|
Name |
Accession |
Description |
Interval |
E-value |
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
59-1258 |
0e+00 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 1715.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 59 DVLGFCGAAEERATQetQWSDLLQLWsrdgpaeeraltlHHPHDAKKDLVFFQLDIANATCHRNVVPaavrarhRALPVS 138
Cdd:PTZ00166 9 ENIDKTFFTSSIPYG--LLFSKLRRP-------------LPPISLQKDLVFFQLDADYTEKDDKSQG-------NPHNTV 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 139 SAPPATvcasyepEVsptpapaavppgaqaaeaaatanslgPMFRVYGVTEDGRSVCANVHGFFPYFYCPVPVSIQESLA 218
Cdd:PTZ00166 67 SGVRHV-------EV--------------------------PIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPEDS 113
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 219 TQpgggvgtnavtarLRSFLDAWLLKTQASaKAYDVRCLDIRMEKKESLMYYTPGQTPSlFFRITLALPNWVAPTRTLIE 298
Cdd:PTZ00166 114 QK-------------LKRELNAQLSEQSQF-KKYQNTVLDIEIVKKESLMYYKGNGEKD-FLKITVQLPKMVPRLRSLIE 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 299 RGISIEaslaatpsseagganctaaqndapaaeaadwpdadgdaaagedaasdaqlleaakalsdVGSGAKVALPPaTFE 378
Cdd:PTZ00166 179 SGVVVC-----------------------------------------------------------GGGWDGIRLFQ-TYE 198
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 379 SNVPFVLRYLVDTKTTGCSWLLGRGGAYVVRPASLQETSAQLELDIHYADLLPLPPAERWQKLPPLRILSFDIECVKLKG 458
Cdd:PTZ00166 199 SNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKTSTCQIEVDCSYEDLIPLPPEGEYLTIAPLRILSFDIECIKLKG 278
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 459 EGFPEAETDPVIQISSIVMLQsvpadlpglsetdtnaatacvakarkkrlsGGLERPLCRVLFALKECASIAGSVVLWFD 538
Cdd:PTZ00166 279 LGFPEAENDPVIQISSVVTNQ------------------------------GDEEEPLTKFIFTLKECASIAGANVLSFE 328
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 539 DEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKVVGFNRLSKLKSLESKIRDSSFSSRALGTHEGKDIATE 618
Cdd:PTZ00166 329 TEKELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIE 408
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 619 GRIQFDLLELVRRDYKLKSYSLNFVSFEFLKEQKEDVHYNMIGDLFRGCPSSRRRIGVYCLKDAYLPLRLLKELLFLYNY 698
Cdd:PTZ00166 409 GRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNY 488
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 699 VEMSRVTGTPLNFLLTRGQQIKVTAQLLRKCKELNYVVPVVKRTGGDNSVQYEGATVLEPRKGFYDKPIATLDFASLYPS 778
Cdd:PTZ00166 489 VEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEGATVLEPKKGFYDEPIATLDFASLYPS 568
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 779 IMIAHNICYSTLVASSAAhtMNNPDDVTvTTTSPPHKFVKKHIRRGVLPMIVEELIAARKAARKEMAAAKDEMTRQVLNG 858
Cdd:PTZ00166 569 IMIAHNLCYSTLVPPNDA--NNYPEDTY-VTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNG 645
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 859 RQLALKISANSVYGYTGTTTGGQLPCLEVATTITCFGRDMIDFTRREVEKMFCRDNQHACNATVIYGDTDSVMVDFGDFS 938
Cdd:PTZ00166 646 RQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDD 725
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 939 IAEAMKLGEEAAQALSEKFVKPIRLEFEKVYCPFLLMNKKRYAGLLYTRPEKYDKIDSKGIETVRRDFSLLVQTMADTVL 1018
Cdd:PTZ00166 726 IQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDKIDCKGIETVRRDNCLLVQQMVETVL 805
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1019 RKMLIDKDVEAAKEYTRRKVAELLQNKIDLSLLVQTKSLGKMDYDTRLPHVELAKKLRKRDAGTAPSVGDRVSYVVIQGA 1098
Cdd:PTZ00166 806 NKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITKSLGKDDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGA 885
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1099 KGQAQYERAEDPLYVLENNLPIDTQHYLEGIKKPLCRIFEGVMSNPESLFSGSHTMKRTVSISTQGALSKFVQRGVQCVG 1178
Cdd:PTZ00166 886 KGAPQYERAEDPLYVLENNIPIDTQYYLDQIKNPLLRIFEGVMDNPDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLG 965
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1179 CRSVIREGALCRRC-QENEAEIVVNKMAEMAEKEKEHSDLWTECQRCQGSLHQDVICINRDCPIFYRRAKVKKDIGTLEE 1257
Cdd:PTZ00166 966 CKSVIKEGALCDNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQE 1045
|
.
gi 237831459 1258 R 1258
Cdd:PTZ00166 1046 L 1046
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
749-1141 |
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: 678.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 749 QYEGATVLEPRKGFYDKPIATLDFASLYPSIMIAHNICYSTLVASSAAHtMNNPDDVTVTTTSppHKFVKKHIRRGVLPM 828
Cdd:cd05533 2 QYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAK-KLPPEDYIKTPNG--DYFVKSSVRKGLLPE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 829 IVEELIAARKAARKEMAAAKDEMTRQVLNGRQLALKISANSVYGYTGTTTGgQLPCLEVATTITCFGRDMIDFTRREVEK 908
Cdd:cd05533 79 ILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVG-KLPCLEISSSVTSFGRQMIEKTKKLVEE 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 909 MFCRDNQHACNATVIYGDTDSVMVDFGDFSIAEAMKLGEEAAQALSEKFVKPIRLEFEKVYCPFLLMNKKRYAGLLYTRP 988
Cdd:cd05533 158 KYTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLWTNP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 989 EKYDKIDSKGIETVRRDFSLLVQTMADTVLRKMLIDKDVEAAKEYTRRKVAELLQNKIDLSLLVQTKSLGK--MDYDTRL 1066
Cdd:cd05533 238 DKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKtaDDYAGKQ 317
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 237831459 1067 PHVELAKKLRKRDAGTAPSVGDRVSYVVIQGAKGQAQYERAEDPLYVLENNLPIDTQHYLEG-IKKPLCRIFEGVM 1141
Cdd:cd05533 318 AHVELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLENNIPIDTQYYLENqLSKPLLRIFEPIL 393
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
708-1138 |
6.42e-172 |
|
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: 516.39 E-value: 6.42e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 708 PLNFLLTRGQQIKVTAQLLRKCKELNYVVPVVKRTGGDNSvQYEGATVLEPRKGFYDKPIATLDFASLYPSIMIAHNICY 787
Cdd:pfam00136 2 PQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGDED-GYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 788 STLVASSAAHTMNNPDD--VTVTTTSPPHKFVKKHIRRGVLPMIVEELIAARKAARKEMAAAKDEMTRQVLNGRQLALKI 865
Cdd:pfam00136 81 TTLVRSVDEANNLPPEDnlITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLALKI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 866 SANSVYGYTGTTTGgQLPCLEVATTITCFGRDMIDFTRREVEKMFCRdnqhacNATVIYGDTDSVMVDFGDFSIAEAMKL 945
