|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1-1087 |
0e+00 |
|
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: 1494.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1 MFIASAGKKTTDKAVDLSKDDLLGDILQDLN-TETAQ--ITPPPVLIPKKKRSTGAL---LNPFSVHTPKAIPSGKPASP 74
Cdd:TIGR00592 85 VRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVVDIVKKAIP 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 75 VLRN---EPLLTPIPLKRAELAGELAQPE-CPEDEQELGVME--FEDGDF----DES-MDTEKVDEK-PVTAKTWDQETE 142
Cdd:TIGR00592 165 VSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDENpADEEIMISTtPVIAKQWDYESE 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 143 PVERVEHEADPERGTT-SYLENFLPDVSC----WD-IDQDDESipQEVQVDSSNLPLVKGADdEQVFQFYWlDAYEDPYN 216
Cdd:TIGR00592 245 PEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD--VEITVNGDNFDLVYLAD-RQVFQFYW-DAYEDPAE 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 217 QPGVVFLFGKVwiesvKTHVSCCVMVKNIERTLYFLPREMKFDLNTGKETAIPVTMKDVYEEFDSKISAKYKIMKFKSKI 296
Cdd:TIGR00592 321 KLGVVLLFGRD-----VDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKP 395
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 297 VEKNYAFEIP--DVPEKSEYLEVRYS-----AEVPQLPQNLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKNPQLL 369
Cdd:TIGR00592 396 IAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPDEL 475
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 370 NQP-ISWCKFEVMALKPDLVNVIKDVSPPPLVVMSFSMKtMQNVQNHQHEIIAMAALVHHSFALDKAPPEPPFQTHFCVV 448
Cdd:TIGR00592 476 EYPrRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVG 554
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 449 SKPKDCIFPCDFK-EVISKKNMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRL 527
Cdd:TIGR00592 555 TRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRL 634
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 528 RRSnmPKLGSRsgFGERnaTCGRMICDVEISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSYLLYLLEHI 607
Cdd:TIGR00592 635 RRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHT 708
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 608 WKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQKLGDEDEEIDG 687
Cdd:TIGR00592 709 WKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKLGDEDEEIDG 787
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 688 dtnkYKKGrKKATYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvtsevQKATEDEeqeqIPELPDPN 767
Cdd:TIGR00592 788 ----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDEDE----LPELPDSE 852
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 768 LEMGILPREIRKLVERRKQVKQLMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILM 847
Cdd:TIGR00592 853 LEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILE 931
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 848 HTKDMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDAVFKSLLLLKKKKYAALVVEPTSD 927
Cdd:TIGR00592 932 HTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYAAIKVEGDSD 1011
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 928 GNYITKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQD 1007
Cdd:TIGR00592 1012 GNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVINKQLTRDPKD 1091
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1008 YPDRKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTATQRAYAPEQLQKLDN-LAIDTQYYLAQQIHPVVARIC 1086
Cdd:TIGR00592 1092 YPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQRKHNnLIYDTQYYLEHQIHPVVLRIL 1171
|
.
gi 1907203014 1087 E 1087
Cdd:TIGR00592 1172 E 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
694-1104 |
0e+00 |
|
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: 719.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 694 KGRKKATYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRvtsevqkATEDEEQEQIPELPDPNLEMGIL 773
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDR-------ADPDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 774 PREIRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMV 853
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 854 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDAVFKSLLLLKKKKYAALVVEPtsDGNYITK 933
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 934 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDRKS 1013
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1014 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTATQRAYAPEQLQKLDNLAIDTQYYLAQQIHPVVARICEPIDGID 1093
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 1907203014 1094 AVLIALWLGLD 1104
Cdd:cd05532 390 AVRLAECLGLD 400
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
636-1089 |
7.20e-167 |
|
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: 504.84 E-value: 7.20e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 636 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKLGDEDeeidgdtnkykkgrkkaTYAGGLVLDPKVGFYD 715
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 716 KFILLLDFNSLYPSIIQEFNICFTTVQRVTSEVQKATEDEEQEQIPELPD------PNLEMGILPREIRKLVERRKQVKQ 789
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 790 LMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKM---NLEVIYGDTD 866
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 867 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDAVFKSLLLLKKKKYAALVVEPTSDGNyitKQELKGLDIVRR 944
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 945 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDRKSLPHVHVALWIN 1024
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907203014 1025 SQGGRKVKAGDTVSYVICQDGS---NLTATQRAYAPE-QLQKldNLAIDTQYYLAQQIHPVVARICEPI 1089
Cdd:pfam00136 373 KRNGEAPEVGDRIPYVIVKAAKglkNLLIYERAEDPEyVLEN--NLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
349-1090 |
7.18e-110 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 365.30 E-value: 7.18e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 349 FLMNRKIKGPCWLEVknpqllnQPISWCKFEVMALKPDLVNVIKDVsPPPLVVMSF----SMKTMQNVQNHQHEIIAMAa 424
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 425 lVHHSFALDKAppeppfqthFCVVSKPKDcifpcdfkeviskknMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSF 504
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 505 ELEVLLQRINECKVPywSKIGRLRRSnmPKLGSRSGFGERNATcGRMICDV-EISAKELIHCKSYHLSELVQQILKTERI 583
Cdd:COG0417 244 DLPYLQKRAERLGIP--LDLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 584 VIPTENIRNMYSESsyLLYLLEHIWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 663
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 664 IVPDKqifrkpqqklgdedEEIDGDTnkykkgrkkatYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqr 743
Cdd:COG0417 397 LAPNK--------------GEIKGEA-----------YPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETL-- 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 744 vtSEVQKATEDEEQEqIPELP-----DPNlemGILPREIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSM 818
Cdd:COG0417 449 --VEGGEEPCGDEDV-APGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 819 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KLYKL 897
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 898 LEIDIDAVFKSllllkkkkyaalVVEPTSDGNY--ITKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 972
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 973 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDRKSLPHVHVALWINSQgGRKVKAGDTVSYVIcqdgsnLTATQ 1052
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI------TKGGG 738
|
730 740 750
....*....|....*....|....*....|....*...
