|
Name |
Accession |
Description |
Interval |
E-value |
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
80-1096 |
0e+00 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 1506.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 80 PLALDPSTEPLIFQQLEIDHYVGTSPPLPEGPPASRN----SVPILRAFGVTDEGFSVCCHIHGFAPYFYTPAPPGFGAE 155
Cdd:PTZ00166 32 PLPPISLQKDLVFFQLDADYTEKDDKSQGNPHNTVSGvrhvEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPE 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 156 HLSELQRELNAAISRDQRGGKELSgpAVLAIELCSRESMFGYHGHGPSPFLRITLALPRLMAPARRLLEQGIRVPGL--- 232
Cdd:PTZ00166 112 DSQKLKRELNAQLSEQSQFKKYQN--TVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVCGGgwd 189
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 233 GTPSFAPYEANVDFEIRFMVDADIVGCNWLELPAGKYVRRAEKKAT-LCQLEVDVLWSDVISHPPEGQWQRIAPLRVLSF 311
Cdd:PTZ00166 190 GIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKTsTCQIEVDCSYEDLIPLPPEGEYLTIAPLRILSF 269
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 312 DIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEREEDLLQAWATFILAMDPDVI 389
Cdd:PTZ00166 270 DIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDPDFL 349
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 390 TGYNIQNFDLPYLISRAQTLKVDRFPFLGRVTGLRSNIRDSSFQSRQVGRRDSKVVSMVGRVQMDMLQVLLREYKLRSYT 469
Cdd:PTZ00166 350 TGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLKSYS 429
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 470 LNAVSFHFLGEQKEDVQHSIITDLQNGNEQTRRRLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTGVPLGYLLSRGQQV 549
Cdd:PTZ00166 430 LNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQI 509
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 550 KVVSQLLRQAMRQGLLMPVVKTEGG---EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKl 626
Cdd:PTZ00166 510 KVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDANN- 588
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 627 gLKPDEFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAQETDPLRRQVLDGRQLALKVSANSVYGFTGAQV-G 705
Cdd:PTZ00166 589 -YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQVgG 667
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 706 KLPCLEISQSVTGFGRQMIEKTKQLVETKYTLENGYDANAKVVYGDTDSVMCRFGVSSVAEAMSLGREAANWVSSHFPSP 785
Cdd:PTZ00166 668 QLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFLKP 747
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 786 IRLEFEKVYFPYLLISKKRYAGLLFsSRSDAHDRMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVAHAKDVIS 865
Cdd:PTZ00166 748 IKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKIS 826
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 866 DLLCNRIDISQLVITKELTRaaADYAGKQAHVELAERMRKRDPGSAPNLGDRVPYVIIGAAKGVAAYMKSEDPLFVLEHS 945
Cdd:PTZ00166 827 DLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVLENN 904
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 946 LPIDTQYYLEqQLAKPLLRIFEPILGEgraESVLLRGDHTRCKTVLTSKVGGLLAFTKRRNSCIGCRSVIDhQGAVCKFC 1025
Cdd:PTZ00166 905 IPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIK-EGALCDNC 979
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564328246 1026 -QPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQERLLQRFG 1096
Cdd:PTZ00166 980 nQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
575-970 |
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: 826.13 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 575 EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLglKPDEFIKTPTGDEFVKASVRKGLLPQ 654
Cdd:cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKL--PPEDYIKTPNGDYFVKSSVRKGLLPE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 655 ILENLLSARKRAKAELAQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVETK 734
Cdd:cd05533 79 ILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 735 YTLENGYDANAKVVYGDTDSVMCRFGVSSVAEAMSLGREAANWVSSHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRS 814
Cdd:cd05533 159 YTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLW-TNP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 815 DAHDRMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVAHAKDVISDLLCNRIDISQLVITKELTRAAADYAGKQ 894
Cdd:cd05533 238 DKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADDYAGKQ 317
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564328246 895 AHVELAERMRKRDPGSAPNLGDRVPYVIIGAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPIL 970
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 ... |
537-969 |
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: 572.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 537 VPLGYLLSRGQQVKVVSQLLRQAMRQGLLMPVVKTEGG--EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 614
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGdeDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 615 TTLLRPGAAQKlGLKPDE----FIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAQETDPLRRQVLDGRQLALK 690
Cdd:pfam00136 81 TTLVRSVDEAN-NLPPEDnlitVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLALK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 691 VSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVETKYTlengydANAKVVYGDTDSVMCRFGVSSVAEAMSL 770
Cdd:pfam00136 160 ITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT------YNFRVIYGDTDSVFIEFGGKDVEEAMKI 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 771 GREAANWVSSH-FPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRSDAHDRMDCKGLEAVRRDNCPLVANLVTSSLRRILV 849
Cdd:pfam00136 234 GDELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKY-TAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLS 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 850 DRDPDGAVAHAKDVI----SDLLCNRIDISQLVITKELTRAAADYAGKQ-AHVELAERMRKRDpGSAPNLGDRVPYVIIG 924
Cdd:pfam00136 313 DRGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEVALRMNKRN-GEAPEVGDRIPYVIVK 391
|
410 420 430 440
....*....|....*....|....*....|....*....|....*...
