|
Name |
Accession |
Description |
Interval |
E-value |
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
80-1099 |
0e+00 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 1480.27 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 80 RPAPPalDPQMEPLIFQQLEIDHYV----APARPLPGAPPPSQDSVPILRAFGVTNEGVSVCCHIHGFAPYFYTPAPPGF 155
Cdd:PTZ00166 31 RPLPP--ISLQKDLVFFQLDADYTEkddkSQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNF 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 156 GPEHLSELQRELSAAISRDQRGGKelTGPAVLAVELCSRESMFGYHGHGPSPFLRITLALPRLMAPARRLLEQGIRL--- 232
Cdd:PTZ00166 109 LPEDSQKLKRELNAQLSEQSQFKK--YQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVcgg 186
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 233 AGLGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYILRPEGKAT-LCQLEADVLWSDVISHPPEGEWQRIAPLRV 311
Cdd:PTZ00166 187 GWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKTsTCQIEVDCSYEDLIPLPPEGEYLTIAPLRI 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 312 LSFDIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEREEDLLQAWSTFIRIMDP 389
Cdd:PTZ00166 267 LSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDP 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 390 DVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVIGLRSNIRESSFQSRQTGRRDSKVVSMVGRVQMDMLQVLLREYKLR 469
Cdd:PTZ00166 347 DFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLK 426
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 470 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGYLLSRG 549
Cdd:PTZ00166 427 SYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRG 506
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 550 QQVKVVSQLLRQAMRQGLLMPVVKTEGG---EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAA 626
Cdd:PTZ00166 507 QQIKVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDA 586
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 627 QKlgLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQ 706
Cdd:PTZ00166 587 NN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQ 664
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 707 V-GRLPCLEISQSVTGFGRQMIEKTKQLVETKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHF 785
Cdd:PTZ00166 665 VgGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKF 744
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 786 PSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQD 865
Cdd:PTZ00166 745 LKPIKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKG 823
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 866 VISDLLCNRIDISQLVITKELTRaaADYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVL 945
Cdd:PTZ00166 824 KISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL 901
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 946 EHSLPIDTQYYLEqQLAKPLLRIFEPILGEgraEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLShQGAVC 1025
Cdd:PTZ00166 902 ENNIPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIK-EGALC 976
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27806073 1026 KFC-QPRESELYQKEVSHLSALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQERLLRRFG 1099
Cdd:PTZ00166 977 DNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
578-973 |
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: 821.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 578 EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLGltEDQFIKTPTGDEFVKASVRKGLLPQ 657
Cdd:cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLP--PEDYIKTPNGDYFVKSSVRKGLLPE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 658 ILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVETK 737
Cdd:cd05533 79 ILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 738 YTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRP 817
Cdd:cd05533 159 YTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLW-TNP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 818 DAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADYAGKQ 897
Cdd:cd05533 238 DKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADDYAGKQ 317
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 27806073 898 AHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPIL 973
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 ... |
540-972 |
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: 568.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 540 VPLGYLLSRGQQVKVVSQLLRQAMRQGLLMPVVKTEGG--EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 617
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGdeDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 618 TTLLRPGAA---QKLGLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKV 694
Cdd:pfam00136 81 TTLVRSVDEannLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLALKI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 695 SANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVETKYTvengysTSAKVVYGDTDSVMCRFGVSSVAEAMALG 774
Cdd:pfam00136 161 TANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT------YNFRVIYGDTDSVFIEFGGKDVEEAMKIG 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 775 REAADWVSGH-FPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLID 853
Cdd:pfam00136 235 DELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKY-TAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSD 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 854 RDPSGAVAHAQDVI----SDLLCNRIDISQLVITKELTRAAADYAGKQ-AHVELAERMRKRDpGSAPSLGDRVPYVIISA 928
Cdd:pfam00136 314 RGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEVALRMNKRN-GEAPEVGDRIPYVIVKA 392
|
410 420 430 440
....*....|....*....|....*....|....*....|....*..
gi 27806073 929 AK---GVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 972
Cdd:pfam00136 393 AKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
119-972 |
1.50e-179 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 544.81 E-value: 1.50e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 119 DSVPILRAFGVTNEGVSVCCHIHGFAPYFYTPAPpgfgpehlselQRELSAAISRDQRGgkeltgpaVLAVELCSRESMF 198
Cdd:COG0417 16 DGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLP-----------DEEKLEELLRDIKE--------ITEVEPVKLKSFF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 199 GyhghGPSPFLRITLALPRLMAPARRLLEQGIrlaglgtpsFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKyilrpEG 278
Cdd:COG0417 77 G----EPVPVLKIYTRDPRDVRELRDRLKEGG---------IDVYEADIRFHDRYLIDRFLTPGVWYEGEVEE-----DG 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 279 KATLCQLEADVLWSDVISHPPegewqriapLRVLSFDIECAGRKGiFPEPERD-PVIQICSlglrwgEPEPFLRLALTLR 357
Cdd:COG0417 139 GKLDYEVKENPRLKPEDYRPK---------LKVLSFDIEVSTPRG-FPDPERDgPIISIGL------AGSDGEKKVLMLG 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 358 pcAPILGAKVQSYEREEDLLQAwstFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVPgfPLLGRViGLRSNIRESS 434
Cdd:COG0417 203 --REGVDFEVEYFDDEKALLEA---FFEIIreyDPDIIIGWNVDNFDLPYLQKRAERLGIP--LDLGRD-GSEPSWREHG 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 435 FQSRqtgrrdskvVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQngnDQTRRRLAVYCLK 513
Cdd:COG0417 275 GQGF---------ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKLIVDGGEIERLW---DDDKPALAEYNLR 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 514 DAFLPLRLLERLMVLVNAMEMARVTGVPLgYLLSRGQQVKVVSQL-LRQAMRQGLLMPVVKTEGGEDYTGATVIEPLKGY 592
Cdd:COG0417 343 DAELTLRIFEKTLLLPFLIELSRITGLPL-DDVGRAGSSAAFENLlLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGL 421
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 593 YDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQklgltEDQFIKTPT-GDEFVKAsvRKGLLPQILENLLSARKRAKA 671
Cdd:COG0417 422 YE-NVLVLDFKSLYPSIIRTFNISPETLVEGGEEP-----CGDEDVAPGfGHRFCRE--PKGILPSILEELWDERDEAKK 493
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 672 ELAK-ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvENGYstsaKV 750
Cdd:COG0417 494 KMKKaKPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAE-----ELGY----KV 564
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 751 VYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLI-SKKRYAGLLfssrPDahDRMDCKGLE 829
Cdd:COG0417 565 IYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPgSKKRYAGLT----ED--GKIDIKGLE 638
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 830 AVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADY-AGKQAHVELAERMRK 908
Cdd:COG0417 639 AVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYeKNVPPHVRAARKLDE 718
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 27806073 909 RdpGSAPSLGDRVPYVIISAAKGVaaymksEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 972
Cdd:COG0417 719 R--GRPYQRGDKISYVITKGGGRV------EPVELAKERESEIDYDYYIEKQLKPTADRILEAF 774
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
303-532 |
1.48e-148 |
|
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues necessary for metal binding and catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation.
