|
Name |
Accession |
Description |
Interval |
E-value |
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
81-1076 |
0e+00 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 1424.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 81 RPTPPalDPQTEPLIFQQLEIDHYVG----PAQPVPGGPPPSRGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPPGF 156
Cdd:PTZ00166 31 RPLPP--ISLQKDLVFFQLDADYTEKddksQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNF 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 157 GPEHMGDLQRELNLAISRDSRGGRelTGPAVLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRV--- 233
Cdd:PTZ00166 109 LPEDSQKLKRELNAQLSEQSQFKK--YQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVcgg 186
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 234 AGLGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALR-LKEKATQCQLEADVLWSDVVSHPPEGPWQRIAPLRV 312
Cdd:PTZ00166 187 GWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRpPKKKTSTCQIEVDCSYEDLIPLPPEGEYLTIAPLRI 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 313 LSFDIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIRIMDP 390
Cdd:PTZ00166 267 LSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDP 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 391 DVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLR 470
Cdd:PTZ00166 347 DFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLK 426
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 471 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRG 550
Cdd:PTZ00166 427 SYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRG 506
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 551 QQVKVVSQLLRQAMHEGLLMPVVKSEGG---EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTA 627
Cdd:PTZ00166 507 QQIKVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDA 586
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 628 QKlgLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALK------------- 694
Cdd:PTZ00166 587 NN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKisansvygytgaq 664
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 695 ------------SVTGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHF 762
Cdd:PTZ00166 665 vggqlpclevstSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKF 744
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 763 PSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQD 842
Cdd:PTZ00166 745 LKPIKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKG 823
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 843 VISDLLCNRIDISQLVITKELTRaaSDYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVL 922
Cdd:PTZ00166 824 KISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL 901
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 923 EHSLPIDTQYYLEqQLAKPLLRIFEPILGEgraEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLShQGAVC 1002
Cdd:PTZ00166 902 ENNIPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIK-EGALC 976
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530416735 1003 EFC-QPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQEQLLRRFG 1076
Cdd:PTZ00166 977 DNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
579-950 |
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: 754.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 579 EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGltEDQFIRTPTGDEFVKTSVRKGLLPQ 658
Cdd:cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLP--PEDYIKTPNGDYFVKSSVRKGLLPE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 659 ILENLLSARKRAKAELAKETDPLRRQVLDGRQLALK------------------------SVTGFGRQMIEKTKQLVESK 714
Cdd:cd05533 79 ILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKisansvygftgatvgklpcleissSVTSFGRQMIEKTKKLVEEK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 715 YTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSsRP 794
Cdd:cd05533 159 YTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLWT-NP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 795 DAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYAGKQ 874
Cdd:cd05533 238 DKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADDYAGKQ 317
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 530416735 875 AHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPIL 950
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 ... |
541-949 |
5.90e-175 |
|
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: 519.09 E-value: 5.90e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 541 VPLSYLLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGG--EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 618
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGdeDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 619 TTLLRPGTA---QKLGLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALK- 694
Cdd:pfam00136 81 TTLVRSVDEannLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLALKi 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 695 -----------------------SVTGFGRQMIEKTKQLVESKYTvengysTSAKVVYGDTDSVMCRFGVSSVAEAMALG 751
Cdd:pfam00136 161 tansvygftgfangrlpclpiaaSVTAIGREMLENTKDLVEGMYT------YNFRVIYGDTDSVFIEFGGKDVEEAMKIG 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 752 REAADWVSGH-FPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLID 830
Cdd:pfam00136 235 DELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKY-TAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSD 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 831 RDPEGAVAHAQDVI----SDLLCNRIDISQLVITKELTRAASDYAGKQ-AHVELAERMRKRDpGSAPSLGDRVPYVIISA 905
Cdd:pfam00136 314 RGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEVALRMNKRN-GEAPEVGDRIPYVIVKA 392
|
410 420 430 440
....*....|....*....|....*....|....*....|....*..
gi 530416735 906 AK---GVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 949
Cdd:pfam00136 393 AKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
119-949 |
1.02e-171 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 524.01 E-value: 1.02e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 119 RGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPpgfgpehmgdlQRELNLAISRDSRGgreltgpaVLAVELCSRESM 198
Cdd:COG0417 15 EDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLP-----------DEEKLEELLRDIKE--------ITEVEPVKLKSF 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 199 FGyhghGPSPFLRITVALPRLVAPAR-RLLEQGIRVaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRL 277
Cdd:COG0417 76 FG----EPVPVLKIYTRDPRDVRELRdRLKEGGIDV----------YEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKL 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 278 KEKatqcqleadvlwsdVVSHPPEGPWQRIAPLRVLSFDIECAGRKGiFPEPERD-PVIQICSlglrwgEPEPFLRLALT 356
Cdd:COG0417 142 DYE--------------VKENPRLKPEDYRPKLKVLSFDIEVSTPRG-FPDPERDgPIISIGL------AGSDGEKKVLM 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 357 LRpcAPILGAKVQSYEKEEDLLQAwstFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRVAGLCSnIR 432
