|
Name |
Accession |
Description |
Interval |
E-value |
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
1-1032 |
0e+00 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 1855.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 1 MSSSALSQWKSIARLPLPSSYLQKDVCFQLLDCCQT------KGNPHETVSRVRHSEVPVVRLYGVTAEGFSVLVHCYNY 74
Cdd:PTZ00166 17 TSSIPYGLLFSKLRRPLPPISLQKDLVFFQLDADYTekddksQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNF 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 75 EPYLWIEAPPNWLPVYSQAFMRELNDQLSNQT---RLQDTVVRVEVHQRRSLMYFKGGQLVPHLKIVVQLPQHIPKLRSL 151
Cdd:PTZ00166 97 FPYFYIEAPPNFLPEDSQKLKRELNAQLSEQSqfkKYQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSL 176
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 152 LSDRGVSCPGAWDGIRVFQTFESNVIFPLRFLVDNDIGGSNWLTLTYGKFFASPVK--TSTCQIEVVCSHEDVQNHEPLG 229
Cdd:PTZ00166 177 IESGVVVCGGGWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKkkTSTCQIEVDCSYEDLIPLPPEG 256
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 230 DYLSIAPFRILSIDIECQGRKGL-FPEPEHDPVIQIANHCVEYGHESEPLTKTIFTLKSCAPIAGAQVLSYETEAEMLLA 308
Cdd:PTZ00166 257 EYLTIAPLRILSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKECASIAGANVLSFETEKELLLA 336
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 309 WATFMKALDPDILTGYNICNFDFPYLLSRATALKASDaFHYWGRQVHERTVARDKKFQSKQMGNREYTELTLEGRIIMDA 388
Cdd:PTZ00166 337 WAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLND-FKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDV 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 389 MVVIQRDYKLRSYSLNSVSQNFLGEQKEDVHHSIISDLQHGDEETRRRLAVYCLKDAFLPVKLLDRLMCIVNNVEMARVT 468
Cdd:PTZ00166 416 MDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVT 495
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 469 GVPVGWLLERGQQIKVFSMLLRKAQKKKLVVPTVEYTG-GSDRGYEGATVIDPIKGFYNCPVATLDFASLYPSIIIAHNL 547
Cdd:PTZ00166 496 GTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSGgGSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNL 575
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 548 CYSTLVRPADARLYPEDALDRSPTSDVFVKKEVFPGILPEVLQDLLAARKHARAMMKDVPmNSLEYKVLNGRQLALKVSA 627
Cdd:PTZ00166 576 CYSTLVPPNDANNYPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK-DPLLKKVLNGRQLALKISA 654
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 628 NSVYGFTGAQV-GKLPCLEISASVTAYGRQMIDRTKNLVEDLYP-------GARVLYGDTDSVMVKCVTDEkasdkerLQ 699
Cdd:PTZ00166 655 NSVYGYTGAQVgGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTkangykhDATVIYGDTDSVMVKFGTDD-------IQ 727
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 700 EAMDFGIEAAEKVSSNFLKPIKLEFEKVYFPYLLMNKKRYAGLLWTNTDRFDKLDAKGIETVRRDNCPLVARMVSGVLNR 779
Cdd:PTZ00166 728 EAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNK 807
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 780 ILIHRSVESAVEFVKGTISDLLLNRLDISNLVITKAFSKaeDEYAGAQAHIALVERMRQRDPASAPTIGDRVAYVIIKAA 859
Cdd:PTZ00166 808 ILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGA 885
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 860 KGAKAYERSEDPIYVLDNNIPIDTQYYLEhQLAPPILRVFEGVLDDPSVLIKGDHTRHIAISAPSKnaGGLMRFVKVQLQ 939
Cdd:PTZ00166 886 KGAPQYERAEDPLYVLENNIPIDTQYYLD-QIKNPLLRIFEGVMDNPDSLFSGEHTRHITISSSSK--GGLSKFVKKQLQ 962
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 940 CISCRAVIKAGALCDNC-QDKAPEVYGKIVAKRNHYEAIYSQVWTQCQQCQGSLNQEVICSSRDCPVFYMRKKVQKDLHE 1018
Cdd:PTZ00166 963 CLGCKSVIKEGALCDNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAE 1042
|
1050
....*....|....
gi 157875046 1019 QQVLLDRFGVvdDW 1032
Cdd:PTZ00166 1043 LQELLSRFGL--DW 1054
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
510-903 |
0e+00 |
|
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: 748.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 510 RGYEGATVIDPIKGFYNCPVATLDFASLYPSIIIAHNLCYSTLVRPADARLYPEDALDRSPTSDVFVKKEVFPGILPEVL 589
Cdd:cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLPPEDYIKTPNGDYFVKSSVRKGLLPEIL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 590 QDLLAARKHARAMMKDvPMNSLEYKVLNGRQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNLVEDLY 669
Cdd:cd05533 81 EELLAARKRAKKDLKE-ETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKY 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 670 P-------GARVLYGDTDSVMVKcvtdekaSDKERLQEAMDFGIEAAEKVSSNFLKPIKLEFEKVYFPYLLMNKKRYAGL 742
Cdd:cd05533 160 TkangyshDAKVIYGDTDSVMVK-------FGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGL 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 743 LWTNTDRFDKLDAKGIETVRRDNCPLVARMVSGVLNRILIHRSVESAVEFVKGTISDLLLNRLDISNLVITKAFSKAEDE 822
Cdd:cd05533 233 LWTNPDKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADD 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 823 YAGAQAHIALVERMRQRDPASAPTIGDRVAYVIIKAAKGAKAYERSEDPIYVLDNNIPIDTQYYLEHQLAPPILRVFEGV 902
Cdd:cd05533 313 YAGKQAHVELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLENNIPIDTQYYLENQLSKPLLRIFEPI 392
|
.
gi 157875046 903 L 903
Cdd:cd05533 393 L 393
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
470-900 |
0e+00 |
|
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: 544.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 470 VPVGWLLERGQQIKVFSMLLRKAQKKKLVVPTVEYTGGSDRGYEGATVIDPIKGFYNCPVATLDFASLYPSIIIAHNLCY 549
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGDEDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 550 STLVRPADA--RLYPEDALD---RSPTSDVFVKKEVFPGILPEVLQDLLAARKHARAMMKDVpMNSLEYKVLNGRQLALK 624
Cdd:pfam00136 81 TTLVRSVDEanNLPPEDNLItveCTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEE-TDPFERAILDKQQLALK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 625 VSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNLVEDLYP-GARVLYGDTDSVMVKCVTDEkasdkerLQEAMD 703
Cdd:pfam00136 160 ITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYTyNFRVIYGDTDSVFIEFGGKD-------VEEAMK 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 704 FGIEAAEKVSS-NFLKPIKLEFEKVYFPYLLMNKKRYAGLLWTNTDRFDKLDAKGIETVRRDNCPLVARMVSGVLNRILI 782
Cdd:pfam00136 233 IGDELAEHVNQdLFKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLS 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 783 HRSVESAVEFVKGTI----SDLLLNRLDISNLVITKAFSKAEDEYAGAQ-AHIALVERMRQRDpASAPTIGDRVAYVIIK 857
Cdd:pfam00136 313 DRGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEVALRMNKRN-GEAPEVGDRIPYVIVK 391
|
410 420 430 440
....*....|....*....|....*....|....*....|....*.