Pssm-ID: 99820 [Multi-domain] Cd Length: 230 Bit Score: 443.17 E-value: 1.48e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 303 WQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWST 382
Cdd:cd05777 1 WSKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 383 FIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVIGLRSNIRESSFQSRQTGRRDSKVVSMVGRVQMDMLQVL 462
Cdd:cd05777 81 FVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVI 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 463 LREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAM 532
Cdd:cd05777 161 QRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLVNYI 230
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
308-763 |
4.91e-148 |
|
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Pssm-ID: 214691 [Multi-domain] Cd Length: 474 Bit Score: 451.60 E-value: 4.91e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 308 PLRVLSFDIECAGRKGIFPEPE--RDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWSTFIR 385
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 386 IMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRV-IGLRSNIRESSFQSRQTGRRDSKVVsMVGRVQMDMLQVLLR 464
Cdd:smart00486 82 KYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLkIGLRIPNKKPLFGSKSFGLSDIKVY-IKGRLVIDLYRLYKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 465 EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGY 544
Cdd:smart00486 161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 545 LLSRGQQVKVVSQLLRQAMRQGLLMPVVKTEGG----------EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHN 614
Cdd:smart00486 241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 615 LCYTTLLRPGAAQKLGLT----EDQFIKTPTG--DEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPL--RRQVLD 686
Cdd:smart00486 321 LCYSTLVGVGEVVIKGDLiipeDLLTIKYEKGnkYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESeeLKKLLD 400
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27806073 687 GRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvENGYST-SAKVVYGDTDSVMCRFG 763
Cdd:smart00486 401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIE-----ENGYPKpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
119-974 |
9.59e-114 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 371.50 E-value: 9.59e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 119 DSVPILRAFGVTNEGVSVCCHIHGFAPYFYtPAppgfgpEHLSELQRELSAAISRDQR--GGKELTGPAVLAVelcsres 196
Cdd:PRK05762 17 PGGPEVELWLATDEGPRVVLLDPQFRPYFI-PA------EQDERAESLLAGEIGVRLSplALKDFHRRPVLGL------- 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 197 mfgyhghgPSPFLRITLALPRlmaparRLLEQGIRLaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLElpaGKYILR- 275
Cdd:PRK05762 83 --------YCRQHRQLTRLPK------RLREGGVDV----------YEADIRFPERYLMERFITPCVWFS---GEVEQYt 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 276 PEGKATLCQLEADVLWsdvishPPegewqriaPLRVLSFDIECAgRKGI-----FPEPERDPVIQIcslglrwGEPEPfl 350
Cdd:PRK05762 136 TDGVLRNARLKPAPDY------RP--------PLKVVSLDIETS-NKGElysigLEGCGQRPVIML-------GPPNG-- 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 351 rlaltlrpCAPILGAKVQSyerEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPgfPLLGRViGLRSNI 430
Cdd:PRK05762 192 --------EALDFLEYVAD---EKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIP--LRLGRD-GSELEW 257
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 431 RESSFQSrQTGrrdskVVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEdvqhsIITDLQNGNDQTRR---- 505
Cdd:PRK05762 258 REHPFRS-GYG-----FASVPGRLVLDGIDALKSaTWVFDSFSLEYVSQRLLGEGKA-----IDDPYDRMDEIDRRfaed 326
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 506 --RLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGyllsR--GQQVKVVSQLLRQAMRQGLLMPVVKTEGGEDYT 581
Cdd:PRK05762 327 kpALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLD----RvgGSVAAFEHLYLPRAHRAGYVAPNLGERPGEASP 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 582 GATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPgaaqkLGLTEDQFIKTPTGDEFVKasvRKGLLPQILEN 661
Cdd:PRK05762 403 GGYVMDSKPGLYD-SVLVLDFKSLYPSIIRTFNIDPDGLVEG-----LAQPPEESVAGFLGARFSR---EKHFLPEIVER 473
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 662 LLSARKRAKAELAKEtdplrrqvldgRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvE 741
Cdd:PRK05762 474 LWEGRDEAKREMNKP-----------LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIE-----A 537
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 742 NGYstsaKVVYGDTDSVMCRFGVS-SVAEAMALGREAADWVSGHFPSPIR----------LEFEKVY----FPYLLI--- 803
Cdd:PRK05762 538 QGY----QVIYGDTDSTFVWLGGAhDEEDAAKIGRALVQEINQWWQEHLQqefglesaleLEFEKHYrrffMPTIRGaee 613
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 804 -SKKRYAGLLfsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVahaQDVISDLLCNRIDiSQLVI 882
Cdd:PRK05762 614 gSKKRYAGLI--QEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEPYVDYV---REVIDKLRAGELD-EKLVY 687
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 883 TKELTRAAADYAGKQA-HV----ELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSedplfvlehslPIDTQYYL 957
Cdd:PRK05762 688 RKRLRRPLDEYQRNVPpHVraarLADEMGYKVGRPLQYQNGGKIGYVITVNGPEPLEYRKS-----------PIDYDYYI 756
|
890
....*....|....*..