Cdd:pfam00136 161 TANSVYGFTGFANG-RLPCLPIAASVTAIGREMLENTKDLVEGMYTY------NFRVIYGDTDSVFIEFGGKDVEEAMKI 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 946 GEEAAQALSEK-FVKPIRLEFEKVYCPFLLMNKKRYAGLLYTRPEKYDKIDSKGIETVRRDFSLLVQTMADTVLRKMLID 1024
Cdd:pfam00136 234 GDELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSD 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1025 KDVEAAKEYTRRKV----AELLQNKIDLSLLVQTKSLGK--MDYD-TRLPHVELAKKLRKRDaGTAPSVGDRVSYVVIQG 1097
Cdd:pfam00136 314 RGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKppDNYKsKNLPHVEVALRMNKRN-GEAPEVGDRIPYVIVKA 392
|
410 420 430 440
....*....|....*....|....*....|....*....|....*
gi 237831459 1098 AKGQAQ---YERAEDPLYVLENNLPIDTQHYLEG-IKKPLCRIFE 1138
Cdd:pfam00136 393 AKGLKNlliYERAEDPEYVLENNLPIDYEYYFSNqLIPPVARLLE 437
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
376-1138 |
4.50e-143 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 453.51 E-value: 4.50e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 376 TFESNVPFVLRYLVDTKTTGCSWLLGRGGAYVVRPASLQETSAQLELDihyadllplppaerwQKLPPLRILSFDIECvk 455
Cdd:COG0417 107 VYEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKLDYEVKENPRLKPE---------------DYRPKLKVLSFDIEV-- 169
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 456 LKGEGFPEAETD-PVIQISSivmlqsvpADLPGLSetdtnaatacvakarkkrlsgglerplcRVLFALKECASIAgsvV 534
Cdd:COG0417 170 STPRGFPDPERDgPIISIGL--------AGSDGEK----------------------------KVLMLGREGVDFE---V 210
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 535 LWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKV---VGfnrlsklksleskiRD-SSFSSRALGTH 610
Cdd:COG0417 211 EYFDDEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAERLGIpldLG--------------RDgSEPSWREHGGQ 276
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 611 EGKDIAteGRIQFDLLELVRRD-YKLKSYSLNFVSFEFLKEQKEDVHYNMIGDLFRgcpSSRRRIGVYCLKDAYLPLRLL 689
Cdd:COG0417 277 GFASIP--GRVVIDLYDALKSAtYKFKSYSLDAVAEELLGEGKLIVDGGEIERLWD---DDKPALAEYNLRDAELTLRIF 351
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 690 KELLFLYNYVEMSRVTGTPLNFLLTRGQQIKVTAQLLRKCKELNYVVPvvkRTGGDNSVQYEGATVLEPRKGFYDKpIAT 769
Cdd:COG0417 352 EKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAP---NKGEIKGEAYPGGYVLDPKPGLYEN-VLV 427
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 770 LDFASLYPSIMIAHNICYSTLVASsaahtMNNPDDVTVTTTSPPHKFVKKhiRRGVLPMIVEELIAARKAARKEMAAAK- 848
Cdd:COG0417 428 LDFKSLYPSIIRTFNISPETLVEG-----GEEPCGDEDVAPGFGHRFCRE--PKGILPSILEELWDERDEAKKKMKKAKp 500
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 849 DEMTRQVLNGRQLALKISANS---VygytGTTTGGQLPCLEVATTITCFGRDMIDFTRREVEKMfcrdnqhacNATVIYG 925
Cdd:COG0417 501 DSEEYRLYDALQQALKILMNSfygV----LGSEGCRFYDPELAESITARGREIIKQTIEKAEEL---------GYKVIYG 567
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 926 DTDSVMVDFGDFSIAEAMKLGEEAAQALSEKFVKPIRLEFEKVYCPFLL-MNKKRYAGLLytrpeKYDKIDSKGIETVRR 1004
Cdd:COG0417 568 DTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFpGSKKRYAGLT-----EDGKIDIKGLEAVRS 642
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1005 DFSLLVQTMADTVLRKMLIDKDVEAAKEYTRRKVAELLQNKIDLSLLVQTKSLGK--MDYD-TRLPHVELAKKLRKRdaG 1081
Cdd:COG0417 643 DWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKplSEYEkNVPPHVRAARKLDER--G 720
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....*...
gi 237831459 1082 TAPSVGDRVSYVVIQGAkgqaqyERAEDPLYVLENNLPIDTQHYLEG-IKKPLCRIFE 1138
Cdd:COG0417 721 RPYQRGDKISYVITKGG------GRVEPVELAKERESEIDYDYYIEKqLKPTADRILE 772
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
442-935 |
1.25e-119 |
|
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: 379.95 E-value: 1.25e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 442 PPLRILSFDIECvKLKGEGFPEAE--TDPVIQISSIVmlqsvpadlpglsetdtnaatacvakarkkrLSGGLERPLCRV 519
Cdd:smart00486 1 PPLKILSFDIET-YTDGGNFPDAEifDDEIIQISLVI-------------------------------NDGDKKGANRRI 48
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 520 LFALKECASIAGSVVLWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKVVGFNRLSKLKSLESKIRD 599
Cdd:smart00486 49 LFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRIPNK 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 600 SSFSSRALGTHEGKDIATEGRIQFDLLELVRRDYKLKSYSLNFVSFEFLKEQKEDVHYNMIGDLFRGCPSSRRRIGVYCL 679
Cdd:smart00486 129 KPLFGSKSFGLSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCI 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 680 KDAYLPLRLLKELLFLYNYVEMSRVTGTPLNFLLTRGQQIKVTAQLLRKCKELNYVVP-------VVKRTGGDNSVQYEG 752
Cdd:smart00486 209 QDAVLTLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPskelydfKGSEPDLKKKVKYEG 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 753 ATVLEPRKGFYDKPIATLDFASLYPSIMIAHNICYSTLVASSAAHTMN----NPDDVTVTTTSP-PHKFVKKHIRRGVLP 827
Cdd:smart00486 289 GKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGdliiPEDLLTIKYEKGnKYRFVKKNIRKGILP 368
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 828 MIVEELIAARKAARKEMAAAKDEM--TRQVLNGRQLALKISANSVYGYTGTTTGGqLPCLEVATTITCFGRDMIDFTRRE 905
Cdd:smart00486 369 KLLKKLLDKRKEIKKLMKKEKDESeeLKKLLDSRQLALKLTANSVYGYLGFTNSR-LPCKPLAASVTALGREILEKTKEL 447
|
490 500 510
....*....|....*....|....*....|
gi 237831459 906 VEKMfcrdNQHACNATVIYGDTDSVMVDFG 935
Cdd:smart00486 448 IEEN----GYPKPGFKVIYGDTDSIFVTKP 473
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
438-683 |
2.64e-112 |
|
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: 350.72 E-value: 2.64e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 438 WQKLPPLRILSFDIECVKLKGeGFPEAETDPVIQISSIVMLQsvpadlpglsetdtnaatacvakarkkrlsgGLERPLC 517
Cdd:cd05777 1 WSKIAPLRILSFDIECAGRKG-VFPEPEKDPVIQIANVVTRQ-------------------------------GEGEPFI 48
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 518 RVLFALKECASIAGSVVLWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKVVGFNRLSKLKSLESKI 597
Cdd:cd05777 49 RNIFTLKTCAPIVGAQVFSFETEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTI 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 598 RDSSFSSRALGTHEGKDIATEGRIQFDLLELVRRDYKLKSYSLNFVSFEFLKEQKEDVHYNMIGDLFRGCPSSRRRIGVY 677
Cdd:cd05777 129 KDTTFSSKQMGTRETKEINIEGRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVY 208
|
....*.