Cdd:COG0417 201 LG--REGVDFEVEYFDDEKALLEA---FFEIIreyDPDIIIGWNVDNFDLPYLQKRAERLGI---PLdLGRDGSEPS-WR 271
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 433 DSSFQSKqtgrrdtkvVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQngnDQTRRRLAVY 511
Cdd:COG0417 272 EHGGQGF---------ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKLIVDGGEIERLW---DDDKPALAEY 339
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 512 CLKDAYLPLRLLERLMVLVNAVEMARVTGVPLsYLLSRGQQVKVVSQL-LRQAMHEGLLMPVVKSEGGEDYTGATVIEPL 590
Cdd:COG0417 340 NLRDAELTLRIFEKTLLLPFLIELSRITGLPL-DDVGRAGSSAAFENLlLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPK 418
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 591 KGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQklgltEDQFIRTPT-GDEFVKTsvRKGLLPQILENLLSARKR 669
Cdd:COG0417 419 PGLYE-NVLVLDFKSLYPSIIRTFNISPETLVEGGEEP-----CGDEDVAPGfGHRFCRE--PKGILPSILEELWDERDE 490
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 670 AKAELAK-ETDPLRRQVLDGRQLALK------------------------SVTGFGRQMIEKTKQLVESKytvenGYsts 724
Cdd:COG0417 491 AKKKMKKaKPDSEEYRLYDALQQALKilmnsfygvlgsegcrfydpelaeSITARGREIIKQTIEKAEEL-----GY--- 562
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 725 aKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLI-SKKRYAGLLfssrPDahDRMDCK 803
Cdd:COG0417 563 -KVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPgSKKRYAGLT----ED--GKIDIK 635
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 804 GLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDY-AGKQAHVELAER 882
Cdd:COG0417 636 GLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYeKNVPPHVRAARK 715
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530416735 883 MRKRdpGSAPSLGDRVPYVIISAAKGVaaymksEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 949
Cdd:COG0417 716 LDER--GRPYQRGDKISYVITKGGGRV------EPVELAKERESEIDYDYYIEKQLKPTADRILEAF 774
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
304-533 |
9.45e-153 |
|
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: 453.19 E-value: 9.45e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 304 WQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWST 383
Cdd:cd05777 1 WSKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 384 FIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVL 463
Cdd:cd05777 81 FVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVI 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 464 LREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAV 533
Cdd:cd05777 161 QRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLVNYI 230
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
309-740 |
6.87e-132 |
|
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: 408.84 E-value: 6.87e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 309 PLRVLSFDIECAGRKGIFPEPE--RDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIR 386
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 387 IMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRV-AGLCSNIRDSSFQSKQTGRRDTKVVsMVGRVQMDMLQVLLR 465
Cdd:smart00486 82 KYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLkIGLRIPNKKPLFGSKSFGLSDIKVY-IKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 466 EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSY 545
Cdd:smart00486 161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 546 LLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGG----------EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHN 615
Cdd:smart00486 241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 616 LCYTTLLRPGTAQKLGLT----EDQFIRTPTG--DEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPL--RRQVLD 687
Cdd:smart00486 321 LCYSTLVGVGEVVIKGDLiipeDLLTIKYEKGnkYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESeeLKKLLD 400
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530416735 688 GRQLALK------------------------SVTGFGRQMIEKTKQLVESKYTVENGYstsaKVVYGDTDSVMCRFG 740
Cdd:smart00486 401 SRQLALKltansvygylgftnsrlpckplaaSVTALGREILEKTKELIEENGYPKPGF----KVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
119-951 |
1.40e-104 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 346.07 E-value: 1.40e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 119 RGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYtPAppgfgpEHMGDLQRELNLAISRDSRggreltgpavlAVELCS--RE 196
Cdd:PRK05762 16 TPGGPEVELWLATDEGPRVVLLDPQFRPYFI-PA------EQDERAESLLAGEIGVRLS-----------PLALKDfhRR 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 197 SMFGYhghgPSPFLRITVALPRlvaparRLLEQGIRVaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLElpaGKYALR 276
Cdd:PRK05762 78 PVLGL----YCRQHRQLTRLPK------RLREGGVDV----------YEADIRFPERYLMERFITPCVWFS---GEVEQY 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 277 LKE-KATQCQLEADVLWsdvvshPPegpwqriaPLRVLSFDIECAgRKGI-----FPEPERDPVIQIcslglrwGEPEPf 350
Cdd:PRK05762 135 TTDgVLRNARLKPAPDY------RP--------PLKVVSLDIETS-NKGElysigLEGCGQRPVIML-------GPPNG- 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 351 lrlaltlrpCAPILGAKVQSyekEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRvAGLCS 429
Cdd:PRK05762 192 ---------EALDFLEYVAD---EKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGI---PLrLGR-DGSEL 255
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 430 NIRDSSFQSkqtgrrDTKVVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEdvqhsIITDLQNGNDQTRR-- 506
Cdd:PRK05762 256 EWREHPFRS------GYGFASVPGRLVLDGIDALKSaTWVFDSFSLEYVSQRLLGEGKA-----IDDPYDRMDEIDRRfa 324
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 507 ----RLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPlsylLSR--GQQVKVVSQLLRQAMHEGLLMPVVKSEGGED 580
Cdd:PRK05762 325 edkpALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLP----LDRvgGSVAAFEHLYLPRAHRAGYVAPNLGERPGEA 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 581 YTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPgtaqkLGLTEDQFIRTPTGDEFVKTsvrKGLLPQIL 660
Cdd:PRK05762 401 SPGGYVMDSKPGLYD-SVLVLDFKSLYPSIIRTFNIDPDGLVEG-----LAQPPEESVAGFLGARFSRE---KHFLPEIV 471
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 661 ENLLSARKRAKAELAKEtdplrrqvldgRQLALK------------------------SVTGFGRQMIEKTKQLVESKyt 716
Cdd:PRK05762 472 ERLWEGRDEAKREMNKP-----------LSQAIKiimnafygvlgssgcrffdprlasSITMRGHEIMKQTRELIEAQ-- 538
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 717 venGYstsaKVVYGDTDSVMCRFGVS-SVAEAMALGREAADWVSGHFPSPIR----------LEFEKVY----FPYLLI- 780
Cdd:PRK05762 539 ---GY----QVIYGDTDSTFVWLGGAhDEEDAAKIGRALVQEINQWWQEHLQqefglesaleLEFEKHYrrffMPTIRGa 611
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 781 ---SKKRYAGLLfsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVahaQDVISDLLCNRIDiSQL 857
Cdd:PRK05762 612 eegSKKRYAGLI--QEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEPYVDYV---REVIDKLRAGELD-EKL 685
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 858 VITKELTRAASDYAGKQA-HV----ELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSedplfvlehslPIDTQY 932
Cdd:PRK05762 686 VYRKRLRRPLDEYQRNVPpHVraarLADEMGYKVGRPLQYQNGGKIGYVITVNGPEPLEYRKS-----------PIDYDY 754
|
890
....*....|....*....