gi 27806073 958 EQQLaKPLLRIFEPILG 974
Cdd:PRK05762 757 EKQL-QPVADRILPFFG 772
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
129-476 |
8.80e-105 |
|
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: 332.07 E-value: 8.80e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 129 VTNEGVSVCCHIHGFAPYFYTPAPPGFGPEHLSELQRELSAAISRdqrggkeltgpaVLAVELCSRESMFGYHGHgPSPF 208
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKELEEVIEEIKELYEGLDK------------IEKIELKLKKSLYGYEED-PVPY 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 209 LRITLALPRLMAPARRLLEQGirlaglgtPSFAPYEANVDFEIRFMVDTDIVGCNWLELPagKYILRPEGKATLCQLEAD 288
Cdd:pfam03104 68 LKVSFANPRPLLKIRKYLSPE--------NISDVYEYDVDYLERFLIDNDIVGFGWYKVK--VYPFRAEGRISNCDVEID 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 289 VLWSDVISHPPEGEWqriAPLRVLSFDIECAGRKGIFPEPER--DPVIQICSLGLRWGEPEPFLRLALTLRPCAPI---- 362
Cdd:pfam03104 138 CDSPDLISVPFEKEW---PPLRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEPRFLFTLRECDSEdied 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 363 ---------LGAKVQSYEREEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRV-IGLRSNIRE 432
Cdd:pfam03104 215 feytpkpiyPGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLnRGGRSKVRE 294
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 27806073 433 SSFqsrqtGRRDSKVVSMVGRVQMDMLQVLLREYKLRSYTLNAV 476
Cdd:pfam03104 295 IGF-----GTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
549-972 |
2.15e-102 |
|
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Pssm-ID: 99917 Cd Length: 451 Bit Score: 329.95 E-value: 2.15e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 549 GQQVKVVSQLLRQAMRQGLLMP-----VVKTEGGEDYTgATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLL-- 621
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPspsrqQVAQQRALECL-PLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLgr 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 622 ------------------RPGAAQKLGLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSAR---KRAKAELAKETDPL 680
Cdd:cd05534 80 veelngggkfgflgvklyLPPPPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRimvKKAMKKYKDDKKLQ 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 681 RRqvLDGRQLALKVSANSVYGFTGAQV-GRLPCLEISQSVTGFGRQMIEKTKQLVETkyTVENGystsAKVVYGDTDSVM 759
Cdd:cd05534 160 RI--LDARQLALKLLANVTYGYTAASFsGRMPCVEIADSIVQTGRETLERAIELIES--TPKWG----AKVVYGDTDSLF 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 760 CRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLV 839
Cdd:cd05534 232 VLLPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAV 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 840 ANLVTASLRRLLIDRDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADYAGK-QAHVELAERMRKRDPGSAPSLG 918
Cdd:cd05534 312 QKILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGATlPAGAIVALRRMEKDPRAEPQYG 391
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 27806073 919 DRVPYVIISAAKGVAAYMKSEDP-LFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 972
Cdd:cd05534 392 ERVPYVVVRGEPGSRLIDLVVSPeEFLADPSLRLDAEYYITKQIIPALDRLFNLV 446
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
206-970 |
2.43e-88 |
|
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: 309.68 E-value: 2.43e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 206 SPFLRITLALPRLMAPARRLLEQGIrlaglGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKyiLRPEGKATLCQL 285
Cdd:TIGR00592 413 SEYLEVTYELGKEFAPMEALPSDLK-----GQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPD--ELEYPRRSWCKY 485
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 286 EADVLWSDVIShppEGEWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTL--RP--CAP 361
Cdd:TIGR00592 486 EGGYVKPPNVE---KGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVgtRPkdCSF 562
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 362 ILG----------AKVQSYEREEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVigLRSNIR 431
Cdd:TIGR00592 563 PLDlkgefpgkkpSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRL--RRSPKF 640
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 432 ESSFQSRQTGRrdskvvsMVGRVQMDMLQVLlreyKLRSYTLNAVSFHFLG-EQKEDVQHSIITDLQNGNDQTRrrLAVY 510
Cdd:TIGR00592 641 GRRFGERTCGR-------MICDVEISAKELI----RCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLTY--LLEH 707
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 511 CLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGYLLSRGQQVKVVSQLLRQAMRQGLLMP----VVKTEGGED------- 579
Cdd:TIGR00592 708 TWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqiFRKQQKLGDedeeidg 787
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 580 --------YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPgaaqklgLTEDQFIKTPtgdefvKASVR 651
Cdd:TIGR00592 788 ykkgkkaaYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQK-------VDEDELPELP------DSELE 854
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 652 KGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTK 731
Cdd:TIGR00592 855 MGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTR 934
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 732 QLVETKYTvengystsaKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPsPIRLEFEKVYFPYLLISKKRYAGL 811
Cdd:TIGR00592 935 QLVEEMNL---------EVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-LLELDIDGVFKRLLLLKKKKYAAI 1004
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 812 LFS--SRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDL----LCNRIDISQLVITKE 885
Cdd:TIGR00592 1005 KVEgdSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQ 1084
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 886 LTRAAADYAGK--QAHVELAERMRKRDPGSAPSlGDRVPYVIISAAKGVAAYMKS---EDPLFvLEHSLPIDTQYYLEQQ 960
Cdd:TIGR00592 1085 LTRDPKDYPDGasLPHVHVALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAyalEELQR-KHNNLIYDTQYYLEHQ 1162
|
810
....*....|
gi 27806073 961 LAKPLLRIFE 970
Cdd:TIGR00592 1163 IHPVVLRILE 1172
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
578-970 |
3.63e-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: 284.26 E-value: 3.63e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 578 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLgltEDqfiktPTGDEFVKASVRKGLLPQ 657