gi 237831459 678 CLKDAY 683
Cdd:cd05777 209 CLKDAY 214
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
377-1127 |
7.86e-89 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 305.63 E-value: 7.86e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 377 FESNVPFVLRYLVDTKTTGCSWLLGRggaYVVRPASLQETSAQLEldihyadllplpPAERWQklPPLRILSFDIECvKL 456
Cdd:PRK05762 105 YEADIRFPERYLMERFITPCVWFSGE---VEQYTTDGVLRNARLK------------PAPDYR--PPLKVVSLDIET-SN 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 457 KGE----GFPEAETDPVIqissivMLQSVPADLPGLSEtdtnaatacvakarkkrlsgglerplcrvlfalkecasiags 532
Cdd:PRK05762 167 KGElysiGLEGCGQRPVI------MLGPPNGEALDFLE------------------------------------------ 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 533 vvlWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKV-VGFNRlsklKSLESKIRDSSFSSralgTHE 611
Cdd:PRK05762 199 ---YVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIpLRLGR----DGSELEWREHPFRS----GYG 267
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 612 GKDIAteGRIQFDLLELVRR-DYKLKSYSLNFVSFEFLKEQKE--DVHYNM--IGDLFRGCPSSRRRigvYCLKDAYLPL 686
Cdd:PRK05762 268 FASVP--GRLVLDGIDALKSaTWVFDSFSLEYVSQRLLGEGKAidDPYDRMdeIDRRFAEDKPALAR---YNLKDCELVT 342
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 687 RLLKELLFLYNYVEMSRVTGTPLNflltR--GQQIKVTAQLLRKCKELNYVVPVVkrtGGDNSVQYEGATVLEPRKGFYD 764
Cdd:PRK05762 343 RIFEKTKLLPFLLERATVTGLPLD----RvgGSVAAFEHLYLPRAHRAGYVAPNL---GERPGEASPGGYVMDSKPGLYD 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 765 KpIATLDFASLYPSIMIAHNICYSTLVASsaahtMNNPDDVTVtttSPP--HKFVKKHirrGVLPMIVEELIAARKAARK 842
Cdd:PRK05762 416 S-VLVLDFKSLYPSIIRTFNIDPDGLVEG-----LAQPPEESV---AGFlgARFSREK---HFLPEIVERLWEGRDEAKR 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 843 EMAAAkdemtrqvlngRQLALKISANS---VygytgtttggqL-------PCLEVATTITCFGRDMIDFTRREVEkmfcr 912
Cdd:PRK05762 484 EMNKP-----------LSQAIKIIMNAfygV-----------LgssgcrfFDPRLASSITMRGHEIMKQTRELIE----- 536
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 913 dnqhACNATVIYGDTDSVMVDFG-DFSIAEAMKLGEEAAQALSEKFVKPIR----------LEFEKVYCPFLLM------ 975
Cdd:PRK05762 537 ----AQGYQVIYGDTDSTFVWLGgAHDEEDAAKIGRALVQEINQWWQEHLQqefglesaleLEFEKHYRRFFMPtirgae 612
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 976 --NKKRYAGLLyTRPEKYDKIDSKGIETVRRDFSLLVQTMADTVLRKMLIDKDVEaakEYTRRKVAELLQNKIDlSLLVQ 1053
Cdd:PRK05762 613 egSKKRYAGLI-QEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEPYV---DYVREVIDKLRAGELD-EKLVY 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1054 TKSLGKM--DYDTR-LPHVELAKKL----RKRDAGTAPSVGDRVSYVVIQGAKGQAQYERAedplyvlennlPIDTQHYL 1126
Cdd:PRK05762 688 RKRLRRPldEYQRNvPPHVRAARLAdemgYKVGRPLQYQNGGKIGYVITVNGPEPLEYRKS-----------PIDYDYYI 756
|
.
gi 237831459 1127 E 1127
Cdd:PRK05762 757 E 757
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
716-1138 |
3.78e-88 |
|
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: 293.35 E-value: 3.78e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 716 GQQIKVTAQLLRKCKELNYVVPvvkrTGGDNSVQYEGAT-----VLEPRKGFYDKPIATLDFASLYPSIMIAHNICYSTL 790
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILP----SPSRQQVAQQRALeclplVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTC 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 791 VASSAAHTMNNP---------------------DDVTVTttspPHK--FVKKHIRRGVLPMIVEELIAARKAARKEMAAA 847
Cdd:cd05534 77 LGRVEELNGGGKfgflgvklylppppldllllkDDVTIS----PNGvmFVKKSVRKGILPKMLEEILDTRIMVKKAMKKY 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 848 KDEMT-RQVLNGRQLALKISANSVYGYTGTTTGGQLPCLEVATTITCFGRDMIDFTRREVEkmfcrdNQHACNATVIYGD 926
Cdd:cd05534 153 KDDKKlQRILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIE------STPKWGAKVVYGD 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 927 TDSVMVDFGDFSIAEAMKLGEEAAQALSEKFVKPIRLEFEKVYCPFLLMNKKRYAGLLY-TRPEKYDKIDSKGIETVRRD 1005
Cdd:cd05534 227 TDSLFVLLPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYeSPDQTEPTFDAKGIETVRRD 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1006 FSLLVQTMADTVLRKMLIDKDVEAAKEYTRRKVAELLQNKIDLSLLVQTKS--LGKMDYDTRLP-HVELAKKLRKRDAGT 1082
Cdd:cd05534 307 GCPAVQKILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEvrLGTYKEGATLPaGAIVALRRMEKDPRA 386
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*...
gi 237831459 1083 APSVGDRVSYVVIQGAKGQAQYERAEDPLYVLEN-NLPIDTQHYLEG-IKKPLCRIFE 1138
Cdd:cd05534 387 EPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLADpSLRLDAEYYITKqIIPALDRLFN 444
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
749-1138 |
7.77e-81 |
|
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: 268.47 E-value: 7.77e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 749 QYEGATVLEPRKGFYDkPIATLDFASLYPSIMIAHNICYSTLVASSAAHTMNNPDDVTvtttspphkFVKKHIRRGVLPM 828
Cdd:cd00145 2 PYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVG---------FRSPKDRKGLLPR 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 829 IVEELIAARKAARKEMAAAKDEM-TRQVLNGRQLALKISANSVYGYTGTTTGgQLPCLEVATTITCFGRDMIDFTRREVE 907
Cdd:cd00145 72 ILEELLNFRDEAKKRMKAAKLAPeERVLYDNRQQALKVLANSFYGYLGAKFF-RFYDPEVAASITSFGREIIQDTIALVE 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 908 KMfcrdnqhacNATVIYGDTDSVMVDFGDF-SIAEAMKLGEEAAQALSEKfvKPIRLEFEKVYCPFLLMNKKRYAGLLYT 986
Cdd:cd00145 151 EH---------GARVIYGDTDSIFVSLPKMgTKEDAIKEGREILQELADE--HLLELEFEKVYLPFFLGKKKRYAGLDIW 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 987 RPEKYDKIDSKGIETVRRD-FSLLVQTMADtVLRKML-IDKDVEAAKEYTRRKvaellqnkidlsllvqtkslgkmdydt 1064
Cdd:cd00145 220 KGQDEGKIDIKGLETRRRDsPPLVKKFQKE-VLELILeEERKVEAVKEYIDEL--------------------------- 271
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 237831459 1065 rlphvelakklrkrdagtapsvgDRVSYVVIQGAKGQAQYERAEDPLYVLENNLPIDTQHYLEG-IKKPLCRIFE 1138
Cdd:cd00145 272 -----------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRHRIDYEYYLERlLQPPLERIFE 323
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
743-1138 |
2.55e-73 |
|
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: 250.19 E-value: 2.55e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 743 GGDNSVQYEGATVLEPRKGFYDKPIATLDFASLYPSIMIAHNICYSTLVASsaahtmNNPDDVTVTTTSPPhkfvkKHIR 822
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRA------DPDDEDDEEPPLPP-----SDQE 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 823 RGVLPMIVEELIAARKAARKEMAAAKDEMTRQVLNGRQLALKISANSVYGytgtttggqlpCL----------EVATTIT 892
Cdd:cd05532 70 KGILPRIIRKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYG-----------CLgfsysrfyakPLAALIT 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 893 CFGRDMIDFTRREVEKMfcrdnqhacNATVIYGDTDSVMVDFGDFSIAEAMKLGEEAAQALSEKFvKPIRLEFEKVYCPF 972
Cdd:cd05532 139 SKGREILQKTKDLVEKM---------NLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSY-KKLEIDIDGVFKRL 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 973 LLMNKKRYAGLLYTRPEKYD-KIDSKGIETVRRDFSLLVQTMADTVLRKMLIDKD----VEAAKEYTRRKVAELLQNKID 1047
Cdd:cd05532 209 LLLKKKKYAALKVVDDDKGKlKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSrediVENIHEYLRKINEDLRNGKIP 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1048 LSLLVQTKSLGK--MDY-DTR-LPHVELAKKLRKRDAGTapSVGDRVSYVVIQGAKGQAQYERAEDPLYV-LENNLPIDT 1122
Cdd:cd05532 289 LEKFIITKQLTKnpEEYpDKKsLPHVQVALRMNKRGRKV--KAGDTIPYIICKDGSSKSLADRAYHPDEVkKNENLKIDI 366
|
410
....*....|....*..
