|
Name |
Accession |
Description |
Interval |
E-value |
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
81-1092 |
0e+00 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 1586.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 81 RPPLSPAYlsNSQSIIFQQLEIDSIIA--ESHKELLPGSSGQA----PIIRMFGVTREGNSVCCFVHGFEPYFYIACPPG 154
Cdd:PTZ00166 30 RRPLPPIS--LQKDLVFFQLDADYTEKddKSQGNPHNTVSGVRhvevPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPN 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 155 MGPDDISNFHQSLEGRMRESNKNAKVPKFVKRIEMVQKRSIMYYQQQKSQTFLKITVALPTMVASCRGILDRGLQI---D 231
Cdd:PTZ00166 108 FLPEDSQKLKRELNAQLSEQSQFKKYQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVcggG 187
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 232 GLGMKSFQTYESNILFVLRFMVDCDIVGGNWIEVPTGKYKKNARTL--SYCQLEFHCLYSDLISHAAEGEYSKMAPFRVL 309
Cdd:PTZ00166 188 WDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKktSTCQIEVDCSYEDLIPLPPEGEYLTIAPLRIL 267
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 310 SFDIECAGRKGH-FPEAKHDPVIQIANLVTLQGED-HPFVRNVMTLKSCAPIVGVDVMSFETEREVLLAWRDLIRDVDPD 387
Cdd:PTZ00166 268 SFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEeEPLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDPD 347
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 388 IIIGYNICKFDLPYLIERAATLGIEEFPLLGRVKNSRVRVRDSTFSSRQQGIRESKETTIEGRFQFDLIQAIHRDHKLSS 467
Cdd:PTZ00166 348 FLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLKS 427
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 468 YSLNSVSAHFLSEQKEDVHHSIITDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIYNYVEMARVTGVPISFLLARGQ 547
Cdd:PTZ00166 428 YSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQ 507
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 548 SIKVLSQLLRKGKQKNLVLPNAKQSGS-EQGTYEGATVLEARTGFYEKPIATLDFASLYPSIMMAYNLCYCTLVTPEDVR 626
Cdd:PTZ00166 508 QIKVTSQLLRKCKKLNYVIPTVKYSGGgSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDAN 587
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 627 klNLPPEHVTKTPSGETFVKQTLQKGILPEILEELLTARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATV 706
Cdd:PTZ00166 588 --NYPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQV 665
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 707 -GQLPCLEISSSVTSYGRQMIEQTKKLVEDKFTTLGGYQYNAEVIYGDTDSVMVQFGVSDVEAAMTLGREAAEHISGTFI 785
Cdd:PTZ00166 666 gGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFL 745
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 786 KPIKLEFEKVYFPYLLINKKRYAGLLWTNPQQFDKMDTKGIETVRRDNCLLVKNLVTESLNKILIDRDVPGAAENVKKTI 865
Cdd:PTZ00166 746 KPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKI 825
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 866 SDLLMNRIDLSLLVITKGLTKtgDDYEVKSAHGELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLQN 945
Cdd:PTZ00166 826 SDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVLEN 903
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 946 NIPIDPNYYLEnQISKPLLRIFEPVLKNASKeLLHGSHTRSISITTPSNSGIMKFAKKQLSCVGCKVPISNGTLCASCK- 1024
Cdd:PTZ00166 904 NIPIDTQYYLD-QIKNPLLRIFEGVMDNPDS-LFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIKEGALCDNCNq 981
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 186532719 1025 GREAELYCKNVSQVAELEEVFGRLWTQCQECQGSLHQDVLCTSRDCPIFYRRMKAQKDMAVARQQLDR 1092
Cdd:PTZ00166 982 NKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSR 1049
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
578-971 |
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: 823.44 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 578 TYEGATVLEARTGFYEKPIATLDFASLYPSIMMAYNLCYCTLVTPEDVRKLnlPPEHVTKTPSGETFVKQTLQKGILPEI 657
Cdd:cd05533 2 QYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKL--PPEDYIKTPNGDYFVKSSVRKGLLPEI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 658 LEELLTARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVEDKF 737
Cdd:cd05533 80 LEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKY 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 738 TTLGGYQYNAEVIYGDTDSVMVQFGVSDVEAAMTLGREAAEHISGTFIKPIKLEFEKVYFPYLLINKKRYAGLLWTNPQQ 817
Cdd:cd05533 160 TKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLWTNPDK 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 818 FDKMDTKGIETVRRDNCLLVKNLVTESLNKILIDRDVPGAAENVKKTISDLLMNRIDLSLLVITKGLTKTGDDYEVKSAH 897
Cdd:cd05533 240 HDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADDYAGKQAH 319
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 186532719 898 GELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLQNNIPIDPNYYLENQISKPLLRIFEPVL 971
Cdd:cd05533 320 VELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLENNIPIDTQYYLENQLSKPLLRIFEPIL 393
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
537-970 |
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: 597.29 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 537 VPISFLLARGQSIKVLSQLLRKGKQKNLVLPNAKQSGSEQGTYEGATVLEARTGFYEKPIATLDFASLYPSIMMAYNLCY 616
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGDEDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 617 CTLVTPEDVRKlNLPPE----HVTKTPSGETFVKQTLQKGILPEILEELLTARKRAKADLKEAKDPLEKAVLDGRQLALK 692
Cdd:pfam00136 81 TTLVRSVDEAN-NLPPEdnliTVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLALK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 693 ISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVEDKfttlggYQYNAEVIYGDTDSVMVQFGVSDVEAAMTL 772
Cdd:pfam00136 160 ITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGM------YTYNFRVIYGDTDSVFIEFGGKDVEEAMKI 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 773 GREAAEHISGT-FIKPIKLEFEKVYFPYLLINKKRYAGLLWTNPQQFDKMDTKGIETVRRDNCLLVKNLVTESLNKILID 851
Cdd:pfam00136 234 GDELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSD 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 852 RDVPGAAENVKKTI----SDLLMNRIDLSLLVITKGLTKTGDDYEVKS-AHGELAERMRKRDAAtAPNVGDRVPYVIIKA 926
Cdd:pfam00136 314 RGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEVALRMNKRNGE-APEVGDRIPYVIVKA 392
|
410 420 430 440
....*....|....*....|....*....|....*....|....*..