gi 530416735 933 YLEQQLaKPLLRIFEPILG 951
Cdd:PRK05762 755 YIEKQL-QPVADRILPFFG 772
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
130-477 |
1.11e-96 |
|
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: 310.12 E-value: 1.11e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 130 VTDEGFSVCCHIHGFAPYFYTPAPPGFGPEHMGDLQRELNLAISRdsrggreltgpaVLAVELCSRESMFGYHGHgPSPF 209
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKELEEVIEEIKELYEGLDK------------IEKIELKLKKSLYGYEED-PVPY 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 210 LRITVALPRLVAPARRLLEQGirvaglgtPSFAPYEANVDFEIRFMVDTDIVGCNWLELPagKYALRLKEKATQCQLEAD 289
Cdd:pfam03104 68 LKVSFANPRPLLKIRKYLSPE--------NISDVYEYDVDYLERFLIDNDIVGFGWYKVK--VYPFRAEGRISNCDVEID 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 290 VLWSDVVSHPPEGPWqriAPLRVLSFDIECAGRKGIFPEPER--DPVIQICSLGLRWGEPEPFLRLALTLRPCAPI---- 363
Cdd:pfam03104 138 CDSPDLISVPFEKEW---PPLRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEPRFLFTLRECDSEdied 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 364 ---------LGAKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVA-GLCSNIRD 433
Cdd:pfam03104 215 feytpkpiyPGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNrGGRSKVRE 294
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 530416735 434 SSFqskqtGRRDTKVVSMVGRVQMDMLQVLLREYKLRSYTLNAV 477
Cdd:pfam03104 295 IGF-----GTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
550-949 |
4.35e-88 |
|
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Pssm-ID: 99917 Cd Length: 451 Bit Score: 291.04 E-value: 4.35e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 550 GQQVKVVSQLLRQAMHEGLLMP-----VVKSEGGEDYTgATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLL-- 622
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPspsrqQVAQQRALECL-PLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLgr 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 623 -----------RPGTAQK-------LGLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSAR---KRAKAELAKETDPL 681
Cdd:cd05534 80 veelngggkfgFLGVKLYlppppldLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRimvKKAMKKYKDDKKLQ 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 682 RRqvLDGRQLALK-------------------------SVTGFGRQMIEKTKQLVESkyTVENGystsAKVVYGDTDSVM 736
Cdd:cd05534 160 RI--LDARQLALKllanvtygytaasfsgrmpcveiadSIVQTGRETLERAIELIES--TPKWG----AKVVYGDTDSLF 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 737 CRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLV 816
Cdd:cd05534 232 VLLPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAV 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 817 ANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYAGK-QAHVELAERMRKRDPGSAPSLG 895
Cdd:cd05534 312 QKILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGATlPAGAIVALRRMEKDPRAEPQYG 391
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 530416735 896 DRVPYVIISAAKGVAAYMKSEDP-LFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 949
Cdd:cd05534 392 ERVPYVVVRGEPGSRLIDLVVSPeEFLADPSLRLDAEYYITKQIIPALDRLFNLV 446
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
581-951 |
1.91e-76 |
|
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: 257.51 E-value: 1.91e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 581 YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQfirtptgdefVKTSVRKGLLPQIL 660
Cdd:cd05532 8 YAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPPL----------PPSDQEKGILPRII 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 661 ENLLSARKRAKAELAKETDPLRRQVLDGRQLALKSVT-------GF-----------------GRQMIEKTKQLVESKyt 716
Cdd:cd05532 78 RKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTAnsmygclGFsysrfyakplaalitskGREILQKTKDLVEKM-- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 717 venGYStsakVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSpIRLEFEKVYFPYLLISKKRYAGLLFSSRPDA 796
Cdd:cd05532 156 ---NLE----VIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKK-LEIDIDGVFKRLLLLKKKKYAALKVVDDDKG 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 797 HDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAV----AHAQDVISDLLCNRIDISQLVITKELTRAASDYAG 872
Cdd:cd05532 228 KLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVenihEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPD 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 873 K--QAHVELAERMRKRDPGSAPslGDRVPYVIIS--AAKGVA--AYMKSEdplFVLEHSLPIDTQYYLEQQLAKPLLRIF 946
Cdd:cd05532 308 KksLPHVQVALRMNKRGRKVKA--GDTIPYIICKdgSSKSLAdrAYHPDE---VKKNENLKIDIEYYLSQQILPPISRLC 382
|
....*
gi 530416735 947 EPILG 951
Cdd:cd05532 383 EPIEG 387
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
253-947 |
1.34e-75 |
|
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: 272.31 E-value: 1.34e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 253 RFMVDTDIVGCNWLELpaGKYALRLKEKATQCQLEADVLWSDVVShppEGPWQRIAPLRVLSFDIECAGRKGIFPEPERD 332
Cdd:TIGR00592 454 RFLLLRKIKGPCWLAV--KGPDELEYPRRSWCKYEGGYVKPPNVE---KGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSI 528
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 333 PVIQICSLGLRWGEPEPFLRLALTL--RP--CAPILG----------AKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNI 398
Cdd:TIGR00592 529 PDTLHREFALDKPPPEPPYDVHPCVgtRPkdCSFPLDlkgefpgkkpSLVEDLATERALIKKFMAKVKKIDPDEIVGHDY 608
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 399 QNFDLPYLISRAQTLKVQTFPFLGRVAglcsnirdssfQSKQTGRRdtKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVS 478
Cdd:TIGR00592 609 QQRALKVLANRINDLKIPTWSKIGRLR-----------RSPKFGRR--FGERTCGRMICDVEISAKELIRCKSYDLSELV 675
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 479 FHFLG-EQKEDVQHSIITDLQNGNDQTRrrLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRGQQVKVVS 557
Cdd:TIGR00592 676 QQILKtERKVIPIDNINNMYSESSSLTY--LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEF 753
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 558 QLLRQAMHEGLLMP----VVKSEGGED---------------YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 618
Cdd:TIGR00592 754 LLLHAFYENNYIVPdkqiFRKQQKLGDedeeidgykkgkkaaYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICF 833
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 619 TTLLRPgtaqklgLTEDQFIRTPtgdefvKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALK---- 694
Cdd:TIGR00592 834 TTVQQK-------VDEDELPELP------DSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKltan 900
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 695 --------------------SVTGFGRQMIEKTKQLVESKYTvengystsaKVVYGDTDSVMCRFGVSSVAEAMALGREA 754
Cdd:TIGR00592 901 smygclgysksrfyakplaaLVTAKGREILEHTRQLVEEMNL---------EVIYGDTDSIMINTPGTKYEEVFKIGKEF 971
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 755 ADWVSGHFPsPIRLEFEKVYFPYLLISKKRYAGLLFS--SRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRD 832
Cdd:TIGR00592 972 KSEVNKLYK-LLELDIDGVFKRLLLLKKKKYAAIKVEgdSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKD 1050
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 833 PEGAVAHAQDVISDL----LCNRIDISQLVITKELTRAASDYAGK--QAHVELAERMRKRDPGSAPSlGDRVPYVIISAA 906
Cdd:TIGR00592 1051 VEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLTRDPKDYPDGasLPHVHVALRINARGGRKVKA-GDVVSYVICKDG 1129
|
730 740 750 760
....*....|....*....|....*....|....*....|....