gi 564328246 925 AAK---GVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 969
Cdd:pfam00136 392 AAKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
119-969 |
2.27e-176 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 536.72 E-value: 2.27e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 119 PILRAFGVTDEGFSVCCHIHGFAPYFYTPAPpgfgaehlselQRELNAAISRDQRGgkelsgpaVLAIELCSRESMFGyh 198
Cdd:COG0417 19 PVIELWGRTEDGPSVLLDVTGFRPYFYVPLP-----------DEEKLEELLRDIKE--------ITEVEPVKLKSFFG-- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 199 ghGPSPFLRITLALPRLMAPAR-RLLEQGIRVpglgtpsfapYEANVDFEIRFMVDADIVGCNWLELPAGKYVRRAEKKa 277
Cdd:COG0417 78 --EPVPVLKIYTRDPRDVRELRdRLKEGGIDV----------YEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKLDYE- 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 278 tlcqlevdvlwsdVISHPPEGQWQRIAPLRVLSFDIECAGRKGiFPEPERD-PVIQICSlglrwgEPEPFLRLALTLRpc 356
Cdd:COG0417 145 -------------VKENPRLKPEDYRPKLKVLSFDIEVSTPRG-FPDPERDgPIISIGL------AGSDGEKKVLMLG-- 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 357 APILGAKVQSYEREEDLLQAWATFILAMDPDVITGYNIQNFDLPYLISRAQTLKVdrfPF-LGRVtGLRSNIRDSSFQSR 435
Cdd:COG0417 203 REGVDFEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAERLGI---PLdLGRD-GSEPSWREHGGQGF 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 436 qvgrrdskvVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQngnEQTRRRLAVYCLKDAFL 514
Cdd:COG0417 279 ---------ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKLIVDGGEIERLW---DDDKPALAEYNLRDAEL 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 515 PLRLLERLMVLVNNVEMARVTGVPLgYLLSRGQQVKVVSQL-LRQAMRQGLLMPVVKTEGGEDYTGATVIEPLKGYYDvP 593
Cdd:COG0417 347 TLRIFEKTLLLPFLIELSRITGLPL-DDVGRAGSSAAFENLlLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGLYE-N 424
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 594 IATLDFSSLYPSIMMAHNLCYTTLLRPGAAqklglKPDEFIKTPT-GDEFVKAsvRKGLLPQILENLLSARKRAKAELAQ 672
Cdd:COG0417 425 VLVLDFKSLYPSIIRTFNISPETLVEGGEE-----PCGDEDVAPGfGHRFCRE--PKGILPSILEELWDERDEAKKKMKK 497
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 673 -ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEtkytlENGYdanaKVVYGD 751
Cdd:COG0417 498 aKPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAE-----ELGY----KVIYGD 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 752 TDSVMCRFGVSSVAEAMSLGREAANWVSSHFPSPIRLEFEKVYFPYLLI-SKKRYAGLLfssrsdAHDRMDCKGLEAVRR 830
Cdd:COG0417 569 TDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPgSKKRYAGLT------EDGKIDIKGLEAVRS 642
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 831 DNCPLVANLVTSSLRRILVDRDPDGAVAHAKDVISDLLCNRIDISQLVITKELTRAAADY-AGKQAHVELAERMRKRdpG 909
Cdd:COG0417 643 DWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYeKNVPPHVRAARKLDER--G 720
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 910 SAPNLGDRVPYVIIGAAKGVaaymksEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 969
Cdd:COG0417 721 RPYQRGDKISYVITKGGGRV------EPVELAKERESEIDYDYYIEKQLKPTADRILEAF 774
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
300-529 |
9.80e-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: 446.25 E-value: 9.80e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 300 WQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWAT 379
Cdd:cd05777 1 WSKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 380 FILAMDPDVITGYNIQNFDLPYLISRAQTLKVDRFPFLGRVTGLRSNIRDSSFQSRQVGRRDSKVVSMVGRVQMDMLQVL 459
Cdd:cd05777 81 FVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVI 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 460 LREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNEQTRRRLAVYCLKDAFLPLRLLERLMVLVNNV 529
Cdd:cd05777 161 QRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLVNYI 230
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
305-760 |
1.74e-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: 452.76 E-value: 1.74e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 305 PLRVLSFDIECAGRKGIFPEPE--RDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWATFIL 382
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 383 AMDPDVITGYNIQNFDLPYLISRAQTLKVDRFPFLGRVT-GLRSNIRDSSFQSRQVGRRDSKVVsMVGRVQMDMLQVLLR 461
Cdd:smart00486 82 KYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKiGLRIPNKKPLFGSKSFGLSDIKVY-IKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 462 EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNEQTRRRLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTGVPLGY 541
Cdd:smart00486 161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 542 LLSRGQQVKVVSQLLRQAMRQGLLMPVVKTEGG----------EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHN 611
Cdd:smart00486 241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 612 LCYTTLLRPGAAQKLGL----KPDEFIKTPTG--DEFVKASVRKGLLPQILENLLSARKRAKAELAQETDPL--RRQVLD 683
Cdd:smart00486 321 LCYSTLVGVGEVVIKGDliipEDLLTIKYEKGnkYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESeeLKKLLD 400
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564328246 684 GRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEtkytlENGYDA-NAKVVYGDTDSVMCRFG 760
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIE-----ENGYPKpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
119-971 |
2.32e-110 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 362.25 E-value: 2.32e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 119 PILRAFGVTDEGFSVCCHIHGFAPYFYTpappgfgAEHLSELQRELNAAISRDQR--GGKELSGPAVLAIelcsresmfg 196
Cdd:PRK05762 20 PEVELWLATDEGPRVVLLDPQFRPYFIP-------AEQDERAESLLAGEIGVRLSplALKDFHRRPVLGL---------- 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 197 yhghgPSPFLRITLALPRlmaparRLLEQGIRVpglgtpsfapYEANVDFEIRFMVDADIVGCNWLElpaGKYVRRAEK- 275
Cdd:PRK05762 83 -----YCRQHRQLTRLPK------RLREGGVDV----------YEADIRFPERYLMERFITPCVWFS---GEVEQYTTDg 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 276 KATLCQLEVDVLWsdvishPPegqwqriaPLRVLSFDIECAgRKGI-----FPEPERDPVIQIcslglrwGEPEpflrla 350
Cdd:PRK05762 139 VLRNARLKPAPDY------RP--------PLKVVSLDIETS-NKGElysigLEGCGQRPVIML-------GPPN------ 190
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 351 ltlrPCAPILGAKVQSyerEEDLLQAWATFILAMDPDVITGYNIQNFDLPYLISRAQTLKVdrfPF-LGRVTGLRSnIRD 429
Cdd:PRK05762 191 ----GEALDFLEYVAD---EKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGI---PLrLGRDGSELE-WRE 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 430 SSFQSRQVgrrdskVVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEdvqhsIITDLQNGNEQTRR------ 502
Cdd:PRK05762 260 HPFRSGYG------FASVPGRLVLDGIDALKSaTWVFDSFSLEYVSQRLLGEGKA-----IDDPYDRMDEIDRRfaedkp 328
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 503 RLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTGVPLGyllsR--GQQVKVVSQLLRQAMRQGLLMPVVKTEGGEDYTGA 580
Cdd:PRK05762 329 ALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLD----RvgGSVAAFEHLYLPRAHRAGYVAPNLGERPGEASPGG 404
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 581 TVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPgaaqkLGLKPDEFIKTPTGDEFVKasvRKGLLPQILENLL 660
Cdd:PRK05762 405 YVMDSKPGLYD-SVLVLDFKSLYPSIIRTFNIDPDGLVEG-----LAQPPEESVAGFLGARFSR---EKHFLPEIVERLW 475