gi 186532719 927 AK---GAKAYERSEDPIYVLQNNIPIDPNYYLENQISKPLLRIFEPV 970
Cdd:pfam00136 393 AKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
119-970 |
0e+00 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 571.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 119 GQAPIIRMFGVTREGNSVCCFVHGFEPYFYIACPPGMGPDDISNFhqslegrmresnknakvPKFVKRIEMVQKRSImyy 198
Cdd:COG0417 16 DGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLPDEEKLEELLRD-----------------IKEITEVEPVKLKSF--- 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 199 qQQKSQTFLKITVALPTMVASCRGILDRGlqidglgmkSFQTYESNILFVLRFMVDCDIVGGNWIEVPTGKYKKnartls 278
Cdd:COG0417 76 -FGEPVPVLKIYTRDPRDVRELRDRLKEG---------GIDVYEADIRFHDRYLIDRFLTPGVWYEGEVEEDGG------ 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 279 ycqlefhcLYSDLISHAAEGEYSKMAP-FRVLSFDIECAGRKGHFPEAKHDPVIQIAnLVTLQGEDHPFVRNvmtlkscA 357
Cdd:COG0417 140 --------KLDYEVKENPRLKPEDYRPkLKVLSFDIEVSTPRGFPDPERDGPIISIG-LAGSDGEKKVLMLG-------R 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 358 PIVGVDVMSFETEREVLLAWRDLIRDVDPDIIIGYNICKFDLPYLIERAATLGIeefPL-LGRvKNSRVRVRDSTFSSRq 436
Cdd:COG0417 204 EGVDFEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKRAERLGI---PLdLGR-DGSEPSWREHGGQGF- 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 437 qgireskeTTIEGRFQFDLIQAIHRD-HKLSSYSLNSVSAHFLSEQKEDVHHSIITDLQNgnaETRRRLAVYCLKDAYLP 515
Cdd:COG0417 279 --------ASIPGRVVIDLYDALKSAtYKFKSYSLDAVAEELLGEGKLIVDGGEIERLWD---DDKPALAEYNLRDAELT 347
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 516 QRLLDKLMFIYNYVEMARVTGVPISFLLARGQSIKVLSQLLRKGKQKNLVLPNAKQSGSEqgTYEGATVLEARTGFYEKp 595
Cdd:COG0417 348 LRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLAPNKGEIKGE--AYPGGYVLDPKPGLYEN- 424
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 596 IATLDFASLYPSIMMAYNLCYCTLVTPEdvrKLNLPPEHVTKTPsGETFVKQtlQKGILPEILEELLTARKRAKADLKEA 675
Cdd:COG0417 425 VLVLDFKSLYPSIIRTFNISPETLVEGG---EEPCGDEDVAPGF-GHRFCRE--PKGILPSILEELWDERDEAKKKMKKA 498
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 676 K-DPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVEDKfttlgGYQynaeVIYGDT 754
Cdd:COG0417 499 KpDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEEL-----GYK----VIYGDT 569
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 755 DSVMVQFGVSDVEAAMTLGREAAEHISGTFIKPIKLEFEKVYFPYLLIN-KKRYAGLlWTNpqqfDKMDTKGIETVRRDN 833
Cdd:COG0417 570 DSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPGsKKRYAGL-TED----GKIDIKGLEAVRSDW 644
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 834 CLLVKNLVTESLNKILIDRDVPGAAENVKKTISDLLMNRIDLSLLVITKGLTKTGDDYEVK-SAHGELAERMRKRDaaTA 912
Cdd:COG0417 645 TELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYEKNvPPHVRAARKLDERG--RP 722
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*...
gi 186532719 913 PNVGDRVPYVIIKAAKGAKAYErsedpiYVLQNNIPIDPNYYLENQISKPLLRIFEPV 970
Cdd:COG0417 723 YQRGDKISYVITKGGGRVEPVE------LAKERESEIDYDYYIEKQLKPTADRILEAF 774
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
300-529 |
1.78e-160 |
|
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: 473.60 E-value: 1.78e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 300 YSKMAPFRVLSFDIECAGRKGHFPEAKHDPVIQIANLVTLQGEDHPFVRNVMTLKSCAPIVGVDVMSFETEREVLLAWRD 379
Cdd:cd05777 1 WSKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 380 LIRDVDPDIIIGYNICKFDLPYLIERAATLGIEEFPLLGRVKNSRVRVRDSTFSSRQQGIRESKETTIEGRFQFDLIQAI 459
Cdd:cd05777 81 FVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVI 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 460 HRDHKLSSYSLNSVSAHFLSEQKEDVHHSIITDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIYNYV 529
Cdd:cd05777 161 QRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLVNYI 230
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
305-762 |
1.86e-143 |
|
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: 439.27 E-value: 1.86e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 305 PFRVLSFDIECAGRKGHFPEAK--HDPVIQIANLVTLQGEDHPFVRNVMTLKSCAPIVGVDVMSFETEREVLLAWRDLIR 382
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 383 DVDPDIIIGYNICKFDLPYLIERAATLGIEEFPLLGRVKNSRVRVRDSTFSSRQQGIRESKETTIEGRFQFDLIQAIHRD 462
Cdd:smart00486 82 KYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLYKNK 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 463 HKLSSYSLNSVSAHFLSEQKEDVHHSIITDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIYNYVEMARVTGVPISFL 542
Cdd:smart00486 162 LKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRRT 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 543 LARGQSIKVLSQLLRKGKQKNLVLPNAKQSGSEQGT--------YEGATVLEARTGFYEKPIATLDFASLYPSIMMAYNL 614
Cdd:smart00486 242 LYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEpdlkkkvkYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHNL 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 615 CYCTLVTPEDVRK--LNLPPEHVTKTPSGET----FVKQTLQKGILPEILEELLTARKRAKADLKEAKDPLE--KAVLDG 686
Cdd:smart00486 322 CYSTLVGVGEVVIkgDLIIPEDLLTIKYEKGnkyrFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEelKKLLDS 401
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 186532719 687 RQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVEDKfttlGGYQYNAEVIYGDTDSVMVQFG 762
Cdd:smart00486 402 RQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEEN----GYPKPGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
119-972 |
6.35e-113 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 368.80 E-value: 6.35e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 119 GQAPIIRMFGVTREGNSVCCFVHGFEPYFYIACPPGMGPDDISNfhqslEGRMRESNknakvpkfVKRIEMVQKRSIMYY 198
Cdd:PRK05762 17 PGGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERAESLLAG-----EIGVRLSP--------LALKDFHRRPVLGLY 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 199 QQQksqtfLKITVALPTMVASCrgildrglqidglgmkSFQTYESNILFVLRFMVDCDIVGGNWIevpTGKY--KKNART 276
Cdd:PRK05762 84 CRQ-----HRQLTRLPKRLREG----------------GVDVYEADIRFPERYLMERFITPCVWF---SGEVeqYTTDGV 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 277 LSYCQLEFHCLYSDlishaaegeyskmaPFRVLSFDIECAgRKGH-----FPEAKHDPVIQIAnlvTLQGEDHPFVRNVm 351
Cdd:PRK05762 140 LRNARLKPAPDYRP--------------PLKVVSLDIETS-NKGElysigLEGCGQRPVIMLG---PPNGEALDFLEYV- 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 352 tlkscapivgvdvmsfETEREVLLAWRDLIRDVDPDIIIGYNICKFDLPYLIERAATLGIeefPL-LGRvKNSRVRVRDS 430
Cdd:PRK05762 201 ----------------ADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGI---PLrLGR-DGSELEWREH 260
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 431 TFSSRQQGIReskettIEGRFQFDLIQAIHR-DHKLSSYSLNSVSAHFLSEQKEdvhhsIITDLQNGNAETRR------R 503
Cdd:PRK05762 261 PFRSGYGFAS------VPGRLVLDGIDALKSaTWVFDSFSLEYVSQRLLGEGKA-----IDDPYDRMDEIDRRfaedkpA 329
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 504 LAVYCLKDAYLPQRLLDKLMFIYNYVEMARVTGVPisflLAR--GQSIKVLSQLLRKGKQKNLVLPNAKQSGSEqgTYEG 581
Cdd:PRK05762 330 LARYNLKDCELVTRIFEKTKLLPFLLERATVTGLP----LDRvgGSVAAFEHLYLPRAHRAGYVAPNLGERPGE--ASPG 403