gi 157875046 858 AAK---GAKAYERSEDPIYVLDNNIPIDTQYYLEHQLAPPILRVFE 900
Cdd:pfam00136 392 AAKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLE 437
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
43-900 |
2.37e-176 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 534.41 E-value: 2.37e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 43 TVSRVRHSEVPVVRLYGVTAEGFSVLVHCYNYEPYLWIEAPPNwlpvysqafmrelnDQLSNQTRLQDTVVRVEVHQRRS 122
Cdd:COG0417 9 DRSYRDEDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLPDE--------------EKLEELLRDIKEITEVEPVKLKS 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 123 LMyfkgGQLVPHLKIVVQLPQHIPKLRSLLSDRGvscpgawdgirvFQTFESNVIFPLRFLVDNDIGGSNWLTLTYGKFF 202
Cdd:COG0417 75 FF----GEPVPVLKIYTRDPRDVRELRDRLKEGG------------IDVYEADIRFHDRYLIDRFLTPGVWYEGEVEEDG 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 203 ASPVKTSTCQIEVVcshedvqnhepLGDYlsIAPFRILSIDIECQGRKGlFPEPEHD-PVIQIANHCvEYGHesepltKT 281
Cdd:COG0417 139 GKLDYEVKENPRLK-----------PEDY--RPKLKVLSFDIEVSTPRG-FPDPERDgPIISIGLAG-SDGE------KK 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 282 IFTLKscAPIAGAQVLSYETEAEMLLAWATFMKALDPDILTGYNICNFDFPYLLSRATALKASdaFhYWGRQVHErtvar 361
Cdd:COG0417 198 VLMLG--REGVDFEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAERLGIP--L-DLGRDGSE----- 267
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 362 dkkfqSKQMGNREYTELTLEGRIIMDAMVVIQRD-YKLRSYSLNSVSQNFLGEQKEDVHHSIISDLQhgdEETRRRLAVY 440
Cdd:COG0417 268 -----PSWREHGGQGFASIPGRVVIDLYDALKSAtYKFKSYSLDAVAEELLGEGKLIVDGGEIERLW---DDDKPALAEY 339
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 441 CLKDAFLPVKLLDRLMCIVNNVEMARVTGVPvgwlLER---GQQIKVF-SMLLRKAQKKKLVVPTVEYtgGSDRGYEGAT 516
Cdd:COG0417 340 NLRDAELTLRIFEKTLLLPFLIELSRITGLP----LDDvgrAGSSAAFeNLLLPEAHRRGYLAPNKGE--IKGEAYPGGY 413
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 517 VIDPIKGFY-NcpVATLDFASLYPSIIIAHNLCYSTLVRPADArlyPEDALDRSPTSD-VFVKKEvfPGILPEVLQDLLA 594
Cdd:COG0417 414 VLDPKPGLYeN--VLVLDFKSLYPSIIRTFNISPETLVEGGEE---PCGDEDVAPGFGhRFCREP--KGILPSILEELWD 486
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 595 ARKHARAMMKDVPMNSLEYKVLNGRQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNLVEDLypGARV 674
Cdd:COG0417 487 ERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEEL--GYKV 564
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 675 LYGDTDSVMVKCvtdekasDKERLQEAMDFGIEAAEKVSSNFLKPIKLEFEKVYfPYLLM--NKKRYAGLlWTNtdrfDK 752
Cdd:COG0417 565 IYGDTDSLFVWL-------PKASLEEAIEIGKELAEEINAWWPSGLELEFEKHY-RRFFFpgSKKRYAGL-TED----GK 631
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 753 LDAKGIETVRRDNCPLVARMVSGVLNRILIHRSVESAVEFVKGTISDLLLNRLDISNLVITKAFSKAEDEY-AGAQAHIA 831
Cdd:COG0417 632 IDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYeKNVPPHVR 711
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157875046 832 LVERMRQRDpaSAPTIGDRVAYVIIKAAKGAKAYErsedpiYVLDNNIPIDTQYYLEHQLAPPILRVFE 900
Cdd:COG0417 712 AARKLDERG--RPYQRGDKISYVITKGGGRVEPVE------LAKERESEIDYDYYIEKQLKPTADRILE 772
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
231-462 |
1.96e-148 |
|
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: 440.86 E-value: 1.96e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 231 YLSIAPFRILSIDIECQGRKGLFPEPEHDPVIQIANHCVEYGhESEPLTKTIFTLKSCAPIAGAQVLSYETEAEMLLAWA 310
Cdd:cd05777 1 WSKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQG-EGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 311 TFMKALDPDILTGYNICNFDFPYLLSRATALKASDaFHYWGRQVHERTVARDKKFQSKQMGNREYTELTLEGRIIMDAMV 390
Cdd:cd05777 80 DFVQEVDPDIITGYNICNFDLPYLLERAKALKLNT-FPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQ 158
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157875046 391 VIQRDYKLRSYSLNSVSQNFLGEQKEDVHHSIISDLQHGDEETRRRLAVYCLKDAFLPVKLLDRLMCIVNNV 462
Cdd:cd05777 159 VIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLVNYI 230
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
236-686 |
9.69e-135 |
|
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: 415.01 E-value: 9.69e-135
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 236 PFRILSIDIECQGRKGLFPEPE--HDPVIQIAnhCVEY-GHESEPLTKTIFTLKSCAPIAGAQVLSYETEAEMLLAWATF 312
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQIS--LVINdGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 313 MKALDPDILTGYNICNFDFPYLLSRATALKASDAFHYwGRQVHERTVARDKKFQSKQMGNREYTELTLEGRIIMDAMVVI 392
Cdd:smart00486 80 IKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKI-GRLKIGLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLY 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 393 QRDYKLRSYSLNSVSQNFLGEQKEDVHHSIISDLQHGDEETRRRLAVYCLKDAFLPVKLLDRLMCIVNNVEMARVTGVPV 472
Cdd:smart00486 159 KNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPL 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 473 GWLLERGQQIKVFSMLLRKAQKKKLVVPTVE--------YTGGSDRGYEGATVIDPIKGFYNCPVATLDFASLYPSIIIA 544
Cdd:smart00486 239 RRTLYYGSQIRVESLLLREAKKNNYILPSKElydfkgsePDLKKKVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIA 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 545 HNLCYSTLVRPADAR-----LYPEDALDR---SPTSDVFVKKEVFPGILPEVLQDLLAARKHARAMMKDVPMNSLE-YKV 615
Cdd:smart00486 319 HNLCYSTLVGVGEVVikgdlIIPEDLLTIkyeKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEElKKL 398
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157875046 616 LNGRQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNLVEDLY---PGARVLYGDTDSVMVKC 686
Cdd:smart00486 399 LDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGypkPGFKVIYGDTDSIFVTK 472
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
479-900 |
1.92e-103 |
|
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: 331.49 E-value: 1.92e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 479 GQQIKVFSMLLRKAQKK--KLVVPTVEytggsDRGYEGAT-----VIDPIKGFYNCPVATLDFASLYPSIIIAHNLCYST 551
Cdd:cd05534 1 GSQFRVESMLLRLAKPEnyILPSPSRQ-----QVAQQRALeclplVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYST 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 552 -------------LVRPADARLYPEDALDR---------SPTSDVFVKKEVFPGILPEVLQDLLAARKHARAMMKDVPMN 609
Cdd:cd05534 76 clgrveelngggkFGFLGVKLYLPPPPLDLlllkddvtiSPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDD 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 610 SLEYKVLNGRQLALKVSANSVYGFTGAQV-GKLPCLEISASVTAYGRQMIDRTKNLVEDL-YPGARVLYGDTDSVMVKCv 687
Cdd:cd05534 156 KKLQRILDARQLALKLLANVTYGYTAASFsGRMPCVEIADSIVQTGRETLERAIELIESTpKWGAKVVYGDTDSLFVLL- 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 688 tdeKASDKErlqEAMDFGIEAAEKVSSNFLKPIKLEFEKVYFPYLLMNKKRYAGLLW-TNTDRFDKLDAKGIETVRRDNC 766
Cdd:cd05534 235 ---PGRTKE---EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYeSPDQTEPTFDAKGIETVRRDGC 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 767 PLVARMVSGVLNRILIHRSVESAVEFVKGTISDLLLNRLDISNLVITKAFSK-AEDEYAGAQAHIALVERMRQRDPASAP 845
Cdd:cd05534 309 PAVQKILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLgTYKEGATLPAGAIVALRRMEKDPRAEP 388
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 157875046 846 TIGDRVAYVIIKAAKGAKAYERSEDPIYVLDN-NIPIDTQYYLEHQLAPPILRVFE 900
Cdd:cd05534 389 QYGERVPYVVVRGEPGSRLIDLVVSPEEFLADpSLRLDAEYYITKQIIPALDRLFN 444
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
48-900 |
1.44e-100 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 334.13 E-value: 1.44e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 48 RHSEV----PVVRLYGVTAEGFSVLVHCYNYEPYLwieappnwlpvYSQAFMRELNDQLSNQTRLQDTVVRVEVHQRRSL 123
Cdd:PRK05762 11 RHYRDtpggPEVELWLATDEGPRVVLLDPQFRPYF-----------IPAEQDERAESLLAGEIGVRLSPLALKDFHRRPV 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 124 MyfkgGQLVPHLKIVVQLPQhipklrsLLSDRGVscpgawdgirvfQTFESNVIFPLRFLVDNDIGGSNWltltygkfFA 203
