD---LSDMYKNYNLEIALemarYCIHDACLCKYLWEYYGIETKIDAGASTYLLPQSMVFEYRASTLIKGPLLKLL 512
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 375 TQRNIAvpMTASQALKDRAIEGGHVESIGAGLYD-MVIVLDFKSMYPSIIMKYNI------------------------- 428
Cdd:PHA03036 513 LEEKTI--LVRSETKNKFPYEGGKVFAPKQKMFDnNVLIFDYNSLYPNVCIFGNLspetlvgvvvndnrleaeinkqelr 590
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 429 ------------CFTTLSEKGTIISPTGARfldpsvRKGLIPELLQTLMARRDQVKKQMKQAT-GDEKDYLDGVQNAIKI 495
Cdd:PHA03036 591 rkypypryiyvhCEPRSPDLVSEIAVFDRR------IEGIIPKLLKTFLEERARYKKLLKEATsSVEKAIYDSMQYTYKI 664
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 496 LMNTFYGVLASSFYRFTNPELGSSVTSFARNTIMGL--------------------------------------IDKLKK 537
Cdd:PHA03036 665 VANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKYLnsvlngsklingklilancpinpffkddrsidtnydtnLPVEYN 744
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 538 KDLKVIYGDTDSVFIESGKKELTDAIKMGNDLSKEISDdlHIL-----IEFEK-----IMDpffshgAKKRYVGKIVYPM 607
Cdd:PHA03036 745 FTFRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINE--KVLfdnfkIEFEAvyknlIMQ------SKKKYTTLKYIAS 816
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1143084521 608 DSAGEMLVRgyevrrtdsfdmqsellESVFDSLMKKDVSGARKNAV----DVIERMISGDR--SIDISKLVISRSVKD 679
Cdd:PHA03036 817 STDGSVPER-----------------VNKGTSETRRDVSKFHKYMIkiykTRLLDMLSEGNmnSNQVCIDILRSLEKD 877
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
161-340 |
1.43e-12 |
|
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis. This explains why in most organisms, that no specific repair role, other than check point control, has been assigned to this enzyme. The exonuclease domain may have a structural role.
Pssm-ID: 99819 [Multi-domain] Cd Length: 234 Bit Score: 68.02 E-value: 1.43e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 161 SFDIENAfPPDEGDTYGKIIVIGYSIRSKKGIETEKGAITGE--------EKEILSNFNKLILEKDPDIIIGYNIDGYDL 232
Cdd:cd05776 33 NVSLDKP-TPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKtkvrifenERALLNFFLAKLQKIDPDVLVGHDLEGFDL 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 233 PVIEYRME------RYRltldIGR--DGSKARRMNGQFWRVK----GRIISDVWWNVKKILKPKHETLNYVAMELLNEGK 300
Cdd:cd05776 112 DVLLSRIQelkvphWSR----IGRlkRSVWPKKKGGGKFGEReltaGRLLCDTYLSAKELIRCKSYDLTELSQQVLGIER 187
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 1143084521 301 DDVDRLNIMEEYKNRPK--EVIDYCIKDADLTLRIMEKMRVV 340
Cdd:cd05776 188 QDIDPEEILNMYNDSESllKLLEHTEKDAYLILQLMFKLNIL 229
|
|
| DNA_polB_like1_exo |
cd05782 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
165-327 |
9.02e-11 |
|
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 99825 [Multi-domain] Cd Length: 208 Bit Score: 62.26 E-value: 9.02e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 165 ENAFPPDEgdtYGKIIVIGYSIRSKKGIE-TEKGAITGEEKEILSNFNKLILEKDPdIIIGYNIDGYDLPVIEYRMERYR 243
Cdd:cd05782 42 GSDFLPLP---FHKVVSISALYRDDDGGFlKVRTLDGADEKELLEDFFQLIEKKNP-RLVSFNGRGFDLPVLHLRALIHG 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 244 LTL----DIGRDGSKARRmngqfwRVKGRIIS--DVW--WNVKKILKpkhetLNYVAmELLN-EGKDDVDRLNIMEEY-K 313
Cdd:cd05782 118 VSApayfDLGNKDWNYRN------RYSERHLDlmDLLafYGARARAS-----LDLLA-KLLGiPGKMDVDGSQVWELYaE 185
|
170
....*....|....