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 582 ATVLEARTGFYEKpIATLDFASLYPSIMMAYNLCYCTLVTPedvrkLNLPPEHVTKTPSGETFVKqtlQKGILPEILEEL 661
Cdd:PRK05762 404 GYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGLVEG-----LAQPPEESVAGFLGARFSR---EKHFLPEIVERL 474
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 662 LTARKRAKADLKEAkdplekavldgRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVEDKfttlg 741
Cdd:PRK05762 475 WEGRDEAKREMNKP-----------LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQ----- 538
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 742 GYQynaeVIYGDTDSVMVQFGVS-DVEAAMTLGREAAEHISGTFIKPIK----------LEFEKVY----FPYLLI---- 802
Cdd:PRK05762 539 GYQ----VIYGDTDSTFVWLGGAhDEEDAAKIGRALVQEINQWWQEHLQqefglesaleLEFEKHYrrffMPTIRGaeeg 614
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 803 NKKRYAGlLWTNPQQFDKMDTKGIETVRRDNCLLVKNLVTESLNKILIDRDVpgaAENVKKTISDLLMNRIDlSLLVITK 882
Cdd:PRK05762 615 SKKRYAG-LIQEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEPY---VDYVREVIDKLRAGELD-EKLVYRK 689
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 883 GLTKTGDDYEVKSA-H---GELAERM-RKRDAATAPNVGDRVPYVIIKAAKGAKAYERSedpiyvlqnniPIDPNYYLEN 957
Cdd:PRK05762 690 RLRRPLDEYQRNVPpHvraARLADEMgYKVGRPLQYQNGGKIGYVITVNGPEPLEYRKS-----------PIDYDYYIEK 758
|
890
....*....|....*
gi 186532719 958 QIsKPLLRIFEPVLK 972
Cdd:PRK05762 759 QL-QPVADRILPFFG 772
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
546-970 |
7.78e-102 |
|
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Pssm-ID: 99917 Cd Length: 451 Bit Score: 328.41 E-value: 7.78e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 546 GQSIKVLSQLLRKGKQKNLVLPNA-KQSGSEQGTYEG-ATVLEARTGFYEKPIATLDFASLYPSIMMAYNLCYCT----- 618
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPSPsRQQVAQQRALEClPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTclgrv 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 619 ---------------LVTPEDVRKLNLPPEHVTKTPSGETFVKQTLQKGILPEILEELLTARKRAKADLKEAKDPLE-KA 682
Cdd:cd05534 81 eelngggkfgflgvkLYLPPPPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKlQR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 683 VLDGRQLALKISANSVYGFTGATV-GQLPCLEISSSVTSYGRQMIEQTKKLVEDkfttlgGYQYNAEVIYGDTDSVMVQF 761
Cdd:cd05534 161 ILDARQLALKLLANVTYGYTAASFsGRMPCVEIADSIVQTGRETLERAIELIES------TPKWGAKVVYGDTDSLFVLL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 762 -GVSdVEAAMTLGREAAEHISGTFIKPIKLEFEKVYFPYLLINKKRYAGLLWTNP-QQFDKMDTKGIETVRRDNCLLVKN 839
Cdd:cd05534 235 pGRT-KEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPdQTEPTFDAKGIETVRRDGCPAVQK 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 840 LVTESLNKILIDRDVPGAAENVKKTISDLLMNRIDLSLLVITKGLtKTGDDYEVKS--AHGELAERMRKRDAATAPNVGD 917
Cdd:cd05534 314 ILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEV-RLGTYKEGATlpAGAIVALRRMEKDPRAEPQYGE 392
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....
gi 186532719 918 RVPYVIIKAAKGAKAYERSEDPIYVLQN-NIPIDPNYYLENQISKPLLRIFEPV 970
Cdd:cd05534 393 RVPYVVVRGEPGSRLIDLVVSPEEFLADpSLRLDAEYYITKQIIPALDRLFNLV 446
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
577-968 |
1.40e-92 |
|
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: 298.90 E-value: 1.40e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 577 GTYEGATVLEARTGFYEkPIATLDFASLYPSIMMAYNLCYCTLVTPEDvrklNLPPEHvtktPSGETFVKQTLQKGILPE 656
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGE----IAAPED----YIGVGFRSPKDRKGLLPR 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 657 ILEELLTARKRAKADLKEAK-DPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVED 735
Cdd:cd00145 72 ILEELLNFRDEAKKRMKAAKlAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEE 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 736 kfttlggyqYNAEVIYGDTDSVMVQFGVS-DVEAAMTLGREAAEHIsgTFIKPIKLEFEKVYFPYLLINKKRYAGLLWTN 814
Cdd:cd00145 152 ---------HGARVIYGDTDSIFVSLPKMgTKEDAIKEGREILQEL--ADEHLLELEFEKVYLPFFLGKKKRYAGLDIWK 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 815 PQQFDKMDTKGIETVRRDNCLLVKNLVTESLNKILIDRDVPGAaenVKKTISDLlmnridlsllvitkgltktgddyevk 894
Cdd:cd00145 221 GQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEA---VKEYIDEL-------------------------- 271
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 186532719 895 sahgelaermrkrdaatapnvgDRVPYVIIKAAKGAKAYERSEDPIYVLQNNIPIDPNYYLENQISKPLLRIFE 968
Cdd:cd00145 272 ----------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
129-473 |
1.03e-88 |
|
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: 288.55 E-value: 1.03e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 129 VTREGNSVCCFVHGFEPYFYIACPPGMGPDDISNfhqslegrmrESNKNAKVPKFVKRIEMVQKRSIMYYQQQKSQtFLK 208
Cdd:pfam03104 1 KTDEGVSVCVNVFGFKPYFYCLAPDGKELEEVIE----------EIKELYEGLDKIEKIELKLKKSLYGYEEDPVP-YLK 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 209 ITVALPTMVASCRGILdrglqidgLGMKSFQTYESNILFVLRFMVDCDIVGGNWIEVPTGKYKKNARtLSYCQLEFHCLY 288
Cdd:pfam03104 70 VSFANPRPLLKIRKYL--------SPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGR-ISNCDVEIDCDS 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 289 SDLISHAAEGEyskMAPFRVLSFDIECAGRKGHFPEAKH--DPVIQIANLVTLQGEDHPFVRNVMTLKSCAPIV------ 360
Cdd:pfam03104 141 PDLISVPFEKE---WPPLRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEPRFLFTLRECDSEDiedfey 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 361 -------GVDVMSFETEREVLLAWRDLIRDVDPDIIIGYNICKFDLPYLIERAATLGIEEFPLLGRV-KNSRVRVRDSTF 432
Cdd:pfam03104 218 tpkpiypGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLnRGGRSKVREIGF 297
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 186532719 433 SSrqqgiRESKETTIEGRFQFDLIQAIHRDHKLSSYSLNSV 473
Cdd:pfam03104 298 GT-----RSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
573-970 |
1.53e-86 |
|
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Pssm-ID: 99915 Cd Length: 400 Bit Score: 285.24 E-value: 1.53e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 573 GSEQGTYEGATVLEARTGFYEKPIATLDFASLYPSIMMAYNLCYCTLVTPEDVRKLNLPPEHVTKTpsgetfvkqtLQKG 652
Cdd:cd05532 2 KKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPPLPPSD----------QEKG 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 653 ILPEILEELLTARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKL 732
Cdd:cd05532 72 ILPRIIRKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDL 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 733 VEDKfttlggyqyNAEVIYGDTDSVMVQFGVSDVEAAMTLGREAAEHISGTFiKPIKLEFEKVYFPYLLINKKRYAGLLW 812
Cdd:cd05532 152 VEKM---------NLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSY-KKLEIDIDGVFKRLLLLKKKKYAALKV 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 813 T-NPQQFDKMDTKGIETVRRDNCLLVKNLVTESLNKILIDRDVPGAAENVKKTI----SDLLMNRIDLSLLVITKGLTKT 887
Cdd:cd05532 222 VdDDKGKLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLrkinEDLRNGKIPLEKFIITKQLTKN 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 888 GDDY-EVKSA-HGELAERMRKRDAATapNVGDRVPYVIIKAAKGAKAYERSEDPIYV-LQNNIPIDPNYYLENQISKPLL 964
Cdd:cd05532 302 PEEYpDKKSLpHVQVALRMNKRGRKV--KAGDTIPYIICKDGSSKSLADRAYHPDEVkKNENLKIDIEYYLSQQILPPIS 379
|
....*.