Cdd:PRK05762 80 L----GLYCRQHRQLTRLPK-------RLREGGV------------DVYEADIRFPERYLMERFITPCVW--------FS 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 204 SPVKTSTCQIEVVCShedvqNHEPLGDYLSiaPFRILSIDIECQGRKGLF----PEPEHDPVIQIAnhcveyghESEPlt 279
Cdd:PRK05762 129 GEVEQYTTDGVLRNA-----RLKPAPDYRP--PLKVVSLDIETSNKGELYsiglEGCGQRPVIMLG--------PPNG-- 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 280 ktiftlkscapiAGAQVLSY-ETEAEMLLAWATFMKALDPDILTGYNICNFDFPYLLSRATALKASDAFhywGRQVHERT 358
Cdd:PRK05762 192 ------------EALDFLEYvADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPLRL---GRDGSELE 256
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 359 VaRDKKFQSkqmgnrEYTELTLEGRIIMDAMVVIQR-DYKLRSYSLNSVSQNFLGEQKEdvhhsIISDLQHGDEETRR-- 435
Cdd:PRK05762 257 W-REHPFRS------GYGFASVPGRLVLDGIDALKSaTWVFDSFSLEYVSQRLLGEGKA-----IDDPYDRMDEIDRRfa 324
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 436 ----RLAVYCLKDA------FLPVKLLDRLMcivnnvEMARVTGVPVGwllERGQQIKVF-SMLLRKAQKKKLVVPTVEY 504
Cdd:PRK05762 325 edkpALARYNLKDCelvtriFEKTKLLPFLL------ERATVTGLPLD---RVGGSVAAFeHLYLPRAHRAGYVAPNLGE 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 505 TGGsdRGYEGATVIDPIKGFYNcPVATLDFASLYPSIIIAHNLCYSTLVRPADArlyPEDALDRSPTSDVFVKKevfPGI 584
Cdd:PRK05762 396 RPG--EASPGGYVMDSKPGLYD-SVLVLDFKSLYPSIIRTFNIDPDGLVEGLAQ---PPEESVAGFLGARFSRE---KHF 466
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 585 LPEVLQDLLAARKHARAMMKdvpmnsleykvlNGRQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNL 664
Cdd:PRK05762 467 LPEIVERLWEGRDEAKREMN------------KPLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTREL 534
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 665 VEDLypGARVLYGDTDSVMvkcVTDEKASDKErlqEAMDFGIEAAEKVSSNFLKPIK----------LEFEKVY----FP 730
Cdd:PRK05762 535 IEAQ--GYQVIYGDTDSTF---VWLGGAHDEE---DAAKIGRALVQEINQWWQEHLQqefglesaleLEFEKHYrrffMP 606
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 731 YLLM----NKKRYAGlLWTNTDRFDKLDAKGIETVRRDNCPLVARMVSGVLNRILIHRSVesaVEFVKGTISDLLLNRLD 806
Cdd:PRK05762 607 TIRGaeegSKKRYAG-LIQEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEPY---VDYVREVIDKLRAGELD 682
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 807 iSNLVITKAFSKAEDEYAGAQA-HIA----LVERMRQRDPASAPTIGDRVAYVIIKAAKGAKAYERSedpiyvldnniPI 881
Cdd:PRK05762 683 -EKLVYRKRLRRPLDEYQRNVPpHVRaarlADEMGYKVGRPLQYQNGGKIGYVITVNGPEPLEYRKS-----------PI 750
|
890 900
....*....|....*....|..
gi 157875046 882 DTQYYLEHQLAP---PILRVFE 900
Cdd:PRK05762 751 DYDYYIEKQLQPvadRILPFFG 772
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
511-900 |
5.59e-96 |
|
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: 306.99 E-value: 5.59e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 511 GYEGATVIDPIKGFYNcPVATLDFASLYPSIIIAHNLCYSTLVRPadarlyPEDALDRSPTSDVFVKKEVFPGILPEVLQ 590
Cdd:cd00145 2 PYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGN------GEIAAPEDYIGVGFRSPKDRKGLLPRILE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 591 DLLAARKHARAMMKDVPMNSLEYKVLNGRQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNLVEDLyp 670
Cdd:cd00145 75 ELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEH-- 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 671 GARVLYGDTDSVMVkcvtdeKASDKERLQEAMDFGIEAAEKVSSNflKPIKLEFEKVYFPYLLMNKKRYAGLLWTNTDRF 750
Cdd:cd00145 153 GARVIYGDTDSIFV------SLPKMGTKEDAIKEGREILQELADE--HLLELEFEKVYLPFFLGKKKRYAGLDIWKGQDE 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 751 DKLDAKGIETVRRDNCPLVARMVSGVLNRILIHrsvESAVEFVKGTISDLllnrldisnlvitkafskaedeyagaqahi 830
Cdd:cd00145 225 GKIDIKGLETRRRDSPPLVKKFQKEVLELILEE---ERKVEAVKEYIDEL------------------------------ 271
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 831 alvermrqrdpasaptigDRVAYVIIKAAKGAKAYERSEDPIYVLDNNIPIDTQYYLEHQLAPPILRVFE 900
Cdd:cd00145 272 ------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
511-901 |
1.05e-82 |
|
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: 273.05 E-value: 1.05e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 511 GYEGATVIDPIKGFYNcPVATLDFASLYPSIIIAHNLCYSTLVRPADarlypEDALDRSPTSDVFVKKevFPGILPEVLQ 590
Cdd:cd05536 3 SYEGGIVLEPEKGLHE-NIVVLDFSSLYPSIMIKYNISPDTLVREGC-----EDCDVEPQVGHKFRKD--PPGFIPSVLE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 591 DLLAARKHARAMMKDVPMNSLEYKVLNGRQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNLVEDLyp 670
Cdd:cd05536 75 DLLEERRRIKEKMKKLDPESEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEK-- 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 671 GARVLYGDTDSVMVKcvtdeKASDKERLQEAMDFGIEAAEKVssnflkPIKLEFEKVYFPYLLMNKKRYAGLlwtntDRF 750
Cdd:cd05536 153 GFKVIYGDTDSLFVK-----IDGADAVKKKVKKLLKYINEEL------PLELEIEKFYKRGFFVTKKRYAGL-----TED 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 751 DKLDAKGIETVRRDNCPLVARMVSGVLNRILIHRSVESAVEFVKGTISDLLLNRLDISNLVITKAFSKAEDEYAGAQAHI 830
Cdd:cd05536 217 GKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYKATGPHV 296
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157875046 831 ALVERMRQRDpaSAPTIGDRVAYVIIKAAkgAKAYERSEDPIYVLDNNiPIDTQYYLEHQLAPPILRVFEG 901
Cdd:cd05536 297 AAAKKLAKRG--YKVRPGTKIGYVIVKGS--GKISDRAYPYDMVDEKH-KYDAEYYIDNQVLPAVLRILEA 362
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
168-900 |
6.67e-82 |
|
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: 289.65 E-value: 6.67e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 168 VFQTFESNVIfplRFLVDNDIGGSNWLTLTYGKFFASPVKtSTCQIEVVCSHEDVQNhepLGDYLSIAPFRILSIDIECQ 247
Cdd:TIGR00592 444 VFGSNTGNLE---RFLLLRKIKGPCWLAVKGPDELEYPRR-SWCKYEGGYVKPPNVE---KGLDKTPPPLVVLDFSMKSL 516
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 248 GRKGLFPE-------PEHDPVIQIANHCVEYGHESEPLTK---TIFTLKSCAPIAG---AQVLSYETEAEMLLAWATFMK 314
Cdd:TIGR00592 517 NPSIIRNEivsipdtLHREFALDKPPPEPPYDVHPCVGTRpkdCSFPLDLKGEFPGkkpSLVEDLATERALIKKFMAKVK 596
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 315 ALDPDILTGYNICNFDFPYLLSRATALKASdafhYWGRqvhertVARDKKFQSKQMGNREYTEltleGRIIMDAMVVIQR 394
Cdd:TIGR00592 597 KIDPDEIVGHDYQQRALKVLANRINDLKIP----TWSK------IGRLRRSPKFGRRFGERTC----GRMICDVEISAKE 662
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 395 DYKLRSYSLNSVSQNFLGEQKEDVHHSIISDlQHGDEETRRRLAVYCLKDAFLPVKLLDRLMCIVNNVEMARVTGVPVGW 474
Cdd:TIGR00592 663 LIRCKSYDLSELVQQILKTERKVIPIDNINN-MYSESSSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSR 741
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 475 LLERGQQIKVFSMLLRKAQKKKLVVPTVE-----------------YTGGSDRGYEGATVIDPIKGFYNCPVATLDFASL 537
Cdd:TIGR00592 742 TLMGGRSERNEFLLLHAFYENNYIVPDKQifrkqqklgdedeeidgYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSL 821
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 538 YPSIIIAHNLCYSTLVRPADarlypEDALDRSPTSdvfvkkEVFPGILPEVLQDLLAARKHARAMMKD--VPMNSLEYKV 615
Cdd:TIGR00592 822 YPSIIQEFNICFTTVQQKVD-----EDELPELPDS------ELEMGILPRELRKLVERRKEVKKLMKQdlNPDLRLQYDI 890
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 616 lngRQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNLVEDLYpgARVLYGDTDSVMVKcvtdekaSDK 695
Cdd:TIGR00592 891 ---RQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMN--LEVIYGDTDSIMIN-------TPG 958
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 696 ERLQEAMDFGIEAAEKVSSNFlKPIKLEFEKVYFPYLLMNKKRYAGL---LWTNTDRFDKLDAKGIETVRRDNCPLvARM 772
Cdd:TIGR00592 959 TKYEEVFKIGKEFKSEVNKLY-KLLELDIDGVFKRLLLLKKKKYAAIkveGDSDGNYTTKQEVKGLDIVRRDWSPL-AKE 1036
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 773 VSG-VLNRILIHRSVESAVEFVKGTISDL----LLNRLDISNLVITKAFSKAEDEYAGA--QAHIALVERMRQRDPASAP 845
Cdd:TIGR00592 1037 TGKkVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLTRDPKDYPDGasLPHVHVALRINARGGRKVK 1116
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....*..