gi 237831459 1123 QHYLEG-IKKPLCRIFE 1138
Cdd:cd05532 367 EYYLSQqILPPISRLCE 383
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
537-1138 |
5.18e-73 |
|
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: 266.15 E-value: 5.18e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 537 FDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKVVGFNRLSKLKsleskiRDSSFSSRALgthegkdIA 616
Cdd:TIGR00592 581 LATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLR------RSPKFGRRFG-------ER 647
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 617 TEGRIQFDLLELVRRDYKLKSYSLNFVSFEFLKEQKEDVHYNMIGDLFRGCPSSRRRIGvYCLKDAYLPLRLLKELLFLY 696
Cdd:TIGR00592 648 TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLE-HTWKDAMFILQIMCELNVLP 726
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 697 NYVEMSRVTGTPLNFLLTRGQQIKVTAQLLRKCKELNYVVP----VVKRTG-GDN-----------SVQYEGATVLEPRK 760
Cdd:TIGR00592 727 LALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqiFRKQQKlGDEdeeidgykkgkKAAYAGGLVLEPKV 806
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 761 GFYDKPIATLDFASLYPSIMIAHNICYSTLvassaahtmNNPDDVTVTTTSPPHKfvkkhIRRGVLPMIVEELIAARKAA 840
Cdd:TIGR00592 807 GLYDKYVLLMDFNSLYPSIIQEFNICFTTV---------QQKVDEDELPELPDSE-----LEMGILPRELRKLVERRKEV 872
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 841 RKEMAAAKDEMTRQVLNGRQLALKISANSVyGYTGTTTGGQLPCLEVATTITCFGRDMIDFTRREVEKMfcrdnqhacNA 920
Cdd:TIGR00592 873 KKLMKQDLNPDLRLQYDIRQKALKLTANSM-YGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEM---------NL 942
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 921 TVIYGDTDSVMVDFGDFSIAEAMKLGEEAAQALSEKFvKPIRLEFEKVYCPFLLMNKKRYAGLLYTRPEK---YDKIDSK 997
Cdd:TIGR00592 943 EVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY-KLLELDIDGVFKRLLLLKKKKYAAIKVEGDSDgnyTTKQEVK 1021
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 998 GIETVRRDFSLLVQTMADTVLRKMLIDKDVEAAKEYTR---RKVAE-LLQNKIDLSLLVQTKSLGK--MDYDTR--LPHV 1069
Cdd:TIGR00592 1022 GLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQevlEKIGKnVLNGEVPLEKFVINKQLTRdpKDYPDGasLPHV 1101
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 237831459 1070 ELAKKLRKRDAGTAPSvGDRVSYVVIQGAKGQAQYERA--EDPLYVLENNLPIDTQHYLEG-IKKPLCRIFE 1138
Cdd:TIGR00592 1102 HVALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAyaLEELQRKHNNLIYDTQYYLEHqIHPVVLRILE 1172
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
750-1139 |
6.25e-64 |
|
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: 222.20 E-value: 6.25e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 750 YEGATVLEPRKGFYDKpIATLDFASLYPSIMIAHNICYSTLvassaahtmnNPDDVTVTTTSPP--HKFVKKhiRRGVLP 827
Cdd:cd05536 4 YEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTL----------VREGCEDCDVEPQvgHKFRKD--PPGFIP 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 828 MIVEELIAARKAARKEMAAAKDEMT-RQVLNGRQLALKISANSvYGYTGTTTGGQLPCLEVATTITCFGRDMIDFTRREV 906
Cdd:cd05536 71 SVLEDLLEERRRIKEKMKKLDPESEeYKLLDERQRAIKILANS-FYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIA 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 907 EKMfcrdnqhacNATVIYGDTDSVMVDFGdfsiaeamklGEEAAQALSEKFVK------PIRLEFEKVYCPFLLMNKKRY 980
Cdd:cd05536 150 EEK---------GFKVIYGDTDSLFVKID----------GADAVKKKVKKLLKyineelPLELEIEKFYKRGFFVTKKRY 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 981 AGLLytrpeKYDKIDSKGIETVRRDFSLLVQTMADTVLRKMLIDKDVEAAKEYTRRKVAELLQNKIDLSLLVQTKSLGK- 1059
Cdd:cd05536 211 AGLT-----EDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKd 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1060 -MDYDTRLPHVELAKKLRKRdaGTAPSVGDRVSYVVIQGAkGQAqYERAEDPLYVLENNlPIDTQHYLEG-IKKPLCRIF 1137
Cdd:cd05536 286 lSEYKATGPHVAAAKKLAKR--GYKVRPGTKIGYVIVKGS-GKI-SDRAYPYDMVDEKH-KYDAEYYIDNqVLPAVLRIL 360
|
..
gi 237831459 1138 EG 1139
Cdd:cd05536 361 EA 362
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
187-643 |
1.73e-60 |
|
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: 210.74 E-value: 1.73e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 187 VTEDGRSVCANVHGFFPYFYCPVPvsiqeslatqpgGGVGTNAVTARLRSFLDawllktqasakaYDVRCLDIRMEKKES 266
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAP------------DGKELEEVIEEIKELYE------------GLDKIEKIELKLKKS 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 267 LMYYTPgqTPSLFFRITLALPNWVAPTRTLIERGISIEaslaatpsseagganctaaqndapaaeaadwpdadgdaaage 346
Cdd:pfam03104 57 LYGYEE--DPVPYLKVSFANPRPLLKIRKYLSPENISD------------------------------------------ 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 347 daasdaqlleaakalsdvgsgakvalppaTFESNVPFVLRYLVDTKTTGCSWLLGRGGAyvvRPASLQETSAQLELDIHY 426
Cdd:pfam03104 93 -----------------------------VYEYDVDYLERFLIDNDIVGFGWYKVKVYP---FRAEGRISNCDVEIDCDS 140
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 427 ADLLPLPPAERWqklPPLRILSFDIECVKLKGeGFPEAE--TDPVIQISSIVMlqsvpadlpglsetdtnaatacvakar 504
Cdd:pfam03104 141 PDLISVPFEKEW---PPLRVLSFDIECTSLPG-KFPDAEnvKDPIIQISCMLD--------------------------- 189
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 505 kkrlSGGLERPLCRVLFALKECASIA-------------GSVVLWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNY 571
Cdd:pfam03104 190 ----GQGEPEPEPRFLFTLRECDSEDiedfeytpkpiypGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPY 265
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 237831459 572 LITRAATLKVVGFNRLSKLKSL-ESKIRDSSFSSRALGThegkdIATEGRIQFDLLELVRRDYKLKSYSLNFV 643
Cdd:pfam03104 266 ILNRAKELYIVKLSSIGRLNRGgRSKVREIGFGTRSYEK-----VKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
752-1134 |
1.59e-41 |
|
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: 157.04 E-value: 1.59e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 752 GATVLEPRKGFYdKPIATLDFASLYPSIMIAHNICYSTLVASSAAhtmNNPDDVTVTttspPH--KFVKKHirrGVLPMI 829
Cdd:cd05537 5 GGYVMDSKPGLY-KNVLVLDFKSLYPSIIRTFLIDPLGLIEGLKA---PDPEDLIPG----FLgaRFSREK---HILPDL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 830 VEELIAARKAARKEmaaaKDEMTRQvlngrqlALKISANS---VYGYTGtttggqlpCL----EVATTITCFGRDMIDFT 902
Cdd:cd05537 74 IARLWAARDEAKRE----KNAPLSQ-------AIKIIMNSfygVLGSTG--------CRffdpRLASSITLRGHEIMKQT 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 903 RREVEKMfcrdnqhacNATVIYGDTDSVMVDFGD-FSIAEAMKLGEEAAQALSEKFVKPIR----------LEFEKVYCP 971
Cdd:cd05537 135 RAWIEQQ---------GYQVIYGDTDSTFVWLGEeLDAAEAQAIGKELASQINQWWAQKLKeefglesfleIEFETHYSR 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 972 FLLM--------NKKRYAGLLYTrpEKYDKIDSKGIETVRRDFSLLVQTMADTVLRKMLIDKDVEaakEYTRRKVAELLQ 1043
Cdd:cd05537 206 FFMPtirgsdegSKKRYAGLKST--DGGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYE---GFIKETVEELLA 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1044 NKIDlSLLVQTKSLGKM--DY-DTRLPHVELAKKL-RKRDAGTAPSVGDRVSYVV-IQGAKGQAQyeraedplyvleNNL 1118
Cdd:cd05537 281 GELD-ELLVYRKRLRRPlsEYtKNVPPHVQAARLAdQINRELGRPRQYQWIEYVItVNGPEPLEY------------RTS 347
|
410
....*....|....*.
