|
Name |
Accession |
Description |
Interval |
E-value |
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
78-1098 |
0e+00 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 1506.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 78 RRPTLRalDPSTEPLIFQQLEIDHYVGSAPPLPEG----PLPSRNSVPILRAFGVTDEGFSVCCHIQGFAPYFYTPAPPG 153
Cdd:PTZ00166 30 RRPLPP--ISLQKDLVFFQLDADYTEKDDKSQGNPhntvSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPN 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 154 FGAEHLSELQQELNAAISRDQRGGKELSgpAVLAIELCSRESMFGYHGHGPSPFLRITLALPRLMAPARRLLEQGVRVPG 233
Cdd:PTZ00166 108 FLPEDSQKLKRELNAQLSEQSQFKKYQN--TVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVCG 185
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 234 L---GTPSFAPYEANVDFEIRFMVDADIVGCNWLELPAGKYVRRAEKKAT-LCQLEVDVLWSDVISHPPEGQWQRIAPLR 309
Cdd:PTZ00166 186 GgwdGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKTsTCQIEVDCSYEDLIPLPPEGEYLTIAPLR 265
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 310 VLSFDIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEREEDLLQAWADFILAMD 387
Cdd:PTZ00166 266 ILSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVD 345
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 388 PDVITGYNIQNFDLPYLISRAQALKVDRFPFLGRVTGLRSNIRDSSFQSRQVGRRDSKVISMVGRVQMDMLQVLLREHKL 467
Cdd:PTZ00166 346 PDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKL 425
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 468 RSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNEQTRRRLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTGVPLGYLLTR 547
Cdd:PTZ00166 426 KSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTR 505
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 548 GQQVKVVSQLLRQAMRQGLLMPVVKTEGS---EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGA 624
Cdd:PTZ00166 506 GQQIKVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPND 585
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 625 AQKlgLKPDEFIKTPTGDEFVKSSVRKGLLPQILENLLSARKRAKAELAQETDPLRRQVLDGRQLALKVSANSVYGFTGA 704
Cdd:PTZ00166 586 ANN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGA 663
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 705 QV-GKLPCLEISQSVTGFGRQMIEKTKQLVESKYTVENGYDANAKVVYGDTDSVMCRFGVSSVAEAMSLGREAANWVSSH 783
Cdd:PTZ00166 664 QVgGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKK 743
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 784 FPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRSDAHDKMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVAHAK 863
Cdd:PTZ00166 744 FLKPIKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTK 822
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 864 DVISDLLCNRIDISQLVITKELTRaaADYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIIGAAKGVAAYMKSEDPLFV 943
Cdd:PTZ00166 823 GKISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYV 900
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 944 LEHSLPIDTQYYLEqQLAKPLLRIFEPILGEgraESVLLRGDHTRCKTVLTSKVGGLLAFTKRRNCCIGCRSVIDhQGAV 1023
Cdd:PTZ00166 901 LENNIPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIK-EGAL 975
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 254587977 1024 CKFC-QPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQERLLQRFG 1098
Cdd:PTZ00166 976 CDNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
577-972 |
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: 828.83 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 577 EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLglKPDEFIKTPTGDEFVKSSVRKGLLPQ 656
Cdd:cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKL--PPEDYIKTPNGDYFVKSSVRKGLLPE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 657 ILENLLSARKRAKAELAQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESK 736
Cdd:cd05533 79 ILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 737 YTVENGYDANAKVVYGDTDSVMCRFGVSSVAEAMSLGREAANWVSSHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRS 816
Cdd:cd05533 159 YTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLW-TNP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 817 DAHDKMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVAHAKDVISDLLCNRIDISQLVITKELTRAAADYAGKQ 896
Cdd:cd05533 238 DKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADDYAGKQ 317
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 254587977 897 AHVELAERMRKRDPGSAPSLGDRVPYVIIGAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPIL 972
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 ... |
539-971 |
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: 574.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 539 VPLGYLLTRGQQVKVVSQLLRQAMRQGLLMPVVK-TEGSED-YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 616
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPsAKGDEDgYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 617 TTLLRPGAAQKlGLKPDE----FIKTPTGDEFVKSSVRKGLLPQILENLLSARKRAKAELAQETDPLRRQVLDGRQLALK 692
Cdd:pfam00136 81 TTLVRSVDEAN-NLPPEDnlitVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLALK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 693 VSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTvengydANAKVVYGDTDSVMCRFGVSSVAEAMSL 772
Cdd:pfam00136 160 ITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT------YNFRVIYGDTDSVFIEFGGKDVEEAMKI 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 773 GREAANWVSSH-FPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRSDAHDKMDCKGLEAVRRDNCPLVANLVTSSLRRILV 851
Cdd:pfam00136 234 GDELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKY-TAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLS 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 852 DRDPDGAVAHAKDVI----SDLLCNRIDISQLVITKELTRAAADYAGKQ-AHVELAERMRKRDpGSAPSLGDRVPYVIIG 926
Cdd:pfam00136 313 DRGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEVALRMNKRN-GEAPEVGDRIPYVIVK 391
|
410 420 430 440
....*....|....*....|....*....|....*....|....*...
gi 254587977 927 AAK---GVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 971
Cdd:pfam00136 392 AAKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
121-971 |
1.48e-176 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 537.10 E-value: 1.48e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 121 PILRAFGVTDEGFSVCCHIQGFAPYFYTPAPpgfgaehlselQQELNAAISRDQRGgkelsgpaVLAIELCSRESMFGyh 200
Cdd:COG0417 19 PVIELWGRTEDGPSVLLDVTGFRPYFYVPLP-----------DEEKLEELLRDIKE--------ITEVEPVKLKSFFG-- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 201 ghGPSPFLRITLALPRLMAPARRLLEQGVrvpglgtpsFAPYEANVDFEIRFMVDADIVGCNWLELPAGKYVRRAEKKat 280
Cdd:COG0417 78 --EPVPVLKIYTRDPRDVRELRDRLKEGG---------IDVYEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKLDYE-- 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 281 lcqlevdvlwsdVISHPPEGQWQRIAPLRVLSFDIECAGRKGiFPEPERD-PVIQICSlglrwgEPEPFLRLALTLRpcA 359
Cdd:COG0417 145 ------------VKENPRLKPEDYRPKLKVLSFDIEVSTPRG-FPDPERDgPIISIGL------AGSDGEKKVLMLG--R 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 360 PILGAKVQSYEREEDLLQAWADFILAMDPDVITGYNIQNFDLPYLISRAQALKVdrfPF-LGRVtGLRSNIRDSSFQSRq 438
Cdd:COG0417 204 EGVDFEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAERLGI---PLdLGRD-GSEPSWREHGGQGF- 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 439 vgrrdskvISMVGRVQMDMLQVLLR-EHKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQngnEQTRRRLAVYCLKDAFLP 517
Cdd:COG0417 279 --------ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKLIVDGGEIERLW---DDDKPALAEYNLRDAELT 347
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 518 LRLLERLMVLVNNVEMARVTGVPLgYLLTRGQQVKVVSQL-LRQAMRQGLLMPVVKTEGSEDYTGATVIEPLKGYYDvPI 596
Cdd:COG0417 348 LRIFEKTLLLPFLIELSRITGLPL-DDVGRAGSSAAFENLlLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYE-NV 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 597 ATLDFSSLYPSIMMAHNLCYTTLLRPGAAqklglKPDEFIKTPT-GDEFVKSsvRKGLLPQILENLLSARKRAKAELAQ- 674
Cdd:COG0417 426 LVLDFKSLYPSIIRTFNISPETLVEGGEE-----PCGDEDVAPGfGHRFCRE--PKGILPSILEELWDERDEAKKKMKKa 498
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 675 ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKytvenGYdanaKVVYGDT 754
Cdd:COG0417 499 KPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEEL-----GY----KVIYGDT 569
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 755 DSVMCRFGVSSVAEAMSLGREAANWVSSHFPSPIRLEFEKVYFPYLLI-SKKRYAGLLfssrsdAHDKMDCKGLEAVRRD 833
Cdd:COG0417 570 DSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPgSKKRYAGLT------EDGKIDIKGLEAVRSD 643
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 834 NCPLVANLVTSSLRRILVDRDPDGAVAHAKDVISDLLCNRIDISQLVITKELTRAAADY-AGKQAHVELAERMRKRdpGS 912
Cdd:COG0417 644 WTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYeKNVPPHVRAARKLDER--GR 721
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*....