gi 1907203014 1053 RAYaPEQLQKLDNLAIDTQYYLAQQIHPVVARICEPID 1090
Cdd:COG0417 739 RVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
397-873 |
1.97e-106 |
|
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: 345.28 E-value: 1.97e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 397 PPLVVMSFSMKTMQNVQNHQHEIIAMAALVHHSFALDKAPPEPPFQtHFCVVSKPKDCIfpcdfkeviskKNMKVEIAAT 476
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 477 ERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRLRRS-----NMPKLGSRSG--FGERNATCG 549
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripnKKPLFGSKSFglSDIKVYIKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 550 RMICDVEISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSYLLY-LLEHIWKDARFILQIMCELNVLPLAL 628
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDeLLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 629 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqklgdedEEIDGDTNKYKKgRKKATYAGGLVLD 708
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSK--------------ELYDFKGSEPDL-KKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 709 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVTSEVQKA-TEDEEQEQIPELPDP--------NLEMGILPREIRK 779
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGdLIIPEDLLTIKYEKGnkyrfvkkNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 780 LVERRKQVKQLMKQ-QDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKM-- 856
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 1907203014 857 ---NLEVIYGDTDSIMINTN 873
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
471-1090 |
5.49e-75 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 266.34 E-value: 5.49e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 471 VEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYwsKIGRLRRSNMPKL-GSRSGFGERNATcG 549
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 550 RMICD-VEISAKELIHCKSYHLsELVQQilkteRIVIPTENIRNMYSESSYL--LY------LLEHIWKDARFILQIMCE 620
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSL-EYVSQ-----RLLGEGKAIDDPYDRMDEIdrRFaedkpaLARYNLKDCELVTRIFEK 347
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 621 LNVLPLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDkqifrkpqqkLGDEDEEidgdtnkykkgrkkaT 700
Cdd:PRK05762 348 TKLLPFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPN----------LGERPGE---------------A 400
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 701 YAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTvqRVtsevqKATEDEEQEQIPelpdPNL------EMGILP 774
Cdd:PRK05762 401 SPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDG--LV-----EGLAQPPEESVA----GFLgarfsrEKHFLP 468
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 775 REIRKLVERRKQVKQLMKQqdlnpdlvlqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQ 854
Cdd:PRK05762 469 EIVERLWEGRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIE 536
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 855 KMNLEVIYGDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDAVFK--------SLLLLKK 914
Cdd:PRK05762 537 AQGYQVIYGDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSK 616
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 915 KKYAALVVEPTSDGNYItkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQ 994
Cdd:PRK05762 617 KRYAGLIQEGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EK 684
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 995 FEINKALTKDPQDYpDRKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGSnltatqrayapeqlQKLDNL--A 1067
Cdd:PRK05762 685 LVYRKRLRRPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNGP--------------EPLEYRksP 749
|
650 660
....*....|....*....|...
gi 1907203014 1068 IDTQYYLAQQIHPVVARICEPID 1090
Cdd:PRK05762 750 IDYDYYIEKQLQPVADRILPFFG 772
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1127-1316 |
7.66e-69 |
|
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain.
Pssm-ID: 462651 Cd Length: 184 Bit Score: 229.03 E-value: 7.66e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1127 AQLTDEEKYKDCEKFKCLCPSCGTENIYDNVFEGS-GLDMEPSLYRCSNvdCKVSPLTFmvQLSNKLIMDIRRCIKKYYD 1205
Cdd:pfam08996 1 SQISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1206 GWLICEEPTCCSRLRRLPLHFSRngplCP-VCMKAVLRPEYSDKSLYTQLCFYRYIFDADCALEKLTEHEKDKLKKQFFP 1284
Cdd:pfam08996 77 GWLVCDDPTCGNRTRQMSVYGKR----CLgPGCKGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLALA 152
|
170 180 190
....*....|....*....|....*....|..