gi 237831459 1119 PIDTQHYLEGIKKPLC 1134
Cdd:cd05537 348 PLDYQHYIDKQLKPIA 363
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
446-683 |
9.69e-39 |
|
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: 143.26 E-value: 9.69e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 446 ILSFDIECVKLKGegFPEAETDPVIQISSIVmlqsvpadlpglsetdtnaatacvakarkkRLSGGLERPLCRVLFALKE 525
Cdd:cd05160 1 VLSFDIETTPPVG--GPEPDRDPIICITYAD------------------------------SFDGVKVVFLLKTSTVGDD 48
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 526 CASIAGSVVLWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLkvvgfnrlsKLKSLESKIRDSSFSSR 605
Cdd:cd05160 49 IEFIDGIEVEYFADEKELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEAL---------GIKLTDGIYRRSGGEKS 119
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 237831459 606 ALGTHEgkdIATEGRIQFDLLELVRRDYKLKSYSLNFVSFEFLKEQKEDVHYNMIGDLFRGcpSSRRRIGVYCLKDAY 683
Cdd:cd05160 120 SGSTER---IAVKGRVVFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDGEIIEDAEWE--EDPERLIEYNLKDAE 192
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
538-1142 |
1.02e-38 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 156.00 E-value: 1.02e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 538 DDEKEMLAKWAEFVRQVDPDFLsgYNCVNFDLNYLITRAATLKVVGFNRLSKLKSLESKI-RDSSFSSRALGTHegkdiA 616
Cdd:PRK05761 208 DSEKELLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIdLYKFFQNKAVRSY-----A 280
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 617 TEGRiqfdllelvrrdYKLKSYSLNFVSFEFLKEQKEDVHYNmIGDLfrgcpsSRRRIGVYCLKDAylplRLLKELLFLY 696
Cdd:PRK05761 281 FYGK------------YRHREARLDAVGRALLGISKVELETN-ISEL------DLEELAEYNFRDA----EITLKLTFFN 337
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 697 NY------VEMSRVTGTPLNfLLTRgQQIK--VTAQLLRKCKELNYVVPV---VKRTGGDNSVQ-------YEGATVLEP 758
Cdd:PRK05761 338 NElvlkliLLLSRISKLPIE-ELSR-ATIStwISNLEYWEHRKRGWLIPWkedILRLDHEVYKKaiikgkkYRGGLVFQP 415
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 759 RKGFYDKpIATLDFASLYPSIMIAHNICYSTLvassaahtmNNP---DDVTVTTTSPPHKFVKKhiRRGVLPMIVEELIA 835
Cdd:PRK05761 416 PPGIFFN-VYVLDFASLYPSIIVKWNLSPETV---------RIPeckCHYDDEVPELGHSVCDD--RPGLTSVLVGLLRD 483
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 836 ARKAARKEMAAAK--DEMTRQVLNGRQLALKISANS---VygytGTTTGGQLPCLEVATTITCFGRDMIDFTRREVEKMf 910
Cdd:PRK05761 484 FRVKIYKKKAKDPnlDEERRAWYDVVQRALKVFLNAsygV----FGAENFKLYRIEVAESITALGREILLSTKKKAEEL- 558
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 911 crdnqhacNATVIYGDTDSVMVdfgdfSIAEAMKLgEEAAQALSEKFvkPIRLEFEKVYcPFLLMN--KKRYAGLLYTrp 988
Cdd:PRK05761 559 --------GLKVLYGDTDSLFV-----WGPTKESL-EELIKEIEERT--GIDLEVDKTY-DWVAFSglKKNYFGVLKD-- 619
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 989 ekyDKIDSKGIETVRRDFSLLVQTMADTVLRKMliDK-----DVEAAKEYTRRKVAELLQN----KIDLSLLVQTKSLGK 1059
Cdd:PRK05761 620 ---GKVKIKGIVAKKRNTPEFVKELQREVLEVL--KSirspeDVEKVKDEIEDVLKRYYEKlrakDYPLDELAIRVRLSK 694
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1060 --MDYDTRLP-HVELAKKLrkRDAGTAPSVGDRVSYVVIQGAKGQ--AQYERAEDplyvlennlpIDTQHYLEGIKkplc 1134
Cdd:PRK05761 695 plDEYTKNTPqHVKAALQL--RDYGVEVSPGDIISYVKVDDKRGVkpVQLAKLSE----------IDVEKYIELLR---- 758
|
....*...
gi 237831459 1135 RIFEGVMS 1142
Cdd:PRK05761 759 SALEQILS 766
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
750-1138 |
8.97e-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: 116.68 E-value: 8.97e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 750 YEGATVLEPRKG-FYDkpIATLDFASLYPSIMIAHNICYSTLVASsaahtmnNPDDVTVTTTSPPHKFVKKhiRRGVLPM 828
Cdd:cd05530 13 YRGAIVLEPPPGiFFN--VVVLDFASLYPSIIKVWNLSYETVNCP-------HCECKTNEVPEVGHWVCKK--RPGITSQ 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 829 IVEEL------IAARKAARKEMaaaKDEMtRQVLNGRQLALKISANSvYGYTGTTTGGQLPCLEVATTITCFGRDMIDFT 902
Cdd:cd05530 82 IIGLLrdlrvkIYKKKAKDKSL---DEEM-RQWYDVVQSAMKVFINA-SYGVFGAENFPLYCPPVAESTTALGRYIITST 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 903 RREVEKMfcrdnqhacNATVIYGDTDSVmvdfgdFSIAEAMKLGEEAAQALSEKFvkPIRLEFEKVYCPFLLMN-KKRYA 981
Cdd:cd05530 157 IKKAREL---------GLKVLYGDTDSL------FLWNPPQEQLEDLVEWVEKEL--GLDLELDKEYRYVVFSGlKKNYL 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 982 GLLytrpeKYDKIDSKGI--------ETVRRDFSLLVQtmadtVLRKMLIDKDVEAAKEYTRRKVAELLQN----KIDLS 1049
Cdd:cd05530 220 GVT-----KDGSVDIKGLlgkkrntpEFVKELFYEVIE-----ILSAVNSPEDFEKAREKIRDIVKGVYKRlkkkEYTLD 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1050 LLVQTKSLGKM--DYDTRLP-HVELAKKLRKrdAGTAPSVGDRVSYVVIQGAKGQAQYERAEDPlyvlennlPIDTQHYL 1126
Cdd:cd05530 290 QLAFKVMLSKPpeEYTKNTPqHVKAARQLEK--YGRNVEAGDIISYVKVKGKEGVKPVQLARLD--------EVDVEKYV 359
|
410
....*....|..