gi 254587977 913 APSLGDRVPYVIIGAAKGVaaymksEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 971
Cdd:COG0417 722 PYQRGDKISYVITKGGGRV------EPVELAKERESEIDYDYYIEKQLKPTADRILEAF 774
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
302-531 |
1.05e-150 |
|
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: 448.56 E-value: 1.05e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 302 WQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWAD 381
Cdd:cd05777 1 WSKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 382 FILAMDPDVITGYNIQNFDLPYLISRAQALKVDRFPFLGRVTGLRSNIRDSSFQSRQVGRRDSKVISMVGRVQMDMLQVL 461
Cdd:cd05777 81 FVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVI 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 462 LREHKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNEQTRRRLAVYCLKDAFLPLRLLERLMVLVNNV 531
Cdd:cd05777 161 QRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLVNYI 230
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
307-762 |
4.27e-148 |
|
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: 451.60 E-value: 4.27e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 307 PLRVLSFDIECAGRKGIFPEPE--RDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWADFIL 384
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 385 AMDPDVITGYNIQNFDLPYLISRAQALKVDRFPFLGRVT-GLRSNIRDSSFQSRQVGRRDSKVIsMVGRVQMDMLQVLLR 463
Cdd:smart00486 82 KYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKiGLRIPNKKPLFGSKSFGLSDIKVY-IKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 464 EHKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNEQTRRRLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTGVPLGY 543
Cdd:smart00486 161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 544 LLTRGQQVKVVSQLLRQAMRQGLLMPVVKTEGS----------EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHN 613
Cdd:smart00486 241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 614 LCYTTLLRPGAAQKLGL----KPDEFIKTPTG--DEFVKSSVRKGLLPQILENLLSARKRAKAELAQETDPL--RRQVLD 685
Cdd:smart00486 321 LCYSTLVGVGEVVIKGDliipEDLLTIKYEKGnkYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESeeLKKLLD 400
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 254587977 686 GRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKytveNGYDANAKVVYGDTDSVMCRFG 762
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEEN----GYPKPGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
121-973 |
2.78e-110 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 362.25 E-value: 2.78e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 121 PILRAFGVTDEGFSVCCHIQGFAPYFYTpappgfgAEHLSELQQELNAAISRDQR--GGKELSGPAVLAIelcsresmfg 198
Cdd:PRK05762 20 PEVELWLATDEGPRVVLLDPQFRPYFIP-------AEQDERAESLLAGEIGVRLSplALKDFHRRPVLGL---------- 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 199 yhghgPSPFLRITLALPRlmaparRLLEQGVRVpglgtpsfapYEANVDFEIRFMVDADIVGCNWLElpaGKYVRRAEK- 277
Cdd:PRK05762 83 -----YCRQHRQLTRLPK------RLREGGVDV----------YEADIRFPERYLMERFITPCVWFS---GEVEQYTTDg 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 278 KATLCQLEVDVLWsdvishPPegqwqriaPLRVLSFDIECAgRKGI-----FPEPERDPVIQIcslglrwGEPEpflrla 352
Cdd:PRK05762 139 VLRNARLKPAPDY------RP--------PLKVVSLDIETS-NKGElysigLEGCGQRPVIML-------GPPN------ 190
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 353 ltlrPCAPILGAKVQSyerEEDLLQAWADFILAMDPDVITGYNIQNFDLPYLISRAQALKVdrfPF-LGRVTGLRSnIRD 431
Cdd:PRK05762 191 ----GEALDFLEYVAD---EKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGI---PLrLGRDGSELE-WRE 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 432 SSFQSRQVgrrdskVISMVGRVQMDMLQVLLR-EHKLRSYTLNAVSFHFLGEQKEdvqhsIITDLQNGNEQTRR------ 504
Cdd:PRK05762 260 HPFRSGYG------FASVPGRLVLDGIDALKSaTWVFDSFSLEYVSQRLLGEGKA-----IDDPYDRMDEIDRRfaedkp 328
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 505 RLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTGVPLGylltR--GQQVKVVSQLLRQAMRQGLLMPVVKTEGSEDYTGA 582
Cdd:PRK05762 329 ALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLD----RvgGSVAAFEHLYLPRAHRAGYVAPNLGERPGEASPGG 404
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 583 TVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPgaaqkLGLKPDEFIKTPTGDEFVKssvRKGLLPQILENLL 662
Cdd:PRK05762 405 YVMDSKPGLYD-SVLVLDFKSLYPSIIRTFNIDPDGLVEG-----LAQPPEESVAGFLGARFSR---EKHFLPEIVERLW 475
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 663 SARKRAKAELAQEtdplrrqvldgRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKytvenG 742
Cdd:PRK05762 476 EGRDEAKREMNKP-----------LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQ-----G 539
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 743 YdanaKVVYGDTDSVMCRFGVS-SVAEAMSLGREAAN----WVSSHF------PSPIRLEFEKVY----FPYLLI----S 803
Cdd:PRK05762 540 Y----QVIYGDTDSTFVWLGGAhDEEDAAKIGRALVQeinqWWQEHLqqefglESALELEFEKHYrrffMPTIRGaeegS 615
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 804 KKRYAGLLfsSRSDAHDKMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVahaKDVISDLLCNRIDiSQLVITK 883
Cdd:PRK05762 616 KKRYAGLI--QEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEPYVDYV---REVIDKLRAGELD-EKLVYRK 689
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 884 ELTRAAADYAGKQA-HV----ELAERMRKRDPGSAPSLGDRVPYVIIGAAKGVAAYMKSedplfvlehslPIDTQYYLEQ 958
Cdd:PRK05762 690 RLRRPLDEYQRNVPpHVraarLADEMGYKVGRPLQYQNGGKIGYVITVNGPEPLEYRKS-----------PIDYDYYIEK 758
|
890
....*....|....*
gi 254587977 959 QLaKPLLRIFEPILG 973
Cdd:PRK05762 759 QL-QPVADRILPFFG 772
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
548-971 |
5.76e-102 |
|
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: 328.79 E-value: 5.76e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 548 GQQVKVVSQLLRQAMRQGLLMP-----VVKTEGSEDYTgATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLL-- 620
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPspsrqQVAQQRALECL-PLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLgr 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 621 ------------------RPGAAQKLGLKPDEFIKTPTGDEFVKSSVRKGLLPQILENLLSARKRAKAELAQETDPLR-R 681
Cdd:cd05534 80 veelngggkfgflgvklyLPPPPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKlQ 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 682 QVLDGRQLALKVSANSVYGFTGAQV-GKLPCLEISQSVTGFGRQMIEKTKQLVESkytvenGYDANAKVVYGDTDSVMCR 760
Cdd:cd05534 160 RILDARQLALKLLANVTYGYTAASFsGRMPCVEIADSIVQTGRETLERAIELIES------TPKWGAKVVYGDTDSLFVL 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 761 FGVSSVAEAMSLGREAANWVSSHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSRSDAHDKMDCKGLEAVRRDNCPLVAN 840
Cdd:cd05534 234 LPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQK 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 841 LVTSSLRRILVDRDPDGAVAHAKDVISDLLCNRIDISQLVITKELTRAAADYAGK-QAHVELAERMRKRDPGSAPSLGDR 919
Cdd:cd05534 314 ILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGATlPAGAIVALRRMEKDPRAEPQYGER 393
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|...