gi 157875046 846 TiGDRVAYVIIKAAKGAKAYERSEDPIYVL--DNNIPIDTQYYLEHQLAPPILRVFE 900
Cdd:TIGR00592 1117 A-GDVVSYVICKDGGNLSARQRAYALEELQrkHNNLIYDTQYYLEHQIHPVVLRILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
512-900 |
2.83e-80 |
|
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: 267.14 E-value: 2.83e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 512 YEGATVIDPIKGFYNCPVATLDFASLYPSIIIAHNLCYSTLVRPADARLYPEDALDRSPTSDvfvkkevfPGILPEVLQD 591
Cdd:cd05532 8 YAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPPLPPSDQE--------KGILPRIIRK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 592 LLAARKHARAMMKDvPMNSLEYKVLNGRQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNLVEDLypG 671
Cdd:cd05532 80 LVERRRQVKKLMKS-EKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKM--N 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 672 ARVLYGDTDSVMVKCVTDEkasdkerLQEAMDFGIEAAEKVSSNFlKPIKLEFEKVYFPYLLMNKKRYAGLLWTNTD-RF 750
Cdd:cd05532 157 LEVIYGDTDSIMINTGTTD-------YEEAKKLGNKIKKEVNKSY-KKLEIDIDGVFKRLLLLKKKKYAALKVVDDDkGK 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 751 DKLDAKGIETVRRDNCPLVARMVSGVLNRILIHRSVESAVEFVKG---TISDLLLN-RLDISNLVITKAFSKAEDEYAGA 826
Cdd:cd05532 229 LKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEylrKINEDLRNgKIPLEKFIITKQLTKNPEEYPDK 308
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157875046 827 --QAHIALVERMRQRDPASAPtiGDRVAYVIIKAAKGAKAYERSEDPIYV-LDNNIPIDTQYYLEHQLAPPILRVFE 900
Cdd:cd05532 309 ksLPHVQVALRMNKRGRKVKA--GDTIPYIICKDGSSKSLADRAYHPDEVkKNENLKIDIEYYLSQQILPPISRLCE 383
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
60-406 |
1.44e-72 |
|
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: 243.86 E-value: 1.44e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 60 VTAEGFSVLVHCYNYEPYLWIEAPPNwlpvysqafmRELNDQLSNQTRL---QDTVVRVEVHQRRSLMYFKGGQlVPHLK 136
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDG----------KELEEVIEEIKELyegLDKIEKIELKLKKSLYGYEEDP-VPYLK 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 137 IVVQLPQHIPKLRSLLSDrgvscpgawdgIRVFQTFESNVIFPLRFLVDNDIGGSNWLTLTYgKFFASPVKTSTCQIEVV 216
Cdd:pfam03104 70 VSFANPRPLLKIRKYLSP-----------ENISDVYEYDVDYLERFLIDNDIVGFGWYKVKV-YPFRAEGRISNCDVEID 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 217 CSHEDVQNHEPLGDylsIAPFRILSIDIECQGRKGLFPEPEH--DPVIQIANHCVEYGhESEPLTKTIFTLKSCAPIA-- 292
Cdd:pfam03104 138 CDSPDLISVPFEKE---WPPLRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQG-EPEPEPRFLFTLRECDSEDie 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 293 -----------GAQVLSYETEAEMLLAWATFMKALDPDILTGYNICNFDFPYLLSRATALKASDAFHYWGRQVHERTVAR 361
Cdd:pfam03104 214 dfeytpkpiypGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNRGGRSKVR 293
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 157875046 362 DKKFqskqmGNREYTELTLEGRIIMDAMVVIQRDYKLRSYSLNSV 406
Cdd:pfam03104 294 EIGF-----GTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
54-904 |
1.90e-58 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 215.71 E-value: 1.90e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 54 VVRLYGVTAEGFSVLVHCYNYEPYLWIEAPPnwlpvysqafmrELNDQLSNQTRLQDtVVRVEVHQRRSLMYFKggqLVP 133
Cdd:PRK05761 34 VVKLYDPETGKIYKWYDRTGHKPYFLTDLDP------------DEIDKIPKILRHPS-FDHLEIVEKYDGLRDK---KVK 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 134 HLKIVVQLPQHIPKLRSLLSDRGvscpgawdgirvfQTFESNVIFPLRFLVDNDIGGSNWLTLTYGKFFASPVKTSTCQI 213
Cdd:PRK05761 98 VTKIVVKDPLAVRRLRLSVRDIP-------------RAWEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEILVEEIK 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 214 EVVCSHEDVQNHEPLGDYLSIAPFRILSIDIECQGR-KGLFPEpehdpviqianhcveyghesepltktiftlkscapia 292
Cdd:PRK05761 165 KAFKDERKLAEDWLPIFEAPIPKIKRIAIDIEVYTPaKGRIPD------------------------------------- 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 293 gaqvlsyETEAEMLLAWATFMKALDPDILtgYNICNFDFPYLLSRATAL---KASDAFHYWGRQVHertVARDKKFQSKQ 369
Cdd:PRK05761 208 -------DSEKELLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKLgipKEEIPIEPGRAGIH---IDLYKFFQNKA 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 370 MgnREYTeltLEGRiimdamvviqrdYKLRSYSLNSVSQNFLGEQKEDVHHSIisdlqhgDEETRRRLAVYCLKDAFLPV 449
Cdd:PRK05761 276 V--RSYA---FYGK------------YRHREARLDAVGRALLGISKVELETNI-------SELDLEELAEYNFRDAEITL 331
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 450 KLLdrlmcIVNN-------VEMARVTGVPVGWL--LERGQQIKvfSMLLRKAQKKKLVVPTVEYTGGSDRG--------- 511
Cdd:PRK05761 332 KLT-----FFNNelvlkliLLLSRISKLPIEELsrATISTWIS--NLEYWEHRKRGWLIPWKEDILRLDHEvykkaiikg 404
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 512 --YEGATVIDPIKGFY-NcpVATLDFASLYPSIIIAHNLCYSTlVRPADARLYPEDALDRSPTSdVFVKKevfPGILPEV 588
Cdd:PRK05761 405 kkYRGGLVFQPPPGIFfN--VYVLDFASLYPSIIVKWNLSPET-VRIPECKCHYDDEVPELGHS-VCDDR---PGLTSVL 477
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 589 LQDLLAARKHARAMMKDVPMNSLEYK-VLNGRQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNLVED 667
Cdd:PRK05761 478 VGLLRDFRVKIYKKKAKDPNLDEERRaWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAEE 557
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 668 LypGARVLYGDTDSVMVKCVTDEKAsdkERLQEAM--DFGIEaaekvssnflkpikLEFEKVY----FPYLlmnKKRYAG 741
Cdd:PRK05761 558 L--GLKVLYGDTDSLFVWGPTKESL---EELIKEIeeRTGID--------------LEVDKTYdwvaFSGL---KKNYFG 615
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 742 LLwtnTDrfDKLDAKGIETVRRDNCPLVARMVSGVLNRILIHRSVESAVEF-------VKGTISDLLLNRLDISNLVITK 814
Cdd:PRK05761 616 VL---KD--GKVKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEKVkdeiedvLKRYYEKLRAKDYPLDELAIRV 690
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 815 AFSKAEDEYA-GAQAHIALVERMRQRDPASAPtiGDRVAYVIIKAAKGAKAYErsedpiyvLDNNIPIDTQYYLEHqlap 893
Cdd:PRK05761 691 RLSKPLDEYTkNTPQHVKAALQLRDYGVEVSP--GDIISYVKVDDKRGVKPVQ--------LAKLSEIDVEKYIEL---- 756
|
890
....*....|.