gi 530416735 907 KGVAAYMKS---EDPLFvLEHSLPIDTQYYLEQQLAKPLLRIFE 947
Cdd:TIGR00592 1130 GNLSARQRAyalEELQR-KHNNLIYDTQYYLEHQIHPVVLRILE 1172
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
579-947 |
5.49e-71 |
|
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: 239.58 E-value: 5.49e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 579 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLgltEDqfirtPTGDEFVKTSVRKGLLPQ 658
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAP---ED-----YIGVGFRSPKDRKGLLPR 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 659 ILENLLSARKRAKAELAK-ETDPLRRQVLDGRQLALK------------------------SVTGFGRQMIEKTKQLVES 713
Cdd:cd00145 72 ILEELLNFRDEAKKRMKAaKLAPEERVLYDNRQQALKvlansfygylgakffrfydpevaaSITSFGREIIQDTIALVEE 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 714 KytvenGYstsaKVVYGDTDSVMCRFGVS-SVAEAMALGREAADWVsgHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsS 792
Cdd:cd00145 152 H-----GA----RVIYGDTDSIFVSLPKMgTKEDAIKEGREILQEL--ADEHLLELEFEKVYLPFFLGKKKRYAGLDI-W 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 793 RPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVIsdllcnridisqlvitkeltraasdyag 872
Cdd:cd00145 220 KGQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL---------------------------- 271
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530416735 873 kqahvelaermrkrdpgsapslgDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 947
Cdd:cd00145 272 -----------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
579-947 |
4.72e-67 |
|
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: 230.29 E-value: 4.72e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 579 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGTaqklgltEDQFIRTPTGDEFVKTsvRKGLLPQ 658
Cdd:cd05536 2 ESYEGGIVLEPEKGLHE-NIVVLDFSSLYPSIMIKYNISPDTLVREGC-------EDCDVEPQVGHKFRKD--PPGFIPS 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 659 ILENLLSARKRAKAELaKETDP--LRRQVLDGRQLALK------------------------SVTGFGRQMIEKTKQLVE 712
Cdd:cd05536 72 VLEDLLEERRRIKEKM-KKLDPesEEYKLLDERQRAIKilansfygymgwanarwyckecaeAVTAWGREYIKTTIKIAE 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 713 skytvENGYstsaKVVYGDTDSVmcrFGVSSVAEA-MALGREAADWVSGHFPspIRLEFEKVYFPYLLISKKRYAGLlfs 791
Cdd:cd05536 151 -----EKGF----KVIYGDTDSL---FVKIDGADAvKKKVKKLLKYINEELP--LELEIEKFYKRGFFVTKKRYAGL--- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 792 srpDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYA 871
Cdd:cd05536 214 ---TEDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYK 290
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 530416735 872 GKQAHVELAERMRKRdpGSAPSLGDRVPYVIIsaaKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 947
Cdd:cd05536 291 ATGPHVAAAKKLAKR--GYKVRPGTKIGYVIV---KGSGKISDRAYPYDMVDEKHKYDAEYYIDNQVLPAVLRILE 361
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
143-951 |
1.16e-55 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 208.00 E-value: 1.16e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 143 GFAPYFYTPAPPgfgpehmgDLQRELNLaISRDsrggreltgPAVLAVELCSRESmfGYHGHgPSPFLRITVALPRLVAP 222
Cdd:PRK05761 53 GHKPYFLTDLDP--------DEIDKIPK-ILRH---------PSFDHLEIVEKYD--GLRDK-KVKVTKIVVKDPLAVRR 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 223 ARRLLEQGIRVaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRLKE------KATQCQLEADVLWSDVV 296
Cdd:PRK05761 112 LRLSVRDIPRA----------WEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEIlveeikKAFKDERKLAEDWLPIF 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 297 SHPPegpwqriAPLRVLSFDIECAGrkgifPEPERDPViqicslglrwgepepflrlaltlrpcapilgakvqsyEKEED 376
Cdd:PRK05761 182 EAPI-------PKIKRIAIDIEVYT-----PAKGRIPD-------------------------------------DSEKE 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 377 LLQAWSTFIRIMDPDVItgYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKqtgrRDTKVVSMVGRvq 456
Cdd:PRK05761 213 LLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQN----KAVRSYAFYGK-- 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 457 mdmlqvllreYKLRSYTLNAVSFHFLGEQKEDVQHSIitdlqngNDQTRRRLAVYCLKDAYLPLRL--LERLMVLVNAVE 534
Cdd:PRK05761 285 ----------YRHREARLDAVGRALLGISKVELETNI-------SELDLEELAEYNFRDAEITLKLtfFNNELVLKLILL 347
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 535 MARVTGVPLSYLlSRGQQVKVVSQLL-RQAMHEGLLMP-----------VVKSEG--GEDYTGATVIEPLKG-YYDVpiA 599
Cdd:PRK05761 348 LSRISKLPIEEL-SRATISTWISNLEyWEHRKRGWLIPwkedilrldheVYKKAIikGKKYRGGLVFQPPPGiFFNV--Y 424
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 600 TLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLgltedqfIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKE-- 677
Cdd:PRK05761 425 VLDFASLYPSIIVKWNLSPETVRIPECKCHY-------DDEVPELGHSVCDDRPGLTSVLVGLLRDFRVKIYKKKAKDpn 497
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 678 TDPLRRQVLDGRQLALK------------------------SVTGFGRQMIEKTKQLVEskytvENGYstsaKVVYGDTD 733
Cdd:PRK05761 498 LDEERRAWYDVVQRALKvflnasygvfgaenfklyrievaeSITALGREILLSTKKKAE-----ELGL----KVLYGDTD 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 734 SVMCRFGVSSVAEAMalgreaADWVSGHFpsPIRLEFEKVYfPYLLIS--KKRYAGLLFSsrpdahDRMDCKGLEAVRRD 811
Cdd:PRK05761 569 SLFVWGPTKESLEEL------IKEIEERT--GIDLEVDKTY-DWVAFSglKKNYFGVLKD------GKVKIKGIVAKKRN 633
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 812 NCPLVANLVTASLRRLLIDRDPEGAV-------AHAQDVISDLLCNRIDISQLVITKELTRAASDYA-GKQAHVELAERM 883
Cdd:PRK05761 634 TPEFVKELQREVLEVLKSIRSPEDVEkvkdeieDVLKRYYEKLRAKDYPLDELAIRVRLSKPLDEYTkNTPQHVKAALQL 713
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 530416735 884 RKRdpGSAPSLGDRVPYVIISAAKGVaaymkseDPLFVLEHSlPIDTQYYLEQqlakpLLRIFEPILG 951
Cdd:PRK05761 714 RDY--GVEVSPGDIISYVKVDDKRGV-------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 ... |
312-524 |
3.03e-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: 184.87 E-value: 3.03e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 312 VLSFDIECAGRKGiFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAP-ILGAKVQSYEKEEDLLQAWSTFIRIMDP 390
Cdd:cd05160 1 VLSFDIETTPPVG-GPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEfIDGIEVEYFADEKELLKRFFDIIREYDP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 391 DVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVaglcSNIRDSSfqskqtgrRDTKVVSMVGRVQMDMLQVLLREYKLR 470
Cdd:cd05160 80 DILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRR----SGGEKSS--------GSTERIAVKGRVVFDLLAAYKRDFKLK 147
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 530416735 471 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDqtRRRLAVYCLKDAYLPLRLLE 524
Cdd:cd05160 148 SYTLDAVAEELLGEGKEKVDGEIIEDAEWEED--PERLIEYNLKDAELTLQILE 199
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