gi 1907203014 1285 LRVLQDYRKVKNIAEQFLSWSGYSEVNLSKLF 1316
Cdd:pfam08996 153 EQNRELFKTLKSVVDKYLDKCGRRWVNLSSLF 184
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1-1087 |
0e+00 |
|
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: 1494.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1 MFIASAGKKTTDKAVDLSKDDLLGDILQDLN-TETAQ--ITPPPVLIPKKKRSTGAL---LNPFSVHTPKAIPSGKPASP 74
Cdd:TIGR00592 85 VRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVVDIVKKAIP 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 75 VLRN---EPLLTPIPLKRAELAGELAQPE-CPEDEQELGVME--FEDGDF----DES-MDTEKVDEK-PVTAKTWDQETE 142
Cdd:TIGR00592 165 VSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDENpADEEIMISTtPVIAKQWDYESE 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 143 PVERVEHEADPERGTT-SYLENFLPDVSC----WD-IDQDDESipQEVQVDSSNLPLVKGADdEQVFQFYWlDAYEDPYN 216
Cdd:TIGR00592 245 PEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD--VEITVNGDNFDLVYLAD-RQVFQFYW-DAYEDPAE 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 217 QPGVVFLFGKVwiesvKTHVSCCVMVKNIERTLYFLPREMKFDLNTGKETAIPVTMKDVYEEFDSKISAKYKIMKFKSKI 296
Cdd:TIGR00592 321 KLGVVLLFGRD-----VDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKP 395
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 297 VEKNYAFEIP--DVPEKSEYLEVRYS-----AEVPQLPQNLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKNPQLL 369
Cdd:TIGR00592 396 IAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPDEL 475
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 370 NQP-ISWCKFEVMALKPDLVNVIKDVSPPPLVVMSFSMKtMQNVQNHQHEIIAMAALVHHSFALDKAPPEPPFQTHFCVV 448
Cdd:TIGR00592 476 EYPrRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVG 554
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 449 SKPKDCIFPCDFK-EVISKKNMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRL 527
Cdd:TIGR00592 555 TRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRL 634
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 528 RRSnmPKLGSRsgFGERnaTCGRMICDVEISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSYLLYLLEHI 607
Cdd:TIGR00592 635 RRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHT 708
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 608 WKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQKLGDEDEEIDG 687
Cdd:TIGR00592 709 WKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKLGDEDEEIDG 787
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 688 dtnkYKKGrKKATYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvtsevQKATEDEeqeqIPELPDPN 767
Cdd:TIGR00592 788 ----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDEDE----LPELPDSE 852
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 768 LEMGILPREIRKLVERRKQVKQLMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILM 847
Cdd:TIGR00592 853 LEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILE 931
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 848 HTKDMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDAVFKSLLLLKKKKYAALVVEPTSD 927
Cdd:TIGR00592 932 HTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYAAIKVEGDSD 1011
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 928 GNYITKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQD 1007
Cdd:TIGR00592 1012 GNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVINKQLTRDPKD 1091
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1008 YPDRKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTATQRAYAPEQLQKLDN-LAIDTQYYLAQQIHPVVARIC 1086
Cdd:TIGR00592 1092 YPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQRKHNnLIYDTQYYLEHQIHPVVLRIL 1171
|
.
gi 1907203014 1087 E 1087
Cdd:TIGR00592 1172 E 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
694-1104 |
0e+00 |
|
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: 719.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 694 KGRKKATYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRvtsevqkATEDEEQEQIPELPDPNLEMGIL 773
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDR-------ADPDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 774 PREIRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMV 853
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 854 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDAVFKSLLLLKKKKYAALVVEPtsDGNYITK 933
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 934 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDRKS 1013
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1014 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTATQRAYAPEQLQKLDNLAIDTQYYLAQQIHPVVARICEPIDGID 1093
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 1907203014 1094 AVLIALWLGLD 1104
Cdd:cd05532 390 AVRLAECLGLD 400
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
636-1089 |
7.20e-167 |
|
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: 504.84 E-value: 7.20e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 636 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKLGDEDeeidgdtnkykkgrkkaTYAGGLVLDPKVGFYD 715
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 716 KFILLLDFNSLYPSIIQEFNICFTTVQRVTSEVQKATEDEEQEQIPELPD------PNLEMGILPREIRKLVERRKQVKQ 789
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 790 LMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKM---NLEVIYGDTD 866
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 867 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDAVFKSLLLLKKKKYAALVVEPTSDGNyitKQELKGLDIVRR 944
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 945 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDRKSLPHVHVALWIN 1024
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907203014 1025 SQGGRKVKAGDTVSYVICQDGS---NLTATQRAYAPE-QLQKldNLAIDTQYYLAQQIHPVVARICEPI 1089
Cdd:pfam00136 373 KRNGEAPEVGDRIPYVIVKAAKglkNLLIYERAEDPEyVLEN--NLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
397-629 |
9.42e-113 |
|
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: 353.07 E-value: 9.42e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 397 PPLVVMSFSMKTMQNVQNHQHEIIAMAALVHHSFALDKAPPEPPFQTHFCVVSKPKDC-IFPCDFKEVISKKNMKVEIAA 475
Cdd:cd05776 1 PPLTVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRsPPPDLFEKNAKKKKTKVRIFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 476 TERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRLRRSNMPKLGSRSGFGERNATCGRMICDV 555
Cdd:cd05776 81 NERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDT 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907203014 556 EISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSYLLYLLEHIWKDARFILQIMCELNVLPLALQ 629
Cdd:cd05776 161 YLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLNILPLTKQ 234
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
349-1090 |
7.18e-110 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 365.30 E-value: 7.18e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 349 FLMNRKIKGPCWLEVknpqllnQPISWCKFEVMALKPDLVNVIKDVsPPPLVVMSF----SMKTMQNVQNHQHEIIAMAa 424
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 425 lVHHSFALDKAppeppfqthFCVVSKPKDcifpcdfkeviskknMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSF 504
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 505 ELEVLLQRINECKVPywSKIGRLRRSnmPKLGSRSGFGERNATcGRMICDV-EISAKELIHCKSYHLSELVQQILKTERI 583
Cdd:COG0417 244 DLPYLQKRAERLGIP--LDLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 584 VIPTENIRNMYSESsyLLYLLEHIWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 663
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 664 IVPDKqifrkpqqklgdedEEIDGDTnkykkgrkkatYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqr 743
Cdd:COG0417 397 LAPNK--------------GEIKGEA-----------YPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETL-- 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 744 vtSEVQKATEDEEQEqIPELP-----DPNlemGILPREIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSM 818
Cdd:COG0417 449 --VEGGEEPCGDEDV-APGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 819 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KLYKL 897
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 898 LEIDIDAVFKSllllkkkkyaalVVEPTSDGNY--ITKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 972
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 973 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDRKSLPHVHVALWINSQgGRKVKAGDTVSYVIcqdgsnLTATQ 1052
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI------TKGGG 738
|
730 740 750
....*....|....*....|....*....|....*...