gi 254587977 920 VPYVIIGAAKGVAAYMKSEDP-LFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 971
Cdd:cd05534 394 VPYVVVRGEPGSRLIDLVVSPeEFLADPSLRLDAEYYITKQIIPALDRLFNLV 446
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
128-475 |
2.37e-100 |
|
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: 320.13 E-value: 2.37e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 128 VTDEGFSVCCHIQGFAPYFYTPAPPGFGAEHLSELQQELNAAISRdqrggkelsgpaVLAIELCSRESMFGYHGHgPSPF 207
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKELEEVIEEIKELYEGLDK------------IEKIELKLKKSLYGYEED-PVPY 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 208 LRITLALPRLMAPARRLL--EQGVRVpglgtpsfapYEANVDFEIRFMVDADIVGCNWLELPagKYVRRAEKKATLCQLE 285
Cdd:pfam03104 68 LKVSFANPRPLLKIRKYLspENISDV----------YEYDVDYLERFLIDNDIVGFGWYKVK--VYPFRAEGRISNCDVE 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 286 VDVLWSDVISHPPEGQWqriAPLRVLSFDIECAGRKGIFPEPER--DPVIQICSLGLRWGEPEPFLRLALTLRPCAPI-- 361
Cdd:pfam03104 136 IDCDSPDLISVPFEKEW---PPLRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEPRFLFTLRECDSEdi 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 362 -----------LGAKVQSYEREEDLLQAWADFILAMDPDVITGYNIQNFDLPYLISRAQALKVDRFPFLGRV-TGLRSNI 429
Cdd:pfam03104 213 edfeytpkpiyPGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLnRGGRSKV 292
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 254587977 430 RDSSFqsrqvGRRDSKVISMVGRVQMDMLQVLLREHKLRSYTLNAV 475
Cdd:pfam03104 293 REIGF-----GTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
205-969 |
1.81e-92 |
|
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: 321.62 E-value: 1.81e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 205 SPFLRITLALPRLMAPARRLLEQGVrvpglGTPSFAPYEANVDFEIRFMVDADIVGCNWLElPAGKYVRrAEKKATLCQL 284
Cdd:TIGR00592 413 SEYLEVTYELGKEFAPMEALPSDLK-----GQTFWHVFGSNTGNLERFLLLRKIKGPCWLA-VKGPDEL-EYPRRSWCKY 485
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 285 EVDVLWSDVIShppEGQWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLrlaltlrPCAPILGA 364
Cdd:TIGR00592 486 EGGYVKPPNVE---KGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPY-------DVHPCVGT 555
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 365 KVQSYEREEDLLQAWADFI-----------------LAM----DPDVITGYNIQNFDLPYLISRAQALKVDRFPFLGRVT 423
Cdd:TIGR00592 556 RPKDCSFPLDLKGEFPGKKpslvedlateralikkfMAKvkkiDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLR 635
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 424 glRSNIRDSSFQSRQVGRrdskvisMVGRVQMDMLQVLlrehKLRSYTLNAVSFHFLG-EQKEDVQHSIITDLQNGNEQT 502
Cdd:TIGR00592 636 --RSPKFGRRFGERTCGR-------MICDVEISAKELI----RCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLT 702
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 503 RrrLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTGVPLGYLLTRGQQVKVVSQLLRQAMRQGLLMP----VVKTEGSED 578
Cdd:TIGR00592 703 Y--LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqiFRKQQKLGD 780
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 579 ---------------YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLGLKPDefiktptgde 643
Cdd:TIGR00592 781 edeeidgykkgkkaaYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDEDELPELPD---------- 850
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 644 fvkSSVRKGLLPQILENLLSARKRAKAELAQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGR 723
Cdd:TIGR00592 851 ---SELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGR 927
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 724 QMIEKTKQLVESKytvengydaNAKVVYGDTDSVMCRFGVSSVAEAMSLGREAANWVSSHFPsPIRLEFEKVYFPYLLIS 803
Cdd:TIGR00592 928 EILEHTRQLVEEM---------NLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-LLELDIDGVFKRLLLLK 997
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 804 KKRYAGLLFSSRSDAH--DKMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVAHAKDVISDL----LCNRIDIS 877
Cdd:TIGR00592 998 KKKYAAIKVEGDSDGNytTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLE 1077
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 878 QLVITKELTRAAADYAGK--QAHVELAERMRKRDPGSAPSlGDRVPYVIIGAAKGVAAYMKS---EDPLFvLEHSLPIDT 952
Cdd:TIGR00592 1078 KFVINKQLTRDPKDYPDGasLPHVHVALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAyalEELQR-KHNNLIYDT 1155
|
810
....*....|....*..