583-947 |
7.70e-40 |
|
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: 152.04 E-value: 7.70e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 583 GATVIEPLKGYYDvPIATLDFSSLYPSIMMahnlcyTTLLRP-GTAQKL-GLTEDQFIRTPTGDEFVKTsvrKGLLPQIL 660
Cdd:cd05537 5 GGYVMDSKPGLYK-NVLVLDFKSLYPSIIR------TFLIDPlGLIEGLkAPDPEDLIPGFLGARFSRE---KHILPDLI 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 661 ENLLSARKRAKaelaKETDPLRRQVL-------------------DGRqLAlKSVTGFGRQMIEKTKQLVEskytvENGY 721
Cdd:cd05537 75 ARLWAARDEAK----REKNAPLSQAIkiimnsfygvlgstgcrffDPR-LA-SSITLRGHEIMKQTRAWIE-----QQGY 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 722 stsaKVVYGDTDSVMCRFG-VSSVAEAMALGREAAD----WVSGH------FPSPIRLEFEKVYFPYLLI--------SK 782
Cdd:cd05537 144 ----QVIYGDTDSTFVWLGeELDAAEAQAIGKELASqinqWWAQKlkeefgLESFLEIEFETHYSRFFMPtirgsdegSK 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 783 KRYAGLlfsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVahaQDVISDLLCNRIDiSQLVITKE 862
Cdd:cd05537 220 KRYAGL---KSTDGGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFI---KETVEELLAGELD-ELLVYRKR 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 863 LTRAASDY-AGKQAHVELAermRKRDPgSAPSLGDRVPYVIISaakgvaaYMKSEDPLFVLEH-SLPIDTQYYLEQQL-- 938
Cdd:cd05537 293 LRRPLSEYtKNVPPHVQAA---RLADQ-INRELGRPRQYQWIE-------YVITVNGPEPLEYrTSPLDYQHYIDKQLkp 361
|
410
....*....|
gi 530416735 939 -AKPLLRIFE 947
Cdd:cd05537 362 iADSILPFLG 371
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
988-1058 |
2.49e-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: 114.39 E-value: 2.49e-30
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530416735 988 CIGCRTVlshQGAVCEFCQPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMR 1058
Cdd:pfam14260 1 CLGCGAP---EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYMR 68
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
579-952 |
3.48e-26 |
|
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99914 Cd Length: 352 Bit Score: 111.28 E-value: 3.48e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 579 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTPtgdefvktsvRKGLLPQ 658
Cdd:cd05531 3 LADRGGLVFQPEPGLYE-NVAQIDFSSMYPSIIVKYNISPETINCRCCECRDHVYLGHRICLK----------RRGFLPE 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 659 ILENLLSARKRAKAELAKETDPlrrqvlDGRQLALK------------------------SVTGFGRQMIEKTKQLVEsk 714
Cdd:cd05531 72 VLEPLLERRLEYKRLKKEEDPY------AGRQKALKwilvtsfgylgyknakfgrievheAITAYGRKILLRAKEIAE-- 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 715 ytvENGYstsaKVVYGDTDSVMCRfgVSSVAEAMALGREAadwvsghfPSPIRLEFEKVY-FPYLLISK------KRYAG 787
Cdd:cd05531 144 ---EMGF----RVLHGIVDSLWIQ--GRGDIEELAREIEE--------RTGIPLKLEGHYdWIVFLPERdglgapNRYFG 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 788 LLFSsrpdahDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPE---GAVAHAQDVIS--DLLCNRIDISQLVITKE 862
Cdd:cd05531 207 RLSD------GEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEellKLREEALDLFRryLQRLREGDLEDLIIEKK 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 863 LTRAASDYAGKQAHVelAERMRKRdpGSAPSLGDRVPYVIISAAKGVAaymksedplfVLEHSLPIDTQYYLEQqlakpL 942
Cdd:cd05531 281 ISKRSSEYKVLASTA--LKALRAK--GVSVVPGMKIEYIVRDGKRPVP----------DLGNDEGYDTKYYREL-----L 341
|
410
....*....|
gi 530416735 943 LRIFEPILGE 952
Cdd:cd05531 342 ERAAEELLFP 351
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
310-526 |
4.38e-24 |
|
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: 100.89 E-value: 4.38e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 310 LRVLSFDIECAGRKGIfPEPERDPVIQI--CSLG----LRW-GEPEPFlrlaltlrpcapilgakVQSYEKEEDLLQaws 382
Cdd:cd05780 3 LKILSFDIEVLNHEGE-PNPEKDPIIMIsfADEGgnkvITWkKFDLPF-----------------VEVVKTEKEMIK--- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 383 TFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVQtFPfLGRVAglcSNIrdssfqsKQTGRRDTKVVSMVGRVQMDM 459
Cdd:cd05780 62 RFIEIVkekDPDVIYTYNGDNFDFPYLKKRAEKLGIE-LD-LGRDG---SEI-------KIQRGGFNNASEIKGRIHVDL 129
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530416735 460 LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNgNDQTRRRLAVYCLKDAYLPLRLLERL 526
Cdd:cd05780 130 YPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWD-SGENLERLFRYSMEDAKYTYEIGKEF 195
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
310-524 |
1.06e-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: 1.06e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 310 LRVLSFDIECAGRKGIFPEPERDPVIQIC----------------SLGLRWGEPEPFLRLALTLRPCapiLGAKVQSYEK 373
Cdd:cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFycidddvspfildankVGVIIVDELKSNASNGRIRSGL---SGIPVEVVES 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 374 EEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPF-LGRVaglcSNIRDSSFQSKQTGRRDTK--VVS 450
Cdd:cd05778 81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDeISRV----PSDSNGKFGDRDDEWGYTHtsGIK 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530416735 451 MVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGND-QTRRRLAVYCLKDAYLPLRLLE 524
Cdd:cd05778 157 IVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSaSERWRVLEYYLKRVRLNLEILD 231
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
309-697 |
6.76e-21 |
|
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: 99.36 E-value: 6.76e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 309 PLRVLSFDIEC--AGRKGIFP--EPERDPVIQI----CSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQA 380
Cdd:TIGR00592 197 ELKLASFDIETyfHDGKDFFPgdENPADEEIMIsttpVIAKQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKR 276
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 381 WSTFIRIMDPDVITGYNIQNFDLPYLISRaqtlkvQTFPF-----------LGRVAGLCSNIRDSSFQSKQTG-RRDTKV 448
Cdd:TIGR00592 277 FWDVIDQEDTDVEITVNGDNFDLVYLADR------QVFQFywdayedpaekLGVVLLFGRDVDHVSPCVQVKGiNRDLFF 350
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 449 VSMVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITdlQNGNDQTRRRLAVYCLKDAYLPLRLLERLMV 528
Cdd:TIGR00592 351 LPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIA--KKYEFEAPDIDAPYSSEYLEVTYELGKEFAP 428
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 529 LVNAVEMARVTGVPLSYLLSRGQQVKVVsqLLRQAMHEGLLMPV------VKSEGGEDYTGATVIEPL--KGYY--DVPI 598
Cdd:TIGR00592 429 MEALPSDLKGQTFWHVFGSNTGNLERFL--LLRKIKGPCWLAVKgpdeleYPRRSWCKYEGGYVKPPNveKGLDktPPPL 506
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 599 ATLDFS--SLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTP-TGDEFVKTSVR-------KGLLPQILENLLSARK 668
Cdd:TIGR00592 507 VVLDFSmkSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPcVGTRPKDCSFPldlkgefPGKKPSLVEDLATERA 586
|
410 420 430
....*....|....*....|....*....|.