gi 1907203014 1053 RAYaPEQLQKLDNLAIDTQYYLAQQIHPVVARICEPID 1090
Cdd:COG0417 739 RVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
397-873 |
1.97e-106 |
|
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: 345.28 E-value: 1.97e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 397 PPLVVMSFSMKTMQNVQNHQHEIIAMAALVHHSFALDKAPPEPPFQtHFCVVSKPKDCIfpcdfkeviskKNMKVEIAAT 476
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 477 ERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRLRRS-----NMPKLGSRSG--FGERNATCG 549
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripnKKPLFGSKSFglSDIKVYIKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 550 RMICDVEISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSYLLY-LLEHIWKDARFILQIMCELNVLPLAL 628
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDeLLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 629 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqklgdedEEIDGDTNKYKKgRKKATYAGGLVLD 708
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSK--------------ELYDFKGSEPDL-KKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 709 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVTSEVQKA-TEDEEQEQIPELPDP--------NLEMGILPREIRK 779
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGdLIIPEDLLTIKYEKGnkyrfvkkNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 780 LVERRKQVKQLMKQ-QDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKM-- 856
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 1907203014 857 ---NLEVIYGDTDSIMINTN 873
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
471-1090 |
5.49e-75 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 266.34 E-value: 5.49e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 471 VEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYwsKIGRLRRSNMPKL-GSRSGFGERNATcG 549
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 550 RMICD-VEISAKELIHCKSYHLsELVQQilkteRIVIPTENIRNMYSESSYL--LY------LLEHIWKDARFILQIMCE 620
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSL-EYVSQ-----RLLGEGKAIDDPYDRMDEIdrRFaedkpaLARYNLKDCELVTRIFEK 347
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 621 LNVLPLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDkqifrkpqqkLGDEDEEidgdtnkykkgrkkaT 700
Cdd:PRK05762 348 TKLLPFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPN----------LGERPGE---------------A 400
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 701 YAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTvqRVtsevqKATEDEEQEQIPelpdPNL------EMGILP 774
Cdd:PRK05762 401 SPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDG--LV-----EGLAQPPEESVA----GFLgarfsrEKHFLP 468
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 775 REIRKLVERRKQVKQLMKQqdlnpdlvlqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQ 854
Cdd:PRK05762 469 EIVERLWEGRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIE 536
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 855 KMNLEVIYGDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDAVFK--------SLLLLKK 914
Cdd:PRK05762 537 AQGYQVIYGDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSK 616
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 915 KKYAALVVEPTSDGNYItkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQ 994
Cdd:PRK05762 617 KRYAGLIQEGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EK 684
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 995 FEINKALTKDPQDYpDRKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGSnltatqrayapeqlQKLDNL--A 1067
Cdd:PRK05762 685 LVYRKRLRRPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNGP--------------EPLEYRksP 749
|
650 660
....*....|....*....|...
gi 1907203014 1068 IDTQYYLAQQIHPVVARICEPID 1090
Cdd:PRK05762 750 IDYDYYIEKQLQPVADRILPFFG 772
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
232-573 |
1.14e-74 |
|
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: 251.57 E-value: 1.14e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 232 VKTHVSCCVMVKNIERTLYFLPREmkfdlnTGKETAIPVTMKDVYEEFdskisakYKIMKFKSKIVEKNYAFEIPDVPek 311
Cdd:pfam03104 2 TDEGVSVCVNVFGFKPYFYCLAPD------GKELEEVIEEIKELYEGL-------DKIEKIELKLKKSLYGYEEDPVP-- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 312 SEYLEVRYSAEVPQLPQNLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVK-NPQLLNQPISWCKFEVMALKPDLVNV 390
Cdd:pfam03104 67 YLKVSFANPRPLLKIRKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKvYPFRAEGRISNCDVEIDCDSPDLISV 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 391 IKDVSPPPLVVMSFSMKTMQ------NVQNHQHEIIAMAALVHhsfalDKAPPEPPFQthfcVVSKPKDCIFPCDFKEVI 464
Cdd:pfam03104 147 PFEKEWPPLRVLSFDIECTSlpgkfpDAENVKDPIIQISCMLD-----GQGEPEPEPR----FLFTLRECDSEDIEDFEY 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 465 SKKNM----KVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRLRRsNMPKLGSRSG 540
Cdd:pfam03104 218 TPKPIypgvKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNR-GGRSKVREIG 296
|
330 340 350
....*....|....*....|....*....|....*..
gi 1907203014 541 FG----ERNATCGRMICDVEISAKELIHCKSYHLSEL 573
Cdd:pfam03104 297 FGtrsyEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
699-1085 |
2.59e-70 |
|
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: 238.81 E-value: 2.59e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 699 ATYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQRvtSEVQKATEDEEQEQIPELPDPNlemGILPREIR 778
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVG--NGEIAAPEDYIGVGFRSPKDRK---GLLPRILE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 779 KLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKMNL 858
Cdd:cd00145 75 ELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGA 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 859 EVIYGDTDSIMINTN-STNLEEVFKLGNKVKSEVNKlYKLLEIDIDAVFKSLLLLKKKKYAALVVEPTSDGNyitKQELK 937
Cdd:cd00145 155 RVIYGDTDSIFVSLPkMGTKEDAIKEGREILQELAD-EHLLELEFEKVYLPFFLGKKKRYAGLDIWKGQDEG---KIDIK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 938 GLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigenvlngsvpvsqfeinkaltkdpqdypdrkslphv 1017
Cdd:cd00145 231 GLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL--------------------------------------- 271
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907203014 1018 hvalwinsqggrkvkagDTVSYVICQDGSNLTATQRAYAPEQLQKlDNLAIDTQYYLAQQIHPVVARI 1085
Cdd:cd00145 272 -----------------DKVKYVVTRGGKGVPDYERADPPLEDLD-KRHRIDYEYYLERLLQPPLERI 321
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1127-1316 |
7.66e-69 |
|
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain.