gi 157875046 894 pILRVFEGVLD 904
Cdd:PRK05761 757 -LRSALEQILS 766
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
514-900 |
1.26e-44 |
|
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: 165.90 E-value: 1.26e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 514 GATVIDPIKGFYNcPVATLDFASLYPSIIIAHNLCYSTLVRPADARlyPEDALDRSPTSDVFVKKEvfpGILPEVLQDLL 593
Cdd:cd05537 5 GGYVMDSKPGLYK-NVLVLDFKSLYPSIIRTFLIDPLGLIEGLKAP--DPEDLIPGFLGARFSREK---HILPDLIARLW 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 594 AARKHARaMMKDVPMnsleykvlngrQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKNLVEDLypGAR 673
Cdd:cd05537 79 AARDEAK-REKNAPL-----------SQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQ--GYQ 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 674 VLYGDTDSVMVK---CVTDEKASDK-------------ERLQEamDFGIEAAekvssnflkpIKLEFEKVYFPYLLM--- 734
Cdd:cd05537 145 VIYGDTDSTFVWlgeELDAAEAQAIgkelasqinqwwaQKLKE--EFGLESF----------LEIEFETHYSRFFMPtir 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 735 -----NKKRYAGLLWTNTDrfDKLDAKGIETVRRDNCPLVARMVSGVLNRILIHRSVEsavEFVKGTISDLLLNRLDiSN 809
Cdd:cd05537 213 gsdegSKKRYAGLKSTDGG--DELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYE---GFIKETVEELLAGELD-EL 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 810 LVITKAFSKAEDEYAG-----AQAHIALVERMRQRDPasaPTIGDRVAYVIIKAakGAKAYErsedpiyvlDNNIPIDTQ 884
Cdd:cd05537 287 LVYRKRLRRPLSEYTKnvpphVQAARLADQINRELGR---PRQYQWIEYVITVN--GPEPLE---------YRTSPLDYQ 352
|
410
....*....|....*....
gi 157875046 885 YYLEHQLAP---PILRVFE 900
Cdd:cd05537 353 HYIDKQLKPiadSILPFLG 371
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
239-452 |
1.13e-43 |
|
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: 157.13 E-value: 1.13e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 239 ILSIDIECQGRKGlFPEPEHDPVIQIAnHCVEY-GHESEPLTKTIFTLKSCAPIAGAQVLSYETEAEMLLAWATFMKALD 317
Cdd:cd05160 1 VLSFDIETTPPVG-GPEPDRDPIICIT-YADSFdGVKVVFLLKTSTVGDDIEFIDGIEVEYFADEKELLKRFFDIIREYD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 318 PDILTGYNICNFDFPYLLSRATALKASdafhywgrqvHERTVARDkkfqSKQMGN-REYTELTLEGRIIMDAMVVIQRDY 396
Cdd:cd05160 79 PDILTGYNIDDFDLPYLLKRAEALGIK----------LTDGIYRR----SGGEKSsGSTERIAVKGRVVFDLLAAYKRDF 144
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 157875046 397 KLRSYSLNSVSQNFLGEQKEDVHHSIISDlqHGDEETRRRLAVYCLKDAFLPVKLL 452
Cdd:cd05160 145 KLKSYTLDAVAEELLGEGKEKVDGEIIED--AEWEEDPERLIEYNLKDAELTLQIL 198
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
508-899 |
2.67e-34 |
|
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: 135.16 E-value: 2.67e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 508 SDRGyeGAtVIDPIKGFYNcPVATLDFASLYPSIIIAHNLCYSTLVRPADARLYPEDALDRSPTSDvfvkkevfPGILPE 587
Cdd:cd05531 4 ADRG--GL-VFQPEPGLYE-NVAQIDFSSMYPSIIVKYNISPETINCRCCECRDHVYLGHRICLKR--------RGFLPE 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 588 VLQDLLAARKHARAMMKdvpmnslEYKVLNGRQLALKVSANSVYGFTG---AQVGKLPCLEisaSVTAYGRQMIDRTKNL 664
Cdd:cd05531 72 VLEPLLERRLEYKRLKK-------EEDPYAGRQKALKWILVTSFGYLGyknAKFGRIEVHE---AITAYGRKILLRAKEI 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 665 VEDLypGARVLYGDTDSVMVKcvtdeKASDKERLqeamdfgieaAEKVSSNFLKPIKLE--FEKVYFPYLLMN---KKRY 739
Cdd:cd05531 142 AEEM--GFRVLHGIVDSLWIQ-----GRGDIEEL----------AREIEERTGIPLKLEghYDWIVFLPERDGlgaPNRY 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 740 AGLLWTntdrfDKLDAKGIETVRRDNCPLVARMVSGVLNRIlihRSVESAVEFvKGTISDLL---------LNRLDISNL 810
Cdd:cd05531 205 FGRLSD-----GEMKVRGIELRRRDTPPFVKKFQEEALDIL---ASAKTPEEL-LKLREEALdlfrrylqrLREGDLEDL 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 811 VITKAFSKAEDEYAGAQAHIAlvERMRQRDPASAPtiGDRVAYVIIkaakgakayeRSEDPIYVLDNNIPIDTQYYLE-- 888
Cdd:cd05531 276 IIEKKISKRSSEYKVLASTAL--KALRAKGVSVVP--GMKIEYIVR----------DGKRPVPDLGNDEGYDTKYYREll 341
|
410
....*....|.