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 661 SARKRAKAELAQEtdplrrqvldgRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEtkytlENG 740
Cdd:PRK05762 476 EGRDEAKREMNKP-----------LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIE-----AQG 539
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 741 YdanaKVVYGDTDSVMCRFGVS-SVAEAMSLGREAAN----WVSSHF------PSPIRLEFEKVY----FPYLLI----S 801
Cdd:PRK05762 540 Y----QVIYGDTDSTFVWLGGAhDEEDAAKIGRALVQeinqWWQEHLqqefglESALELEFEKHYrrffMPTIRGaeegS 615
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 802 KKRYAGLLfsSRSDAHDRMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVahaKDVISDLLCNRIDiSQLVITK 881
Cdd:PRK05762 616 KKRYAGLI--QEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEPYVDYV---REVIDKLRAGELD-EKLVYRK 689
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 882 ELTRAAADYAGKQA-HV----ELAERMRKRDPGSAPNLGDRVPYVIIGAAKGVAAYMKSedplfvlehslPIDTQYYLEQ 956
Cdd:PRK05762 690 RLRRPLDEYQRNVPpHVraarLADEMGYKVGRPLQYQNGGKIGYVITVNGPEPLEYRKS-----------PIDYDYYIEK 758
|
890
....*....|....*
gi 564328246 957 QLaKPLLRIFEPILG 971
Cdd:PRK05762 759 QL-QPVADRILPFFG 772
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
126-473 |
6.43e-103 |
|
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: 327.07 E-value: 6.43e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 126 VTDEGFSVCCHIHGFAPYFYTPAPPGFGAEHLSELQRELNAAISRdqrggkelsgpaVLAIELCSRESMFGYHGHgPSPF 205
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKELEEVIEEIKELYEGLDK------------IEKIELKLKKSLYGYEED-PVPY 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 206 LRITLALPRLMAPARRLLEQGirvpglgtPSFAPYEANVDFEIRFMVDADIVGCNWLELPagKYVRRAEKKATLCQLEVD 285
Cdd:pfam03104 68 LKVSFANPRPLLKIRKYLSPE--------NISDVYEYDVDYLERFLIDNDIVGFGWYKVK--VYPFRAEGRISNCDVEID 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 286 VLWSDVISHPPEGQWqriAPLRVLSFDIECAGRKGIFPEPER--DPVIQICSLGLRWGEPEPFLRLALTLRPCAPI---- 359
Cdd:pfam03104 138 CDSPDLISVPFEKEW---PPLRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEPRFLFTLRECDSEdied 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 360 ---------LGAKVQSYEREEDLLQAWATFILAMDPDVITGYNIQNFDLPYLISRAQTLKVDRFPFLGRV-TGLRSNIRD 429
Cdd:pfam03104 215 feytpkpiyPGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLnRGGRSKVRE 294
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 564328246 430 SSFqsrqvGRRDSKVVSMVGRVQMDMLQVLLREYKLRSYTLNAV 473
Cdd:pfam03104 295 IGF-----GTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
546-969 |
4.84e-101 |
|
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: 326.48 E-value: 4.84e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 546 GQQVKVVSQLLRQAMRQGLLMP-----VVKTEGGEDYTgATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLL-- 618
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPspsrqQVAQQRALECL-PLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLgr 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 619 ------------------RPGAAQKLGLKPDEFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAQETDPLR-R 679
Cdd:cd05534 80 veelngggkfgflgvklyLPPPPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKlQ 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 680 QVLDGRQLALKVSANSVYGFTGAQV-GKLPCLEISQSVTGFGRQMIEKTKQLVEtkytleNGYDANAKVVYGDTDSVMCR 758
Cdd:cd05534 160 RILDARQLALKLLANVTYGYTAASFsGRMPCVEIADSIVQTGRETLERAIELIE------STPKWGAKVVYGDTDSLFVL 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 759 FGVSSVAEAMSLGREAANWVSSHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSRSDAHDRMDCKGLEAVRRDNCPLVAN 838
Cdd:cd05534 234 LPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQK 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 839 LVTSSLRRILVDRDPDGAVAHAKDVISDLLCNRIDISQLVITKELTRAAADYAGK-QAHVELAERMRKRDPGSAPNLGDR 917
Cdd:cd05534 314 ILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGATlPAGAIVALRRMEKDPRAEPQYGER 393
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|...
gi 564328246 918 VPYVIIGAAKGVAAYMKSEDP-LFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 969
Cdd:cd05534 394 VPYVVVRGEPGSRLIDLVVSPeEFLADPSLRLDAEYYITKQIIPALDRLFNLV 446
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
203-967 |
1.79e-90 |
|
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: 315.84 E-value: 1.79e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 203 SPFLRITLALPRLMAPARRLLEQGIrvpglGTPSFAPYEANVDFEIRFMVDADIVGCNWLElPAGKYVRrAEKKATLCQL 282
Cdd:TIGR00592 413 SEYLEVTYELGKEFAPMEALPSDLK-----GQTFWHVFGSNTGNLERFLLLRKIKGPCWLA-VKGPDEL-EYPRRSWCKY 485
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 283 EVDVLWSDVIShppEGQWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLrlaltlrPCAPILGA 362
Cdd:TIGR00592 486 EGGYVKPPNVE---KGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPY-------DVHPCVGT 555
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 363 KVQSYEREEDL-----------------LQAWATFILAM----DPDVITGYNIQNFDLPYLISRAQTLKVDRFPFLGRVT 421
Cdd:TIGR00592 556 RPKDCSFPLDLkgefpgkkpslvedlatERALIKKFMAKvkkiDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLR 635
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 422 glRSNIRDSSFQSRQVGRrdskvvsMVGRVQMDMLQVLlreyKLRSYTLNAVSFHFLG-EQKEDVQHSIITDLQNGNEQT 500
Cdd:TIGR00592 636 --RSPKFGRRFGERTCGR-------MICDVEISAKELI----RCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLT 702
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 501 RrrLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTGVPLGYLLSRGQQVKVVSQLLRQAMRQGLLMP----VVKTEGGED 576
Cdd:TIGR00592 703 Y--LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqiFRKQQKLGD 780
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 577 ---------------YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLGLKPDefiktptgde 641
Cdd:TIGR00592 781 edeeidgykkgkkaaYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDEDELPELPD---------- 850
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 642 fvkASVRKGLLPQILENLLSARKRAKAELAQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGR 721
Cdd:TIGR00592 851 ---SELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGR 927
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 722 QMIEKTKQLVETKytlengydaNAKVVYGDTDSVMCRFGVSSVAEAMSLGREAANWVSSHFPsPIRLEFEKVYFPYLLIS 801
Cdd:TIGR00592 928 EILEHTRQLVEEM---------NLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-LLELDIDGVFKRLLLLK 997
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 802 KKRYAGLLFSSRSDAH--DRMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVAHAKDVISDL----LCNRIDIS 875
Cdd:TIGR00592 998 KKKYAAIKVEGDSDGNytTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLE 1077
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 876 QLVITKELTRAAADYAGK--QAHVELAERMRKRDpGSAPNLGDRVPYVIIGAAKGVAAYMKS---EDPLFvLEHSLPIDT 950
Cdd:TIGR00592 1078 KFVINKQLTRDPKDYPDGasLPHVHVALRINARG-GRKVKAGDVVSYVICKDGGNLSARQRAyalEELQR-KHNNLIYDT 1155
|
810
....*....|....*..
gi 564328246 951 QYYLEQQLAKPLLRIFE 967
Cdd:TIGR00592 1156 QYYLEHQIHPVVLRILE 1172
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
575-967 |
1.25e-87 |
|
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.