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAP---ED-----YIGVGFRSPKDRKGLLPR 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 658 ILENLLSARKRAKAELAK-ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEt 736
Cdd:cd00145 72 ILEELLNFRDEAKKRMKAaKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVE- 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 737 kytvengySTSAKVVYGDTDSVMCRFGVS-SVAEAMALGREAADWVsgHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsS 815
Cdd:cd00145 151 --------EHGARVIYGDTDSIFVSLPKMgTKEDAIKEGREILQEL--ADEHLLELEFEKVYLPFFLGKKKRYAGLDI-W 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 816 RPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVIsdllcnridisqlvitkeltraaadyag 895
Cdd:cd00145 220 KGQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL---------------------------- 271
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27806073 896 kqahvelaermrkrdpgsapslgDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 970
Cdd:cd00145 272 -----------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
580-974 |
7.25e-83 |
|
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: 275.23 E-value: 7.25e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 580 YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLGLTEDQfiktptgdefVKASVRKGLLPQIL 659
Cdd:cd05532 8 YAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPPL----------PPSDQEKGILPRII 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 660 ENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVETKyt 739
Cdd:cd05532 78 RKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKM-- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 740 venGYStsakVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSpIRLEFEKVYFPYLLISKKRYAGLLFSSRPDA 819
Cdd:cd05532 156 ---NLE----VIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKK-LEIDIDGVFKRLLLLKKKKYAALKVVDDDKG 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 820 HDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAV----AHAQDVISDLLCNRIDISQLVITKELTRAAADYAG 895
Cdd:cd05532 228 KLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVenihEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPD 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 896 K--QAHVELAERMRKRDPGSAPslGDRVPYVIIS--AAKGVA--AYMKSEdplFVLEHSLPIDTQYYLEQQLAKPLLRIF 969
Cdd:cd05532 308 KksLPHVQVALRMNKRGRKVKA--GDTIPYIICKdgSSKSLAdrAYHPDE---VKKNENLKIDIEYYLSQQILPPISRLC 382
|
....*
gi 27806073 970 EPILG 974
Cdd:cd05532 383 EPIEG 387
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
578-970 |
2.41e-76 |
|
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: 256.48 E-value: 2.41e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 578 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAaqklgltEDQFIKTPTGDEFVKAsvRKGLLPQ 657
Cdd:cd05536 2 ESYEGGIVLEPEKGLHE-NIVVLDFSSLYPSIMIKYNISPDTLVREGC-------EDCDVEPQVGHKFRKD--PPGFIPS 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 658 ILENLLSARKRAKAELaKETDP--LRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVE 735
Cdd:cd05536 72 VLEDLLEERRRIKEKM-KKLDPesEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAE 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 736 tkytvENGYstsaKVVYGDTDSVmcrFGVSSVAEA-MALGREAADWVSGHFPspIRLEFEKVYFPYLLISKKRYAGLlfs 814
Cdd:cd05536 151 -----EKGF----KVIYGDTDSL---FVKIDGADAvKKKVKKLLKYINEELP--LELEIEKFYKRGFFVTKKRYAGL--- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 815 srpDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADYA 894
Cdd:cd05536 214 ---TEDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYK 290
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 27806073 895 GKQAHVELAERMRKRdpGSAPSLGDRVPYVIIsaaKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 970
Cdd:cd05536 291 ATGPHVAAAKKLAKR--GYKVRPGTKIGYVIV---KGSGKISDRAYPYDMVDEKHKYDAEYYIDNQVLPAVLRILE 361
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
243-974 |
3.88e-64 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 233.04 E-value: 3.88e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 243 YEANVDFEIRFMVDTDIVGCNWLELPAGKYILRPE------GKATLCQLEADVLWSDVISHPPegewqriAPLRVLSFDI 316
Cdd:PRK05761 123 WEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEilveeiKKAFKDERKLAEDWLPIFEAPI-------PKIKRIAIDI 195
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 317 ECAGrkgifPEPERDPViqicslglrwgepepflrlaltlrpcapilgakvqsyEREEDLLQAWSTFIRIMDPDVItgYN 396
Cdd:PRK05761 196 EVYT-----PAKGRIPD-------------------------------------DSEKELLAELFDIILEYPPVVT--FN 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 397 IQNFDLPYLISRAQTLKVPGFPLLGRVIGLRSNIRESSFQSRqtgrRDSKVVSMVGRvqmdmlqvllreYKLRSYTLNAV 476
Cdd:PRK05761 232 GDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQN----KAVRSYAFYGK------------YRHREARLDAV 295
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 477 SFHFLGEQKEDVQHSIitdlqngNDQTRRRLAVYCLKDAFLPLRL--LERLMVLVNAMEMARVTGVPLGYLlSRGQQVKV 554
Cdd:PRK05761 296 GRALLGISKVELETNI-------SELDLEELAEYNFRDAEITLKLtfFNNELVLKLILLLSRISKLPIEEL-SRATISTW 367
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 555 VSQLL-RQAMRQGLLMP-----------VVK--TEGGEDYTGATVIEPLKG-YYDVpiATLDFSSLYPSIMMAHNLCYTT 619
Cdd:PRK05761 368 ISNLEyWEHRKRGWLIPwkedilrldheVYKkaIIKGKKYRGGLVFQPPPGiFFNV--YVLDFASLYPSIIVKWNLSPET 445
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 620 LLRPGAAQKLGLTEDQFIKTPTGDefvkasvRKGLLPQILENLLSARKRAKAELAKE--TDPLRRQVLDGRQLALKVSAN 697
Cdd:PRK05761 446 VRIPECKCHYDDEVPELGHSVCDD-------RPGLTSVLVGLLRDFRVKIYKKKAKDpnLDEERRAWYDVVQRALKVFLN 518
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 698 SVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvENGYstsaKVVYGDTDSVMCRFGVSSVAEAMalgrea 777
Cdd:PRK05761 519 ASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAE-----ELGL----KVLYGDTDSLFVWGPTKESLEEL------ 583
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 778 ADWVSGHFpsPIRLEFEKVYfPYLLIS--KKRYAGLLFSsrpdahDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRD 855
Cdd:PRK05761 584 IKEIEERT--GIDLEVDKTY-DWVAFSglKKNYFGVLKD------GKVKIKGIVAKKRNTPEFVKELQREVLEVLKSIRS 654
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 856 PSGAV-------AHAQDVISDLLCNRIDISQLVITKELTRAAADYA-GKQAHVELAERMRKRdpGSAPSLGDRVPYVIIS 927
Cdd:PRK05761 655 PEDVEkvkdeieDVLKRYYEKLRAKDYPLDELAIRVRLSKPLDEYTkNTPQHVKAALQLRDY--GVEVSPGDIISYVKVD 732
|
730 740 750 760
....*....|....*....|....*....|....*....|....*..