gi 254587977 953 QYYLEQQLAKPLLRIFE 969
Cdd:TIGR00592 1156 QYYLEHQIHPVVLRILE 1172
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
577-969 |
2.13e-88 |
|
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: 287.73 E-value: 2.13e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 577 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAqklglKPDEFiktPTGDEFVKSSVRKGLLPQ 656
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEI-----AAPED---YIGVGFRSPKDRKGLLPR 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 657 ILENLLSARKRAKAE-LAQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVES 735
Cdd:cd00145 72 ILEELLNFRDEAKKRmKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEE 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 736 KytvengydaNAKVVYGDTDSVMCRFGVS-SVAEAMSLGREAANWVSShfPSPIRLEFEKVYFPYLLISKKRYAGLLFSS 814
Cdd:cd00145 152 H---------GARVIYGDTDSIFVSLPKMgTKEDAIKEGREILQELAD--EHLLELEFEKVYLPFFLGKKKRYAGLDIWK 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 815 RSDaHDKMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVahaKDVISDLlcnridisqlvitkeltraaadyag 894
Cdd:cd00145 221 GQD-EGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAV---KEYIDEL------------------------- 271
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 254587977 895 kqahvelaermrkrdpgsapslgDRVPYVIIGAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 969
Cdd:cd00145 272 -----------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
579-973 |
9.18e-86 |
|
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: 283.32 E-value: 9.18e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 579 YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPgaaqklglKPDEFIKTPTGDEFvkSSVRKGLLPQIL 658
Cdd:cd05532 8 YAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRA--------DPDDEDDEEPPLPP--SDQEKGILPRII 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 659 ENLLSARKRAKAELAQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKyt 738
Cdd:cd05532 78 RKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKM-- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 739 venGYDanakVVYGDTDSVMCRFGVSSVAEAMSLGREAANWVSSHFPSpIRLEFEKVYFPYLLISKKRYAGLLFSSRSDA 818
Cdd:cd05532 156 ---NLE----VIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKK-LEIDIDGVFKRLLLLKKKKYAALKVVDDDKG 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 819 HDKMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAV----AHAKDVISDLLCNRIDISQLVITKELTRAAADYAG 894
Cdd:cd05532 228 KLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVenihEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPD 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 895 K--QAHVELAERMRKRDPGSAPslGDRVPYVII--GAAKGVA--AYMKSEdplFVLEHSLPIDTQYYLEQQLAKPLLRIF 968
Cdd:cd05532 308 KksLPHVQVALRMNKRGRKVKA--GDTIPYIICkdGSSKSLAdrAYHPDE---VKKNENLKIDIEYYLSQQILPPISRLC 382
|
....*
gi 254587977 969 EPILG 973
Cdd:cd05532 383 EPIEG 387
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
577-969 |
1.98e-78 |
|
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: 262.26 E-value: 1.98e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 577 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGaaqklglKPDEFIKTPTGDEFVKSsvRKGLLPQ 656
Cdd:cd05536 2 ESYEGGIVLEPEKGLHE-NIVVLDFSSLYPSIMIKYNISPDTLVREG-------CEDCDVEPQVGHKFRKD--PPGFIPS 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 657 ILENLLSARKRAKAELAQETDP-LRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEs 735
Cdd:cd05536 72 VLEDLLEERRRIKEKMKKLDPEsEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAE- 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 736 kytvENGYdanaKVVYGDTDSVmcrFGVSSVAEA-MSLGREAANWVSSHFPspIRLEFEKVYFPYLLISKKRYAGLlfss 814
Cdd:cd05536 151 ----EKGF----KVIYGDTDSL---FVKIDGADAvKKKVKKLLKYINEELP--LELEIEKFYKRGFFVTKKRYAGL---- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 815 rsDAHDKMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVAHAKDVISDLLCNRIDISQLVITKELTRAAADYAG 894
Cdd:cd05536 214 --TEDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYKA 291
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 254587977 895 KQAHVELAERMRKRdpGSAPSLGDRVPYVIIgaaKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 969
Cdd:cd05536 292 TGPHVAAAKKLAKR--GYKVRPGTKIGYVIV---KGSGKISDRAYPYDMVDEKHKYDAEYYIDNQVLPAVLRILE 361
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
242-973 |
1.04e-65 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 237.66 E-value: 1.04e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 242 YEANVDFEIRFMVDADIVGCNWLELPAGKYVRRAE------KKATLCQLEVDVLWSDVISHPPegqwqriAPLRVLSFDI 315
Cdd:PRK05761 123 WEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEilveeiKKAFKDERKLAEDWLPIFEAPI-------PKIKRIAIDI 195
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 316 ECAGrkgifPEPERDPViqicslglrwgepepflrlaltlrpcapilgakvqsyEREEDLLQAWADFILAMDPDVItgYN 395
Cdd:PRK05761 196 EVYT-----PAKGRIPD-------------------------------------DSEKELLAELFDIILEYPPVVT--FN 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 396 IQNFDLPYLISRAQALKVDRFPFLGRVTGLRSNIRDSSFQSRqvgrRDSKVISMVGRVQMdmlqvllrehklRSYTLNAV 475
Cdd:PRK05761 232 GDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQN----KAVRSYAFYGKYRH------------REARLDAV 295
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 476 SFHFLGEQKEDVQHSIitdlqngNEQTRRRLAVYCLKDAFLPLRLL----ERLMVLVnnVEMARVTGVPLGYLlTRGQQV 551
Cdd:PRK05761 296 GRALLGISKVELETNI-------SELDLEELAEYNFRDAEITLKLTffnnELVLKLI--LLLSRISKLPIEEL-SRATIS 365
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 552 KVVSQLL-RQAMRQGLLMP-----------VVKTEGSED--YTGATVIEPLKG-YYDVpiATLDFSSLYPSIMMAHNLCY 616
Cdd:PRK05761 366 TWISNLEyWEHRKRGWLIPwkedilrldheVYKKAIIKGkkYRGGLVFQPPPGiFFNV--YVLDFASLYPSIIVKWNLSP 443
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 617 TTLLRPGAAQKLGLKPDEFIKTPTGDefvkssvRKGLLPQILENLLSARKRAKAELAQE--TDPLRRQVLDGRQLALKVS 694
Cdd:PRK05761 444 ETVRIPECKCHYDDEVPELGHSVCDD-------RPGLTSVLVGLLRDFRVKIYKKKAKDpnLDEERRAWYDVVQRALKVF 516
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 695 ANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEskytvENGYdanaKVVYGDTDSVMCRFGVSSVAEAMslgr 774
Cdd:PRK05761 517 LNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAE-----ELGL----KVLYGDTDSLFVWGPTKESLEEL---- 583
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 775 eaANWVSSHFpsPIRLEFEKVYfPYLLIS--KKRYAGLLFSsrsdahDKMDCKGLEAVRRDNCPLVANLVTSSLRRILVD 852
Cdd:PRK05761 584 --IKEIEERT--GIDLEVDKTY-DWVAFSglKKNYFGVLKD------GKVKIKGIVAKKRNTPEFVKELQREVLEVLKSI 652
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 853 RDPDGAV-------AHAKDVISDLLCNRIDISQLVITKELTRAAADYA-GKQAHVELAERMRKRdpGSAPSLGDRVPYVI 924
Cdd:PRK05761 653 RSPEDVEkvkdeieDVLKRYYEKLRAKDYPLDELAIRVRLSKPLDEYTkNTPQHVKAALQLRDY--GVEVSPGDIISYVK 730
|
730 740 750 760
....*....|....*....|....*....|....*....|....*....