Pssm-ID: 99912 [Multi-domain] Cd Length: 323 Bit Score: 285.42 E-value: 1.25e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 575 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAqklglKPDEFiktPTGDEFVKASVRKGLLPQ 654
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEI-----AAPED---YIGVGFRSPKDRKGLLPR 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 655 ILENLLSARKRAKAE-LAQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEt 733
Cdd:cd00145 72 ILEELLNFRDEAKKRmKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVE- 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 734 kytlengyDANAKVVYGDTDSVMCRFGVS-SVAEAMSLGREAANWVSShfPSPIRLEFEKVYFPYLLISKKRYAGLLFSS 812
Cdd:cd00145 151 --------EHGARVIYGDTDSIFVSLPKMgTKEDAIKEGREILQELAD--EHLLELEFEKVYLPFFLGKKKRYAGLDIWK 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 813 RSDaHDRMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVahaKDVISDLlcnridisqlvitkeltraaadyag 892
Cdd:cd00145 221 GQD-EGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAV---KEYIDEL------------------------- 271
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564328246 893 kqahvelaermrkrdpgsapnlgDRVPYVIIGAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 967
Cdd:cd00145 272 -----------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
577-971 |
5.28e-84 |
|
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: 278.31 E-value: 5.28e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 577 YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPgaaqklglKPDEFIKTPTGDEFvkASVRKGLLPQIL 656
Cdd:cd05532 8 YAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRA--------DPDDEDDEEPPLPP--SDQEKGILPRII 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 657 ENLLSARKRAKAELAQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVETKyt 736
Cdd:cd05532 78 RKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKM-- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 737 lenGYDanakVVYGDTDSVMCRFGVSSVAEAMSLGREAANWVSSHFPSpIRLEFEKVYFPYLLISKKRYAGLLFSSRSDA 816
Cdd:cd05532 156 ---NLE----VIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKK-LEIDIDGVFKRLLLLKKKKYAALKVVDDDKG 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 817 HDRMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAV----AHAKDVISDLLCNRIDISQLVITKELTRAAADYAG 892
Cdd:cd05532 228 KLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVenihEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPD 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 893 K--QAHVELAERMRKRDPGSAPnlGDRVPYVII--GAAKGVA--AYMKSEdplFVLEHSLPIDTQYYLEQQLAKPLLRIF 966
Cdd:cd05532 308 KksLPHVQVALRMNKRGRKVKA--GDTIPYIICkdGSSKSLAdrAYHPDE---VKKNENLKIDIEYYLSQQILPPISRLC 382
|
....*
gi 564328246 967 EPILG 971
Cdd:cd05532 383 EPIEG 387
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
575-967 |
2.95e-77 |
|
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: 258.79 E-value: 2.95e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 575 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGaaqklglKPDEFIKTPTGDEFVKAsvRKGLLPQ 654
Cdd:cd05536 2 ESYEGGIVLEPEKGLHE-NIVVLDFSSLYPSIMIKYNISPDTLVREG-------CEDCDVEPQVGHKFRKD--PPGFIPS 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 655 ILENLLSARKRAKAELAQETDP-LRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEt 733
Cdd:cd05536 72 VLEDLLEERRRIKEKMKKLDPEsEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAE- 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 734 kytlENGYdanaKVVYGDTDSVmcrFGVSSVAEA-MSLGREAANWVSSHFPspIRLEFEKVYFPYLLISKKRYAGLlfss 812
Cdd:cd05536 151 ----EKGF----KVIYGDTDSL---FVKIDGADAvKKKVKKLLKYINEELP--LELEIEKFYKRGFFVTKKRYAGL---- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 813 rsDAHDRMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVAHAKDVISDLLCNRIDISQLVITKELTRAAADYAG 892
Cdd:cd05536 214 --TEDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYKA 291
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564328246 893 KQAHVELAERMRKRdpGSAPNLGDRVPYVIIgaaKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 967
Cdd:cd05536 292 TGPHVAAAKKLAKR--GYKVRPGTKIGYVIV---KGSGKISDRAYPYDMVDEKHKYDAEYYIDNQVLPAVLRILE 361
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
240-971 |
2.74e-64 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 233.81 E-value: 2.74e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 240 YEANVDFEIRFMVDADIVGCNWLELPAGKYVRRAE------KKATLCQLEVDVLWSDVISHPPegqwqriAPLRVLSFDI 313
Cdd:PRK05761 123 WEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEilveeiKKAFKDERKLAEDWLPIFEAPI-------PKIKRIAIDI 195
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 314 ECAGrkgifPEPERDPViqicslglrwgepepflrlaltlrpcapilgakvqsyEREEDLLQAWATFILAMDPDVItgYN 393
Cdd:PRK05761 196 EVYT-----PAKGRIPD-------------------------------------DSEKELLAELFDIILEYPPVVT--FN 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 394 IQNFDLPYLISRAQTLKVDRFPFLGRVTGLRSNIRDSSFQSRqvgrRDSKVVSMVGRvqmdmlqvllreYKLRSYTLNAV 473
Cdd:PRK05761 232 GDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQN----KAVRSYAFYGK------------YRHREARLDAV 295
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 474 SFHFLGEQKEDVQHSIitdlqngNEQTRRRLAVYCLKDAFLPLRLL----ERLMVLVnnVEMARVTGVPLGYLlSRGQQV 549
Cdd:PRK05761 296 GRALLGISKVELETNI-------SELDLEELAEYNFRDAEITLKLTffnnELVLKLI--LLLSRISKLPIEEL-SRATIS 365
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 550 KVVSQLL-RQAMRQGLLMP-----------VVK--TEGGEDYTGATVIEPLKG-YYDVpiATLDFSSLYPSIMMAHNLCY 614
Cdd:PRK05761 366 TWISNLEyWEHRKRGWLIPwkedilrldheVYKkaIIKGKKYRGGLVFQPPPGiFFNV--YVLDFASLYPSIIVKWNLSP 443
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 615 TTLLRPGAAQKLGLKPDEFIKTPTGDefvkasvRKGLLPQILENLLSARKRAKAELAQE--TDPLRRQVLDGRQLALKVS 692
Cdd:PRK05761 444 ETVRIPECKCHYDDEVPELGHSVCDD-------RPGLTSVLVGLLRDFRVKIYKKKAKDpnLDEERRAWYDVVQRALKVF 516
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 693 ANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEtkytlENGYdanaKVVYGDTDSVMCRFGVSSVAEAMslgr 772
Cdd:PRK05761 517 LNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAE-----ELGL----KVLYGDTDSLFVWGPTKESLEEL---- 583
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 773 eaANWVSSHFpsPIRLEFEKVYfPYLLIS--KKRYAGLLFSsrsdahDRMDCKGLEAVRRDNCPLVANLVTSSLRRILVD 850
Cdd:PRK05761 584 --IKEIEERT--GIDLEVDKTY-DWVAFSglKKNYFGVLKD------GKVKIKGIVAKKRNTPEFVKELQREVLEVLKSI 652
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 851 RDPDGAV-------AHAKDVISDLLCNRIDISQLVITKELTRAAADYA-GKQAHVELAERMRKRdpGSAPNLGDRVPYVI 922
Cdd:PRK05761 653 RSPEDVEkvkdeieDVLKRYYEKLRAKDYPLDELAIRVRLSKPLDEYTkNTPQHVKAALQLRDY--GVEVSPGDIISYVK 730
|
730 740 750 760
....*....|....*....|....*....|....*....|....*....