gi 27806073 928 AAKGVaaymkseDPLFVLEHSlPIDTQYYLEQqlakpLLRIFEPILG 974
Cdd:PRK05761 733 DKRGV-------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 ... |
311-523 |
2.75e-54 |
|
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: 187.56 E-value: 2.75e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 311 VLSFDIECAGRKGiFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAP-ILGAKVQSYEREEDLLQAWSTFIRIMDP 389
Cdd:cd05160 1 VLSFDIETTPPVG-GPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEfIDGIEVEYFADEKELLKRFFDIIREYDP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 390 DVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVIGlrsNIRESSFQSRqtgrrdskvVSMVGRVQMDMLQVLLREYKLR 469
Cdd:cd05160 80 DILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSG---GEKSSGSTER---------IAVKGRVVFDLLAAYKRDFKLK 147
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 27806073 470 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDqtRRRLAVYCLKDAFLPLRLLE 523
Cdd:cd05160 148 SYTLDAVAEELLGEGKEKVDGEIIEDAEWEED--PERLIEYNLKDAELTLQILE 199
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
582-970 |
1.24e-43 |
|
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99920 Cd Length: 371 Bit Score: 163.21 E-value: 1.24e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 582 GATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKlgltEDQFIKTPTGDEFvkaSVRKGLLPQILEN 661
Cdd:cd05537 5 GGYVMDSKPGLYK-NVLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPD----PEDLIPGFLGARF---SREKHILPDLIAR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 662 LLSARKRAKaelaKETDPLRRQvldgrqlALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvE 741
Cdd:cd05537 77 LWAARDEAK----REKNAPLSQ-------AIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIE-----Q 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 742 NGYstsaKVVYGDTDSVMCRFG-VSSVAEAMALGREAAD----WVSGH------FPSPIRLEFEKVYFPYLLI------- 803
Cdd:cd05537 141 QGY----QVIYGDTDSTFVWLGeELDAAEAQAIGKELASqinqWWAQKlkeefgLESFLEIEFETHYSRFFMPtirgsde 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 804 -SKKRYAGLlfsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVahaQDVISDLLCNRIDiSQLVI 882
Cdd:cd05537 217 gSKKRYAGL---KSTDGGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFI---KETVEELLAGELD-ELLVY 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 883 TKELTRAAADY-AGKQAHVELAermRKRDPgSAPSLGDRVPYVIISaakgvaaYMKSEDPLFVLEH-SLPIDTQYYLEQQ 960
Cdd:cd05537 290 RKRLRRPLSEYtKNVPPHVQAA---RLADQ-INRELGRPRQYQWIE-------YVITVNGPEPLEYrTSPLDYQHYIDKQ 358
|
410
....*....|...
gi 27806073 961 L---AKPLLRIFE 970
Cdd:cd05537 359 LkpiADSILPFLG 371
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
1011-1081 |
3.78e-30 |
|
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.
Pssm-ID: 464119 Cd Length: 68 Bit Score: 113.62 E-value: 3.78e-30
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 27806073 1011 CIGCRTVlshQGAVCKFCQPRESELYQKEVSHLSALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMR 1081
Cdd:pfam14260 1 CLGCGAP---EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYMR 68
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
578-975 |
1.34e-29 |
|
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: 121.30 E-value: 1.34e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 578 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLGLTEDQFIKTPtgdefvkasvRKGLLPQ 657
Cdd:cd05531 3 LADRGGLVFQPEPGLYE-NVAQIDFSSMYPSIIVKYNISPETINCRCCECRDHVYLGHRICLK----------RRGFLPE 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 658 ILENLLSARKRAKAELAKETDPlrrqvlDGRQLALKVSANSVYGFTG---AQVGRLPCLEisqSVTGFGRQMIEKTKQLV 734
Cdd:cd05531 72 VLEPLLERRLEYKRLKKEEDPY------AGRQKALKWILVTSFGYLGyknAKFGRIEVHE---AITAYGRKILLRAKEIA 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 735 EtkytvENGYstsaKVVYGDTDSVMCRfgVSSVAEAMALGREAadwvsghfPSPIRLEFEKVY-FPYLLISK------KR 807
Cdd:cd05531 143 E-----EMGF----RVLHGIVDSLWIQ--GRGDIEELAREIEE--------RTGIPLKLEGHYdWIVFLPERdglgapNR 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 808 YAGLLFSsrpdahDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPS---GAVAHAQDVIS--DLLCNRIDISQLVI 882
Cdd:cd05531 204 YFGRLSD------GEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEellKLREEALDLFRryLQRLREGDLEDLII 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 883 TKELTRAAADYAGKQAHVelAERMRKRdpGSAPSLGDRVPYVIISAAKGVAaymksedplfVLEHSLPIDTQYYLEQqla 962
Cdd:cd05531 278 EKKISKRSSEYKVLASTA--LKALRAK--GVSVVPGMKIEYIVRDGKRPVP----------DLGNDEGYDTKYYREL--- 340
|
410
....*....|...
gi 27806073 963 kpLLRIFEPILGE 975
Cdd:cd05531 341 --LERAAEELLFP 351
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
577-932 |
3.99e-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: 114.76 E-value: 3.99e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 577 GEDYTGATVIEPLKG-YYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPGAaqklgltEDQFIKTPTGDEFVKASvRKGLL 655
Cdd:cd05530 10 GKKYRGAIVLEPPPGiFFNV--VVLDFASLYPSIIKVWNLSYETVNCPHC-------ECKTNEVPEVGHWVCKK-RPGIT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 656 PQILENLLSAR-----KRAKAelaKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKT 730
Cdd:cd05530 80 SQIIGLLRDLRvkiykKKAKD---KSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITST 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 731 kqlveTKYTVENGYstsaKVVYGDTDSVMCRFGVSSVAEamalgrEAADWVSGHFpsPIRLEFEKVYfPYLLIS--KKRY 808
Cdd:cd05530 157 -----IKKARELGL----KVLYGDTDSLFLWNPPQEQLE------DLVEWVEKEL--GLDLELDKEY-RYVVFSglKKNY 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 809 AGLLFSSrpdahdRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSgAVAHAQDVISDL-------LCNR-IDISQL 880
Cdd:cd05530 219 LGVTKDG------SVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPE-DFEKAREKIRDIvkgvykrLKKKeYTLDQL 291
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|...
gi 27806073 881 VITKELTRAAADYA-GKQAHVELAERMRKRdpGSAPSLGDRVPYVIISAAKGV 932
Cdd:cd05530 292 AFKVMLSKPPEEYTkNTPQHVKAARQLEKY--GRNVEAGDIISYVKVKGKEGV 342
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
309-782 |
1.59e-26 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 117.48 E-value: 1.59e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 309 LRVLSFDIECAGRKGiFPEPERDPViQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQ----------SYEREEDLLQ 378
Cdd:PHA02528 106 IRIANLDIEVTAEDG-FPDPEEAKY-EIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPqeildkvvymPFDTEREMLL 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 379 AWSTFIRIMDPDVITGYNIQNFDLPYLISRaqtlkvpgfplLGRVIGLRSNIRESSF---QSRQT----GRRDSKvVSMV 451
Cdd:PHA02528 184 EYINFWEENTPVIFTGWNVELFDVPYIINR-----------IKNILGEKTAKRLSPWgkvKERTIenmyGREEIA-YDIS 251
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 452 GRVQMDMLQVllreYK------LRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQtrrRLAVYCLKDAFLPLRLLERL 525
Cdd:PHA02528 252 GISILDYLDL----YKkftftnQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQ---KYIEYNIIDVELVDRLDDKR 324
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 526 MVLVNAMEMARVTGVPLGYLLSrgqQVKVVSQLLRQAMR-QGLLMPVVKTEGGEDYTGATVIEPLKGYYDVpIATLDFSS 604
Cdd:PHA02528 325 KLIELVLSMAYYAKINFEDVFS---PIKTWDAIIFNSLKeEKIVIPENKSHKKQKYAGAFVKEPVPGAYRW-VVSFDLTS 400
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 605 LYPSIMMAHNLCYTTLL--RPGA------AQKLGLTEDQFIKTPTGDEFVKAsvRKGLLPQILENLLSARKRAK------ 670
Cdd:PHA02528 401 LYPSIIRQVNISPETIAgtFHVApvheyiNKTAPRPSDEYSCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIYKkkmlaa 478
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 671 ---AELAKET----------------------------DPLRRQVLDGR--------------QLALKVSANSVYGFTGA 705
Cdd:PHA02528 479 ernAELIKTIledlndsvdtpidvdyyfdfsdefkaelKTLTKSSLKALleecekeialcntiQMARKILINSLYGALGN 558
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 706 QVGRLPCLEISQSVTGFG--------RQMIEKTKQLVETKytvengysTSAKVVYGDTDSVMCRFGvsSVAEAMALGR-- 775
Cdd:PHA02528 559 EHFRYYDLRNAEAITLFGqlaiqwieRKMNEYLNKLCKTE--------DEDYVIYGDTDSIYVNLD--PLVEKVGEDKfk 628
|
....*..