gi 254587977 925 IGAAKGVaaymkseDPLFVLEHSlPIDTQYYLEQqlakpLLRIFEPILG 973
Cdd:PRK05761 731 VDDKRGV-------KPVQLAKLS-EIDVEKYIEL-----LRSALEQILS 766
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
310-522 |
3.74e-53 |
|
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: 184.48 E-value: 3.74e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 310 VLSFDIECAGRKGiFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAP-ILGAKVQSYEREEDLLQAWADFILAMDP 388
Cdd:cd05160 1 VLSFDIETTPPVG-GPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEfIDGIEVEYFADEKELLKRFFDIIREYDP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 389 DVITGYNIQNFDLPYLISRAQALKVDRFPFLGRvtglRSNIRDSSfqsrqvgrRDSKVISMVGRVQMDMLQVLLREHKLR 468
Cdd:cd05160 80 DILTGYNIDDFDLPYLLKRAEALGIKLTDGIYR----RSGGEKSS--------GSTERIAVKGRVVFDLLAAYKRDFKLK 147
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 254587977 469 SYTLNAVSFHFLGEQKEDVQHSIITDlqNGNEQTRRRLAVYCLKDAFLPLRLLE 522
Cdd:cd05160 148 SYTLDAVAEELLGEGKEKVDGEIIED--AEWEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
581-969 |
1.64e-43 |
|
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: 162.82 E-value: 1.64e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 581 GATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKlglkPDEFIKTPTGDEFvksSVRKGLLPQILEN 660
Cdd:cd05537 5 GGYVMDSKPGLYK-NVLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPD----PEDLIPGFLGARF---SREKHILPDLIAR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 661 LLSARKRAKaelaQETDPLRRQvldgrqlALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEskytve 740
Cdd:cd05537 77 LWAARDEAK----REKNAPLSQ-------AIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIE------ 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 741 ngyDANAKVVYGDTDSVMCRFG-VSSVAEAMSLGREAA----NWVSSH------FPSPIRLEFEKVYFPYLLI------- 802
Cdd:cd05537 140 ---QQGYQVIYGDTDSTFVWLGeELDAAEAQAIGKELAsqinQWWAQKlkeefgLESFLEIEFETHYSRFFMPtirgsde 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 803 -SKKRYAGLlfsSRSDAHDKMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVahaKDVISDLLCNRIDiSQLVI 881
Cdd:cd05537 217 gSKKRYAGL---KSTDGGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFI---KETVEELLAGELD-ELLVY 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 882 TKELTRAAADY-AGKQAHVELAermRKRDPgSAPSLGDRVPYVIIgaakgvaAYMKSEDPLFVLEH-SLPIDTQYYLEQQ 959
Cdd:cd05537 290 RKRLRRPLSEYtKNVPPHVQAA---RLADQ-INRELGRPRQYQWI-------EYVITVNGPEPLEYrTSPLDYQHYIDKQ 358
|
410
....*....|...
gi 254587977 960 L---AKPLLRIFE 969
Cdd:cd05537 359 LkpiADSILPFLG 371
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
577-974 |
8.21e-31 |
|
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: 125.15 E-value: 8.21e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 577 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTllrpgaaqkLGLKPDEFIKTPTGDEFVKSSvRKGLLPQ 656
Cdd:cd05531 3 LADRGGLVFQPEPGLYE-NVAQIDFSSMYPSIIVKYNISPET---------INCRCCECRDHVYLGHRICLK-RRGFLPE 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 657 ILENLLSARKRAKAELAQETDPlrrqvlDGRQLALKVSANSVYGFTG---AQVGKLPCLEisqSVTGFGRQMIEKTKQLV 733
Cdd:cd05531 72 VLEPLLERRLEYKRLKKEEDPY------AGRQKALKWILVTSFGYLGyknAKFGRIEVHE---AITAYGRKILLRAKEIA 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 734 EskytvENGYdanaKVVYGDTDSVMCRFGVSSVAEAMSLGREAAnwvsshfpspIRLEFEKVY-FPYLLISK------KR 806
Cdd:cd05531 143 E-----EMGF----RVLHGIVDSLWIQGRGDIEELAREIEERTG----------IPLKLEGHYdWIVFLPERdglgapNR 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 807 YAGLLFSsrsdahDKMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPD---GAVAHAKDVIS--DLLCNRIDISQLVI 881
Cdd:cd05531 204 YFGRLSD------GEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEellKLREEALDLFRryLQRLREGDLEDLII 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 882 TKELTRAAADYAGKQAHVelAERMRKRdpGSAPSLGDRVPYVIIGAAKGVAaymksedplfVLEHSLPIDTQYYLEQqla 961
Cdd:cd05531 278 EKKISKRSSEYKVLASTA--LKALRAK--GVSVVPGMKIEYIVRDGKRPVP----------DLGNDEGYDTKYYREL--- 340
|
410
....*....|...
gi 254587977 962 kpLLRIFEPILGE 974
Cdd:cd05531 341 --LERAAEELLFP 351
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
1010-1080 |
4.33e-30 |
|
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: 113.62 E-value: 4.33e-30
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 254587977 1010 CIGCRSVidhQGAVCKFCQPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMR 1080
Cdd:pfam14260 1 CLGCGAP---EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYMR 68
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
579-931 |
9.73e-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: 116.30 E-value: 9.73e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 579 YTGATVIEPLKG-YYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPgaaqklglkPDEFIKTPTGDefVKSSV---RKGLL 654
Cdd:cd05530 13 YRGAIVLEPPPGiFFNV--VVLDFASLYPSIIKVWNLSYETVNCP---------HCECKTNEVPE--VGHWVckkRPGIT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 655 PQILENLLSAR-----KRAKAelaQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKT 729
Cdd:cd05530 80 SQIIGLLRDLRvkiykKKAKD---KSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITST 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 730 kqlveSKYTVENGYdanaKVVYGDTDSVMCRFGVSSVAEamslgrEAANWVSSHFpsPIRLEFEKVYfPYLLIS--KKRY 807
Cdd:cd05530 157 -----IKKARELGL----KVLYGDTDSLFLWNPPQEQLE------DLVEWVEKEL--GLDLELDKEY-RYVVFSglKKNY 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 808 AGLLFSSrsdahdKMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDgAVAHAKDVISDL-------LCNR-IDISQL 879
Cdd:cd05530 219 LGVTKDG------SVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPE-DFEKAREKIRDIvkgvykrLKKKeYTLDQL 291
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|...