gi 186532719 965 RIFEPV 970
Cdd:cd05532 380 RLCEPI 385
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
250-968 |
2.09e-84 |
|
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: 298.12 E-value: 2.09e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 250 RFMVDCDIVGGNWIEvPTGKYKKNARTLSYCQLEFHCLYSDLIShaaEGEYSKMAPFRVLSFDI---------------- 313
Cdd:TIGR00592 454 RFLLLRKIKGPCWLA-VKGPDELEYPRRSWCKYEGGYVKPPNVE---KGLDKTPPPLVVLDFSMkslnpsiirneivsip 529
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 314 ECAGRKGHFPEAKHDPVIQIANLVTLQGEDHPFVrnvMTLKSCAP-IVGVDVMSFETEREVLLAWRDLIRDVDPDIIIGY 392
Cdd:TIGR00592 530 DTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFP---LDLKGEFPgKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGH 606
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 393 NICKFDLPYLIERAATLGIEEFPLLGRVknsrvrvRDSTFSSRQQGIRESkettieGRFQFDLIQAIHRDHKLSSYSLNS 472
Cdd:TIGR00592 607 DYQQRALKVLANRINDLKIPTWSKIGRL-------RRSPKFGRRFGERTC------GRMICDVEISAKELIRCKSYDLSE 673
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 473 VSAHFL-SEQKEDVHHSIITDLQNGNAETRrrLAVYCLKDAYLPQRLLDKLMFIYNYVEMARVTGVPISFLLARGQSIKV 551
Cdd:TIGR00592 674 LVQQILkTERKVIPIDNINNMYSESSSLTY--LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERN 751
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 552 LSQLLRKGKQKNLVLPNAKQSGSEQG-----------------TYEGATVLEARTGFYEKPIATLDFASLYPSIMMAYNL 614
Cdd:TIGR00592 752 EFLLLHAFYENNYIVPDKQIFRKQQKlgdedeeidgykkgkkaAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNI 831
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 615 CYCTLVTPEDVRKLNLPPEhvtktpsgetfvkQTLQKGILPEILEELLTARKRAKADLKEAKDPLEKAVLDGRQLALKIS 694
Cdd:TIGR00592 832 CFTTVQQKVDEDELPELPD-------------SELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLT 898
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 695 ANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVEDKfttlggyqyNAEVIYGDTDSVMVQFGVSDVEAAMTLGR 774
Cdd:TIGR00592 899 ANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEM---------NLEVIYGDTDSIMINTPGTKYEEVFKIGK 969
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 775 EAAEHISGTFiKPIKLEFEKVYFPYLLINKKRYAGL---LWTNPQQFDKMDTKGIETVRRDNCLLVKNLVTESLNKILID 851
Cdd:TIGR00592 970 EFKSEVNKLY-KLLELDIDGVFKRLLLLKKKKYAAIkveGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSD 1048
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 852 RDVPGAAENVKKTISDL----LMNRIDLSLLVITKGLTKTGDDYEVKSA--HGELAERMRKRDAATAPNvGDRVPYVIIK 925
Cdd:TIGR00592 1049 KDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLTRDPKDYPDGASlpHVHVALRINARGGRKVKA-GDVVSYVICK 1127
|
730 740 750 760
....*....|....*....|....*....|....*....|....*
gi 186532719 926 AAKGAKAYERSEDPIYVL--QNNIPIDPNYYLENQISKPLLRIFE 968
Cdd:TIGR00592 1128 DGGNLSARQRAYALEELQrkHNNLIYDTQYYLEHQIHPVVLRILE 1172
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
577-968 |
2.73e-77 |
|
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Pssm-ID: 99919 Cd Length: 371 Bit Score: 258.79 E-value: 2.73e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 577 GTYEGATVLEARTGFYEKpIATLDFASLYPSIMMAYNLCYCTLVTPEDvrklnlpPEHVTKTPSGETFVKQtlQKGILPE 656
Cdd:cd05536 2 ESYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVREGC-------EDCDVEPQVGHKFRKD--PPGFIPS 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 657 ILEELLTARKRAKADLKEAKDP-LEKAVLDGRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVED 735
Cdd:cd05536 72 VLEDLLEERRRIKEKMKKLDPEsEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEE 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 736 KfttlgGYQynaeVIYGDTDSVMVQFgvSDVEAAMTLGREAAEHISGTFikPIKLEFEKVYFPYLLINKKRYAGLLwtnp 815
Cdd:cd05536 152 K-----GFK----VIYGDTDSLFVKI--DGADAVKKKVKKLLKYINEEL--PLELEIEKFYKRGFFVTKKRYAGLT---- 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 816 qQFDKMDTKGIETVRRDNCLLVKNLVTESLNKILIDRDVPGAAENVKKTISDLLMNRIDLSLLVITKGLTKTGDDYEVKS 895
Cdd:cd05536 215 -EDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYKATG 293
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 186532719 896 AHGELAERMRKRDAATAPnvGDRVPYVIIKAAkgAKAYERSEDPIYVLQNNiPIDPNYYLENQISKPLLRIFE 968
Cdd:cd05536 294 PHVAAAKKLAKRGYKVRP--GTKIGYVIVKGS--GKISDRAYPYDMVDEKH-KYDAEYYIDNQVLPAVLRILE 361
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
142-972 |
8.46e-53 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 199.14 E-value: 8.46e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 142 GFEPYFYIACPPGmgpddisnfhqslegRMRESNKNAKVPKFVkRIEMVQKRSIMYYQQQKSqtfLKITVALPTMVASCR 221
Cdd:PRK05761 53 GHKPYFLTDLDPD---------------EIDKIPKILRHPSFD-HLEIVEKYDGLRDKKVKV---TKIVVKDPLAVRRLR 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 222 GILDrglqidglgmKSFQTYESNILFVLRFMVDCDIVGGNWIEVPTGKYKKNARTLSYCQLEFHCLYSDLISHAAEGEYS 301
Cdd:PRK05761 114 LSVR----------DIPRAWEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEILVEEIKKAFKDERKLAEDWLPIFEA 183
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 302 KMAPFRVLSFDIECAGR-KGHFPEakhdpviqianlvtlqgedhpfvrnvmtlkscapivgvdvmsfETEREVLLAWRDL 380
Cdd:PRK05761 184 PIPKIKRIAIDIEVYTPaKGRIPD-------------------------------------------DSEKELLAELFDI 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 381 IRDVDPDIIigYNICKFDLPYLIERAATLGIEEFPLLGRVKNSRVRVRDSTFssrqQGIRESKETTIEGRFQfdliqaiH 460
Cdd:PRK05761 221 ILEYPPVVT--FNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKF----FQNKAVRSYAFYGKYR-------H 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 461 RDhklssYSLNSVSAHFLSEQKEDVHHSIitdlqngNAETRRRLAVYCLKDAylpqRLLDKLMFIYNY------VEMARV 534