gi 1143084521 314 NRPKEVIDYCIKDA 327
Cdd:cd05782 186 GKLDEIAEYCETDV 199
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
59-498 |
1.50e-10 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 65.08 E-value: 1.50e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 59 QEFKRMENLELWVKGETRKAIRIYVNHPYKVPELRSLFVSTVMAA-----DIPFHHRFIYDLDLGACIEVEGEEVIDRNR 133
Cdd:TIGR00592 112 QELNKTETAQRKITPRLVSVPKLKFSSPADVPAINDFSNHHPAVVdivkkAIPVSTRYLLEKILIPVPLKRAEFAGGDVQ 191
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 134 YHTDMVLKADIKGIRT----TDDFTPD-------VRVLSFDIENAFPPD-EGDTYGKIIVIGYSIRSKKGIETEkgaITG 201
Cdd:TIGR00592 192 MEGDPELKLASFDIETyfhdGKDFFPGdenpadeEIMISTTPVIAKQWDyESEPEARVVTWKKPDKPTTGSYVE---SVS 268
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 202 EEKEILSNFNKLILEKDPDIIIGYNIDGYDLPVIEYRMERYR-------------LTLDIGRDGS----KARRMNGQ--- 261
Cdd:TIGR00592 269 EEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLADRQVFQFywdayedpaeklgVVLLFGRDVDhvspCVQVKGINrdl 348
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 262 -FWRVKGRIISDVWWNVKKILKPKHETLNYVAMELLNEGKDDVDRLNIMEEYK-NRPKEVIDYCIKDADLTLRIMEKMRV 339
Cdd:TIGR00592 349 fFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEfEAPDIDAPYSSEYLEVTYELGKEFAP 428
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 340 VDRNMFMSTVTKLPleDTTNGGTSNYVDSLLIRLATQRN---IAVPMTASQALKDR-AIEGGHVE--SIGAGLY---DMV 410
Cdd:TIGR00592 429 MEALPSDLKGQTFW--HVFGSNTGNLERFLLLRKIKGPCwlaVKGPDELEYPRRSWcKYEGGYVKppNVEKGLDktpPPL 506
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 411 IVLDF--KSMYPSIIMKYNICFTTLSEKGTIISP------------TGARFLDPSVR-------KGLIPELLQTLMARRD 469
Cdd:TIGR00592 507 VVLDFsmKSLNPSIIRNEIVSIPDTLHREFALDKpppeppydvhpcVGTRPKDCSFPldlkgefPGKKPSLVEDLATERA 586
|
490 500 510
....*....|....*....|....*....|..
gi 1143084521 470 QVKKQMKQATG---DEKDYLDGVQNAIKILMN 498
Cdd:TIGR00592 587 LIKKFMAKVKKidpDEIVGHDYQQRALKVLAN 618
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
202-428 |
1.00e-08 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 58.47 E-value: 1.00e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 202 EEKEILSNFNKLILEKDPDIIIGYNIDGYDLPVIEYRMeryrltldIGRDGSKARRMNGQFWRVKGRIISDVWWnvKKIL 281
Cdd:PHA02524 179 DEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRI--------TNILGEKAANQLSPYGKITSKTITNLYG--EKII 248
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 282 KPKH-----------ETLNYVAM---ELLNEGKDDV--DRLN----IMEEYKNRPKEVIDYCIKDADLTLRIMEKMRVVD 341
Cdd:PHA02524 249 YKIHgialmdymdvfKKFSFTPMpdyKLGNVGYREVkaDKLDyegpINKFRKADHQRYVDYCVRDTDIILLIDGRRCFID 328
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 342 RNMFMSTVTKLPLEDTTngGTSNYVDSLLIRLATQRNIAVPMTasQALKDRAIEGGHVESIGAGLYDMVIVLDFKSMYPS 421
Cdd:PHA02524 329 LILSLSYYAKIRFDDVL--GTIKVWDSIIFNSLVESNVVIPAM--KASPKQSFPGAYVKEPVPGGYRYGLSFDLTSLYPS 404
|
....*..