Pssm-ID: 462651 Cd Length: 184 Bit Score: 229.03 E-value: 7.66e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1127 AQLTDEEKYKDCEKFKCLCPSCGTENIYDNVFEGS-GLDMEPSLYRCSNvdCKVSPLTFmvQLSNKLIMDIRRCIKKYYD 1205
Cdd:pfam08996 1 SQISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1206 GWLICEEPTCCSRLRRLPLHFSRngplCP-VCMKAVLRPEYSDKSLYTQLCFYRYIFDADCALEKLTEHEKDKLKKQFFP 1284
Cdd:pfam08996 77 GWLVCDDPTCGNRTRQMSVYGKR----CLgPGCKGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLALA 152
|
170 180 190
....*....|....*....|....*....|..
gi 1907203014 1285 LRVLQDYRKVKNIAEQFLSWSGYSEVNLSKLF 1316
Cdd:pfam08996 153 EQNRELFKTLKSVVDKYLDKCGRRWVNLSSLF 184
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
700-1087 |
3.56e-65 |
|
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: 225.67 E-value: 3.56e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 700 TYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQRvtsevqkateDEEQEQIPELP-------DPnleMGI 772
Cdd:cd05536 3 SYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVR----------EGCEDCDVEPQvghkfrkDP---PGF 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 773 LPREIRKLVERRKQVKQLMKQ-QDLNPDLVLqYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKD 851
Cdd:cd05536 69 IPSVLEDLLEERRRIKEKMKKlDPESEEYKL-LDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIK 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 852 MVQKMNLEVIYGDTDSIM--INTNSTNLEEVFKLGNKVKSEVNklyklLEIDIDAVFKSLLLLKKKKYAALvvepTSDGN 929
Cdd:cd05536 148 IAEEKGFKVIYGDTDSLFvkIDGADAVKKKVKKLLKYINEELP-----LELEIEKFYKRGFFVTKKRYAGL----TEDGK 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 930 YITkqelKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYp 1009
Cdd:cd05536 219 IDV----VGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVK----EVIEKLKRGEVPPEKLVIWKQLTKDLSEY- 289
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907203014 1010 dRKSLPHVHVALWInSQGGRKVKAGDTVSYVICQDGSNLtaTQRAYAPEQLQKLDNlaIDTQYYLAQQIHPVVARICE 1087
Cdd:cd05536 290 -KATGPHVAAAKKL-AKRGYKVRPGTKIGYVIVKGSGKI--SDRAYPYDMVDEKHK--YDAEYYIDNQVLPAVLRILE 361
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
700-1089 |
1.11e-63 |
|
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: 222.14 E-value: 1.11e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 700 TYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVqrVTSEVQKATEDEEQEQIP---ELPDPNLEMGILPRE 776
Cdd:cd05533 2 QYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTL--LNKNTAKKLPPEDYIKTPngdYFVKSSVRKGLLPEI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 777 IRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQ-- 854
Cdd:cd05533 80 LEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEek 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 855 -------KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDAVFKSLLLLKKKKYAALVVepTS 926
Cdd:cd05533 159 ytkangySHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFiKPIKLEFEKVYFPYLLINKKRYAGLLW--TN 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 927 DGNYiTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIqKRLIeigENVLNGSVPVSQFEINKALTKDPQ 1006
Cdd:cd05533 237 PDKH-DKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFV-KGVI---SDLLQNKIDISLLVITKALTKTAD 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1007 DYPDRksLPHVHVALWINSQG-GRKVKAGDTVSYVICQDGSNLTATQRAYAPeqLQKLD-NLAIDTQYYLAQQIHPVVAR 1084
Cdd:cd05533 312 DYAGK--QAHVELAERMRKRDpGSAPNVGDRVPYVIIKGAKGAKAYEKAEDP--IYVLEnNIPIDTQYYLENQLSKPLLR 387
|
....*
gi 1907203014 1085 ICEPI 1089
Cdd:cd05533 388 IFEPI 392
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
349-1089 |
2.92e-63 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 235.31 E-value: 2.92e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 349 FLMNRKIKGPCWLEVKNPQ----LLNQPISWCKFEVmALKPDLVNVIKDV----SPPPLVVMSFSMKTMQNV-----QNH 415
Cdd:PTZ00166 207 FLIDNNITGGSWLTLPKGKykirPPKKKTSTCQIEV-DCSYEDLIPLPPEgeylTIAPLRILSFDIECIKLKglgfpEAE 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 416 QHEIIAMAALVHhsfaLDKAPPEPPFQTHFCVvskpKDC--IFPCdfkEVISKKNMKVEIAATERTLIgfflakvhKIDP 493
Cdd:PTZ00166 286 NDPVIQISSVVT----NQGDEEEPLTKFIFTL----KECasIAGA---NVLSFETEKELLLAWAEFVI--------AVDP 346
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 494 DILVGHNICSFELEVLLQRINECKVP---YWSKIGRLRRSNMPKLGSRSGFGERNATC----GRMICDVeisaKELIH-- 564
Cdd:PTZ00166 347 DFLTGYNIINFDLPYLLNRAKALKLNdfkYLGRIKSTRSVIKDSKFSSKQMGTRESKEinieGRIQFDV----MDLIRrd 422
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 565 --CKSYHLSELVQQILKTERIVIPTENIRNMYSES--------SYLLyllehiwKDARFILQIMCELNVLPLALQITNIA 634
Cdd:PTZ00166 423 ykLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSpetrrriaVYCL-------KDAILPLRLLDKLLLIYNYVEMARVT 495
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 635 GNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqifrkpqqklgdedeeidgdTNKYKKGRKKATYAGGLVLDPKVGFY 714
Cdd:PTZ00166 496 GTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIP----------------------TVKYSGGGSEEKYEGATVLEPKKGFY 553
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 715 DKFILLLDFNSLYPSIIQEFNICFTTVqrVTSEVQKATEDEEQEQIP---ELPDPNLEMGILPREIRKLVERRKQVKQLM 791
Cdd:PTZ00166 554 DEPIATLDFASLYPSIMIAHNLCYSTL--VPPNDANNYPEDTYVTTPtgdKFVKKEVRKGILPLIVEELIAARKKAKKEM 631
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 792 KQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYakP---LAALVTYKGREILMHTKDMVQKM---------NLE 859
Cdd:PTZ00166 632 KDEK-DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQL--PcleVSTSITSFGRQMIDKTKELVEKHytkangykhDAT 708
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 860 VIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDAVFKSLLLLKKKKYAALVVepTSDGNYiTKQELKG 938
Cdd:PTZ00166 709 VIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFlKPIKLEFEKVYCPYLLMNKKRYAGLLY--TNPEKY-DKIDCKG 785
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 939 LDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNgsvpVSQFEINKALTKDpqDYPDRksLPHVH 1018
Cdd:PTZ00166 786 IETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRID----ISLLVITKSLGKD--DYEGR--LAHVE 857
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1019 VAlwinsqggRKVKA---------GDTVSYVICQDGSNLTATQRAYAPeqLQKLDN-LAIDTQYYLaQQIHPVVARICEP 1088
Cdd:PTZ00166 858 LA--------KKLRQrdpgsapnvGDRVSYVIVKGAKGAPQYERAEDP--LYVLENnIPIDTQYYL-DQIKNPLLRIFEG 926
|
.