Cdd:PRK05761 288 RE-----ARLDAVGRALLGISKVELETNI-------SELDLEELAEYNFRDA----EITLKLTFFNNElvlkliLLLSRI 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 535 TGVPISfLLARGQSIKVLSQLL-RKGKQKNLVLPNAK---QSGSEQGT--------YEGATVLEARTGFYEKpIATLDFA 602
Cdd:PRK05761 352 SKLPIE-ELSRATISTWISNLEyWEHRKRGWLIPWKEdilRLDHEVYKkaiikgkkYRGGLVFQPPPGIFFN-VYVLDFA 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 603 SLYPSIMMAYNLCYCTLVTPEDVRKLNLPPEHVTKTPSGEtfvkqtlQKGILPEILEELLTARKRAKAdlKEAKDP---- 678
Cdd:PRK05761 430 SLYPSIIVKWNLSPETVRIPECKCHYDDEVPELGHSVCDD-------RPGLTSVLVGLLRDFRVKIYK--KKAKDPnlde 500
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 679 LEKAVLDGRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVEDkfttLGGyqynaEVIYGDTDSVM 758
Cdd:PRK05761 501 ERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAEE----LGL-----KVLYGDTDSLF 571
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 759 VQfGVS--DVEaamtlgrEAAEHISGTFikPIKLEFEKVY----FPYLlinKKRYAGLLWTnpqqfDKMDTKGIETVRRD 832
Cdd:PRK05761 572 VW-GPTkeSLE-------ELIKEIEERT--GIDLEVDKTYdwvaFSGL---KKNYFGVLKD-----GKVKIKGIVAKKRN 633
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 833 NCLLVKNLVTESLNKILIDRDvPGAAENVKKTISDLL--------MNRIDLSLLVITKGLTKTGDDYEV-KSAHGELAER 903
Cdd:PRK05761 634 TPEFVKELQREVLEVLKSIRS-PEDVEKVKDEIEDVLkryyeklrAKDYPLDELAIRVRLSKPLDEYTKnTPQHVKAALQ 712
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 186532719 904 MRKRDAATAPnvGDRVPYVIIKAAKGAKAYErsedpiyvLQNNIPIDPNYYLENqiskpLLRIFEPVLK 972
Cdd:PRK05761 713 LRDYGVEVSP--GDIISYVKVDDKRGVKPVQ--------LAKLSEIDVEKYIEL-----LRSALEQILS 766
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
308-519 |
9.44e-51 |
|
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: 177.55 E-value: 9.44e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 308 VLSFDIECAGRKGhFPEAKHDPVIQIANLVTLQGEDHPFVRNVMTLKSCAP-IVGVDVMSFETEREVLLAWRDLIRDVDP 386
Cdd:cd05160 1 VLSFDIETTPPVG-GPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEfIDGIEVEYFADEKELLKRFFDIIREYDP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 387 DIIIGYNICKFDLPYLIERAATLGIEEFPLLGRvknsrvRVRDSTFSsrqqgiRESKETTIEGRFQFDLIQAIHRDHKLS 466
Cdd:cd05160 80 DILTGYNIDDFDLPYLLKRAEALGIKLTDGIYR------RSGGEKSS------GSTERIAVKGRVVFDLLAAYKRDFKLK 147
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 186532719 467 SYSLNSVSAHFLSEQKEDVHHSIITDlqNGNAETRRRLAVYCLKDAYLPQRLL 519
Cdd:cd05160 148 SYTLDAVAEELLGEGKEKVDGEIIED--AEWEEDPERLIEYNLKDAELTLQIL 198
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
581-968 |
2.77e-48 |
|
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: 176.69 E-value: 2.77e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 581 GATVLEARTGFYeKPIATLDFASLYPSIMMAYNLCYCTLVTPEDvrklNLPPEHVTKTPSGETFVKQtlqKGILPEILEE 660
Cdd:cd05537 5 GGYVMDSKPGLY-KNVLVLDFKSLYPSIIRTFLIDPLGLIEGLK----APDPEDLIPGFLGARFSRE---KHILPDLIAR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 661 LLTARKRAKadlKEAKDPLekavldgrQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVEDKfttl 740
Cdd:cd05537 77 LWAARDEAK---REKNAPL--------SQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQ---- 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 741 gGYQynaeVIYGDTDSVMVQFG-VSDVEAAMTLGREAAEHISGTFIKPIK----------LEFEKVYFPYLLI------- 802
Cdd:cd05537 142 -GYQ----VIYGDTDSTFVWLGeELDAAEAQAIGKELASQINQWWAQKLKeefglesfleIEFETHYSRFFMPtirgsde 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 803 -NKKRYAGLLWTNPQqfDKMDTKGIETVRRDNCLLVKNLVTESLNKILIDRDVPGAaenVKKTISDLLMNRIDlSLLVIT 881
Cdd:cd05537 217 gSKKRYAGLKSTDGG--DELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGF---IKETVEELLAGELD-ELLVYR 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 882 KGLTKTGDDYEVKSAHGELAERMRK--RDAATAPNVGDRVPYVIIKAakGAKAYErsedpiyvlQNNIPIDPNYYLENQI 959
Cdd:cd05537 291 KRLRRPLSEYTKNVPPHVQAARLADqiNRELGRPRQYQWIEYVITVN--GPEPLE---------YRTSPLDYQHYIDKQL 359
|
410
....*....|..
gi 186532719 960 S---KPLLRIFE 968
Cdd:cd05537 360 KpiaDSILPFLG 371
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
578-972 |
1.58e-33 |
|
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: 132.85 E-value: 1.58e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 578 TYEGATVLEARTGFYEKpIATLDFASLYPSIMMAYNLcyctlvTPEDVRKlnlpPEHVTKTPSGETFVKQTLQKGILPEI 657
Cdd:cd05531 4 ADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNI------SPETINC----RCCECRDHVYLGHRICLKRRGFLPEV 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 658 LEELLTARKRAKADLKEAKDPlekavlDGRQLALKISANSVYGFTG---ATVGQLPCLEissSVTSYGRQMIEQTKKLVE 734
Cdd:cd05531 73 LEPLLERRLEYKRLKKEEDPY------AGRQKALKWILVTSFGYLGyknAKFGRIEVHE---AITAYGRKILLRAKEIAE 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 735 DKfttlgGYqynaEVIYGDTDSVMVQfGVSDVEaamtlgrEAAEHISGTFIKPIKLE--FEKVYFPYLLIN---KKRYAG 809
Cdd:cd05531 144 EM-----GF----RVLHGIVDSLWIQ-GRGDIE-------ELAREIEERTGIPLKLEghYDWIVFLPERDGlgaPNRYFG 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 810 LLWTnpqqfDKMDTKGIETVRRDNCLLVKNLVTESLNKILIDRDvpgaAENVKKTISDLL---------MNRIDLSLLVI 880
Cdd:cd05531 207 RLSD-----GEMKVRGIELRRRDTPPFVKKFQEEALDILASAKT----PEELLKLREEALdlfrrylqrLREGDLEDLII 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 881 TKGLTKTGDDYEVKSAHgeLAERMRKRDAATAPnvGDRVPYVIIkaakgakayeRSEDPIYVLQNNIPIDPNYYLENqis 960
Cdd:cd05531 278 EKKISKRSSEYKVLAST--ALKALRAKGVSVVP--GMKIEYIVR----------DGKRPVPDLGNDEGYDTKYYREL--- 340
|
410
....*....|..