gi 27806073 776 EAADWVS 782
Cdd:PHA02528 629 DTNHWVD 635
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
312-837 |
1.35e-25 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 114.73 E-value: 1.35e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 312 LSFDIECAGRKGiFPEPERDPV--IQICSLGLRWGEpepfLRLALT---LRPCAPILGAKVQSYEREEDLLQAWSTFIRI 386
Cdd:PHA03036 163 LFLDIECHFDKK-FPSVFINPVshISCCYIDLSGKE----KRFTLInedMLSEDEIEEAVKRGYYEIESLLDMDYSKELI 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 387 ----------------MDPDVITGYNIQNFDLPYLISRAQTLKvpgfplLGRVIgLRS-----NIRESSFQSRQTGRRDS 445
Cdd:PHA03036 238 lcseivllriakklleLEFDYVVTFNGHNFDLRYISNRLELLT------GEKII-FRSpdgkeTVHLCIYERNLSSHKGV 310
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 446 KVVSMV--------GRVQMDMLQVLLREYKLRSYTLNAVS---FHFLGEqKEDVQHSIITDLQNGNDQTRRRLAV----- 509
Cdd:PHA03036 311 GGVANTtyhinnnnGTIFFDLYTFIQKTEKLDSYKLDSISknaFNCNAK-VLSENNNEVTFIGDNTTDAKGKASIfsevl 389
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 510 ----YCLKDAFLPLRLLE--------RLMVLVN-------------------------------AMEMAR---------- 536
Cdd:PHA03036 390 stgnYVTINDDDICKILDkdiiensfTVKVICKnnyipgdtytlsfgkddvdlsdmyknynleiALEMARycihdaclck 469
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 537 -----------VTGVPLGYLLSRGQQVKVVS------QLLRQAMRQGLLMPVVKTEGGEDYTGATVIEPLKGYYDVPIAT 599
Cdd:PHA03036 470 ylweyygietkIDAGASTYLLPQSMVFEYRAstlikgPLLKLLLEEKTILVRSETKNKFPYEGGKVFAPKQKMFDNNVLI 549
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 600 LDFSSLYPSIMMAHNLCYTTLL-------RPGAAQKLGLTEDQF-------IK-TPTGDEFV-KASV----RKGLLPQIL 659
Cdd:PHA03036 550 FDYNSLYPNVCIFGNLSPETLVgvvvndnRLEAEINKQELRRKYpypryiyVHcEPRSPDLVsEIAVfdrrIEGIIPKLL 629
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 660 ENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIE----------- 728
Cdd:PHA03036 630 KTFLEERARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKylnsvlngskl 709
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 729 ----------------KTKQLVETKY--TVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGH-FPSPI 789
Cdd:PHA03036 710 ingklilancpinpffKDDRSIDTNYdtNLPVEYNFTFRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINEKvLFDNF 789
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|
gi 27806073 790 RLEFEKVYFPYLLISKKRYAGLLF--SSRPDAHDRMDCKGLEAVRRDNCP 837
Cdd:PHA03036 790 KIEFEAVYKNLIMQSKKKYTTLKYiaSSTDGSVPERVNKGTSETRRDVSK 839
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
308-730 |
2.46e-24 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 110.53 E-value: 2.46e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 308 PLRVLSFDIEC--AGRKGIFP--EPERDPVIQI----CSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQA 379
Cdd:TIGR00592 197 ELKLASFDIETyfHDGKDFFPgdENPADEEIMIsttpVIAKQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKR 276
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 380 WSTFIRIMDPDVITGYNIQNFDLPYLISRA----------QTLKVPGFPLLGRviglRSNIRESSFQSRQTGRRDSKVVS 449
Cdd:TIGR00592 277 FWDVIDQEDTDVEITVNGDNFDLVYLADRQvfqfywdayeDPAEKLGVVLLFG----RDVDHVSPCVQVKGINRDLFFLP 352
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 450 MVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITdlQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLV 529
Cdd:TIGR00592 353 REGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIA--KKYEFEAPDIDAPYSSEYLEVTYELGKEFAPME 430
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 530 NAMEMARVTGVPLGYLLSRGQQVKVVSQL-------LRQAMRQGLLMPVV---KTEGGedYTGATVIEPLKGYYDVPIAT 599
Cdd:TIGR00592 431 ALPSDLKGQTFWHVFGSNTGNLERFLLLRkikgpcwLAVKGPDELEYPRRswcKYEGG--YVKPPNVEKGLDKTPPPLVV 508
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 600 LDFS--SLYPSIMMAHNLCYT-TLLRPGAAQKLGLTEDQFIKTPTGDEFVKASVR-------KGLLPQILENLLSARKRA 669
Cdd:TIGR00592 509 LDFSmkSLNPSIIRNEIVSIPdTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPldlkgefPGKKPSLVEDLATERALI 588
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 27806073 670 KAELA--KETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSvtgFGRQMIEKT 730
Cdd:TIGR00592 589 KKFMAkvKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPK---FGRRFGERT 648
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
309-525 |
5.18e-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: 5.18e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 309 LRVLSFDIECAGRKGIfPEPERDPVIQI--CSLG----LRW-GEPEPFlrlaltlrpcapilgakVQSYEREEDLLQaws 381