gi 1907203014 1089 I 1089
Cdd:PTZ00166 927 V 927
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
401-619 |
5.99e-52 |
|
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 176646 [Multi-domain] Cd Length: 199 Bit Score: 181.40 E-value: 5.99e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 401 VMSFSMKTMQNVQ---NHQHEIIAMAALVhhSFALDKAPPEPPFQTHFCVVSKpkdcifpcdfkevisKKNMKVEIAATE 477
Cdd:cd05160 1 VLSFDIETTPPVGgpePDRDPIICITYAD--SFDGVKVVFLLKTSTVGDDIEF---------------IDGIEVEYFADE 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 478 RTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWskIGRLRRSNMPKlgsRSGFGERNATCGRMICDVEI 557
Cdd:cd05160 64 KELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLT--DGIYRRSGGEK---SSGSTERIAVKGRVVFDLLA 138
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907203014 558 SAKELIHCKSYHLSELVQQILK-TERIVIPTENIRNMysESSYLLYLLEHIWKDARFILQIMC 619
Cdd:cd05160 139 AYKRDFKLKSYTLDAVAEELLGeGKEKVDGEIIEDAE--WEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
705-1093 |
2.95e-44 |
|
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: 167.39 E-value: 2.95e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 705 LVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTT-VQRVTSEVQKATEDEEQEQIPELPDPNLEM------------- 770
Cdd:cd05534 40 LVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTcLGRVEELNGGGKFGFLGVKLYLPPPPLDLLllkddvtispngv 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 771 ---------GILPREIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYS-RFYAKPLAALVTY 840
Cdd:cd05534 120 mfvkksvrkGILPKMLEEILDTRIMVKKAMKKYKDDKKLQRILDARQLALKLLANVTYGYTAASFSgRMPCVEIADSIVQ 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 841 KGREILMHTKDMVQ---KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDAVFKSLLLLKKKK 916
Cdd:cd05534 200 TGRETLERAIELIEstpKWGAKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVTAANpSPIKLKFEKVYHPCVLVTKKR 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 917 YAALVVE------PTSDGnyitkqelKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigENVLNGSV 990
Cdd:cd05534 280 YVGYKYEspdqtePTFDA--------KGIETVRRDGCPAVQKILEKSLRILFETKDLSTVKSYLQRQW----SKLLQGRV 347
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 991 PVSQFEINKALTKDpQDYPDRKSLPHVHVAL-WINSQGGRKVKAGDTVSYVICQDGSNLTATQRAYAPEQLQKLDNLAID 1069
Cdd:cd05534 348 SIQDFIFAKEVRLG-TYKEGATLPAGAIVALrRMEKDPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLADPSLRLD 426
|
410 420
....*....|....*....|....