gi 530416735 669 RAKAELA--KETDPLRRQVLDGRQLALKSVT 697
Cdd:TIGR00592 587 LIKKFMAkvKKIDPDEIVGHDYQQRALKVLA 617
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
310-678 |
8.02e-21 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 98.99 E-value: 8.02e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 310 LRVLSFDIECAGRKGiFPEPERDPViQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQ----------SYEKEEDLLQ 379
Cdd:PHA02528 106 IRIANLDIEVTAEDG-FPDPEEAKY-EIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPqeildkvvymPFDTEREMLL 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 380 AWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLkvqtfpfLG-RVAGLCSNIRdsSFQSKQT----GRRDTKvVSMVGR 454
Cdd:PHA02528 184 EYINFWEENTPVIFTGWNVELFDVPYIINRIKNI-------LGeKTAKRLSPWG--KVKERTIenmyGREEIA-YDISGI 253
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 455 VQMDMLQVllreYK------LRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQtrrRLAVYCLKDAYLPLRLLERLMV 528
Cdd:PHA02528 254 SILDYLDL----YKkftftnQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQ---KYIEYNIIDVELVDRLDDKRKL 326
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 529 LVNAVEMARVTGVPLSYLLSrgqQVK-----VVSQLLRQamheGLLMPVVKSEGGEDYTGATVIEPLKGYYDVpIATLDF 603
Cdd:PHA02528 327 IELVLSMAYYAKINFEDVFS---PIKtwdaiIFNSLKEE----KIVIPENKSHKKQKYAGAFVKEPVPGAYRW-VVSFDL 398
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 604 SSLYPSIMMAHNLCYTTLLrpGT----------AQKLGLTEDQFIRTPTGDEFVKTsvRKGLLPQILENLLSARKRAK-- 671
Cdd:PHA02528 399 TSLYPSIIRQVNISPETIA--GTfhvapvheyiNKTAPRPSDEYSCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIYKkk 474
|
410
....*....|....
gi 530416735 672 -------AELAKET 678
Cdd:PHA02528 475 mlaaernAELIKTI 488
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
578-909 |
3.17e-20 |
|
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: 93.95 E-value: 3.17e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 578 GEDYTGATVIEPLKG-YYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPGtaqklglTEDQFIRTPTGDEFVKTSvRKGLL 656
Cdd:cd05530 10 GKKYRGAIVLEPPPGiFFNV--VVLDFASLYPSIIKVWNLSYETVNCPH-------CECKTNEVPEVGHWVCKK-RPGIT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 657 PQILENLLSAR-----KRAKaelAKETDPLRRQVLDGRQLALK------------------------SVTGFGRQMIEKT 707
Cdd:cd05530 80 SQIIGLLRDLRvkiykKKAK---DKSLDEEMRQWYDVVQSAMKvfinasygvfgaenfplycppvaeSTTALGRYIITST 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 708 kqlveSKYTVENGYstsaKVVYGDTDSVMCRFGVSSVAEamalgrEAADWVSGHFpsPIRLEFEKVYfPYLLIS--KKRY 785
Cdd:cd05530 157 -----IKKARELGL----KVLYGDTDSLFLWNPPQEQLE------DLVEWVEKEL--GLDLELDKEY-RYVVFSglKKNY 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 786 AGLLFSSrpdahdRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEgAVAHAQDVISDL-------LCNR-IDISQL 857
Cdd:cd05530 219 LGVTKDG------SVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPE-DFEKAREKIRDIvkgvykrLKKKeYTLDQL 291
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|...