gi 186532719 961 kpLLRIFEPVLK 972
Cdd:cd05531 341 --LERAAEELLF 350
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
305-949 |
2.82e-33 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 139.39 E-value: 2.82e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 305 PFRVLSFDIECAGRKgHFPEAKHDPVIQIA----------NLVTLQGED--------HPFVRNVMTLKSCAPIVGVDVMS 366
Cdd:PHA03036 159 PRSYLFLDIECHFDK-KFPSVFINPVSHISccyidlsgkeKRFTLINEDmlsedeieEAVKRGYYEIESLLDMDYSKELI 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 367 FETEREVLLAWRDLIRdVDPDIIIGYNICKFDLPYLIERAATLGIEE--FPLLGRVKNSRVRVRDSTFSSRQQGIRESKE 444
Cdd:PHA03036 238 LCSEIVLLRIAKKLLE-LEFDYVVTFNGHNFDLRYISNRLELLTGEKiiFRSPDGKETVHLCIYERNLSSHKGVGGVANT 316
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 445 TT-IE---GRFQFDLIQAIHRDHKLSSYSLNSVSAHFLS--EQKEDVHHSIITDLQNGNAETRRRLAV---------YCL 509
Cdd:PHA03036 317 TYhINnnnGTIFFDLYTFIQKTEKLDSYKLDSISKNAFNcnAKVLSENNNEVTFIGDNTTDAKGKASIfsevlstgnYVT 396
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 510 KDAYLPQRLLDK------------------------LMF---------IY-NY-----VEMAR----------------- 533
Cdd:PHA03036 397 INDDDICKILDKdiiensftvkvicknnyipgdtytLSFgkddvdlsdMYkNYnleiaLEMARycihdaclckylweyyg 476
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 534 ----VTGVPISFLLARGQSIKVLSQLLRKGKQKNLVLPNA---KQSGSEQ-GTYEGATVLEARTGFYEKPIATLDFASLY 605
Cdd:PHA03036 477 ietkIDAGASTYLLPQSMVFEYRASTLIKGPLLKLLLEEKtilVRSETKNkFPYEGGKVFAPKQKMFDNNVLIFDYNSLY 556
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 606 PSIMMAYNLCYCTLV-------------TPEDVRKLNLPPE--HVTKTPSGETFVKQTL-----QKGILPEILEELLTAR 665
Cdd:PHA03036 557 PNVCIFGNLSPETLVgvvvndnrleaeiNKQELRRKYPYPRyiYVHCEPRSPDLVSEIAvfdrrIEGIIPKLLKTFLEER 636
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 666 KRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTK------KLVEDKFTT 739
Cdd:PHA03036 637 ARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKYLNsvlngsKLINGKLIL 716
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 740 L-----------------------GGYQYNAEVIYGDTDSVMVQFGVSDVEAAMTLGREAAEHIS-GTFIKPIKLEFEKV 795
Cdd:PHA03036 717 AncpinpffkddrsidtnydtnlpVEYNFTFRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINeKVLFDNFKIEFEAV 796
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 796 YFPYLLINKKRYAGLLWTN---PQQFDKMDTKGIETVRRDNCLLVKNLVteslnKILIDRdvpgaaenVKKTISDLLMNR 872
Cdd:PHA03036 797 YKNLIMQSKKKYTTLKYIAsstDGSVPERVNKGTSETRRDVSKFHKYMI-----KIYKTR--------LLDMLSEGNMNS 863
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 873 IDLSLLVITKGLTKTGDDYEVKSAHGE--LAERMRKRD--AATAPNV----------------GDRVPYVIIKAAKGA-- 930
Cdd:PHA03036 864 NQVCIDILRSLEKDLIIEFDSRSAPLEmfLLSRTHHCNykSPDNPNMylvneynknnpekieiGERYYFAYICPINLPwq 943
|
810 820
....*....|....*....|....*
gi 186532719 931 ------KAYERSEDPIYVLQNNIPI 949
Cdd:PHA03036 944 kklvniKTYERIIDRSFKLKSNERI 968
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
579-956 |
2.93e-29 |
|
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: 120.92 E-value: 2.93e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 579 YEGATVLEARTGFYEKpIATLDFASLYPSIMMAYNLCYCTLVTPEDVRKLNLPPE---HVTKTpsgetfvkqtlQKGILP 655
Cdd:cd05530 13 YRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVNCPHCECKTNEVPEvghWVCKK-----------RPGITS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 656 EILEELLTAR-----KRAKadlKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQT- 729
Cdd:cd05530 81 QIIGLLRDLRvkiykKKAK---DKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTi 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 730 KKLVEdkfttlggyqYNAEVIYGDTDSVMVQfgvsdvEAAMTLGREAAEHISGTFikPIKLEFEKVYFPYLLIN-KKRYA 808
Cdd:cd05530 158 KKARE----------LGLKVLYGDTDSLFLW------NPPQEQLEDLVEWVEKEL--GLDLELDKEYRYVVFSGlKKNYL 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 809 GLLwtnpqQFDKMDTKGIETVRRDNCLLVKNLVTESLnKILIDRDVPGAAENVKKTISDL-------LMNR-IDLSLLVI 880
Cdd:cd05530 220 GVT-----KDGSVDIKGLLGKKRNTPEFVKELFYEVI-EILSAVNSPEDFEKAREKIRDIvkgvykrLKKKeYTLDQLAF 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 881 TKGLTKTGDDY------EVKSAhgELAERMRKRdaataPNVGDRVPYVIIKAAKGAKAYERSEDPiyvlqnniPIDPNYY 954
Cdd:cd05530 294 KVMLSKPPEEYtkntpqHVKAA--RQLEKYGRN-----VEAGDIISYVKVKGKEGVKPVQLARLD--------EVDVEKY 358
|
..
gi 186532719 955 LE 956
Cdd:cd05530 359 VE 360
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
577-965 |
3.55e-29 |
|
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: 119.90 E-value: 3.55e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 577 GTYEGATVLEARTGFYeKPIATLDFASLYPSIMMAYNLCyctlvtpedvrklnlppehvtktPSGETFvkqtlqkGILPE 656
Cdd:cd05538 1 GKFEGGYAYVFITGVL-GPIVHADVASLYPSIMLAYRIC-----------------------PARDSL-------GIFLA 49
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 657 ILEELLTARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIeqtkKLVEDK 736
Cdd:cd05538 50 LLKYLVELRLAAKESARAAARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELL----KLMIRW 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 737 FTtlggyQYNAEVIYGDTDSV--MVQFGVSDVEAAMTLGREaaehISGTFIKPIKLEFEKVYFPYLLINKKRYAGLLwtn 814
Cdd:cd05538 126 LR-----RRGATPVEVDTDGIyfIPPNGVDTEDEEEELVRE----LSSTLPKGITVEFDGRYRAMFSYKIKNYALLD--- 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 815 pqQFDKMDTKGIETVRRDNCLLVKNLVTESLnKILIDRDVPGAAENVKKTISDLLMNRIDLSLLVITKGLTKTGDDY--- 891
Cdd:cd05538 194 --YDGKLIVKGSAFRSRGIEPFLREFLREAV-RLLLQGDGAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYlqk 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 892 -----EVKSAHGELAERMRKRDAAtapnvGDRVPYVIIKAAKGAKAYER-SEDPIYvlqnnipiDPNYYLEN-------- 957
Cdd:cd05538 271 vragkRNPAAAYEIALARPREWRA-----GDRVTYYVSGTGKGVSVYENcRLVADY--------DPAHPDENtgfyaerl 337
|
....*....
gi 186532719 958 -QISKPLLR 965
Cdd:cd05538 338 lQLAARLLP 346
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
292-849 |
5.07e-29 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 125.19 E-value: 5.07e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 292 ISHAAEGEYS-KMAPFRVLSFDIECAGRKGhFPEAKHDPV----IQIANLVTlqgeDHPFV---RNVMTLKSCAPIVG-- 361
Cdd:PHA02528 91 ISDTYPGEIKyDRSKIRIANLDIEVTAEDG-FPDPEEAKYeidaITHYDSID----DRFYVfdlGSVEEWDAKGDEVPqe 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 362 ----VDVMSFETEREVLLAWRDLIRDVDPDIIIGYNICKFDLPYLIERAATlgieefpLLG-RVKNS-----RVRVRDST 431
Cdd:PHA02528 166 ildkVVYMPFDTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKN-------ILGeKTAKRlspwgKVKERTIE 238
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 432 FssrQQGiRESKETTIEGRFQFDLIQAIhrdHKLS-----SYSLNSVSAHFLSEQKEDVHHSIITDLQNGNAEtrrRLAV 506
Cdd:PHA02528 239 N---MYG-REEIAYDISGISILDYLDLY---KKFTftnqpSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQ---KYIE 308
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 507 YCLKDAYLPQRLLDKLMFIYNYVEMARVTGVPISfllargqsiKVLSQL-------LRKGKQKNLVLPnaKQSGSEQGTY 579
Cdd:PHA02528 309 YNIIDVELVDRLDDKRKLIELVLSMAYYAKINFE---------DVFSPIktwdaiiFNSLKEEKIVIP--ENKSHKKQKY 377
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 580 EGATVLEARTGFYeKPIATLDFASLYPSIMMAYNLCYCTLVTPEDVRKLNlppEHVTKT-----------PSGETFVKQt 648
Cdd:PHA02528 378 AGAFVKEPVPGAY-RWVVSFDLTSLYPSIIRQVNISPETIAGTFHVAPVH---EYINKTaprpsdeyscsPNGWMYRKD- 452
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 649 lQKGILPEILEELLTARKRAK-------------------------------------------------ADLKEAKDPL 679
Cdd:PHA02528 453 -IRGVIPTEIKKVFDQRKIYKkkmlaaernaeliktiledlndsvdtpidvdyyfdfsdefkaelktltkSSLKALLEEC 531
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 680 EK--AVLDGRQLALKISANSVYGFTGATVGQLPCLEISSSVTSYGRQMIEQTKKLVEDKFTTLGGYQYNAEVIYGDTDSV 757
Cdd:PHA02528 532 EKeiALCNTIQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQLAIQWIERKMNEYLNKLCKTEDEDYVIYGDTDSI 611
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 758 MVQFGvsDVEAAMTLGREA-AEHISGTFIKPIKLEFEKV----------YF----------------PYLLINKKRYAGL 810
Cdd:PHA02528 612 YVNLD--PLVEKVGEDKFKdTNHWVDFLDKFCKERMEPYidssyrelceYMnnyehlmfmdreaiagPGFWTAKKRYALN 689
|
650 660 670 680
....*....|....*....|....*....|....*....|..