gi 1907203014 1070 TQYYLAQQIHPVVARICEPIdGID 1093
Cdd:cd05534 427 AEYYITKQIIPALDRLFNLV-GVD 449
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
694-1074 |
4.06e-42 |
|
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: 159.05 E-value: 4.06e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 694 KGRKkatYAGGLVLDPKVG-FYDkfILLLDFNSLYPSIIQEFNICFTTVQRVTsevqkatEDEEQEQIPELP-----DPN 767
Cdd:cd05530 9 KGKK---YRGAIVLEPPPGiFFN--VVVLDFASLYPSIIKVWNLSYETVNCPH-------CECKTNEVPEVGhwvckKRP 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 768 LEMGILPREIRKLveRRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILM 847
Cdd:cd05530 77 GITSQIIGLLRDL--RVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIIT 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 848 HTKDMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDAVFKsllllkkkkyaaLVVEPTS 926
Cdd:cd05530 155 STIKKARELGLKVLYGDTDSLFLwNPPQEQLEDLVE---WVEKELG-----LDLELDKEYR------------YVVFSGL 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 927 DGNYI-----TKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRD---TIVENIQKRLIEIGENVLNGSVPVSQFEIN 998
Cdd:cd05530 215 KKNYLgvtkdGSVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPEdfeKAREKIRDIVKGVYKRLKKKEYTLDQLAFK 294
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907203014 999 KALTKDPQDYpdRKSLP-HVHVALWINSQgGRKVKAGDTVSYVicqdgsnLTATQRAYAPEQLQKLDNlaIDTQYYL 1074
Cdd:cd05530 295 VMLSKPPEEY--TKNTPqHVKAARQLEKY-GRNVEAGDIISYV-------KVKGKEGVKPVQLARLDE--VDVEKYV 359
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
681-1074 |
1.20e-40 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 162.17 E-value: 1.20e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 681 EDEEIDGDTNKYKKGRKKATYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvtsevqkatEDEEQEQI 760
Cdd:PRK05761 387 EDILRLDHEVYKKAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETV-----------RIPECKCH 454
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 761 PELPDPNL------EMGILPREIRKLV--ERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAK 832
Cdd:PRK05761 455 YDDEVPELghsvcdDRPGLTSVLVGLLrdFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRI 534
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 833 PLAALVTYKGREILMHTKDMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDAVFKslll 911
Cdd:PRK05761 535 EVAESITALGREILLSTKKKAEELGLKVLYGDTDSLFVwGPTKESLEELIK---EIEERTG-----IDLEVDKTYD---- 602
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 912 lkkkkyaaLVVEPTSDGNYITKQ-----ELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQK---RLIEIGE 983
Cdd:PRK05761 603 --------WVAFSGLKKNYFGVLkdgkvKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEKVKDEiedVLKRYYE 674
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 984 NVLNGSVPVSQFEINKALTKDPQDYpDRKSLPHVHVALWINSQGGrKVKAGDTVSYVICQDgsnltatQRAYAPEQLQKL 1063
Cdd:PRK05761 675 KLRAKDYPLDELAIRVRLSKPLDEY-TKNTPQHVKAALQLRDYGV-EVSPGDIISYVKVDD-------KRGVKPVQLAKL 745
|
410
....*....|.
gi 1907203014 1064 DNlaIDTQYYL 1074
Cdd:PRK05761 746 SE--IDVEKYI 754
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
702-1089 |
9.48e-40 |
|
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99920 Cd Length: 371 Bit Score: 152.04 E-value: 9.48e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 702 AGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNIcfTTVQRVtsEVQKAteDEEQEQIPELPDPNL--EMGILPREIRK 779
Cdd:cd05537 4 PGGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI--DPLGLI--EGLKA--PDPEDLIPGFLGARFsrEKHILPDLIAR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 780 LVERRKQVKQlmkqqDLNPDLvlqydirQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKMNLE 859
Cdd:cd05537 77 LWAARDEAKR-----EKNAPL-------SQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQ 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 860 VIYGDTDSIMINTNST-NLEEVFKLGNKVKSEVN--------KLYKL---LEIDIDAVF--------KSLLLLKKKKYAA 919
Cdd:cd05537 145 VIYGDTDSTFVWLGEElDAAEAQAIGKELASQINqwwaqklkEEFGLesfLEIEFETHYsrffmptiRGSDEGSKKRYAG 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 920 LVVEPTSDgnyitKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEiGEnvLNgsvpvSQFEINK 999
Cdd:cd05537 225 LKSTDGGD-----ELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLA-GE--LD-----ELLVYRK 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1000 ALTKDPQDYpDRKSLPHVHVALW---INSQGGRKvKAGDTVSYVICQDGsnltatqrayaPEQLQKlDNLAIDTQYYLAQ 1076
Cdd:cd05537 292 RLRRPLSEY-TKNVPPHVQAARLadqINRELGRP-RQYQWIEYVITVNG-----------PEPLEY-RTSPLDYQHYIDK 357
|
410
....*....|...
gi 1907203014 1077 QIHPvvarICEPI 1089
Cdd:cd05537 358 QLKP----IADSI 366
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
699-1092 |
3.13e-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: 120.53 E-value: 3.13e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 699 ATYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQrvtsevqkaTEDEEQEQIPELPDP--NLEMGILPRE 776
Cdd:cd05531 3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETIN---------CRCCECRDHVYLGHRicLKRRGFLPEV 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 777 IRKLVERRKQVKQLMKQQDlnpdlvlQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKM 856
Cdd:cd05531 73 LEPLLERRLEYKRLKKEED-------PYAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEM 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 857 NLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKsevnklyklLEIDIDAVFKsllllkkkkyaALVVEPTSDG-----NYI 931
Cdd:cd05531 146 GFRVLHGIVDSLWIQGRGDIEELAREIEERTG---------IPLKLEGHYD-----------WIVFLPERDGlgapnRYF 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 932 TKQE-----LKGLDIVRRDWCDLAKDTGNFVIgQILSdQSRDtiVENIQKRLIEIgENVLNGSV------PVSQFEINKA 1000
Cdd:cd05531 206 GRLSdgemkVRGIELRRRDTPPFVKKFQEEAL-DILA-SAKT--PEELLKLREEA-LDLFRRYLqrlregDLEDLIIEKK 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 1001 LTKDPQDYpdrKSLPHvHVALWINSQgGRKVKAGDTVSYVICQDGSNLTATQrayapeqlqklDNLAIDTQYYLAQQIHP 1080
Cdd:cd05531 281 ISKRSSEY---KVLAS-TALKALRAK-GVSVVPGMKIEYIVRDGKRPVPDLG-----------NDEGYDTKYYRELLERA 344
|
410
....*....|..