gi 530416735 858 VITKELTRAASDYA-GKQAHVELAERMRKRdpGSAPSLGDRVPYVIISAAKGV 909
Cdd:cd05530 292 AFKVMLSKPPEEYTkNTPQHVKAARQLEKY--GRNVEAGDIISYVKVKGKEGV 342
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
313-814 |
6.61e-19 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 92.78 E-value: 6.61e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 313 LSFDIECAGRKGiFPEPERDPV--IQICSLGLRWGEpepfLRLALT---LRPCAPILGAKVQSYEKEEDLLQAWSTFIRI 387
Cdd:PHA03036 163 LFLDIECHFDKK-FPSVFINPVshISCCYIDLSGKE----KRFTLInedMLSEDEIEEAVKRGYYEIESLLDMDYSKELI 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 388 ----------------MDPDVITGYNIQNFDLPYLISRAQTLKVQTF----PFLGRVAGLCSNIRDSSFQSKQTGRRDT- 446
Cdd:PHA03036 238 lcseivllriakklleLEFDYVVTFNGHNFDLRYISNRLELLTGEKIifrsPDGKETVHLCIYERNLSSHKGVGGVANTt 317
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 447 -KVVSMVGRVQMDMLQVLLREYKLRSYTLNAVS---FH--------------FLGEQKEDVQ------------------ 490
Cdd:PHA03036 318 yHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISknaFNcnakvlsennnevtFIGDNTTDAKgkasifsevlstgnyvti 397
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 491 ------------------------------HSIIT--------DLQ----NGNDQTRRRLAVYCLKDAYLPLRLLERLMV 528
Cdd:PHA03036 398 ndddickildkdiiensftvkvicknnyipGDTYTlsfgkddvDLSdmykNYNLEIALEMARYCIHDACLCKYLWEYYGI 477
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 529 lvnaveMARVTGVPLSYLLSRGQQVKVVS------QLLRQAMHEGLLMPVVKSEGGEDYTGATVIEPLKGYYDVPIATLD 602
Cdd:PHA03036 478 ------ETKIDAGASTYLLPQSMVFEYRAstlikgPLLKLLLEEKTILVRSETKNKFPYEGGKVFAPKQKMFDNNVLIFD 551
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 603 FSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTE--DQFIR-------------TPTGDEFVKTSV-----RKGLLPQILEN 662
Cdd:PHA03036 552 YNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEinKQELRrkypypryiyvhcEPRSPDLVSEIAvfdrrIEGIIPKLLKT 631
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 663 LLSARKRAKAELAKETDPLRRQVLDGRQL------------------AL------KSVTGFGRQMIE------------- 705
Cdd:PHA03036 632 FLEERARYKKLLKEATSSVEKAIYDSMQYtykivansvyglmgfrnsALysyasaKSCTAIGRNMIKylnsvlngsklin 711
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 706 --------------KTKQLVESKYT--VENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGH-FPSPIRL 768
Cdd:PHA03036 712 gklilancpinpffKDDRSIDTNYDtnLPVEYNFTFRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINEKvLFDNFKI 791
|
650 660 670 680
....*....|....*....|....*....|....*....|....*...
gi 530416735 769 EFEKVYFPYLLISKKRYAGLLF--SSRPDAHDRMDCKGLEAVRRDNCP 814
Cdd:PHA03036 792 EFEAVYKNLIMQSKKKYTTLKYiaSSTDGSVPERVNKGTSETRRDVSK 839
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
309-524 |
2.10e-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: 84.54 E-value: 2.10e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 309 PLRVLSFDIECagrkgifpeperDPVIQICSLGLrWGEPEpflRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIRIM 388
Cdd:cd05784 2 KLKVVSLDIET------------SMDGELYSIGL-YGEGQ---ERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQY 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 389 DPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRvAGLCSNIRDSSFQSKQTgrrdtkvVSMVGRVQMDMLQvLLRE- 466
Cdd:cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAHGL---PLrLGR-GGSPLNWRQSGKPGQGF-------LSLPGRVVLDGID-ALKTa 133
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 530416735 467 -YKLRSYTLNAVSFHFLGEQKedvqhsIITDLQNGNDQTRRR-------LAVYCLKDAYLPLRLLE 524
Cdd:cd05784 134 tYHFESFSLENVAQELLGEGK------LIHDVDDRGAEIERLfredklaLARYNLQDCELVWRIFE 193
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
597-944 |
7.56e-16 |
|
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: 80.22 E-value: 7.56e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 597 PIATLDFSSLYPSIMMAHNLCyttllrpgtaqklgltedqfirtPTGDEFvktsvrkGLLPQILENLLSARKRAKAELAK 676
Cdd:cd05538 18 PIVHADVASLYPSIMLAYRIC-----------------------PARDSL-------GIFLALLKYLVELRLAAKESARA 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 677 ETDPLRRQVLDGRQLALK------------------------SVTGFGRQMIEKTKQLVESKytvengystSAKVVYGDT 732
Cdd:cd05538 68 AARPAERDAFKAKQAAFKvlinsfygylgtglhafsdpeaaaEVTRLGRELLKLMIRWLRRR---------GATPVEVDT 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 733 DSV--MCRFGVSSVAEAMALGREaadwVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSsrpdahDRMDCKGLEAVRR 810
Cdd:cd05538 139 DGIyfIPPNGVDTEDEEEELVRE----LSSTLPKGITVEFDGRYRAMFSYKIKNYALLDYD------GKLIVKGSAFRSR 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 811 DNCPLVANLVTASLRRLLIDrDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDY-----AGKQAHVELAERMRK 885
Cdd:cd05538 209 GIEPFLREFLREAVRLLLQG-DGAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYlqkvrAGKRNPAAAYEIALA 287
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530416735 886 RDPGSAPslGDRVPYVIISAAKGVAAYMK-SEDPLFVLEHSLpIDTQYYLEQ--QLAKPLLR 944
Cdd:cd05538 288 RPREWRA--GDRVTYYVSGTGKGVSVYENcRLVADYDPAHPD-ENTGFYAERllQLAARLLP 346
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
309-483 |
9.37e-16 |
|
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: 76.60 E-value: 9.37e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 309 PLRVLSFDIECAGRKGiFPEPERDPVIQIcSLGLRWGEPEPFLrlaltlrpcapilgakvQSYEKEEDLLQAWSTFIRIM 388
Cdd:cd05781 2 DLKTLAFDIEVYSKYG-TPNPRRDPIIVI-SLATSNGDVEFIL-----------------AEGLDDRKIIREFVKYVKEY 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 389 DPDVITGYNIQNFDLPYLISRAQTLKVQTfpFLGRVAGlcsnirDSSFQSKqTGRrdtkvVSMVGRVQMDMLQVLLREYK 468
Cdd:cd05781 63 DPDIIVGYNSNAFDWPYLVERARVLGVKL--DVGRRGG------SEPSTGV-YGH-----YSITGRLNVDLYDFAEEIPE 128
|
170
....*....|....*
gi 530416735 469 LRSYTLNAVSfHFLG 483
Cdd:cd05781 129 VKVKTLENVA-EYLG 142
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
307-522 |
2.33e-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: 75.82 E-value: 2.33e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 307 IAPLRVLSFDIEC-AGRKGIFPEPERD--PVIQIC---SLGLRwgepepflRLALTLRPCAPIL------GAKVQSYEKE 374