gi 237831459 1127 EGIKKPLCRIFE 1138
Cdd:cd05530 360 EIMRSTLEQILG 371
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
1176-1245 |
7.31e-27 |
|
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: 104.38 E-value: 7.31e-27
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1176 CVGCRSVirEGALCRRCQENEAEIVVNKMAEMAEKEKEHSDLWTECQRCQGSLHQDVICINRDCPIFYRR 1245
Cdd:pfam14260 1 CLGCGAP--EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYMR 68
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
752-1132 |
1.08e-26 |
|
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: 113.21 E-value: 1.08e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 752 GATVLEPRKGFYDKpIATLDFASLYPSIMIAHNICYSTLvassaahtmNNPDDVTVTTTSPPHKFVKKhiRRGVLPMIVE 831
Cdd:cd05531 7 GGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETI---------NCRCCECRDHVYLGHRICLK--RRGFLPEVLE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 832 ELIAARKAARKEMAaakdemTRQVLNGRQLALKIS----------ANSVYGYtgtttggqlpcLEVATTITCFGRDMIDF 901
Cdd:cd05531 75 PLLERRLEYKRLKK------EEDPYAGRQKALKWIlvtsfgylgyKNAKFGR-----------IEVHEAITAYGRKILLR 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 902 TRREVEKMFCRdnqhacnatVIYGDTDSVMVDFGDFSIAEAMKLGEEAAqalsekfvkpIRLEFEKVY--CPFLLMN--- 976
Cdd:cd05531 138 AKEIAEEMGFR---------VLHGIVDSLWIQGRGDIEELAREIEERTG----------IPLKLEGHYdwIVFLPERdgl 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 977 --KKRYAGLLYTrpekyDKIDSKGIETVRRDFSLLVQTMADTVLRKMLIDKDVEAAKEyTRRKVAELLQ------NKIDL 1048
Cdd:cd05531 199 gaPNRYFGRLSD-----GEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEELLK-LREEALDLFRrylqrlREGDL 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1049 SLLVQTKSLGKMDYDTRLPHVELAKKLRKRdaGTAPSVGDRVSYVVIQGAKgqaqyeraedPLYVLENNLPIDTQHYLEG 1128
Cdd:cd05531 273 EDLIIEKKISKRSSEYKVLASTALKALRAK--GVSVVPGMKIEYIVRDGKR----------PVPDLGNDEGYDTKYYREL 340
|
....
gi 237831459 1129 IKKP 1132
Cdd:cd05531 341 LERA 344
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
439-1025 |
1.13e-24 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 112.04 E-value: 1.13e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 439 QKLPPLRI----LSFDIECvKLKGEgFPEAETDPVIQISSIVMlqsvpaDLPG----LSETDTNAATACVAKARKKRlsg 510
Cdd:PHA03036 151 NKIPRFDIprsyLFLDIEC-HFDKK-FPSVFINPVSHISCCYI------DLSGkekrFTLINEDMLSEDEIEEAVKR--- 219
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 511 glerplcrvlfALKECASIAG---SVVLWFDDEKEMLaKWAEFVRQVDPDFLSGYNCVNFDLNYLItraatlkvvgfNRL 587
Cdd:PHA03036 220 -----------GYYEIESLLDmdySKELILCSEIVLL-RIAKKLLELEFDYVVTFNGHNFDLRYIS-----------NRL 276
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 588 SKLKSleSKIR-DSSFSS---------RALGTHEGKDIA---------TEGRIQFDLLELVRRDYKLKSYSLNFVSFE-- 646
Cdd:PHA03036 277 ELLTG--EKIIfRSPDGKetvhlciyeRNLSSHKGVGGVanttyhinnNNGTIFFDLYTFIQKTEKLDSYKLDSISKNaf 354
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 647 ---FLKEQKEDVHYNMIGD----------LFRG---------------------------------CPSSRRRIGVYC-- 678
Cdd:PHA03036 355 ncnAKVLSENNNEVTFIGDnttdakgkasIFSEvlstgnyvtindddickildkdiiensftvkviCKNNYIPGDTYTls 434
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 679 -------LKDAYLplrllkellflyNY-----VEMSR---------------------VTGTPLNFLLTRGQQIKVTAQL 725
Cdd:PHA03036 435 fgkddvdLSDMYK------------NYnleiaLEMARycihdaclckylweyygietkIDAGASTYLLPQSMVFEYRAST 502
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 726 LRKCKELNYVVP---VVKRTGGDNSVQYEGATVLEPRKGFYDKPIATLDFASLYPSIMIAHNICYSTLV----------- 791
Cdd:PHA03036 503 LIKGPLLKLLLEektILVRSETKNKFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVgvvvndnrlea 582
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 792 ---ASSAAHTMNNPDDVTVTTTSPPHKFVKKHI---RR--GVLPMIVEELIAARKAARKEMAAAKDEMTRQVLNGRQLAL 863
Cdd:PHA03036 583 einKQELRRKYPYPRYIYVHCEPRSPDLVSEIAvfdRRieGIIPKLLKTFLEERARYKKLLKEATSSVEKAIYDSMQYTY 662
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 864 KISANSVYGYTGTTTGGqLPCLEVATTITCFGRDMIDFTRREV----------------EKMFCRDNQHA--CNAT---- 921
Cdd:PHA03036 663 KIVANSVYGLMGFRNSA-LYSYASAKSCTAIGRNMIKYLNSVLngsklingklilancpINPFFKDDRSIdtNYDTnlpv 741
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 922 -------VIYGDTDSVMVDFGDFSIAEAMKLGEEAAQALSEK-FVKPIRLEFEKVYCPFLLMNKKRYAGLLY---TRPEK 990
Cdd:PHA03036 742 eynftfrSVYGDTDSVFLEINTKDVDKSIKIAKELERIINEKvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYiasSTDGS 821
|
730 740 750
....*....|....*....|....*....|....*...
gi 237831459 991 YDKIDSKGIETVRRDFSLLVQTMAD---TVLRKMLIDK 1025
Cdd:PHA03036 822 VPERVNKGTSETRRDVSKFHKYMIKiykTRLLDMLSEG 859
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
442-912 |
1.28e-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: 105.52 E-value: 1.28e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 442 PPLRILSFDIECVKLKGEGFPeaetdpviqissivmlqsvPADLPGLSETDTNAATACVAKARKKRlsgglERPLCRVLF 521
Cdd:TIGR00592 196 PELKLASFDIETYFHDGKDFF-------------------PGDENPADEEIMISTTPVIAKQWDYE-----SEPEARVVT 251
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 522 ALKECASIAGSVVLWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKVVG-----FNRLSKLKSLESK 596
Cdd:TIGR00592 252 WKKPDKPTTGSYVESVSEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLADRQVFQFYWDayedpAEKLGVVLLFGRD 331
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 597 IRDSSFSSRALG-THEGKDIATEGRIQFDLLELVRRDYKLKSYSLNFVSFEFLKEQKEDVHYNMIGDLFRG------CPS 669
Cdd:TIGR00592 332 VDHVSPCVQVKGiNRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEFeapdidAPY 411
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 670 SRRRIGV-YCLKDAYLPLRLLKELLflyNYVEMSRVTGTplnfllTRGQQikVTAQLLRKCK---ELNYVVPVVKRTGGD 745
Cdd:TIGR00592 412 SSEYLEVtYELGKEFAPMEALPSDL---KGQTFWHVFGS------NTGNL--ERFLLLRKIKgpcWLAVKGPDELEYPRR 480
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 746 NSVQYEGATVLEPR----KGFYDKPIATLDFA--SLYPSIMIAHNICYSTLVASSAAHTMNNP----DDVTVTTTSP--- 812
Cdd:TIGR00592 481 SWCKYEGGYVKPPNvekgLDKTPPPLVVLDFSmkSLNPSIIRNEIVSIPDTLHREFALDKPPPeppyDVHPCVGTRPkdc 560
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 813 PHKFVKKHIRRGVLPMIVEELIAARKAARKEMAAAK--DEMTRQVLNGRQLALKISAN-----SVYGYTGTTTGGQLPCL 885
Cdd:TIGR00592 561 SFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVKkiDPDEIVGHDYQQRALKVLANrindlKIPTWSKIGRLRRSPKF 640
|
490 500
....*....|....*....|....*..