gi 186532719 811 LWTNP-QQFD--KMDTKGIETVRRDNCLLVKNLVTESLNKIL 849
Cdd:PHA02528 690 VWDSEgTRYAepKLKIMGIETQRSSTPKAVQKALKEAIRRIL 731
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
306-522 |
9.27e-28 |
|
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: 111.29 E-value: 9.27e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 306 FRVLSFDIECAGRKGHfPEAKHDPVIQI-------ANLVTLQGEDHPFVRNVmtlkscapivgvdvmsfETEREVLLAWR 378
Cdd:cd05780 3 LKILSFDIEVLNHEGE-PNPEKDPIIMIsfadeggNKVITWKKFDLPFVEVV-----------------KTEKEMIKRFI 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 379 DLIRDVDPDIIIGYNICKFDLPYLIERAATLGIeEFPlLGRvknsrvrvRDSTFSSRQQGIRESKEttIEGRFQFDLIQA 458
Cdd:cd05780 65 EIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGI-ELD-LGR--------DGSEIKIQRGGFNNASE--IKGRIHVDLYPV 132
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 186532719 459 IHRDHKLSSYSLNSVSAHFLSEQKEDVHHSIITDLQNgNAETRRRLAVYCLKDAYLPQRLLDKL 522
Cdd:cd05780 133 ARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWD-SGENLERLFRYSMEDAKYTYEIGKEF 195
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
1007-1076 |
3.02e-26 |
|
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: 102.45 E-value: 3.02e-26
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 1007 CVGCKVPisNGTLCASCKGREAELYCKNVSQVAELEEVFGRLWTQCQECQGSLHQDVLCTSRDCPIFYRR 1076
Cdd:pfam14260 1 CLGCGAP--EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYMR 68
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
303-696 |
5.17e-26 |
|
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: 115.92 E-value: 5.17e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 303 MAPFRVLSFDIEC--AGRKGHFP--EAKHDPVIQIANLVTLQ----GEDHPFVRNVMTLKSCAPIVGVDVMSFETEREVL 374
Cdd:TIGR00592 195 DPELKLASFDIETyfHDGKDFFPgdENPADEEIMISTTPVIAkqwdYESEPEARVVTWKKPDKPTTGSYVESVSEEISMI 274
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 375 LAWRDLIRDVDPDIIIGYNICKFDLPYLIERAATLGIEEFPLLGRVKNSRV-----RVRDSTFSSRQQGI-RESKETTIE 448
Cdd:TIGR00592 275 KRFWDVIDQEDTDVEITVNGDNFDLVYLADRQVFQFYWDAYEDPAEKLGVVllfgrDVDHVSPCVQVKGInRDLFFLPRE 354
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 449 GRFQFDLIQAIHRDHKLSSYSLNSVSAHFLSEQKEDVHHSIITdlQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIYNy 528
Cdd:TIGR00592 355 GKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIA--KKYEFEAPDIDAPYSSEYLEVTYELGKEFAPMEA- 431
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 529 vEMARVTGVPISFLLARGQSIKVLSQLLRKGKQKNLVLPNAKQSGS----EQGTYEGATVLEAR----TGFYEKPIATLD 600
Cdd:TIGR00592 432 -LPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPDELEyprrSWCKYEGGYVKPPNvekgLDKTPPPLVVLD 510
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 601 FA--SLYPSIMMAYNlCYCTLVTPEDVRKLNLPPE-------------HVTKTPSGETFvkqtLQKGILPEILEELLTAR 665
Cdd:TIGR00592 511 FSmkSLNPSIIRNEI-VSIPDTLHREFALDKPPPEppydvhpcvgtrpKDCSFPLDLKG----EFPGKKPSLVEDLATER 585
|
410 420 430
....*....|....*....|....*....|...
gi 186532719 666 KRAKADLKEAK--DPLEKAVLDGRQLALKISAN 696
Cdd:TIGR00592 586 ALIKKFMAKVKkiDPDEIVGHDYQQRALKVLAN 618
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
308-520 |
2.10e-23 |
|
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: 100.00 E-value: 2.10e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 308 VLSFDIECAGRKGHFPEAKHDPVIQIAnlVTLQGEDHPF------------------VRNVMTLKSCapiVGVDVMSFET 369
Cdd:cd05778 6 ILSLEVHVNTRGDLLPDPEFDPISAIF--YCIDDDVSPFildankvgviivdelksnASNGRIRSGL---SGIPVEVVES 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 370 EREVLLAWRDLIRDVDPDIIIGYNICKFDLPYLIERAATLGIEEF-PLLGRVK-NSRVRVRDSTfssRQQGIRESKETTI 447
Cdd:cd05778 81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLlDEISRVPsDSNGKFGDRD---DEWGYTHTSGIKI 157
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 186532719 448 EGRFQFDLIQAIHRDHKLSSYSLNSVSAHFLSEQKEDVHHSIITD-LQNGNAETRRRLAVYCLKDAYLPQRLLD 520
Cdd:cd05778 158 VGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEwYKSGSASERWRVLEYYLKRVRLNLEILD 231
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
454-767 |
9.40e-19 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 92.61 E-value: 9.40e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 454 DLIQAIHR---DHKLSSYSLNSVSAHFLSEQK-----------EDVHHSIITDLQNGNAETRRRLAVYCLKDAYLPQRLL 519
Cdd:PHA03334 473 DLMRVCNTksiKAKCSSRKLDTVARLIISKSKphknppkigkmDDVKYTEMDGMFTAGGAALARYLIYNLVDSELLIRIA 552
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 520 DKLMFIYNYVEMARVT-GVPISfLLARG--------QSIKVLSQLLRKGKQKN------------LVLPNAKQSGSEQG- 577
Cdd:PHA03334 553 KNLDPVIEFLNRLRATyNIDYV-AHGRGvmnfcgfvQSTKSVEVPLLKARLRIgifvatgriaesLCMPEKYARDCRQKi 631
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 578 TYEGATVLEARTGF-----YEKPIATLDFASLYPSIMMAYNlcyctlVTPE---DVRKLN------------LPPE---- 633
Cdd:PHA03334 632 KLKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDAN------ISPEaivDPDCTArvrgwvvfdwkkIDRGfgka 705
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 634 --------HVTKTPSGETFVKQTLQKgilpeiLEELLTARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGftgat 705
Cdd:PHA03334 706 tlmytilrTKPEEPSWRRFTTYTTSS------LNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNEMKICANSHYG----- 774
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 186532719 706 VGQLPCleiSSSVTSYGRQMIeqtkKLVEDKFTTLGGYQynaeVIYGDTDSVMVQFGVSDVE 767
Cdd:PHA03334 775 VAPHAC---QHLITTLGRHKI----KLVEEFIKKEPGMT----VNYGDTDSVMFQLPPDDAE 825
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
305-520 |
3.65e-16 |
|
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: 77.99 E-value: 3.65e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 305 PFRVLSFDIECAGrkghfpeakHDPVIQIAnlvtLQGEDHPFVRNVMTLKSCAPivgVDVMSFETEREVLLAWRDLIRDV 384
Cdd:cd05784 2 KLKVVSLDIETSM---------DGELYSIG----LYGEGQERVLMVGDPEDDAP---DNIEWFADEKSLLLALIAWFAQY 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 385 DPDIIIGYNICKFDLPYLIERAATLGIEefPLLGRvKNSRVRVRDSTFSsrQQGIreskeTTIEGRFQFDLIQAI----- 459
Cdd:cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAHGLP--LRLGR-GGSPLNWRQSGKP--GQGF-----LSLPGRVVLDGIDALktaty 135
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 186532719 460 HrdhkLSSYSLNSVSAHFLSEQKeDVHHS-----IITDLQNgnaETRRRLAVYCLKDAYLPQRLLD 520
Cdd:cd05784 136 H----FESFSLENVAQELLGEGK-LIHDVddrgaEIERLFR---EDKLALARYNLQDCELVWRIFE 193
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
305-477 |
7.09e-15 |
|
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: 74.29 E-value: 7.09e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 305 PFRVLSFDIECAGRKGhFPEAKHDPVIQIAnlvtLQGEDHPfvrnvmtlkscapiVGVDVMSFETEREVLLAWRDLIRDV 384
Cdd:cd05781 2 DLKTLAFDIEVYSKYG-TPNPRRDPIIVIS----LATSNGD--------------VEFILAEGLDDRKIIREFVKYVKEY 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 385 DPDIIIGYNICKFDLPYLIERAATLGIeefPL-LGRVKNSRVRVrdSTFSsrqqgireskETTIEGRFQFDLIQAIHRDH 463
Cdd:cd05781 63 DPDIIVGYNSNAFDWPYLVERARVLGV---KLdVGRRGGSEPST--GVYG----------HYSITGRLNVDLYDFAEEIP 127
|
170
....*....|....