gi 564328246 923 IGAAKGVaaymkseDPLFVLEHSlPIDTQYYLEQqlakpLLRIFEPILG 971
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 ... |
308-520 |
5.86e-52 |
|
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: 181.01 E-value: 5.86e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 308 VLSFDIECAGRKGiFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAP-ILGAKVQSYEREEDLLQAWATFILAMDP 386
Cdd:cd05160 1 VLSFDIETTPPVG-GPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEfIDGIEVEYFADEKELLKRFFDIIREYDP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 387 DVITGYNIQNFDLPYLISRAQTLKVDRFPFLGRvtglRSNIRDSSfqsrqvgrRDSKVVSMVGRVQMDMLQVLLREYKLR 466
Cdd:cd05160 80 DILTGYNIDDFDLPYLLKRAEALGIKLTDGIYR----RSGGEKSS--------GSTERIAVKGRVVFDLLAAYKRDFKLK 147
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 564328246 467 SYTLNAVSFHFLGEQKEDVQHSIITDlqNGNEQTRRRLAVYCLKDAFLPLRLLE 520
Cdd:cd05160 148 SYTLDAVAEELLGEGKEKVDGEIIED--AEWEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
579-967 |
1.42e-44 |
|
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99920 Cd Length: 371 Bit Score: 165.90 E-value: 1.42e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 579 GATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKlglkPDEFIKTPTGDEFvkaSVRKGLLPQILEN 658
Cdd:cd05537 5 GGYVMDSKPGLYK-NVLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPD----PEDLIPGFLGARF---SREKHILPDLIAR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 659 LLSARKRAKaelaQETDPLRRQvldgrqlALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEtkytle 738
Cdd:cd05537 77 LWAARDEAK----REKNAPLSQ-------AIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIE------ 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 739 ngyDANAKVVYGDTDSVMCRFG-VSSVAEAMSLGREAA----NWVSSH------FPSPIRLEFEKVYFPYLLI------- 800
Cdd:cd05537 140 ---QQGYQVIYGDTDSTFVWLGeELDAAEAQAIGKELAsqinQWWAQKlkeefgLESFLEIEFETHYSRFFMPtirgsde 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 801 -SKKRYAGLlfsSRSDAHDRMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDGAVahaKDVISDLLCNRIDiSQLVI 879
Cdd:cd05537 217 gSKKRYAGL---KSTDGGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFI---KETVEELLAGELD-ELLVY 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 880 TKELTRAAADY-AGKQAHVELAermRKRDPgSAPNLGDRVPYVIIgaakgvaAYMKSEDPLFVLEH-SLPIDTQYYLEQQ 957
Cdd:cd05537 290 RKRLRRPLSEYtKNVPPHVQAA---RLADQ-INRELGRPRQYQWI-------EYVITVNGPEPLEYrTSPLDYQHYIDKQ 358
|
410
....*....|...
gi 564328246 958 L---AKPLLRIFE 967
Cdd:cd05537 359 LkpiADSILPFLG 371
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
575-972 |
1.88e-30 |
|
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: 123.99 E-value: 1.88e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 575 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTllrpgaaqkLGLKPDEFIKTPTGDEFVKASvRKGLLPQ 654
Cdd:cd05531 3 LADRGGLVFQPEPGLYE-NVAQIDFSSMYPSIIVKYNISPET---------INCRCCECRDHVYLGHRICLK-RRGFLPE 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 655 ILENLLSARKRAKAELAQETDPlrrqvlDGRQLALKVSANSVYGFTG---AQVGKLPCLEisqSVTGFGRQMIEKTKQLV 731
Cdd:cd05531 72 VLEPLLERRLEYKRLKKEEDPY------AGRQKALKWILVTSFGYLGyknAKFGRIEVHE---AITAYGRKILLRAKEIA 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 732 EtkytlENGYdanaKVVYGDTDSVMCRFGVSSVAEAMSLGREAAnwvsshfpspIRLEFEKVY-FPYLLISK------KR 804
Cdd:cd05531 143 E-----EMGF----RVLHGIVDSLWIQGRGDIEELAREIEERTG----------IPLKLEGHYdWIVFLPERdglgapNR 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 805 YAGLLFSsrsdahDRMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPD---GAVAHAKDVIS--DLLCNRIDISQLVI 879
Cdd:cd05531 204 YFGRLSD------GEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEellKLREEALDLFRryLQRLREGDLEDLII 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 880 TKELTRAAADYAGKQAHVelAERMRKRdpGSAPNLGDRVPYVIIGAAKGVAaymksedplfVLEHSLPIDTQYYLEQqla 959
Cdd:cd05531 278 EKKISKRSSEYKVLASTA--LKALRAK--GVSVVPGMKIEYIVRDGKRPVP----------DLGNDEGYDTKYYREL--- 340
|
410
....*....|...
gi 564328246 960 kpLLRIFEPILGE 972
Cdd:cd05531 341 --LERAAEELLFP 351
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
1008-1078 |
2.74e-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: 114.01 E-value: 2.74e-30
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564328246 1008 CIGCRSVidhQGAVCKFCQPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMR 1078
Cdd:pfam14260 1 CLGCGAP---EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYMR 68
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
309-834 |
1.86e-27 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 120.51 E-value: 1.86e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 309 LSFDIECAGRKGiFPEPERDPV--IQICSLGLRWGEpepfLRLALT--------------LRPCAPILGAKVQSYERE-- 370
Cdd:PHA03036 163 LFLDIECHFDKK-FPSVFINPVshISCCYIDLSGKE----KRFTLInedmlsedeieeavKRGYYEIESLLDMDYSKEli 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 371 ---EDLLQAWATFILAMDPDVITGYNIQNFDLPYLISRAQTLK--------VDRFPFLGRVTGLRSniRDSSFQSRQVGR 439
Cdd:PHA03036 238 lcsEIVLLRIAKKLLELEFDYVVTFNGHNFDLRYISNRLELLTgekiifrsPDGKETVHLCIYERN--LSSHKGVGGVAN 315
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 440 RDSKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVS---FH--------------FLGEQKEDVQ---------------- 486
Cdd:PHA03036 316 TTYHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISknaFNcnakvlsennnevtFIGDNTTDAKgkasifsevlstgnyv 395
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 487 --------------------------------HSIIT--------DLQ----NGNEQTRRRLAVYCLKDAFLPLRLLERL 522
Cdd:PHA03036 396 tindddickildkdiiensftvkvicknnyipGDTYTlsfgkddvDLSdmykNYNLEIALEMARYCIHDACLCKYLWEYY 475
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 523 MVlvnnveMARVTGVPLGYLLSRGQQVKVVS------QLLRQAMRQGLLMPVVKTEGGEDYTGATVIEPLKGYYDVPIAT 596
Cdd:PHA03036 476 GI------ETKIDAGASTYLLPQSMVFEYRAstlikgPLLKLLLEEKTILVRSETKNKFPYEGGKVFAPKQKMFDNNVLI 549
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 597 LDFSSLYPSIMMAHNLCYTTLL----------RPGAAQKL--GLKPDEFIK---TPTGDEFV-KASV----RKGLLPQIL 656
Cdd:PHA03036 550 FDYNSLYPNVCIFGNLSPETLVgvvvndnrleAEINKQELrrKYPYPRYIYvhcEPRSPDLVsEIAVfdrrIEGIIPKLL 629
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 657 ENLLSARKRAKAELAQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIE----------- 725
Cdd:PHA03036 630 KTFLEERARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKylnsvlngskl 709
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 726 ----------------KTKQLVETKY--TLENGYDANAKVVYGDTDSVMCRFGVSSVAEAMSLGREAANWVSSH-FPSPI 786
Cdd:PHA03036 710 ingklilancpinpffKDDRSIDTNYdtNLPVEYNFTFRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINEKvLFDNF 789
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|
gi 564328246 787 RLEFEKVYFPYLLISKKRYAGLLFSSRSDAHD--RMDCKGLEAVRRDNCP 834