gi 254587977 880 VITKELTRAAADYA-GKQAHVELAERMRKRdpGSAPSLGDRVPYVIIGAAKGV 931
Cdd:cd05530 292 AFKVMLSKPPEEYTkNTPQHVKAARQLEKY--GRNVEAGDIISYVKVKGKEGV 342
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
466-836 |
5.74e-27 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 118.97 E-value: 5.74e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 466 KLRSYTLNAV-SFHFLGEQKEDVQhsiITDL-QNGNEQTRRRLAVYCLKDAFLPLRLLERLMVlvnnveMARVTGVPLGY 543
Cdd:PHA03036 418 KVICKNNYIPgDTYTLSFGKDDVD---LSDMyKNYNLEIALEMARYCIHDACLCKYLWEYYGI------ETKIDAGASTY 488
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 544 LLTRGQQVKVVS------QLLRQAMRQGLLMPVVKTEGSEDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYT 617
Cdd:PHA03036 489 LLPQSMVFEYRAstlikgPLLKLLLEEKTILVRSETKNKFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPE 568
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 618 TLL----------RPGAAQKL--GLKPDEFIK---TPTGDEFVkSSV------RKGLLPQILENLLSARKRAKAELAQET 676
Cdd:PHA03036 569 TLVgvvvndnrleAEINKQELrrKYPYPRYIYvhcEPRSPDLV-SEIavfdrrIEGIIPKLLKTFLEERARYKKLLKEAT 647
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 677 DPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYtVENG-------------- 742
Cdd:PHA03036 648 SSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKYLNSVLNGSK-LINGklilancpinpffk 726
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 743 --------YDANA--------KVVYGDTDSVMCRFGVSSVAEAMSLGREAANWVSSH-FPSPIRLEFEKVYFPYLLISKK 805
Cdd:PHA03036 727 ddrsidtnYDTNLpveynftfRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINEKvLFDNFKIEFEAVYKNLIMQSKK 806
|
410 420 430
....*....|....*....|....*....|...
gi 254587977 806 RYAGLLFSSRSDAHD--KMDCKGLEAVRRDNCP 836
Cdd:PHA03036 807 KYTTLKYIASSTDGSvpERVNKGTSETRRDVSK 839
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
595-966 |
2.46e-25 |
|
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: 108.73 E-value: 2.46e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 595 PIATLDFSSLYPSIMMAHNLCyttllrpgaaqklglkpdefiktPTGDEFvkssvrkGLLPQILENLLSARKRAKAELAQ 674
Cdd:cd05538 18 PIVHADVASLYPSIMLAYRIC-----------------------PARDSL-------GIFLALLKYLVELRLAAKESARA 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 675 ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKytvengydaNAKVVYGDT 754
Cdd:cd05538 68 AARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRR---------GATPVEVDT 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 755 DSVMcrFGVSSVAEAMSLGREAANWVSSHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSsrsdahDKMDCKGLEAVRRDN 834
Cdd:cd05538 139 DGIY--FIPPNGVDTEDEEEELVRELSSTLPKGITVEFDGRYRAMFSYKIKNYALLDYD------GKLIVKGSAFRSRGI 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 835 CPLVANLVTSSLRRILVDrdpDGAVAHA--KDVISDLLCNRIDISQLVITKELTRAAADY-----AGKQAHVELAERMRK 907
Cdd:cd05538 211 EPFLREFLREAVRLLLQG---DGAGVHDlyEDYLRRLRSHELPISDLARTETLKESPEEYlqkvrAGKRNPAAAYEIALA 287
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 254587977 908 RDPGSAPslGDRVPYVIIGAAKGVAAYMK-SEDPLFVLEHSLpIDTQYYLEQ--QLAKPLLR 966
Cdd:cd05538 288 RPREWRA--GDRVTYYVSGTGKGVSVYENcRLVADYDPAHPD-ENTGFYAERllQLAARLLP 346
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
267-729 |
1.39e-24 |
|
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: 111.30 E-value: 1.39e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 267 PAGKYVRRAEKKATLCQLEVDVLWSDVISHPPEGQWQRIAPLRVLSFDIEC--AGRKGIFP--EPERDPVIQI----CSL 338
Cdd:TIGR00592 157 DIVKKAIPVSTRYLLEKILIPVPLKRAEFAGGDVQMEGDPELKLASFDIETyfHDGKDFFPgdENPADEEIMIsttpVIA 236
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 339 GLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWADFILAMDPDVITGYNIQNFDLPYLISRAQ-----ALKV 413
Cdd:TIGR00592 237 KQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLADRQVfqfywDAYE 316
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 414 DRFPFLGRVTGL-RSNIRDSSFQSRQVGRRDSKVISMVGRVQMDMLQVLLREHKLRSYTLNAVSFHFLGEQKEDVQHSII 492
Cdd:TIGR00592 317 DPAEKLGVVLLFgRDVDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPI 396
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 493 TDLQNGNEQTrrRLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTGVPLGYLLTRGQQVKVVsqLLRQAMRQGLLMPVVK 572
Cdd:TIGR00592 397 AKKYEFEAPD--IDAPYSSEYLEVTYELGKEFAPMEALPSDLKGQTFWHVFGSNTGNLERFL--LLRKIKGPCWLAVKGP 472
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 573 TEGS------EDYTGATVIEPL--KGYY--DVPIATLDFS--SLYPSIMMAHNLCYT-TLLRPGAAQKLGLKPDEFIKTP 639
Cdd:TIGR00592 473 DELEyprrswCKYEGGYVKPPNveKGLDktPPPLVVLDFSmkSLNPSIIRNEIVSIPdTLHREFALDKPPPEPPYDVHPC 552
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 640 TGDEFVKSSVR-------KGLLPQILENLLSARKRAKAELA--QETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLP 710
Cdd:TIGR00592 553 VGTRPKDCSFPldlkgefPGKKPSLVEDLATERALIKKFMAkvKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIG 632
|
490
....*....|....*....
gi 254587977 711 CLEISQSvtgFGRQMIEKT 729
Cdd:TIGR00592 633 RLRRSPK---FGRRFGERT 648
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
308-850 |
1.15e-23 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 108.24 E-value: 1.15e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 308 LRVLSFDIECAGRKGiFPEPERDPViQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQ----------SYEREEDLLQ 377
Cdd:PHA02528 106 IRIANLDIEVTAEDG-FPDPEEAKY-EIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPqeildkvvymPFDTEREMLL 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 378 AWADFILAMDPDVITGYNIQNFDLPYLISRaqalkvdrfpfLGRVTGLRSNIRDSSFQSRQV-------GRRDSKvISMV 450
Cdd:PHA02528 184 EYINFWEENTPVIFTGWNVELFDVPYIINR-----------IKNILGEKTAKRLSPWGKVKErtienmyGREEIA-YDIS 251
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 451 GRVQMDMLQVllreHK------LRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNEQtrrRLAVYCLKDAFLPLRLLER- 523
Cdd:PHA02528 252 GISILDYLDL----YKkftftnQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQ---KYIEYNIIDVELVDRLDDKr 324
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 524 -LMVLVnnVEMARVTGVPLGYLLTrgqQVKVVSQLLRQAMR-QGLLMPVVKTEGSEDYTGATVIEPLKGYYDVpIATLDF 601
Cdd:PHA02528 325 kLIELV--LSMAYYAKINFEDVFS---PIKTWDAIIFNSLKeEKIVIPENKSHKKQKYAGAFVKEPVPGAYRW-VVSFDL 398
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 602 SSLYPSIMMAHNLCYTTLL--RPGA------AQKLGLKPDEFIKTPTGDEFVKSsvRKGLLPQILENLLSARKRAK---- 669
Cdd:PHA02528 399 TSLYPSIIRQVNISPETIAgtFHVApvheyiNKTAPRPSDEYSCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIYKkkml 476
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 670 -----AELAQET----------------------------DPLRRQVLDGR--------------QLALKVSANSVYGFT 702
Cdd:PHA02528 477 aaernAELIKTIledlndsvdtpidvdyyfdfsdefkaelKTLTKSSLKALleecekeialcntiQMARKILINSLYGAL 556
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 703 GAQVGKLPCLEISQSVTGFGRQMIektkQLVESKYtveNGY-------DANAKVVYGDTDSVMCRFG--VSSVAEAMSlg 773
Cdd:PHA02528 557 GNEHFRYYDLRNAEAITLFGQLAI----QWIERKM---NEYlnklcktEDEDYVIYGDTDSIYVNLDplVEKVGEDKF-- 627
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 774 REAANWVSshFPSPI-RLEFEKV----------YF----------------PYLLISKKRYAGLLFSSRSD--AHDKMDC 824
Cdd:PHA02528 628 KDTNHWVD--FLDKFcKERMEPYidssyrelceYMnnyehlmfmdreaiagPGFWTAKKRYALNVWDSEGTryAEPKLKI 705
|
650 660
....*....|....*....|....*.