Cdd:cd05780 3 LKILSFDIEVLNHEGE-PNPEKDPIIMIsfADEGgnkvITWkKFDLPF-----------------VEVVKTEKEMIK--- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 382 TFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVPgFPlLGRviglrsNIRESSFQsRQTGRRDSKVvsmVGRVQMDM 458
Cdd:cd05780 62 RFIEIVkekDPDVIYTYNGDNFDFPYLKKRAEKLGIE-LD-LGR------DGSEIKIQ-RGGFNNASEI---KGRIHVDL 129
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 27806073 459 LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNgNDQTRRRLAVYCLKDAFLPLRLLERL 525
Cdd:cd05780 130 YPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWD-SGENLERLFRYSMEDAKYTYEIGKEF 195
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
596-967 |
4.43e-23 |
|
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99921 Cd Length: 347 Bit Score: 102.18 E-value: 4.43e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 596 PIATLDFSSLYPSIMMAHNLCyttllrpgaaqklgltedqfiktPTGDEFvkasvrkGLLPQILENLLSARKRAKAELAK 675
Cdd:cd05538 18 PIVHADVASLYPSIMLAYRIC-----------------------PARDSL-------GIFLALLKYLVELRLAAKESARA 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 676 ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvengySTSAKVVYGDT 755
Cdd:cd05538 68 AARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLR---------RRGATPVEVDT 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 756 DSV--MCRFGVSSVAEAMALGREaadwVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSsrpdahDRMDCKGLEAVRR 833
Cdd:cd05538 139 DGIyfIPPNGVDTEDEEEELVRE----LSSTLPKGITVEFDGRYRAMFSYKIKNYALLDYD------GKLIVKGSAFRSR 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 834 DNCPLVANLVTASLRRLLIDrDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADY-----AGKQAHVELAERMRK 908
Cdd:cd05538 209 GIEPFLREFLREAVRLLLQG-DGAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYlqkvrAGKRNPAAAYEIALA 287
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 27806073 909 RDPGSAPslGDRVPYVIISAAKGVAAYMK-SEDPLFVLEHSLpIDTQYYLEQ--QLAKPLLR 967
Cdd:cd05538 288 RPREWRA--GDRVTYYVSGTGKGVSVYENcRLVADYDPAHPD-ENTGFYAERllQLAARLLP 346
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
309-523 |
4.18e-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: 96.15 E-value: 4.18e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 309 LRVLSFDIECAGRKGIFPEPERDPVIQIC----------------SLGLRWGEPEPFLRLALTLRPCapiLGAKVQSYER 372
Cdd:cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFycidddvspfildankVGVIIVDELKSNASNGRIRSGL---SGIPVEVVES 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 373 EEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPGF-PLLGRVIglrSNiRESSFQSRQTGRRDSK--VVS 449
Cdd:cd05778 81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLlDEISRVP---SD-SNGKFGDRDDEWGYTHtsGIK 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27806073 450 MVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGND-QTRRRLAVYCLKDAFLPLRLLE 523
Cdd:cd05778 157 IVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSaSERWRVLEYYLKRVRLNLEILD 231
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
308-523 |
4.81e-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: 4.81e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 308 PLRVLSFDIECagrkgifpeperDPVIQICSLGLrWGEPEpflRLALTLRPCAPILGAKVQSYEREEDLLQAWSTFIRIM 387
Cdd:cd05784 2 KLKVVSLDIET------------SMDGELYSIGL-YGEGQ---ERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQY 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 388 DPDVITGYNIQNFDLPYLISRAQTLKVPgfPLLGRViGLRSNIRESSFQSRQTgrrdskvVSMVGRVQMDMLQvLLRE-- 465
Cdd:cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAHGLP--LRLGRG-GSPLNWRQSGKPGQGF-------LSLPGRVVLDGID-ALKTat 134
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27806073 466 YKLRSYTLNAVSFHFLGEQKedvqhsIITDLQNGNDQTRRR-------LAVYCLKDAFLPLRLLE 523
Cdd:cd05784 135 YHFESFSLENVAQELLGEGK------LIHDVDDRGAEIERLfredklaLARYNLQDCELVWRIFE 193
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
308-482 |
5.73e-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: 80.06 E-value: 5.73e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 308 PLRVLSFDIECAGRKGiFPEPERDPVIQIcSLGLRWGEPEPFLrlaltlrpcapilgakvQSYEREEDLLQAWSTFIRIM 387
Cdd:cd05781 2 DLKTLAFDIEVYSKYG-TPNPRRDPIIVI-SLATSNGDVEFIL-----------------AEGLDDRKIIREFVKYVKEY 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 388 DPDVITGYNIQNFDLPYLISRAqtlKVPGFPL-LGRVIGlrsnirESSFQSRqTGRrdskvVSMVGRVQMDMLQVLLREY 466
Cdd:cd05781 63 DPDIIVGYNSNAFDWPYLVERA---RVLGVKLdVGRRGG------SEPSTGV-YGH-----YSITGRLNVDLYDFAEEIP 127
|
170
....*....|....*.