Cdd:PHA03036 790 KIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSvpERVNKGTSETRRDVSK 839
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
574-929 |
1.97e-27 |
|
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: 115.53 E-value: 1.97e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 574 GEDYTGATVIEPLKG-YYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPgaaqklglkPDEFIKTPTGDefVKASV---RK 649
Cdd:cd05530 10 GKKYRGAIVLEPPPGiFFNV--VVLDFASLYPSIIKVWNLSYETVNCP---------HCECKTNEVPE--VGHWVckkRP 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 650 GLLPQILENLLSAR-----KRAKAelaQETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMI 724
Cdd:cd05530 77 GITSQIIGLLRDLRvkiykKKAKD---KSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYII 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 725 EKTkqlveTKYTLENGYdanaKVVYGDTDSVMCRFGVSSVAEamslgrEAANWVSSHFpsPIRLEFEKVYfPYLLIS--K 802
Cdd:cd05530 154 TST-----IKKARELGL----KVLYGDTDSLFLWNPPQEQLE------DLVEWVEKEL--GLDLELDKEY-RYVVFSglK 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 803 KRYAGLLFSSrsdahdRMDCKGLEAVRRDNCPLVANLVTSSLRRILVDRDPDgAVAHAKDVISDL-------LCNR-IDI 874
Cdd:cd05530 216 KNYLGVTKDG------SVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPE-DFEKAREKIRDIvkgvykrLKKKeYTL 288
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 564328246 875 SQLVITKELTRAAADYA-GKQAHVELAERMRKRdpGSAPNLGDRVPYVIIGAAKGV 929
Cdd:cd05530 289 DQLAFKVMLSKPPEEYTkNTPQHVKAARQLEKY--GRNVEAGDIISYVKVKGKEGV 342
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
265-727 |
8.88e-25 |
|
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: 112.07 E-value: 8.88e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 265 PAGKYVRRAEKKATLCQLEVDVLWSDVISHPPEGQWQRIAPLRVLSFDIEC--AGRKGIFP--EPERDPVIQI----CSL 336
Cdd:TIGR00592 157 DIVKKAIPVSTRYLLEKILIPVPLKRAEFAGGDVQMEGDPELKLASFDIETyfHDGKDFFPgdENPADEEIMIsttpVIA 236
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 337 GLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWATFILAMDPDVITGYNIQNFDLPYLISRAQ-----TLKV 411
Cdd:TIGR00592 237 KQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLADRQVfqfywDAYE 316
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 412 DRFPFLGRVTGL-RSNIRDSSFQSRQVGRRDSKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSII 490
Cdd:TIGR00592 317 DPAEKLGVVLLFgRDVDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPI 396
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 491 TDLQNGNEQTrrRLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTGVPLGYLLSRGQQVKVVSQL-------LRQAMRQG 563
Cdd:TIGR00592 397 AKKYEFEAPD--IDAPYSSEYLEVTYELGKEFAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRkikgpcwLAVKGPDE 474
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 564 LLMPVV---KTEGGedYTGATVIEPLKGYYDVPIATLDFS--SLYPSIMMAHNLCYT-TLLRPGAAQKLGLKPDEFIKTP 637
Cdd:TIGR00592 475 LEYPRRswcKYEGG--YVKPPNVEKGLDKTPPPLVVLDFSmkSLNPSIIRNEIVSIPdTLHREFALDKPPPEPPYDVHPC 552
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 638 TGDEFVKASVR-------KGLLPQILENLLSARKRAKAELA--QETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLP 708
Cdd:TIGR00592 553 VGTRPKDCSFPldlkgefPGKKPSLVEDLATERALIKKFMAkvKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIG 632
|
490
....*....|....*....
gi 564328246 709 CLEISQSvtgFGRQMIEKT 727
Cdd:TIGR00592 633 RLRRSPK---FGRRFGERT 648
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
593-964 |
2.27e-24 |
|
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99921 Cd Length: 347 Bit Score: 106.03 E-value: 2.27e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 593 PIATLDFSSLYPSIMMAHNLCyttllrpgaaqklglkpdefiktPTGDEFvkasvrkGLLPQILENLLSARKRAKAELAQ 672
Cdd:cd05538 18 PIVHADVASLYPSIMLAYRIC-----------------------PARDSL-------GIFLALLKYLVELRLAAKESARA 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 673 ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIektKQLVEtkYTLENGydanAKVVYGDT 752
Cdd:cd05538 68 AARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELL---KLMIR--WLRRRG----ATPVEVDT 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 753 DSVMcrFGVSSVAEAMSLGREAANWVSSHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSsrsdahDRMDCKGLEAVRRDN 832
Cdd:cd05538 139 DGIY--FIPPNGVDTEDEEEELVRELSSTLPKGITVEFDGRYRAMFSYKIKNYALLDYD------GKLIVKGSAFRSRGI 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 833 CPLVANLVTSSLRRILVDrdpDGAVAHA--KDVISDLLCNRIDISQLVITKELTRAAADY-----AGKQAHVELAERMRK 905
Cdd:cd05538 211 EPFLREFLREAVRLLLQG---DGAGVHDlyEDYLRRLRSHELPISDLARTETLKESPEEYlqkvrAGKRNPAAAYEIALA 287
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564328246 906 RDPGSAPnlGDRVPYVIIGAAKGVAAYMK-SEDPLFVLEHSLpIDTQYYLEQ--QLAKPLLR 964
Cdd:cd05538 288 RPREWRA--GDRVTYYVSGTGKGVSVYENcRLVADYDPAHPD-ENTGFYAERllQLAARLLP 346
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
306-779 |
2.67e-24 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 110.17 E-value: 2.67e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 306 LRVLSFDIECAGRKGiFPEPERDPViQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQ----------SYEREEDLLQ 375
Cdd:PHA02528 106 IRIANLDIEVTAEDG-FPDPEEAKY-EIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPqeildkvvymPFDTEREMLL 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 376 AWATFILAMDPDVITGYNIQNFDLPYLISRAQTL----KVDRFPFLGRVTglrSNIRDSSFQSRQVGrrdskvVSMVGRV 451
Cdd:PHA02528 184 EYINFWEENTPVIFTGWNVELFDVPYIINRIKNIlgekTAKRLSPWGKVK---ERTIENMYGREEIA------YDISGIS 254
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 452 QMDMLQVllreYK------LRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNEQtrrRLAVYCLKDAFLPLRLLER--LM 523
Cdd:PHA02528 255 ILDYLDL----YKkftftnQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQ---KYIEYNIIDVELVDRLDDKrkLI 327
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 524 VLVnnVEMARVTGVPLGYLLSrgqQVKVVSQLLRQAMR-QGLLMPVVKTEGGEDYTGATVIEPLKGYYDVpIATLDFSSL 602
Cdd:PHA02528 328 ELV--LSMAYYAKINFEDVFS---PIKTWDAIIFNSLKeEKIVIPENKSHKKQKYAGAFVKEPVPGAYRW-VVSFDLTSL 401
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 603 YPSIMMAHNLCYTTLL--RPGA------AQKLGLKPDEFIKTPTGDEFVKAsvRKGLLPQILENLLSARKRAK------- 667
Cdd:PHA02528 402 YPSIIRQVNISPETIAgtFHVApvheyiNKTAPRPSDEYSCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIYKkkmlaae 479
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 668 --AELAQET----------------------------DPLRRQVLDGR--------------QLALKVSANSVYGFTGAQ 703
Cdd:PHA02528 480 rnAELIKTIledlndsvdtpidvdyyfdfsdefkaelKTLTKSSLKALleecekeialcntiQMARKILINSLYGALGNE 559
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 704 VGKLPCLEISQSVTGFG--------RQMIEKTKQLVETKytlenGYDAnakVVYGDTDSVMCRFG--VSSVAEAMSlgRE 773
Cdd:PHA02528 560 HFRYYDLRNAEAITLFGqlaiqwieRKMNEYLNKLCKTE-----DEDY---VIYGDTDSIYVNLDplVEKVGEDKF--KD 629
|
....*.