Cdd:cd05783 2 IPKLKRIAIDIEVyTPIKGRIPDPKTAeyPVISVAlagSDGLK--------RVLVLKREGVEGLegllpeGAEVEFFDSE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 375 EDLLQAwstFIRIMD--PDVITgYNIQNFDLPYLISRAQTLKV--QTFPFLGRvaglcsniRDSsfqskqtgrrdtkvVS 450
Cdd:cd05783 74 KELIRE---AFKIISeyPIVLT-FNGDNFDLPYLYNRALKLGIpkEEIPIYLK--------RDY--------------AT 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 451 MVGRVQMDM--------LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIitdlqngNDQTRRRLAVYCLKDAYLPLRL 522
Cdd:cd05783 128 LKHGIHIDLykffsnraIQVYAFGNKYREYTLDAVAKALLGEGKVELEKNI-------SELNLYELAEYNYRDAELTLEL 200
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
327-529 |
4.11e-13 |
|
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: 69.95 E-value: 4.11e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 327 PEPERDPVIQICSLGL---RWGEPEPFLRLALTLRPcapilgaKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDL 403
Cdd:cd05776 39 PTPPPPFQSHTCTLTRplgRSPPPDLFEKNAKKKKT-------KVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDL 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 404 PYLISRAQTLKVQTFPFLGRVaglcsnIRDSSFQSKQTGRRDTKVVsMVGRVQMDMlQVLLRE-YKLRSYTLNAVSFHFL 482
Cdd:cd05776 112 DVLLSRIQELKVPHWSRIGRL------KRSVWPKKKGGGKFGEREL-TAGRLLCDT-YLSAKElIRCKSYDLTELSQQVL 183
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 530416735 483 GEQKEDVqhsIITDLQNGNDQTRR--RLAVYCLKDAYLPLRLLERLMVL 529
Cdd:cd05776 184 GIERQDI---DPEEILNMYNDSESllKLLEHTEKDAYLILQLMFKLNIL 229
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
310-515 |
4.32e-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: 69.36 E-value: 4.32e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 310 LRVLSFDIECAGRKGIF---PEPERDPVIQIcslGLRwgEPEPFlRLALTLRPCApilgakvqsyekEEDLLQAWSTFIR 386
Cdd:cd05785 9 LRRLQLDIETYSLPGFFfsnPDRGDDRIIIV---ALR--DNRGW-EEVLHAEDAA------------EKELLEELVAIIR 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 387 IMDPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRVaGLCSNIRDSSFQSKQtGRRDTKVVSMVGRVQMDMLQVLLR 465
Cdd:cd05785 71 ERDPDVIEGHNIFRFDLPYLRRRCRRHGV---PLaIGRD-GSIPRQRPSRFRFAE-RLIDYPRYDIPGRHVIDTYFLVQL 145
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 530416735 466 ----EYKLRSYTLNAVSFHF--LGEQKEDVQHSIITDLQNGNdqtRRRLAVYCLKD 515
Cdd:cd05785 146 fdvsSRDLPSYGLKAVAKHFglASPDRTYIDGRQIAEVWRSD---PARLLAYALDD 198
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
366-737 |
5.22e-12 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 70.66 E-value: 5.22e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 366 AKVQSYEKEEDLLQAWSTFI----RIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPfLGRVAGLCSnIRDSSFQSKQT 441
Cdd:PHA03334 370 FKQRPHPLTKALMEAWEAFLskdpQLVPAQLLFGSDILNSNYLELLDVIESHKAQFKA-TCRKAAARK-EEIGSYMKTRD 447
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 442 GRRDTKVVSMV---------GRVQMDMLQVLLR---EYKLRSYTLNAVSFHFLGEQK-----------EDVQHSIITDLQ 498
Cdd:PHA03334 448 TVQDFNDNDKKylnstshgfGAHIIDLMRVCNTksiKAKCSSRKLDTVARLIISKSKphknppkigkmDDVKYTEMDGMF 527
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 499 NGNDQTRRRLAVYCLKDAYLPLRL----------LERLMVLVNA---------------VEMARVTGVPLSYllSRGQQV 553
Cdd:PHA03334 528 TAGGAALARYLIYNLVDSELLIRIaknldpviefLNRLRATYNIdyvahgrgvmnfcgfVQSTKSVEVPLLK--ARLRIG 605
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 554 KVVSQLlRQAmhEGLLMP-VVKSEGGEDYT--GATVIEPLKGY-----YDVPIATLDFSSLYPSIMMAHNLCYTTLLRPG 625
Cdd:PHA03334 606 IFVATG-RIA--ESLCMPeKYARDCRQKIKlkGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIVDPD 682
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 626 TA---------------QKLGLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQ 690
Cdd:PHA03334 683 CTarvrgwvvfdwkkidRGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQ 762
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530416735 691 LALKS----------------VTGFGRQMIektkQLVESKYTVENGYStsakVVYGDTDSVMC 737
Cdd:PHA03334 763 NEMKIcanshygvaphacqhlITTLGRHKI----KLVEEFIKKEPGMT----VNYGDTDSVMF 817
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
371-671 |
1.11e-06 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 52.69 E-value: 1.11e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 371 YEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLkvqtfpfLG-RVAGLCSNIRDSSFQSKQTGRRDTKVV 449
Cdd:PHA02524 177 FEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNI-------LGeKAANQLSPYGKITSKTITNLYGEKIIY 249
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 450 SMVGRVQMDMLQVLlREYK---LRSYTLNAVSFHFLGEQKEDVQHSIiTDLQNGNDQtrrRLAVYCLKDAYLPLRLLERL 526
Cdd:PHA02524 250 KIHGIALMDYMDVF-KKFSftpMPDYKLGNVGYREVKADKLDYEGPI-NKFRKADHQ---RYVDYCVRDTDIILLIDGRR 324
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 527 MVLVNAVEMARVTGVPLSYLLSrgqQVKVVSQLLRQAMHE-GLLMPVVKSEGGEDYTGATVIEPLKGYYDVPIaTLDFSS 605
Cdd:PHA02524 325 CFIDLILSLSYYAKIRFDDVLG---TIKVWDSIIFNSLVEsNVVIPAMKASPKQSFPGAYVKEPVPGGYRYGL-SFDLTS 400
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530416735 606 LYPSIMMAHNLC---YTTLLRP--------GTAQKlglTEDQFIRTPTGDEFVKTSVrkGLLPQILENLLSARKRAK 671
Cdd:PHA02524 401 LYPSILRLLNISpemIAGMFSParledyinKVAPK---PSDQFSCAPNGMMYKKGVV--GVLPNETEKVFLQRKSEK 472
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
309-413 |
6.93e-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: 6.93e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530416735 309 PLRVLSFDIECAGRKGIFPEPERDPVIQIcSLGLrwgEPEPFLrlaLTLRPcapILGAKVQSYE---------------- 372
Cdd:cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMI-SYMI---DGQGYL---IVNRE---IVSEDIEDFEytpkpeyegpfkvfne 70
|
90 100 110 120
....*....|....*....|....*....|....*....|..
gi 530416735 373 -KEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTL 413
Cdd:cd05779 71 pDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIH 112
|
|
| |