gi 254587977 825 KGLEAVRRDNCPLVANLVTSSLRRIL 850
Cdd:PHA02528 706 MGIETQRSSTPKAVQKALKEAIRRIL 731
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
308-524 |
6.44e-23 |
|
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: 97.43 E-value: 6.44e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 308 LRVLSFDIECAGRKGIfPEPERDPVIQI--CSLG----LRW-GEPEPFlrlaltlrpcapilgakVQSYEREEDLLQAWA 380
Cdd:cd05780 3 LKILSFDIEVLNHEGE-PNPEKDPIIMIsfADEGgnkvITWkKFDLPF-----------------VEVVKTEKEMIKRFI 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 381 DFILAMDPDVITGYNIQNFDLPYLISRAQALKVDrFPfLGRvtglrsniRDSSFQSRQVGRRDSKVISmvGRVQMDMLQV 460
Cdd:cd05780 65 EIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIE-LD-LGR--------DGSEIKIQRGGFNNASEIK--GRIHVDLYPV 132
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 254587977 461 LLREHKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNEQtRRRLAVYCLKDAFLPLRLLERL 524
Cdd:cd05780 133 ARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGEN-LERLFRYSMEDAKYTYEIGKEF 195
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
308-522 |
1.07e-22 |
|
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: 98.08 E-value: 1.07e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 308 LRVLSFDIECAGRKGIFPEPERDPVIQIC----------------SLGLRWGEPEPFLRLALTLRPCapiLGAKVQSYER 371
Cdd:cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFycidddvspfildankVGVIIVDELKSNASNGRIRSGL---SGIPVEVVES 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 372 EEDLLQAWADFILAMDPDVITGYNIQNFDLPYLISRAQALKVDRFPF-LGRV-TGLRSNIRDSsfqSRQVGRRDSKVISM 449
Cdd:cd05778 81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDeISRVpSDSNGKFGDR---DDEWGYTHTSGIKI 157
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 254587977 450 VGRVQMDMLQVLLREHKLRSYTLNAVSFHFLGEQKEDVQHSIITD-LQNGNEQTRRRLAVYCLKDAFLPLRLLE 522
Cdd:cd05778 158 VGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEwYKSGSASERWRVLEYYLKRVRLNLEILD 231
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
307-481 |
5.45e-18 |
|
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: 83.14 E-value: 5.45e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 307 PLRVLSFDIECAGRKGiFPEPERDPVIQIcSLGLRWGEPEPFLrlaltlrpcapilgakvQSYEREEDLLQAWADFILAM 386
Cdd:cd05781 2 DLKTLAFDIEVYSKYG-TPNPRRDPIIVI-SLATSNGDVEFIL-----------------AEGLDDRKIIREFVKYVKEY 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 387 DPDVITGYNIQNFDLPYLISRAQALkvdrfpflgrvtglrsNIRdssfqsRQVGRRDSKV--------ISMVGRVQMDML 458
Cdd:cd05781 63 DPDIIVGYNSNAFDWPYLVERARVL----------------GVK------LDVGRRGGSEpstgvyghYSITGRLNVDLY 120
|
170 180
....*....|....*....|...
gi 254587977 459 QVLLREHKLRSYTLNAVSfHFLG 481
Cdd:cd05781 121 DFAEEIPEVKVKTLENVA-EYLG 142
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
307-522 |
1.01e-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: 82.62 E-value: 1.01e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 307 PLRVLSFDIECagrkgifpeperDPVIQICSLGLrWGEPEpflRLALTLRPCAPILGAKVQSYEREEDLLQAWADFILAM 386
Cdd:cd05784 2 KLKVVSLDIET------------SMDGELYSIGL-YGEGQ---ERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQY 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 387 DPDVITGYNIQNFDLPYLISRAQALkvdRFPF-LGRvTGLRSNIRDSSFQsrQVGRrdskvISMVGRVQMDMLQvLLRE- 464
Cdd:cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAH---GLPLrLGR-GGSPLNWRQSGKP--GQGF-----LSLPGRVVLDGID-ALKTa 133
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 254587977 465 -HKLRSYTLNAVSFHFLGEQKedvqhsIITDLQN-GNEQTRR------RLAVYCLKDAFLPLRLLE 522
Cdd:cd05784 134 tYHFESFSLENVAQELLGEGK------LIHDVDDrGAEIERLfredklALARYNLQDCELVWRIFE 193
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
305-520 |
3.18e-15 |
|
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: 75.43 E-value: 3.18e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 305 IAPLRVLSFDIEC-AGRKGIFPEPERD--PVIQIC---SLGLRwgepepflRLALTLRPCAPIL------GAKVQSYERE 372
Cdd:cd05783 2 IPKLKRIAIDIEVyTPIKGRIPDPKTAeyPVISVAlagSDGLK--------RVLVLKREGVEGLegllpeGAEVEFFDSE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 373 EDLLQAWADFILAMdPDVITgYNIQNFDLPYLISRAQALkvdrfpflgrvtGLRSNIRDSSFqsrqvgRRDSkvISMVGR 452
Cdd:cd05783 74 KELIREAFKIISEY-PIVLT-FNGDNFDLPYLYNRALKL------------GIPKEEIPIYL------KRDY--ATLKHG 131
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 254587977 453 VQMDM--------LQVLLREHKLRSYTLNAVSFHFLGEQKEDVQHSIitdlqngNEQTRRRLAVYCLKDAFLPLRL 520
Cdd:cd05783 132 IHIDLykffsnraIQVYAFGNKYREYTLDAVAKALLGEGKVELEKNI-------SELNLYELAEYNYRDAELTLEL 200
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
364-759 |
3.82e-15 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 80.67 E-value: 3.82e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 364 AKVQSYEREEDLLQAWADFIL----AMDPDVITGYNIQNFDLPYLISRAQALKvDRFPFLGRVTGLRSNIRDS------- 432
Cdd:PHA03334 370 FKQRPHPLTKALMEAWEAFLSkdpqLVPAQLLFGSDILNSNYLELLDVIESHK-AQFKATCRKAAARKEEIGSymktrdt 448
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 433 --SFQSRQVGRRDSKVISMvGRVQMDMLQVLLR---EHKLRSYTLNAVSFHFLGEQK-----------EDVQHSIITDLQ 496