gi 157875046 889 HQLAPPILRVF 899
Cdd:cd05531 342 ERAAEELLFPL 352
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
509-889 |
2.43e-32 |
|
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: 129.78 E-value: 2.43e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 509 DRGYEGATVIDPIKG-FYNcpVATLDFASLYPSIIIAHNLCYSTlVRPAdarlYPEDALDRSPTSDVFVKKEvFPGILPE 587
Cdd:cd05530 10 GKKYRGAIVLEPPPGiFFN--VVVLDFASLYPSIIKVWNLSYET-VNCP----HCECKTNEVPEVGHWVCKK-RPGITSQ 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 588 V---LQDLLAARKHARAMMKDVPMNSLE-YKVLngrQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIDRTKN 663
Cdd:cd05530 82 IiglLRDLRVKIYKKKAKDKSLDEEMRQwYDVV---QSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 664 LVEDLypGARVLYGDTDSVMVKCVTDEKASDKERLQEAmDFGIEaaekvssnflkpikLEFEKVYFPYLLMN-KKRYAGL 742
Cdd:cd05530 159 KAREL--GLKVLYGDTDSLFLWNPPQEQLEDLVEWVEK-ELGLD--------------LELDKEYRYVVFSGlKKNYLGV 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 743 LwtnTDRfdKLDAKGIETVRRDNCPLVARMVSGVLNrILIHRSVESAVEFVKGTISDL---LLNRL-----DISNLVITK 814
Cdd:cd05530 222 T---KDG--SVDIKGLLGKKRNTPEFVKELFYEVIE-ILSAVNSPEDFEKAREKIRDIvkgVYKRLkkkeyTLDQLAFKV 295
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157875046 815 AFSKAEDEYA-GAQAHIA---LVERMRQRDPAsaptiGDRVAYVIIKAAKGAKAYERSEDPiyvldnniPIDTQYYLEH 889
Cdd:cd05530 296 MLSKPPEEYTkNTPQHVKaarQLEKYGRNVEA-----GDIISYVKVKGKEGVKPVQLARLD--------EVDVEKYVEI 361
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
190-795 |
2.89e-31 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 132.51 E-value: 2.89e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 190 GSNWLTLtYGKF-----FASPVKTStcqiEVVCSHEDVqNHEPLG------DYLS----------IAPFRILSIDIECQG 248
Cdd:PHA02528 44 ESKYKDI-YGKNcrpkkFDSMRDAR----KWMKRMKDV-GFEALGmddfklQYISdtypgeikydRSKIRIANLDIEVTA 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 249 RKGlFPEPEH--DPVIQIanhcveyGHESEPLTK-TIFTLKSCAP--IAGAQV----------LSYETEAEMLLAWATFM 313
Cdd:PHA02528 118 EDG-FPDPEEakYEIDAI-------THYDSIDDRfYVFDLGSVEEwdAKGDEVpqeildkvvyMPFDTEREMLLEYINFW 189
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 314 KALDPDILTGYNICNFDFPYLLSRATAL---KASDAFHYWGRqVHERTVARDkkfqskqMGNREYTeLTLEGRIIMDAMV 390
Cdd:PHA02528 190 EENTPVIFTGWNVELFDVPYIINRIKNIlgeKTAKRLSPWGK-VKERTIENM-------YGREEIA-YDISGISILDYLD 260
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 391 VIQR-DYKLR-SYSLNSVSQNFLGEQKEDVHHSIISDLQHGDEEtrrRLAVYCLKDAFLPVKLLDRLMCIVNNVEMARVT 468
Cdd:PHA02528 261 LYKKfTFTNQpSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQ---KYIEYNIIDVELVDRLDDKRKLIELVLSMAYYA 337
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 469 GVPVGWLLergQQIKVF-SMLLRKAQKKKLVVPTVEYTggSDRGYEGATVIDPIKGFYNCpVATLDFASLYPSIIIAHNL 547
Cdd:PHA02528 338 KINFEDVF---SPIKTWdAIIFNSLKEEKIVIPENKSH--KKQKYAGAFVKEPVPGAYRW-VVSFDLTSLYPSIIRQVNI 411
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 548 CYSTL-----VRPADARL-----YPEDALDRSPTSDVFVKKEvfPGILPEVLQDLLAARKHARAMM----------KDVP 607
Cdd:PHA02528 412 SPETIagtfhVAPVHEYInktapRPSDEYSCSPNGWMYRKDI--RGVIPTEIKKVFDQRKIYKKKMlaaernaeliKTIL 489
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 608 MN--------------------------SLEYKVLNGR--------------QLALKVSANSVYGFTGAQVGKLPCLEIS 647
Cdd:PHA02528 490 EDlndsvdtpidvdyyfdfsdefkaelkTLTKSSLKALleecekeialcntiQMARKILINSLYGALGNEHFRYYDLRNA 569
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 648 ASVTAYGR---QMIDRTKNL-------VEDLypgARVLYGDTDSVMV------------KCVTDEKASD------KERLQ 699
Cdd:PHA02528 570 EAITLFGQlaiQWIERKMNEylnklckTEDE---DYVIYGDTDSIYVnldplvekvgedKFKDTNHWVDfldkfcKERME 646
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 700 EAMDFGIEAAEKVSSNFLKPIKLEFEKVYFPYLLMNKKRYAGLLWTNTD-RFD--KLDAKGIETVRRDNCPLVARMVSGV 776
Cdd:PHA02528 647 PYIDSSYRELCEYMNNYEHLMFMDREAIAGPGFWTAKKRYALNVWDSEGtRYAepKLKIMGIETQRSSTPKAVQKALKEA 726
|
730
....*....|....*....
gi 157875046 777 LNRILIhRSVESAVEFVKG 795
Cdd:PHA02528 727 IRRILQ-EGEESLQEYIKE 744
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
940-1009 |
3.63e-25 |
|
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.
Pssm-ID: 464119 Cd Length: 68 Bit Score: 99.37 E-value: 3.63e-25
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 940 CISCRAVikAGALCDNCQDKAPEVYGKIVAKRNHYEAIYSQVWTQCQQCQGSLNQEVICSSRDCPVFYMR 1009
Cdd:pfam14260 1 CLGCGAP--EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYMR 68
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
234-881 |
8.23e-25 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 112.04 E-value: 8.23e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 234 IAPFRI----LSIDIECQGRKGlFPEPEHDPVIQIanhCVEYghESEPLTKTIFTL----------------------KS 287
Cdd:PHA03036 153 IPRFDIprsyLFLDIECHFDKK-FPSVFINPVSHI---SCCY--IDLSGKEKRFTLinedmlsedeieeavkrgyyeiES 226
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 288 CAPIAGAQVLSYETEAEMLLawatFMKAL---DPDILTGYNICNFDFPYLLSRATALKAS-------DAFHYWGRQVHER 357
Cdd:PHA03036 227 LLDMDYSKELILCSEIVLLR----IAKKLlelEFDYVVTFNGHNFDLRYISNRLELLTGEkiifrspDGKETVHLCIYER 302
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 358 TVARDKkfQSKQMGNREYTELTLEGRIIMDAMVVIQRDYKLRSYSLNSVSQN-----------------FLGEQKED--- 417
Cdd:PHA03036 303 NLSSHK--GVGGVANTTYHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISKNafncnakvlsennnevtFIGDNTTDakg 380
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 418 -------------------------VHHSIIS----------------------------DLQ----HGDEETRRRLAVY 440
Cdd:PHA03036 381 kasifsevlstgnyvtindddickiLDKDIIEnsftvkvicknnyipgdtytlsfgkddvDLSdmykNYNLEIALEMARY 460
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 441 CLKDAFLPVKLLDRLMcivnnVEmARVTGVPVGWLLErgqQIKVFSM---------LLRKAQKKKLVVptVEYTGGSDRG 511
Cdd:PHA03036 461 CIHDACLCKYLWEYYG-----IE-TKIDAGASTYLLP---QSMVFEYrastlikgpLLKLLLEEKTIL--VRSETKNKFP 529
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 512 YEGATVIDPIKGFYNCPVATLDFASLYPSIIIAHNLCYSTLVR--PADARL------------YPED---ALDRSPTSDV 574
Cdd:PHA03036 530 YEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGvvVNDNRLeaeinkqelrrkYPYPryiYVHCEPRSPD 609
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 575 FVKK-EVF----PGILPEVLQDLLAARKHARAMMKDVPmNSLEYKVLNGRQLALKVSANSVYGFTGAQVGKLPCLEISAS 649
Cdd:PHA03036 610 LVSEiAVFdrriEGIIPKLLKTFLEERARYKKLLKEAT-SSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKS 688
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 650 VTAYGRQMI---DRTKN------------------LVEDLYPGA---------------RVLYGDTDSVMVKCVTDEkas 693
Cdd:PHA03036 689 CTAIGRNMIkylNSVLNgsklingklilancpinpFFKDDRSIDtnydtnlpveynftfRSVYGDTDSVFLEINTKD--- 765
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 694 dkerlqeaMDFGIEAA---EKVSSN--FLKPIKLEFEKVYFPYLLMNKKRYAGLLWTNTDRFD---KLDAKGIETVRRDN 765
Cdd:PHA03036 766 --------VDKSIKIAkelERIINEkvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGsvpERVNKGTSETRRDV 837
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 766 CPLVARMVSGVLNRILihrsvesavefvkGTISDLLLNRLDISNLVITKAFSKAEDEYAGAQAHIA--LVERMRQRDPAS 843
Cdd:PHA03036 838 SKFHKYMIKIYKTRLL-------------DMLSEGNMNSNQVCIDILRSLEKDLIIEFDSRSAPLEmfLLSRTHHCNYKS 904
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157875046 844 AP------------------TIGDRVAYVIIKAAKGA--------KAYERSEDPIYVLDNNIPI 881
Cdd:PHA03036 905 PDnpnmylvneynknnpekiEIGERYYFAYICPINLPwqkklvniKTYERIIDRSFKLKSNERI 968
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
512-897 |
7.41e-23 |
|