gi 237831459 886 EVATTITCFGRDMIDFTRREVEKMFCR 912
Cdd:TIGR00592 641 GRRFGERTCGRMICDVEISAKELIRCK 667
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
444-1033 |
2.06e-22 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 104.39 E-value: 2.06e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 444 LRILSFDIEcVKLKGeGFPEAETDPViQISSIVMLQSVPA-----DLPGLSETDtnaatacvaKARKKRLSGGLERplcr 518
Cdd:PHA02528 106 IRIANLDIE-VTAED-GFPDPEEAKY-EIDAITHYDSIDDrfyvfDLGSVEEWD---------AKGDEVPQEILDK---- 169
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 519 vlfalkecasiagsVVLW-FDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRaaTLKVVG---FNRLSKLKSLE 594
Cdd:PHA02528 170 --------------VVYMpFDTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINR--IKNILGektAKRLSPWGKVK 233
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 595 SKIRDSSFSSRalgtHEGKDIAteGRIQFDLLELvrrdYK------LKSYSLNFVSFEFLKEQKEDVHYNMIGDLFRgcp 668
Cdd:PHA02528 234 ERTIENMYGRE----EIAYDIS--GISILDYLDL----YKkftftnQPSYRLDYIAEVELGKKKLDYSDGPFKKFRE--- 300
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 669 SSRRRIGVYCLKDAYLPLRLLKELLFLYNYVEMSRVTGTPLNFLLTrgqQIKV-TAQLLRKCKELNYVVPVVKRTGGDns 747
Cdd:PHA02528 301 TDHQKYIEYNIIDVELVDRLDDKRKLIELVLSMAYYAKINFEDVFS---PIKTwDAIIFNSLKEEKIVIPENKSHKKQ-- 375
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 748 vQYEGATVLEPRKGFYDKpIATLDFASLYPSIMIAHNICYSTLVASSAAHTMNN--------PDDvtVTTTSPPHKFVKK 819
Cdd:PHA02528 376 -KYAGAFVKEPVPGAYRW-VVSFDLTSLYPSIIRQVNISPETIAGTFHVAPVHEyinktaprPSD--EYSCSPNGWMYRK 451
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 820 HIrRGVLPMIVEELIAARKAARKEMAAAK-------------------------------------DEMTRQVLNGR--- 859
Cdd:PHA02528 452 DI-RGVIPTEIKKVFDQRKIYKKKMLAAErnaeliktiledlndsvdtpidvdyyfdfsdefkaelKTLTKSSLKALlee 530
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 860 -----------QLALKISANSVYGYTGTTTGGQLPcLEVATTITCFGRDMIDFTRREV-EKM--FCRDNQHacnATVIYG 925
Cdd:PHA02528 531 cekeialcntiQMARKILINSLYGALGNEHFRYYD-LRNAEAITLFGQLAIQWIERKMnEYLnkLCKTEDE---DYVIYG 606
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 926 DTDSVMVDFGDFsIAEAMKLGEEAAQALSEKFVKPIRLEFEKV--------------YCPFLLMN------------KKR 979
Cdd:PHA02528 607 DTDSIYVNLDPL-VEKVGEDKFKDTNHWVDFLDKFCKERMEPYidssyrelceymnnYEHLMFMDreaiagpgfwtaKKR 685
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 237831459 980 YA-------GLLYTRPekydKIDSKGIETVRRDFSLLVQTMADTVLRKMLIdKDVEAAKEY 1033
Cdd:PHA02528 686 YAlnvwdseGTRYAEP----KLKIMGIETQRSSTPKAVQKALKEAIRRILQ-EGEESLQEY 741
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
442-683 |
1.06e-18 |
|
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: 85.48 E-value: 1.06e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 442 PPLRILSFDIECvkLKGEGFPEAETDPVIQISsivmlqsvpadlpglsetdtnaatacvakarkkrlsgglerplcrvlF 521
Cdd:cd05780 1 EDLKILSFDIEV--LNHEGEPNPEKDPIIMIS-----------------------------------------------F 31
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 522 ALKECASiagsVVLW--FD--------DEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKVVgfnrlSKLK 591
Cdd:cd05780 32 ADEGGNK----VITWkkFDlpfvevvkTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIE-----LDLG 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 592 SLESKIRDSsfssralgtHEGKDIATE--GRIQFDLLELVRRDYKLKSYSLNFVSFEFLKEQKEDVHYNMIGDLF-RGcp 668
Cdd:cd05780 103 RDGSEIKIQ---------RGGFNNASEikGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWdSG-- 171
|
250
....*....|....*
gi 237831459 669 SSRRRIGVYCLKDAY 683
Cdd:cd05780 172 ENLERLFRYSMEDAK 186
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
749-1131 |
5.12e-15 |
|
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: 77.91 E-value: 5.12e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 749 QYEGATVLEPRKGFYdKPIATLDFASLYPSIMIAHNICystlvassaahtmnnpddvtvtttspPHkfvkkHIRRGVLPM 828
Cdd:cd05538 2 KFEGGYAYVFITGVL-GPIVHADVASLYPSIMLAYRIC--------------------------PA-----RDSLGIFLA 49
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 829 IVEELIAARKAARKEMAAAKDEMTRQVLNGRQLALKISANSVYGYTGTTTGGqLPCLEVATTITCFGR----DMIDFTRR 904
Cdd:cd05538 50 LLKYLVELRLAAKESARAAARPAERDAFKAKQAAFKVLINSFYGYLGTGLHA-FSDPEAAAEVTRLGRellkLMIRWLRR 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 905 EvekmfcrdnqhacNATVIYGDTDSV--MVDFGDFSIAEAmklgEEAAQALSEKFVKPIRLEFEKVYCPFLLMNKKRYAG 982
Cdd:cd05538 129 R-------------GATPVEVDTDGIyfIPPNGVDTEDEE----EELVRELSSTLPKGITVEFDGRYRAMFSYKIKNYAL 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 983 LLYTrpekyDKIDSKGIETVRRDFSLLVQTMADTVLRkMLIDKDVEAAKEYTRRKVAELLQNKIDLSLLVQTKSLGKMDy 1062
Cdd:cd05538 192 LDYD-----GKLIVKGSAFRSRGIEPFLREFLREAVR-LLLQGDGAGVHDLYEDYLRRLRSHELPISDLARTETLKESP- 264
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 1063 DTRLPHVELAKKLR------KRDAGTAPSVGDRVSYVVIQGAKGQAQYERAE-----DPLYVLENnlpidTQHYLEGIKK 1131
Cdd:cd05538 265 EEYLQKVRAGKRNPaaayeiALARPREWRAGDRVTYYVSGTGKGVSVYENCRlvadyDPAHPDEN-----TGFYAERLLQ 339
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
442-665 |
2.37e-14 |
|
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: 72.99 E-value: 2.37e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 442 PPLRILSFDIECvklkgegfpeaetdpviqissivmlqSVPADLpglsetdtnaatacvakarkkrLSGGLERPLCRVLF 521
Cdd:cd05784 1 PKLKVVSLDIET--------------------------SMDGEL----------------------YSIGLYGEGQERVL 32
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 522 ALKECASIAGSVVLWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKV---VGFNRlsklKSLEskIR 598
Cdd:cd05784 33 MVGDPEDDAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLplrLGRGG----SPLN--WR 106
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 237831459 599 DSSFSSRALgthegkdIATEGRIQFDLLELVRR-DYKLKSYSLNFVSFEFLKEQK--EDVHYNM--IGDLFR 665
Cdd:cd05784 107 QSGKPGQGF-------LSLPGRVVLDGIDALKTaTYHFESFSLENVAQELLGEGKliHDVDDRGaeIERLFR 171
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
442-664 |
8.55e-14 |
|
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: 72.26 E-value: 8.55e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 442 PPLRILSFDIECVklkgegFPEAETDPVIQISSIVMLQSVPADlpglsetDTNAatacvaKARKKRLSGGLERPLCRVLF 521