gi 1143084521 422 IIMKYNI 428
Cdd:PHA02524 405 ILRLLNI 411
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
148-335 |
1.90e-06 |
|
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Pssm-ID: 99821 [Multi-domain] Cd Length: 231 Bit Score: 49.54 E-value: 1.90e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 148 RTTDDFTPD-----VRVLSFDIENAFPPDEGDTY--GKIIV--IGYSIRSKKGIETEKG---AITGEEKEILSNFNKLIL 215
Cdd:cd05778 14 NTRGDLLPDpefdpISAIFYCIDDDVSPFILDANkvGVIIVdeLKSNASNGRIRSGLSGipvEVVESELELFEELIDLVR 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 216 EKDPDIIIGYNID----GYdlpVIeyrmERYR------LTLDIGR-----DGSKARRMNGQFW------RVKGRIISDVW 274
Cdd:cd05778 94 RFDPDILSGYEIQrsswGY---LI----ERAAalgiddLLDEISRvpsdsNGKFGDRDDEWGYthtsgiKIVGRHILNVW 166
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1143084521 275 WNVKKILKPKHETLNYVAMELLNEGKDDVDRLNIMEEYK-NRPKE---VIDYCIKDADLTLRIME 335
Cdd:cd05778 167 RLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKsGSASErwrVLEYYLKRVRLNLEILD 231
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
385-550 |
8.37e-06 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 49.47 E-value: 8.37e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 385 ASQALKDRAIEGGHVESIGAGLY------DMVIVLDFKSMYPSIIMKYNI------------------------------ 428
Cdd:PHA03334 624 ARDCRQKIKLKGGYVFAPLTGLTfagpyqGTELTLDFASLYPSNMCDANIspeaivdpdctarvrgwvvfdwkkidrgfg 703
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 429 CFTTL--SEKGTIISPTGARFLDPSVRKglipelLQTLMARRDQVKKQMKQATG-DEKDYLDGVQNAIKILMNTFYGVla 505
Cdd:PHA03334 704 KATLMytILRTKPEEPSWRRFTTYTTSS------LNHYLSMRTEYKGAMKQAKDpKLKSYHNQLQNEMKICANSHYGV-- 775
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 1143084521 506 ssfyrftNPELGSS-VTSFARNTIMGLIDKLKKKD-LKVIYGDTDSV 550
Cdd:PHA03334 776 -------APHACQHlITTLGRHKIKLVEEFIKKEPgMTVNYGDTDSV 815
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
156-246 |
6.64e-05 |
|
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique large C-terminal domain with an unknown function. Phylogenetic analyses indicate that it is orthologous to the archaeal DNA polymerase B3 rather than to the eukaryotic alpha, delta, or zeta polymerases. The exonuclease domain of family-B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation
Pssm-ID: 99822 [Multi-domain] Cd Length: 204 Bit Score: 44.56 E-value: 6.64e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 156 DVRVLSFDIENA-----FPPDEGDtygKIIVIGYSIRSK-----------KGIE----TEKGAITGE--------EKEIL 207
Cdd:cd05779 1 DPRVLAFDIETTklplkFPDAETD---QIMMISYMIDGQgylivnreivsEDIEdfeyTPKPEYEGPfkvfnepdEKALL 77
|
90 100 110
....*....|....*....|....*....|....*....
gi 1143084521 208 SNFNKLILEKDPDIIIGYNIDGYDLPVIEYRMERYRLTL 246
Cdd:cd05779 78 QRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSM 116
|
|
| RNase_H_2 |
pfam13482 |
RNase_H superfamily; |
162-244 |
4.01e-03 |
|
RNase_H superfamily;
Pssm-ID: 433246 [Multi-domain] Cd Length: 163 Bit Score: 38.73 E-value: 4.01e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143084521 162 FDIE-NAFPPDEGDtygkIIVIG-YSIRSKKGIETEKGAITG--EEKEILSNFnkLILEKDPDIIIgYNIDGYDLPVIEY 237
Cdd:pfam13482 3 FDIEtTGLSPGKNT----IYLIGvYDVDGDKVRTFVQYLAEGptEEAAILQLF--ELLADYPLLVT-FNGKSFDVPFIKR 75
|
....*..
gi 1143084521 238 RMERYRL 244
Cdd:pfam13482 76 RFKRYDL 82
|
|
| |