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: 101.41 E-value: 7.41e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 512 YEGATVIDPIKGFYNcPVATLDFASLYPSIIIAHNLCystlvrPADARLypedaldrsptsdvfvkkEVFPGILPEVLQD 591
Cdd:cd05538 3 FEGGYAYVFITGVLG-PIVHADVASLYPSIMLAYRIC------PARDSL------------------GIFLALLKYLVEL 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 592 LLAARKHARAMMKdvpmnSLEYKVLNGRQLALKVSANSVYGFTGAQVGKLPCLEISASVTAYGRQMIdrtKNLVEDLYP- 670
Cdd:cd05538 58 RLAAKESARAAAR-----PAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELL---KLMIRWLRRr 129
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 671 GARVLYGDTDSVMVKCVTDEKASDKERlqeamdfgiEAAEKVSSNFLKPIKLEFEKVYFPYLLMNKKRYAglLWtntDRF 750
Cdd:cd05538 130 GATPVEVDTDGIYFIPPNGVDTEDEEE---------ELVRELSSTLPKGITVEFDGRYRAMFSYKIKNYA--LL---DYD 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 751 DKLDAKGIETVRRDNCPLV-ARMVSGVlnRILIHRSVESAVEFVKGTISDLLLNRLDISNLVITKAFSKAEDEY-----A 824
Cdd:cd05538 196 GKLIVKGSAFRSRGIEPFLrEFLREAV--RLLLQGDGAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYlqkvrA 273
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157875046 825 GAQAHIALVE-RMRQRDPASAptiGDRVAYVIIKAAKGAKAYErSEDPIYVLDNNIP-IDTQYYLE--HQLAPPILR 897
Cdd:cd05538 274 GKRNPAAAYEiALARPREWRA---GDRVTYYVSGTGKGVSVYE-NCRLVADYDPAHPdENTGFYAErlLQLAARLLP 346
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
237-445 |
1.06e-22 |
|
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: 96.66 E-value: 1.06e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 237 FRILSIDIECQGRKGLfPEPEHDPVIQIanhcveyGHESEPLTKTIFTLKSCAPiagaQVLSYETEAEMLLAWATFMKAL 316
Cdd:cd05780 3 LKILSFDIEVLNHEGE-PNPEKDPIIMI-------SFADEGGNKVITWKKFDLP----FVEVVKTEKEMIKRFIEIVKEK 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 317 DPDILTGYNICNFDFPYLLSRATALKAsdafhywgrqvhERTVARDK-KFQSKQMGNREYTEltLEGRIIMDAMVVIQRD 395
Cdd:cd05780 71 DPDVIYTYNGDNFDFPYLKKRAEKLGI------------ELDLGRDGsEIKIQRGGFNNASE--IKGRIHVDLYPVARRT 136
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 157875046 396 YKLRSYSLNSVSQNFLGEQKEDVHHSIISDLQHGDEEtRRRLAVYCLKDA 445
Cdd:cd05780 137 LNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGEN-LERLFRYSMEDA 185
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
236-700 |
7.09e-22 |
|
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: 102.44 E-value: 7.09e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 236 PFRILSIDIECQ--GRKGLFP--EPEHDPVIQIANHCV---EYGHESEPLTKTIFTLKSCAPIAGAQVLSYETEAEMLLA 308
Cdd:TIGR00592 197 ELKLASFDIETYfhDGKDFFPgdENPADEEIMISTTPViakQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKR 276
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 309 WATFMKALDPDILTGYNICNFDFPYLLSRATALKASDAFHYWGRQVHERTV-ARDKKFQSKQM----GNREYTELTLEGR 383
Cdd:TIGR00592 277 FWDVIDQEDTDVEITVNGDNFDLVYLADRQVFQFYWDAYEDPAEKLGVVLLfGRDVDHVSPCVqvkgINRDLFFLPREGK 356
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 384 IIMDAMVVIQRDYKLRSYSLNSVSQNFLGEQKEDVHHSIISDLQHGdeETRRRLAVYCLKDAFLPVKLLDRLMCIVNNVE 463
Cdd:TIGR00592 357 IDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEF--EAPDIDAPYSSEYLEVTYELGKEFAPMEALPS 434
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 464 MARVTGVPVGWLLERGQQIKVFsmLLRKAQKKKLVVPTV----EYTGGSDRGYEGATV----IDPIKGFYNCPVATLDFA 535
Cdd:TIGR00592 435 DLKGQTFWHVFGSNTGNLERFL--LLRKIKGPCWLAVKGpdelEYPRRSWCKYEGGYVkppnVEKGLDKTPPPLVVLDFS 512
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 536 --SLYPSIIIAHNLCYSTLV--RPADARLYPEDALDRSPTSDVFVK--------KEVFPGILPEVLQDLLAARKHARAMM 603
Cdd:TIGR00592 513 mkSLNPSIIRNEIVSIPDTLhrEFALDKPPPEPPYDVHPCVGTRPKdcsfpldlKGEFPGKKPSLVEDLATERALIKKFM 592
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 604 KDVPMN-SLEYKVLNGRQLALKVSANSVYGFTGAQVGKLPCLEISASVTayGRQMIDRTKNLVEDLYPGARVL-----YG 677
Cdd:TIGR00592 593 AKVKKIdPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFG--RRFGERTCGRMICDVEISAKELircksYD 670
|
490 500
....*....|....*....|...
gi 157875046 678 DTDSVMVKCVTDEKASDKERLQE 700
Cdd:TIGR00592 671 LSELVQQILKTERKVIPIDNINN 693
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
239-453 |
7.12e-18 |
|
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: 83.82 E-value: 7.12e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 239 ILSIDIECQGRKGLFPEPEHDPV--------------IQIANHC-VEYGHESEPLTKTIFTLKSCApiaGAQVLSYETEA 303
Cdd:cd05778 6 ILSLEVHVNTRGDLLPDPEFDPIsaifycidddvspfILDANKVgVIIVDELKSNASNGRIRSGLS---GIPVEVVESEL 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 304 EMLLAWATFMKALDPDILTGYNI---------------CNFDFPYLLSR---ATALKASDAFHYWGrqvHERTvardkkf 365
Cdd:cd05778 83 ELFEELIDLVRRFDPDILSGYEIqrsswgylieraaalGIDDLLDEISRvpsDSNGKFGDRDDEWG---YTHT------- 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 366 qskqmgnreyTELTLEGRIIMDAMVVIQRDYKLRSYSLNSVSQNFLGEQKEDVHHSIISD-LQHGDEETRRRLAVYCLKD 444
Cdd:cd05778 153 ----------SGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEwYKSGSASERWRVLEYYLKR 222
|
....*....
gi 157875046 445 AFLPVKLLD 453
Cdd:cd05778 223 VRLNLEILD 231
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
236-447 |
2.34e-17 |
|
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: 81.46 E-value: 2.34e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 236 PFRILSIDIECQGRKGLFpepehdpviQIANHcveygheSEPLtKTIFTLKSCAPIAGAQVLSYETEAEMLLAWATFMKA 315
Cdd:cd05784 2 KLKVVSLDIETSMDGELY---------SIGLY-------GEGQ-ERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQ 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 316 LDPDILTGYNICNFDFPYLLSRATALKASDAfhyWGRQvhertvarDKKFQSKQMGNREYTELTLEGRIIMDAMVVIqRD 395
Cdd:cd05784 65 YDPDIIIGWNVINFDLRLLQRRAEAHGLPLR---LGRG--------GSPLNWRQSGKPGQGFLSLPGRVVLDGIDAL-KT 132
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 396 --YKLRSYSLNSVSQNFLGEQKedvhhSIISDLQHGDEETRR------RLAVYCLKDAFL 447
Cdd:cd05784 133 atYHFESFSLENVAQELLGEGK-----LIHDVDDRGAEIERLfredklALARYNLQDCEL 187
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
298-713 |
7.34e-15 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 79.90 E-value: 7.34e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 298 SYETEAEMLLAWATFM----KALDPDILTGYNICNFDFPYLLSraTALKASDAFHYWGRQVHERTVARD------KKFQS 367
Cdd:PHA03334 374 PHPLTKALMEAWEAFLskdpQLVPAQLLFGSDILNSNYLELLD--VIESHKAQFKATCRKAAARKEEIGsymktrDTVQD 451
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 368 KQMGNREYTELTLE--GRIIMDAMVVIQR---DYKLRSYSLNSVSQNFLGEQK-----------EDVHHSIISDLQHGDE 431
Cdd:PHA03334 452 FNDNDKKYLNSTSHgfGAHIIDLMRVCNTksiKAKCSSRKLDTVARLIISKSKphknppkigkmDDVKYTEMDGMFTAGG 531
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 432 ETRRRLAVYCLKDAFLPVKLLDRLMCIVNNVEMARVT----GVPVGwlleRG--------QQIKVFSMLLRKAQKKKLVV 499
Cdd:PHA03334 532 AALARYLIYNLVDSELLIRIAKNLDPVIEFLNRLRATynidYVAHG----RGvmnfcgfvQSTKSVEVPLLKARLRIGIF 607
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 500 PTVEYTGGS-------DRGY------EGATVIDPIKGF-----YNCPVATLDFASLYPSIIIAHNLCYSTLVRPADA--- 558
Cdd:PHA03334 608 VATGRIAESlcmpekyARDCrqkiklKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIVDPDCTarv 687
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 559 ------------RLYP--EDALDRSPTSDVFVKKEVFPGILPEVLQDLLAARKHARAMMKDVPMNSLeYKVLNGRQLALK 624
Cdd:PHA03334 688 rgwvvfdwkkidRGFGkaTLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKL-KSYHNQLQNEMK 766
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 625 VSANSVYGftgaqVGKLPCleiSASVTAYGRQMIdrtkNLVEDLY---PGARVLYGDTDSVMVKCVTDEK----ASDKER 697
Cdd:PHA03334 767 ICANSHYG-----VAPHAC---QHLITTLGRHKI----KLVEEFIkkePGMTVNYGDTDSVMFQLPPDDAetylEDTVTL 834
|
490
....*....|....*.