gi 564328246 774 AANWVS 779
Cdd:PHA02528 630 TNHWVD 635
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
306-522 |
1.02e-22 |
|
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family-B DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99823 [Multi-domain] Cd Length: 195 Bit Score: 97.04 E-value: 1.02e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 306 LRVLSFDIECAGRKGIfPEPERDPVIQI--CSLG----LRW-GEPEPFlrlaltlrpcapilgakVQSYEREEDLLQAWA 378
Cdd:cd05780 3 LKILSFDIEVLNHEGE-PNPEKDPIIMIsfADEGgnkvITWkKFDLPF-----------------VEVVKTEKEMIKRFI 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 379 TFILAMDPDVITGYNIQNFDLPYLISRAQTLKVDrFPfLGRVTglrSNIRdssfQSRQVGRRDSKVvsmVGRVQMDMLQV 458
Cdd:cd05780 65 EIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIE-LD-LGRDG---SEIK----IQRGGFNNASEI---KGRIHVDLYPV 132
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564328246 459 LLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNEQtRRRLAVYCLKDAFLPLRLLERL 522
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 ... |
306-520 |
2.63e-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: 96.92 E-value: 2.63e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 306 LRVLSFDIECAGRKGIFPEPERDPVIQIC----------------SLGLRWGEPEPFLRLALTLRPCapiLGAKVQSYER 369
Cdd:cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFycidddvspfildankVGVIIVDELKSNASNGRIRSGL---SGIPVEVVES 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 370 EEDLLQAWATFILAMDPDVITGYNIQNFDLPYLISRAQTLKVDRFPF-LGRV-TGLRSNIRDSsfqSRQVGRRDSKVVSM 447
Cdd:cd05778 81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDeISRVpSDSNGKFGDR---DDEWGYTHTSGIKI 157
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564328246 448 VGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITD-LQNGNEQTRRRLAVYCLKDAFLPLRLLE 520
Cdd:cd05778 158 VGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEwYKSGSASERWRVLEYYLKRVRLNLEILD 231
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
305-520 |
4.53e-18 |
|
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Pol II is also involved in lagging strand synthesis.
Pssm-ID: 99827 [Multi-domain] Cd Length: 193 Bit Score: 83.39 E-value: 4.53e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 305 PLRVLSFDIECagrkgifpeperDPVIQICSLGLrWGEPEpflRLALTLRPCAPILGAKVQSYEREEDLLQAWATFILAM 384
Cdd:cd05784 2 KLKVVSLDIET------------SMDGELYSIGL-YGEGQ---ERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQY 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 385 DPDVITGYNIQNFDLPYLISRAQTLkvdRFPF-LGRvTGLRSNIRDSSFQsrQVGRrdskvVSMVGRVQMDMLQvLLRE- 462
Cdd:cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAH---GLPLrLGR-GGSPLNWRQSGKP--GQGF-----LSLPGRVVLDGID-ALKTa 133
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564328246 463 -YKLRSYTLNAVSFHFLGEQKedvqhsIITDLQN-GNEQTRR------RLAVYCLKDAFLPLRLLE 520
Cdd:cd05784 134 tYHFESFSLENVAQELLGEGK------LIHDVDDrGAEIERLfredklALARYNLQDCELVWRIFE 193
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
305-479 |
3.18e-17 |
|
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99824 [Multi-domain] Cd Length: 188 Bit Score: 80.83 E-value: 3.18e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 305 PLRVLSFDIECAGRKGiFPEPERDPVIQIcSLGLRWGEPEPFLrlaltlrpcapilgakvQSYEREEDLLQAWATFILAM 384
Cdd:cd05781 2 DLKTLAFDIEVYSKYG-TPNPRRDPIIVI-SLATSNGDVEFIL-----------------AEGLDDRKIIREFVKYVKEY 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 385 DPDVITGYNIQNFDLPYLISRAqtlkvdrfpflgRVTGLRsnirdssfqsRQVGRRDSKVV--------SMVGRVQMDML 456
Cdd:cd05781 63 DPDIIVGYNSNAFDWPYLVERA------------RVLGVK----------LDVGRRGGSEPstgvyghySITGRLNVDLY 120
|
170 180
....*....|....*....|...