Cdd:cd05776 1 PPLTVMSLSIKTV------LNSKTNKNEIVMISMLVHRNVSLD-------KPTP------PPPFQSHTCTLTRPLGRSPP 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 522 ALKE--CASIAGSVVLWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKVVGFNRLSKLKsleskiRD 599
Cdd:cd05776 62 PDLFekNAKKKKTKVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLK------RS 135
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 237831459 600 SSFSSRALGTHEGKDIaTEGRIQFDLL----ELVRRdyklKSYSLNFVSFEFLKEQKEDVHYNMIGDLF 664
Cdd:cd05776 136 VWPKKKGGGKFGEREL-TAGRLLCDTYlsakELIRC----KSYDLTELSQQVLGIERQDIDPEEILNMY 199
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
537-680 |
1.36e-11 |
|
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: 65.72 E-value: 1.36e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 537 FDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKVVGF-NRLSKLKS-LESKIRDssfSSRALGTHEGKD 614
Cdd:cd05778 78 VESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLlDEISRVPSdSNGKFGD---RDDEWGYTHTSG 154
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 237831459 615 IATEGRIQFDLLELVRRDYKLKSYSLNFVSFEFLKEQKEDVHYNMIGDLFR-GCPSSRRRIGVYCLK 680
Cdd:cd05778 155 IKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKsGSASERWRVLEYYLK 221
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
442-682 |
4.22e-09 |
|
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: 57.34 E-value: 4.22e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 442 PPLRILSFDIECvkLKGEGFPEAETDPVIQISsivmLQSvpadlpglsetdtnaatacvakarkkrlSGGlerplcRVLF 521
Cdd:cd05781 1 PDLKTLAFDIEV--YSKYGTPNPRRDPIIVIS----LAT----------------------------SNG------DVEF 40
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 522 ALKECAsiagsvvlwfdDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKVvgfnRLSKLKsleskiRDSS 601
Cdd:cd05781 41 ILAEGL-----------DDRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGV----KLDVGR------RGGS 99
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 602 FSSRALGTHegkdIATEGRIQFDLLELVRRDYKLKSYSLNFVSfEFL----KEQKEDVHYNMIGDLFRGcPSSRRRIGVY 677
Cdd:cd05781 100 EPSTGVYGH----YSITGRLNVDLYDFAEEIPEVKVKTLENVA-EYLgvmkKSERVLIEWYRIYEYWDD-EKKRDILLKY 173
|
....*
gi 237831459 678 CLKDA 682
Cdd:cd05781 174 NRDDA 178
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
533-863 |
6.47e-08 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 56.93 E-value: 6.47e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 533 VVLWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAAT-LKVVGFNRLSKLKSLESKIRDSSFSSRALGTHE 611
Cdd:PHA02524 173 VYMPFEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNiLGEKAANQLSPYGKITSKTITNLYGEKIIYKIH 252
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 612 GKDIATEGRIQFDLLELVRRDYKLKSyslnfVSFEFLKEQKEDvhYNMIGDLFRGCPSSR------RRIGVYCLKDAYLP 685
Cdd:PHA02524 253 GIALMDYMDVFKKFSFTPMPDYKLGN-----VGYREVKADKLD--YEGPINKFRKADHQRyvdycvRDTDIILLIDGRRC 325
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 686 LRLLKELLFLYNYVEMSRVTGTplnflltrgqqIKV-TAQLLRKCKELNYVVPVVKRTGGDNsvqYEGATVLEPRKGFYD 764
Cdd:PHA02524 326 FIDLILSLSYYAKIRFDDVLGT-----------IKVwDSIIFNSLVESNVVIPAMKASPKQS---FPGAYVKEPVPGGYR 391
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 765 KPIaTLDFASLYPSIMIAHNICYSTLVASSAAHTMNnpDDVTVTTTSPPHKF-------VKKHIRRGVLPMIVEELIAAR 837
Cdd:PHA02524 392 YGL-SFDLTSLYPSILRLLNISPEMIAGMFSPARLE--DYINKVAPKPSDQFscapngmMYKKGVVGVLPNETEKVFLQR 468
|
330 340
....*....|....*....|....*...
gi 237831459 838 KAARKEMAAA--KDEMTRQVLNGRQLAL 863
Cdd:PHA02524 469 KSEKKMMLAAirNQEAIKKILASRGVKL 496
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
539-681 |
1.36e-06 |
|
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: 50.49 E-value: 1.36e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 539 DEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATLKV---VGFNRlSKLKSLESKIRdssFSSRaLGTHEGKDI 615
Cdd:cd05785 57 AEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVplaIGRDG-SIPRQRPSRFR---FAER-LIDYPRYDI 131
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 237831459 616 AteGRIQFDLLELVRR----DYKLKSYSLNFVS--FEFLKEQKEDVHYNMIGDLFRGCPSSRRRigvYCLKD 681
Cdd:cd05785 132 P--GRHVIDTYFLVQLfdvsSRDLPSYGLKAVAkhFGLASPDRTYIDGRQIAEVWRSDPARLLA---YALDD 198
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
649-933 |
4.54e-06 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 51.40 E-value: 4.54e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 649 KEQK-EDVHYNMIGDLFRGCPSSRRRIGVYCLKDAYLPLRLLKELLFLYNYVEMSRVTGTPLNFLLTRG--------QQI 719
Cdd:PHA03334 511 KIGKmDDVKYTEMDGMFTAGGAALARYLIYNLVDSELLIRIAKNLDPVIEFLNRLRATYNIDYVAHGRGvmnfcgfvQST 590
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 720 KVTAQLLRKCKELNYVV------------PVVKRTGGDNSVQYEGATVLEPRKGF-----YDKPIATLDFASLYPSIMIA 782
Cdd:PHA03334 591 KSVEVPLLKARLRIGIFvatgriaeslcmPEKYARDCRQKIKLKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCD 670
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 783 HNIC-----------------------------YSTLVASSAAHTMNNPDDV--TVTTTSPPHKFvkkhirrgvLPMive 831
Cdd:PHA03334 671 ANISpeaivdpdctarvrgwvvfdwkkidrgfgKATLMYTILRTKPEEPSWRrfTTYTTSSLNHY---------LSM--- 738
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 832 eliaaRKAARKEMAAAKDEMTRQVLNGRQLALKISANSvygytgTTTGGQLPClevATTITCFGRDMIDFTRREVEKmfc 911
Cdd:PHA03334 739 -----RTEYKGAMKQAKDPKLKSYHNQLQNEMKICANS------HYGVAPHAC---QHLITTLGRHKIKLVEEFIKK--- 801
|
330 340
....*....|....*....|..
gi 237831459 912 rdnqhACNATVIYGDTDSVMVD 933
Cdd:PHA03334 802 -----EPGMTVNYGDTDSVMFQ 818
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
443-589 |
2.13e-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: 46.87 E-value: 2.13e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 443 PLRILSFDIECVK--LKgegFPEAETDPVIQISS--------IVMLQSVPADLPGLSETDtnaatacvakarKKRLSGgl 512
Cdd:cd05779 1 DPRVLAFDIETTKlpLK---FPDAETDQIMMISYmidgqgylIVNREIVSEDIEDFEYTP------------KPEYEG-- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237831459 513 erPLCrvlfalkecasiagsvVLWFDDEKEMLAKWAEFVRQVDPDFLSGYNCVNFDLNYLITRAATL-----KVVGFNRL 587
Cdd:cd05779 64 --PFK----------------VFNEPDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHglsmeEEIGFRKD 125
|
..
gi 237831459 588 SK 589
Cdd:cd05779 126 SE 127
|
|
| |