gi 157875046 698 LQEAMDFGIEAAEKVS 713
Cdd:PHA03334 835 EDEERAPLEYTLEEWS 850
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
295-458 |
3.05e-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: 67.25 E-value: 3.05e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 295 QVLSYETEAEMLLAWATFMKALDPDILTGYNICNFDFPYLLSRATALKASDafhyW---GRQvhERTVARdKKFQSKQMG 371
Cdd:cd05776 75 KVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPH----WsriGRL--KRSVWP-KKKGGGKFG 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 372 NREytelTLEGRIIMDamvvIQRDYK----LRSYSLNSVSQNFLGEQKEDVhhsIISDLQHGDEETRR--RLAVYCLKDA 445
Cdd:cd05776 148 ERE----LTAGRLLCD----TYLSAKelirCKSYDLTELSQQVLGIERQDI---DPEEILNMYNDSESllKLLEHTEKDA 216
|
170
....*....|...
gi 157875046 446 FLPVKLLDRLMCI 458
Cdd:cd05776 217 YLILQLMFKLNIL 229
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
236-445 |
7.81e-11 |
|
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: 62.34 E-value: 7.81e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 236 PFRILSIDIECQGRKGlFPEPEHDPVIQIanhcveyGHESEPLTKTIFTLkscapiagaqvlSYETEAEMLLAWATFMKA 315
Cdd:cd05781 2 DLKTLAFDIEVYSKYG-TPNPRRDPIIVI-------SLATSNGDVEFILA------------EGLDDRKIIREFVKYVKE 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 316 LDPDILTGYNICNFDFPYLLSRATALKASDAFhywGRQVHErtvardKKFQSKqmgnreYTELTLEGRIIMDAMVVIQRD 395
Cdd:cd05781 62 YDPDIIVGYNSNAFDWPYLVERARVLGVKLDV---GRRGGS------EPSTGV------YGHYSITGRLNVDLYDFAEEI 126
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 157875046 396 YKLRSYSLNSVSqNFLG----EQKEDVHHSIISdlQHGDEETRRRLAV-YCLKDA 445
Cdd:cd05781 127 PEVKVKTLENVA-EYLGvmkkSERVLIEWYRIY--EYWDDEKKRDILLkYNRDDA 178
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
234-451 |
9.07e-11 |
|
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 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. B1displays thermostable 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. Family-B DNA polymerases from thermophilic archaea are unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthesis. This is an additional safeguard mechanism against increased levels of deaminated bases during genome duplication at high temperatures. S. solfataricus B1 also interacts with DNA polymerase Y and may contribute to genome stability mechanisms.
Pssm-ID: 99826 [Multi-domain] Cd Length: 204 Bit Score: 62.34 E-value: 9.07e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 234 IAPFRILSIDIECQG-RKGLFPEPEHD--PVIQIAnhcvEYGheSEPLtKTIFTLKSCAPIA-------GAQVLSYETEA 303
Cdd:cd05783 2 IPKLKRIAIDIEVYTpIKGRIPDPKTAeyPVISVA----LAG--SDGL-KRVLVLKREGVEGlegllpeGAEVEFFDSEK 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 304 EMLLAWATFMKALdPDILTgYNICNFDFPYLLSRATALKASDAFhywgRQVHertVARDkkfqskqmgnreytELTLEGR 383
Cdd:cd05783 75 ELIREAFKIISEY-PIVLT-FNGDNFDLPYLYNRALKLGIPKEE----IPIY---LKRD--------------YATLKHG 131
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157875046 384 IIMD--------AMVVIQRDYKLRSYSLNSVSQNFLGEQKEDvHHSIISDLqhgdeeTRRRLAVYCLKDAFLPVKL 451
Cdd:cd05783 132 IHIDlykffsnrAIQVYAFGNKYREYTLDAVAKALLGEGKVE-LEKNISEL------NLYELAEYNYRDAELTLEL 200
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
297-603 |
1.25e-10 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 65.02 E-value: 1.25e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 297 LSYETEAEMLLAWATFMKALDPDILTGYNICNFDFPYLLSRATAL---KASDAFHYWGrqvhertvardkKFQSKQMGNR 373
Cdd:PHA02524 175 MPFEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNIlgeKAANQLSPYG------------KITSKTITNL 242
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 374 --EYTELTLEGRIIMDAMVVIQR-------DYKLRSYSLNSVSQNFLGeqkedvHHSIISDLQHGDEEtrrRLAVYCLKD 444
Cdd:PHA02524 243 ygEKIIYKIHGIALMDYMDVFKKfsftpmpDYKLGNVGYREVKADKLD------YEGPINKFRKADHQ---RYVDYCVRD 313
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 445 AFLpVKLLDRLMCIVN---------NVEMARVTGVpvgwllergqqIKVF-SMLLRKAQKKKLVVPTVEytGGSDRGYEG 514
Cdd:PHA02524 314 TDI-ILLIDGRRCFIDlilslsyyaKIRFDDVLGT-----------IKVWdSIIFNSLVESNVVIPAMK--ASPKQSFPG 379
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 515 ATVIDPIKGFYNCPVaTLDFASLYPSIIIAHNLC---YSTLVRPADARLY-------PEDALDRSPTSDVFVKKEVfpGI 584
Cdd:PHA02524 380 AYVKEPVPGGYRYGL-SFDLTSLYPSILRLLNISpemIAGMFSPARLEDYinkvapkPSDQFSCAPNGMMYKKGVV--GV 456
|
330
....*....|....*....
gi 157875046 585 LPEVLQDLLAARKHARAMM 603
Cdd:PHA02524 457 LPNETEKVFLQRKSEKKMM 475
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
238-444 |
2.37e-09 |
|
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: 58.19 E-value: 2.37e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 238 RILSIDIECQGRKGLF---PEPEHDPVIQIANHCveyghesepltktiftlkscaPIAGAQVLSYE--TEAEMLLAWATF 312
Cdd:cd05785 10 RRLQLDIETYSLPGFFfsnPDRGDDRIIIVALRD---------------------NRGWEEVLHAEdaAEKELLEELVAI 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 313 MKALDPDILTGYNICNFDFPYLLSRATALKASDAfhyWGRqvhERTVARdkkFQSKQMGNRE----YTELTLEGRIIMDA 388
Cdd:cd05785 69 IRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLA---IGR---DGSIPR---QRPSRFRFAErlidYPRYDIPGRHVIDT 139
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157875046 389 MVVIQR----DYKLRSYSLNSVSQNF--LGEQKEDVHHSIISDLQHGDEETRRRlavYCLKD 444
Cdd:cd05785 140 YFLVQLfdvsSRDLPSYGLKAVAKHFglASPDRTYIDGRQIAEVWRSDPARLLA---YALDD 198
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
238-341 |
1.02e-03 |
|
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: 41.48 E-value: 1.02e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157875046 238 RILSIDIECQGRKGLFPEPEHDPVIQIAnhcveYGHE------------SEPLTKTIFTLKscAPIAGA-QVLSYETEAE 304
Cdd:cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMIS-----YMIDgqgylivnreivSEDIEDFEYTPK--PEYEGPfKVFNEPDEKA 75
|
90 100 110
....*....|....*....|....*....|....*..
gi 157875046 305 MLLAWATFMKALDPDILTGYNICNFDFPYLLSRATAL 341
Cdd:cd05779 76 LLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIH 112
|
|
| |