gi 564328246 457 QVLLREYKLRSYTLNAVSfHFLG 479
Cdd:cd05781 121 DFAEEIPEVKVKTLENVA-EYLG 142
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
362-757 |
9.19e-15 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 79.52 E-value: 9.19e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 362 AKVQSYEREEDLLQAWATFIL----AMDPDVITGYNIQNFDLPYLISRAQTLKvDRFPFLGRVTGLRSNIRDS------- 430
Cdd:PHA03334 370 FKQRPHPLTKALMEAWEAFLSkdpqLVPAQLLFGSDILNSNYLELLDVIESHK-AQFKATCRKAAARKEEIGSymktrdt 448
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 431 --SFQSRQVGRRDSKVVSMvGRVQMDMLQVLLR---EYKLRSYTLNAVSFHFLGEQK-----------EDVQHSIITDLQ 494
Cdd:PHA03334 449 vqDFNDNDKKYLNSTSHGF-GAHIIDLMRVCNTksiKAKCSSRKLDTVARLIISKSKphknppkigkmDDVKYTEMDGMF 527
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 495 NGNEQTRRRLAVYCLKDAFLPLRLLERLMVLVNNVEMARVTgVPLGYL-LSRG--------QQVKVVS-QLLRQAMRQG- 563
Cdd:PHA03334 528 TAGGAALARYLIYNLVDSELLIRIAKNLDPVIEFLNRLRAT-YNIDYVaHGRGvmnfcgfvQSTKSVEvPLLKARLRIGi 606
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 564 ----------LLMP-VVKTEGGEDYT--GATVIEPLKGY-----YDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQK 625
Cdd:PHA03334 607 fvatgriaesLCMPeKYARDCRQKIKlkGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIVDPDCTAR 686
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 626 L-------------GLKPDEFIKTPTGDEFVKASVRKglLPQI----LENLLSARKRAKAELAQETDPLRRQVLDGRQLA 688
Cdd:PHA03334 687 VrgwvvfdwkkidrGFGKATLMYTILRTKPEEPSWRR--FTTYttssLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNE 764
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564328246 689 LKVSANSVYGftgaqVGKLPCleiSQSVTGFGRQMIektkQLVETKYTLENGYdanaKVVYGDTDSVMC 757
Cdd:PHA03334 765 MKICANSHYG-----VAPHAC---QHLITTLGRHKI----KLVEEFIKKEPGM----TVNYGDTDSVMF 817
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
303-518 |
1.67e-14 |
|
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: 73.51 E-value: 1.67e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 303 IAPLRVLSFDIEC-AGRKGIFPEPERD--PVIQIC---SLGLRwgepepflRLALTLRPCAPIL------GAKVQSYERE 370
Cdd:cd05783 2 IPKLKRIAIDIEVyTPIKGRIPDPKTAeyPVISVAlagSDGLK--------RVLVLKREGVEGLegllpeGAEVEFFDSE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 371 EDLLQAwATFILAMDPDVITgYNIQNFDLPYLISRAQTLkvdrfpflgrvtGLRSNIRDSSFqsrqvgRRDSkvVSMVGR 450
Cdd:cd05783 74 KELIRE-AFKIISEYPIVLT-FNGDNFDLPYLYNRALKL------------GIPKEEIPIYL------KRDY--ATLKHG 131
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564328246 451 VQMDM--------LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIitdlqngNEQTRRRLAVYCLKDAFLPLRL 518
Cdd:cd05783 132 IHIDLykffsnraIQVYAFGNKYREYTLDAVAKALLGEGKVELEKNI-------SELNLYELAEYNYRDAELTLEL 200
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
323-525 |
1.85e-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: 74.19 E-value: 1.85e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 323 PEPERDPVIQICSLGL---RWGEPEPFLRLALTLRPcapilgaKVQSYEREEDLLQAWATFILAMDPDVITGYNIQNFDL 399
Cdd:cd05776 39 PTPPPPFQSHTCTLTRplgRSPPPDLFEKNAKKKKT-------KVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDL 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 400 PYLISRAQTLKVDRFPFLGRV--TGLRSNIRDSSFQSRQVgrrdskvvsMVGRVQMDMlQVLLRE-YKLRSYTLNAVSFH 476
Cdd:cd05776 112 DVLLSRIQELKVPHWSRIGRLkrSVWPKKKGGGKFGEREL---------TAGRLLCDT-YLSAKElIRCKSYDLTELSQQ 181
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 564328246 477 FLGEQKEDVqhsIITDLQNGNEQTRR--RLAVYCLKDAFLPLRLLERLMVL 525
Cdd:cd05776 182 VLGIERQDI---DPEEILNMYNDSESllKLLEHTEKDAYLILQLMFKLNIL 229
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|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
306-505 |
3.05e-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: 69.75 E-value: 3.05e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 306 LRVLSFDIECAGRKGIF---PEPERDPVIQIcslGLRwgEPEPFlRLALTLRPCApilgakvqsyerEEDLLQAWATFIL 382
Cdd:cd05785 9 LRRLQLDIETYSLPGFFfsnPDRGDDRIIIV---ALR--DNRGW-EEVLHAEDAA------------EKELLEELVAIIR 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 383 AMDPDVITGYNIQNFDLPYLISRAQTLKVdrfPF-LGRVtGLRSNIRDSSFqsrQVGRR--DSKVVSMVGRVQMDMLQVL 459
Cdd:cd05785 71 ERDPDVIEGHNIFRFDLPYLRRRCRRHGV---PLaIGRD-GSIPRQRPSRF---RFAERliDYPRYDIPGRHVIDTYFLV 143
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 564328246 460 LR----EYKLRSYTLNAVSFHF--LGEQKEDVQHSIITDLQNGNEQTRRRLA 505
Cdd:cd05785 144 QLfdvsSRDLPSYGLKAVAKHFglASPDRTYIDGRQIAEVWRSDPARLLAYA 195
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|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
367-667 |
6.26e-07 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 53.46 E-value: 6.26e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 367 YEREEDLLQAWATFILAMDPDVITGYNIQNFDLPYLISRAQTL----KVDRFPFLGRVTglrsnirdSSFQSRQVGRRds 442
Cdd:PHA02524 177 FEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNIlgekAANQLSPYGKIT--------SKTITNLYGEK-- 246
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 443 KVVSMVGRVQMDMLQVLlREYK---LRSYTLNAVSFHFLGEQKEDVQHSIiTDLQNGNEQtrrRLAVYCLKDAFLPLRLL 519
Cdd:PHA02524 247 IIYKIHGIALMDYMDVF-KKFSftpMPDYKLGNVGYREVKADKLDYEGPI-NKFRKADHQ---RYVDYCVRDTDIILLID 321
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 520 ERLMVLVNNVEMARVTGVPLGYLLSrgqQVKVVSQLLRQAM-RQGLLMPVVKTEGGEDYTGATVIEPLKGYYDVPIaTLD 598
Cdd:PHA02524 322 GRRCFIDLILSLSYYAKIRFDDVLG---TIKVWDSIIFNSLvESNVVIPAMKASPKQSFPGAYVKEPVPGGYRYGL-SFD 397
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564328246 599 FSSLYPSIMMAHNLC---YTTLLRPGAAQ----KLGLKP-DEFIKTPTGDEFVKASVrkGLLPQILENLLSARKRAK 667
Cdd:PHA02524 398 LTSLYPSILRLLNISpemIAGMFSPARLEdyinKVAPKPsDQFSCAPNGMMYKKGVV--GVLPNETEKVFLQRKSEK 472
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|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
305-442 |
6.81e-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: 48.03 E-value: 6.81e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 305 PLRVLSFDIECAGRKGIFPEPERDPVIQIcSLGLrwgEPEPFLrlaLTLRPcapILGAKVQSYE---------------- 368
Cdd:cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMI-SYMI---DGQGYL---IVNRE---IVSEDIEDFEytpkpeyegpfkvfne 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328246 369 -REEDLLQAWATFILAMDPDVITGYNIQNFDLPYLISRAQTLKVDrfpfLGRVTGLRSNIRDsSFQSRQVG--------R 439
Cdd:cd05779 71 pDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLS----MEEEIGFRKDSEG-EYKSRYIIhmdcfrwvK 145
|
...
gi 564328246 440 RDS 442
Cdd:cd05779 146 RDS 148
|
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