gi 27806073 467 KLRSYTLNAVSfHFLG 482
Cdd:cd05781 128 EVKVKTLENVA-EYLG 142
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
306-521 |
4.21e-16 |
|
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: 78.13 E-value: 4.21e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 306 IAPLRVLSFDIEC-AGRKGIFPEPERD--PVIQIC---SLGLRwgepepflRLALTLRPCAPIL------GAKVQSYERE 373
Cdd:cd05783 2 IPKLKRIAIDIEVyTPIKGRIPDPKTAeyPVISVAlagSDGLK--------RVLVLKREGVEGLegllpeGAEVEFFDSE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 374 EDLLQAwstFIRIMD--PDVITgYNIQNFDLPYLISRAQTLkvpGFPLLGRVIGLrsniressfqsrqtgRRDSkvVSMV 451
Cdd:cd05783 74 KELIRE---AFKIISeyPIVLT-FNGDNFDLPYLYNRALKL---GIPKEEIPIYL---------------KRDY--ATLK 129
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27806073 452 GRVQMDM--------LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIitdlqngNDQTRRRLAVYCLKDAFLPLRL 521
Cdd:cd05783 130 HGIHIDLykffsnraIQVYAFGNKYREYTLDAVAKALLGEGKVELEKNI-------SELNLYELAEYNYRDAELTLEL 200
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
365-760 |
6.52e-15 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 79.90 E-value: 6.52e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 365 AKVQSYEREEDLLQAWSTFI----RIMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVIGLRSNI--------RE 432
Cdd:PHA03334 370 FKQRPHPLTKALMEAWEAFLskdpQLVPAQLLFGSDILNSNYLELLDVIESHKAQFKATCRKAAARKEEIgsymktrdTV 449
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 433 SSFQSRQTGRRDSKVVSMvGRVQMDMLQVLLR---EYKLRSYTLNAVSFHFLGEQK-----------EDVQHSIITDLQN 498
Cdd:PHA03334 450 QDFNDNDKKYLNSTSHGF-GAHIIDLMRVCNTksiKAKCSSRKLDTVARLIISKSKphknppkigkmDDVKYTEMDGMFT 528
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 499 GNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTgVPLGYL-LSRG--------QQVKVVS-QLLRQAMRQG-- 566
Cdd:PHA03334 529 AGGAALARYLIYNLVDSELLIRIAKNLDPVIEFLNRLRAT-YNIDYVaHGRGvmnfcgfvQSTKSVEvPLLKARLRIGif 607
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 567 ---------LLMP-VVKTEGGEDYT--GATVIEPLKGY-----YDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAA--- 626
Cdd:PHA03334 608 vatgriaesLCMPeKYARDCRQKIKlkGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIVDPDCTarv 687
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 627 ------------QKLGLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKV 694
Cdd:PHA03334 688 rgwvvfdwkkidRGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNEMKI 767
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 27806073 695 SANSVYGftgaqVGRLPCleiSQSVTGFGRQMIektkQLVETKYTVENGYStsakVVYGDTDSVMC 760
Cdd:PHA03334 768 CANSHYG-----VAPHAC---QHLITTLGRHKI----KLVEEFIKKEPGMT----VNYGDTDSVMF 817
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
326-528 |
3.88e-14 |
|
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis. This explains why in most organisms, that no specific repair role, other than check point control, has been assigned to this enzyme. The exonuclease domain may have a structural role.
Pssm-ID: 99819 [Multi-domain] Cd Length: 234 Bit Score: 73.03 E-value: 3.88e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 326 PEPERDPVIQICSLGL---RWGEPEPFLRLALTLRPcapilgaKVQSYEREEDLLQAWSTFIRIMDPDVITGYNIQNFDL 402
Cdd:cd05776 39 PTPPPPFQSHTCTLTRplgRSPPPDLFEKNAKKKKT-------KVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDL 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 403 PYLISRAQTLKVPGFPLLGRVigLRSNIRE----SSFQSRQTgrrdskvvsMVGRVQMDMlQVLLRE-YKLRSYTLNAVS 477
Cdd:cd05776 112 DVLLSRIQELKVPHWSRIGRL--KRSVWPKkkggGKFGEREL---------TAGRLLCDT-YLSAKElIRCKSYDLTELS 179
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 27806073 478 FHFLGEQKEDVqhsIITDLQNGNDQTRR--RLAVYCLKDAFLPLRLLERLMVL 528
Cdd:cd05776 180 QQVLGIERQDI---DPEEILNMYNDSESllKLLEHTEKDAYLILQLMFKLNIL 229
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
309-514 |
3.24e-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: 3.24e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 309 LRVLSFDIECAGRKGIF---PEPERDPVIQIcslGLRwgEPEPFlRLALTLRPCApilgakvqsyerEEDLLQAWSTFIR 385
Cdd:cd05785 9 LRRLQLDIETYSLPGFFfsnPDRGDDRIIIV---ALR--DNRGW-EEVLHAEDAA------------EKELLEELVAIIR 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 386 IMDPDVITGYNIQNFDLPYLISRAQTLKVPgfPLLGRvIGLRSNIRESSFQSRQtGRRDSKVVSMVGRVQMDMLQVLLR- 464
Cdd:cd05785 71 ERDPDVIEGHNIFRFDLPYLRRRCRRHGVP--LAIGR-DGSIPRQRPSRFRFAE-RLIDYPRYDIPGRHVIDTYFLVQLf 146
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 27806073 465 ---EYKLRSYTLNAVSFHF--LGEQKEDVQHSIITDLQNGNdqtRRRLAVYCLKD 514
Cdd:cd05785 147 dvsSRDLPSYGLKAVAKHFglASPDRTYIDGRQIAEVWRSD---PARLLAYALDD 198
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|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
308-439 |
1.26e-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: 50.34 E-value: 1.26e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 308 PLRVLSFDIECAGRKGIFPEPERDPVIQIcSLGLrwgEPEPFLrlaLTLRPcapILGAKVQSYE---------------- 371
Cdd:cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMI-SYMI---DGQGYL---IVNRE---IVSEDIEDFEytpkpeyegpfkvfne 70
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 27806073 372 -REEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLkvpGFPLLgRVIGLRSNiRESSFQSRQ 439
Cdd:cd05779 71 pDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIH---GLSME-EEIGFRKD-SEGEYKSRY 134
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
370-670 |
1.37e-06 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 52.31 E-value: 1.37e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 370 YEREEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLkvpgfplLGRviglrsnirESSFQSRQTGRRDSKVVS 449
Cdd:PHA02524 177 FEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNI-------LGE---------KAANQLSPYGKITSKTIT 240
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 450 MV----------GRVQMDMLQVLlREYK---LRSYTLNAVSFHFLGEQKEDVQHSIiTDLQNGNDQtrrRLAVYCLKDAF 516
Cdd:PHA02524 241 NLygekiiykihGIALMDYMDVF-KKFSftpMPDYKLGNVGYREVKADKLDYEGPI-NKFRKADHQ---RYVDYCVRDTD 315
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 517 LPLRLLERLMVLVNAMEMARVTGVPLGYLLSrgqQVKVVSQLLRQAM-RQGLLMPVVKTEGGEDYTGATVIEPLKGYYDV 595
Cdd:PHA02524 316 IILLIDGRRCFIDLILSLSYYAKIRFDDVLG---TIKVWDSIIFNSLvESNVVIPAMKASPKQSFPGAYVKEPVPGGYRY 392
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073 596 PIaTLDFSSLYPSIMMAHNLC---YTTLLRP--------GAAQKlglTEDQFIKTPTGDEFVKASVrkGLLPQILENLLS 664
Cdd:PHA02524 393 GL-SFDLTSLYPSILRLLNISpemIAGMFSParledyinKVAPK---PSDQFSCAPNGMMYKKGVV--GVLPNETEKVFL 466
|
....*.
gi 27806073 665 ARKRAK 670
Cdd:PHA02524 467 QRKSEK 472
|
|
|