Cdd:PHA03334 449 vqDFNDNDKKYLNSTSHGF-GAHIIDLMRVCNTksiKAKCSSRKLDTVARLIISKSKphknppkigkmDDVKYTEMDGMF 527
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 497 NGNEQTRRRLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTgVPLGYL-LTRG--------QQVKVVS-QLLRQAMRQGL 566
Cdd:PHA03334 528 TAGGAALARYLIYNLVDSELLIRIAKNLDPVIEFLNRLRAT-YNIDYVaHGRGvmnfcgfvQSTKSVEvPLLKARLRIGI 606
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 567 LMPVVKTEGS----EDYT----------GATVIEPLKGY-----YDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQK 627
Cdd:PHA03334 607 FVATGRIAESlcmpEKYArdcrqkiklkGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIVDPDCTAR 686
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 628 L-------------GLKPDEFIKTPTGDEFVKSSVRKglLPQI----LENLLSARKRAKAELAQETDPLRRQVLDGRQLA 690
Cdd:PHA03334 687 VrgwvvfdwkkidrGFGKATLMYTILRTKPEEPSWRR--FTTYttssLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNE 764
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 254587977 691 LKVSANSVYGftgaqVGKLPCleiSQSVTGFGRQMIektkQLVESKYTVENGYdanaKVVYGDTDSVMC 759
Cdd:PHA03334 765 MKICANSHYG-----VAPHAC---QHLITTLGRHKI----KLVEEFIKKEPGM----TVNYGDTDSVMF 817
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
325-527 |
4.73e-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: 73.03 E-value: 4.73e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 325 PEPERDPVIQICSLGL---RWGEPEPFLRLALTLRPcapilgaKVQSYEREEDLLQAWADFILAMDPDVITGYNIQNFDL 401
Cdd:cd05776 39 PTPPPPFQSHTCTLTRplgRSPPPDLFEKNAKKKKT-------KVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDL 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 402 PYLISRAQALKVDRFPFLGRV--TGLRSNIRDSSFQSRQVgrrdskvisMVGRVQMDMlQVLLRE-HKLRSYTLNAVSFH 478
Cdd:cd05776 112 DVLLSRIQELKVPHWSRIGRLkrSVWPKKKGGGKFGEREL---------TAGRLLCDT-YLSAKElIRCKSYDLTELSQQ 181
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 254587977 479 FLGEQKEDVqhsIITDLQNGNEQTRR--RLAVYCLKDAFLPLRLLERLMVL 527
Cdd:cd05776 182 VLGIERQDI---DPEEILNMYNDSESllKLLEHTEKDAYLILQLMFKLNIL 229
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
308-507 |
1.51e-13 |
|
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: 70.90 E-value: 1.51e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 308 LRVLSFDIECAGRKGIF---PEPERDPVIQIcslGLRwgEPEPFlRLALTLRPCApilgakvqsyerEEDLLQAWADFIL 384
Cdd:cd05785 9 LRRLQLDIETYSLPGFFfsnPDRGDDRIIIV---ALR--DNRGW-EEVLHAEDAA------------EKELLEELVAIIR 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 385 AMDPDVITGYNIQNFDLPYLISRAQALKVdrfPF-LGRVtGLRSNIRDSSFqsrQVGRR--DSKVISMVGRVQMDMLQVL 461
Cdd:cd05785 71 ERDPDVIEGHNIFRFDLPYLRRRCRRHGV---PLaIGRD-GSIPRQRPSRF---RFAERliDYPRYDIPGRHVIDTYFLV 143
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 254587977 462 LR----EHKLRSYTLNAVSFHF--LGEQKEDVQHSIITDLQNGNEQTRRRLA 507
Cdd:cd05785 144 QLfdvsSRDLPSYGLKAVAKHFglASPDRTYIDGRQIAEVWRSDPARLLAYA 195
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
369-669 |
4.33e-07 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 53.85 E-value: 4.33e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 369 YEREEDLLQAWADFILAMDPDVITGYNIQNFDLPYLISRAQALkvdrfpfLGRvtglrsnirDSSFQSRQVGRRDSKVIS 448
Cdd:PHA02524 177 FEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNI-------LGE---------KAANQLSPYGKITSKTIT 240
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 449 MV----------GRVQMDMLQVLLREH--KLRSYTLNAVSFHFLGEQKEDVQHSIiTDLQNGNEQtrrRLAVYCLKDAFL 516
Cdd:PHA02524 241 NLygekiiykihGIALMDYMDVFKKFSftPMPDYKLGNVGYREVKADKLDYEGPI-NKFRKADHQ---RYVDYCVRDTDI 316
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 517 PLRLLERLMVLVNNVEMARVTGVPLGYLLTrgqQVKVVSQLLRQAM-RQGLLMPVVKTEGSEDYTGATVIEPLKGYYDVP 595
Cdd:PHA02524 317 ILLIDGRRCFIDLILSLSYYAKIRFDDVLG---TIKVWDSIIFNSLvESNVVIPAMKASPKQSFPGAYVKEPVPGGYRYG 393
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 596 IaTLDFSSLYPSIMMAHNLC---YTTLLRPGAAQ----KLGLKP-DEFIKTPTGDEFVKSSVrkGLLPQILENLLSARKR 667
Cdd:PHA02524 394 L-SFDLTSLYPSILRLLNISpemIAGMFSPARLEdyinKVAPKPsDQFSCAPNGMMYKKGVV--GVLPNETEKVFLQRKS 470
|
..
gi 254587977 668 AK 669
Cdd:PHA02524 471 EK 472
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
307-514 |
4.25e-06 |
|
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: 48.80 E-value: 4.25e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 307 PLRVLSFDIECAGRKGIFPEPERDPVIQIcSLGLrwgEPEPFLrlaLTLRPcapILGAKVQSYE---------------- 370
Cdd:cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMI-SYMI---DGQGYL---IVNRE---IVSEDIEDFEytpkpeyegpfkvfne 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254587977 371 -REEDLLQAWADFILAMDPDVITGYNIQNFDLPYLISRAQALKVDrfpfLGRVTGLRSNIRDsSFQSRQVgrrdskvism 449
Cdd:cd05779 71 pDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLS----MEEEIGFRKDSEG-EYKSRYI---------- 135
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 254587977 450 vgrVQMDMLQVLLREHKLR--SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNEQTrrrLAVYCLKDA 514
Cdd:cd05779 136 ---IHMDCFRWVKRDSYLPqgSQGLKAVTKAKLGYDPVELDPEDMVPLAREDPQT---LASYSVSDA 196
|
|
| |