gi 186532719 464 KLSSYSLNSVSAHF 477
Cdd:cd05781 128 EVKVKTLENVAEYL 141
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
307-511 |
1.73e-14 |
|
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: 73.60 E-value: 1.73e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 307 RVLSFDIECAGRKGHF---PEAKHDPVIQIAnLVTLQGEDHpfvrnvmtlkscapivgvdVMSFE--TEREVLLAWRDLI 381
Cdd:cd05785 10 RRLQLDIETYSLPGFFfsnPDRGDDRIIIVA-LRDNRGWEE-------------------VLHAEdaAEKELLEELVAII 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 382 RDVDPDIIIGYNICKFDLPYLIERAATLGIeefPL-LGRVkNSRVRVRDSTFSSRQQGIRESKeTTIEGRFQFDLIQAIH 460
Cdd:cd05785 70 RERDPDVIEGHNIFRFDLPYLRRRCRRHGV---PLaIGRD-GSIPRQRPSRFRFAERLIDYPR-YDIPGRHVIDTYFLVQ 144
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 186532719 461 R----DHKLSSYSLNSVSAHF--LSEQKEDVHHSIITDLQNGNAETRRRlavYCLKD 511
Cdd:cd05785 145 LfdvsSRDLPSYGLKAVAKHFglASPDRTYIDGRQIAEVWRSDPARLLA---YALDD 198
|
|
| DNA_polB_B1_exo |
cd05783 |
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ... |
307-518 |
8.89e-13 |
|
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: 68.50 E-value: 8.89e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 307 RVLSFDIEC-AGRKGHFPEAKHD--PVIQIAnLVTLQGEDHPFV---RNVMTLKSCAPIvGVDVMSFETEREVLLAWRDL 380
Cdd:cd05783 6 KRIAIDIEVyTPIKGRIPDPKTAeyPVISVA-LAGSDGLKRVLVlkrEGVEGLEGLLPE-GAEVEFFDSEKELIREAFKI 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 381 IRDVdPdIIIGYNICKFDLPYLIERAATLGI--EEFPLlgRVKNSRVRVRDS-------TFSSRQqgireskettiegrf 451
Cdd:cd05783 84 ISEY-P-IVLTFNGDNFDLPYLYNRALKLGIpkEEIPI--YLKRDYATLKHGihidlykFFSNRA--------------- 144
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 186532719 452 qfdlIQAIHRDHKLSSYSLNSVSAHFLSEQKEDvHHSIITDLqngnaeTRRRLAVYCLKDAYLPQRL 518
Cdd:cd05783 145 ----IQVYAFGNKYREYTLDAVAKALLGEGKVE-LEKNISEL------NLYELAEYNYRDAELTLEL 200
|
|
| DNA_polB_epsilon_exo |
cd05779 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ... |
307-423 |
2.22e-12 |
|
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: 67.29 E-value: 2.22e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 307 RVLSFDIECAGRKGHFPEAKHDPVIQIANLVTLQGEdhpfvrnvmtLKSCAPIVGVDVMSFE-----------------T 369
Cdd:cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGY----------LIVNREIVSEDIEDFEytpkpeyegpfkvfnepD 72
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 186532719 370 EREVLLAWRDLIRDVDPDIIIGYNICKFDLPYLIERAATLGIEEFPLLGRVKNS 423
Cdd:cd05779 73 EKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDS 126
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
364-522 |
4.82e-11 |
|
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: 64.17 E-value: 4.82e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 364 VMSFETEREVLLAWRDLIRDVDPDIIIGYNICKFDLPYLIERAATLGIEEFPLLGRVKNSRVRvrdSTFSSRQQGIREsk 443
Cdd:cd05776 76 VRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWP---KKKGGGKFGERE-- 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 444 etTIEGRFQFDL-IQAihRD-HKLSSYSLNSVSAHFLSEQKEDVhhsIITDLQN--GNAETRRRLAVYCLKDAYLPQRLL 519
Cdd:cd05776 151 --LTAGRLLCDTyLSA--KElIRCKSYDLTELSQQVLGIERQDI---DPEEILNmyNDSESLLKLLEHTEKDAYLILQLM 223
|
...
gi 186532719 520 DKL 522
Cdd:cd05776 224 FKL 226
|
|
| 43A |
PHA02524 |
DNA polymerase subunit A; Provisional |
365-669 |
2.69e-07 |
|
DNA polymerase subunit A; Provisional
Pssm-ID: 164925 [Multi-domain] Cd Length: 498 Bit Score: 54.62 E-value: 2.69e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 365 MSFETEREVLLAWRDLIRDVDPDIIIGYNICKFDLPYLIERAATL----GIEEFPLLGRVKNSRV-RVRDSTFSSRQQGI 439
Cdd:PHA02524 175 MPFEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNIlgekAANQLSPYGKITSKTItNLYGEKIIYKIHGI 254
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 440 RESKETTIEGRFQFDLIQaihrDHKLSSYSLNSVSAHFLSEQKEdvhhsiitdLQNGNAETRRRLAVYCLKDAYLPQRLL 519
Cdd:PHA02524 255 ALMDYMDVFKKFSFTPMP----DYKLGNVGYREVKADKLDYEGP---------INKFRKADHQRYVDYCVRDTDIILLID 321
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 520 DKLMFIYNYVEMARVTGVPISFLLArgqSIKVLSQLLRKG-KQKNLVLPNAKQSGSEqgTYEGATVLEARTGFYEKPIaT 598
Cdd:PHA02524 322 GRRCFIDLILSLSYYAKIRFDDVLG---TIKVWDSIIFNSlVESNVVIPAMKASPKQ--SFPGAYVKEPVPGGYRYGL-S 395
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186532719 599 LDFASLYPSIMMAYNLC---------------YCTLVTPEdvrklnlPPEHVTKTPSGETFVKQTLqkGILPEILEELLT 663
Cdd:PHA02524 396 FDLTSLYPSILRLLNISpemiagmfsparledYINKVAPK-------PSDQFSCAPNGMMYKKGVV--GVLPNETEKVFL 466
|
....*.
gi 186532719 664 ARKRAK 669
Cdd:PHA02524 467 QRKSEK 472
|
|
| |