gi 1907203014 1081 VvaricEPIDGI 1092
Cdd:cd05531 345 A-----EELLFP 351
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
697-1015 |
3.60e-21 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 100.48 E-value: 3.60e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 697 KKATYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNIC-FTTVQRVTSEVQKATEDEEQEQIPELPDP--------- 766
Cdd:PHA03036 526 NKFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSpETLVGVVVNDNRLEAEINKQELRRKYPYPryiyvhcep 605
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 767 ---NL----------EMGILPREIRKLVERRKQVKQLMKQQDLNPDLVLqYDIRQKALKLTANSMYGCLGFSYSRFYAKP 833
Cdd:PHA03036 606 rspDLvseiavfdrrIEGIIPKLLKTFLEERARYKKLLKEATSSVEKAI-YDSMQYTYKIVANSVYGLMGFRNSALYSYA 684
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 834 LAALVTYKGREILMHTKDMV--------------------------------------QKMNLEVIYGDTDSIMINTNST 875
Cdd:PHA03036 685 SAKSCTAIGRNMIKYLNSVLngsklingklilancpinpffkddrsidtnydtnlpveYNFTFRSVYGDTDSVFLEINTK 764
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 876 NLEEVFKLGNKVKSEVNK--LYKLLEIDIDAVFKSLLLLKKKKYAALVVEPTSDGNYITKQELKGLDIVRRDWCDLAKdt 953
Cdd:PHA03036 765 DVDKSIKIAKELERIINEkvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVPERVNKGTSETRRDVSKFHK-- 842
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907203014 954 gnfvigqilsdqsrdTIVENIQKRLIEIGENVLNGSVPVSqFEINKALTKDPQDYPDRKSLP 1015
Cdd:PHA03036 843 ---------------YMIKIYKTRLLDMLSEGNMNSNQVC-IDILRSLEKDLIIEFDSRSAP 888
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
693-871 |
1.72e-15 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 82.05 E-value: 1.72e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 693 KKGRKKATYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQRVTSEvqkATEDEEQEQIPELPD------P 766
Cdd:PHA02528 369 NKSHKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFHV---APVHEYINKTAPRPSdeyscsP 444
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 767 NLEM------GILPREIRKLVERRKQVKQLMKQQDLNPDL---------------------------------------- 800
Cdd:PHA02528 445 NGWMyrkdirGVIPTEIKKVFDQRKIYKKKMLAAERNAELiktiledlndsvdtpidvdyyfdfsdefkaelktltkssl 524
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 801 ----------VLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGR-EILMHTKDMVQKMNL--------EVI 861
Cdd:PHA02528 525 kalleecekeIALCNTIQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQlAIQWIERKMNEYLNKlcktededYVI 604
|
250
....*....|
gi 1907203014 862 YGDTDSIMIN 871
Cdd:PHA02528 605 YGDTDSIYVN 614
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
722-1050 |
6.39e-14 |
|
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: 74.83 E-value: 6.39e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 722 DFNSLYPSIIQEFNICfttvqrvtsevqkATEDEEqeqipelpdpnlemGILPREIRKLVERRKQVKQLMKQQDLnPDLV 801
Cdd:cd05538 23 DVASLYPSIMLAYRIC-------------PARDSL--------------GIFLALLKYLVELRLAAKESARAAAR-PAER 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 802 LQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILmhtKDMVQKM---NLEVIYGDTDSIMI---NTNST 875
Cdd:cd05538 75 DAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELL---KLMIRWLrrrGATPVEVDTDGIYFippNGVDT 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 876 NLEEvfklgNKVKSEVNK-LYKLLEIDIDAVFKSLLLLKKKKYAALvveptsdgNYITKQELKGLDIVRRDWCDLAKDTG 954
Cdd:cd05538 152 EDEE-----EELVRELSStLPKGITVEFDGRYRAMFSYKIKNYALL--------DYDGKLIVKGSAFRSRGIEPFLREFL 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 955 NFVIGQILSDQSrdtivENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPD----RKSLPhvHVALWINSQGGRK 1030
Cdd:cd05538 219 REAVRLLLQGDG-----AGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYLQkvraGKRNP--AAAYEIALARPRE 291
|
330 340
....*....|....*....|
gi 1907203014 1031 VKAGDTVSYVICQDGSNLTA 1050
Cdd:cd05538 292 WRAGDRVTYYVSGTGKGVSV 311
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
459-617 |
1.07e-09 |
|
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: 59.29 E-value: 1.07e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 459 DFKEVISKKNM---KVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPywSKIGRLRRSnmPKL 535
Cdd:cd05780 35 GGNKVITWKKFdlpFVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIE--LDLGRDGSE--IKI 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 536 gSRSGFGERNATCGRMICDVEISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSYLLYLLEHIWKDARFIL 615
Cdd:cd05780 111 -QRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTY 189
|
..
gi 1907203014 616 QI 617
Cdd:cd05780 190 EI 191
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
689-869 |
3.85e-08 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 58.33 E-value: 3.85e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 689 TNKYKKG-RKKATYAGGLVLDPKVGF-----YDKFILLLDFNSLYPSIIQEFNICFTTV--QRVTSEVQkATEDEEQEQI 760
Cdd:PHA03334 620 PEKYARDcRQKIKLKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIvdPDCTARVR-GWVVFDWKKI 698
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 761 PE-LPDPNLEMGIL---PRE-------------IRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGclg 823
Cdd:PHA03334 699 DRgFGKATLMYTILrtkPEEpswrrfttyttssLNHYLSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYG--- 774
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 1907203014 824 fsysrfyAKPLAA--LVTYKGREILMHTKDMVQKM-NLEVIYGDTDSIM 869
Cdd:PHA03334 775 -------VAPHACqhLITTLGRHKIKLVEEFIKKEpGMTVNYGDTDSVM 816
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
445-544 |
4.72e-07 |
|
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: 52.03 E-value: 4.72e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 445 FCVVSKPKDCIF------PCDFKEVISKKNMkveiaaTERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKV 518
Cdd:cd05785 26 FSNPDRGDDRIIivalrdNRGWEEVLHAEDA------AEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGV 99
|
90 100
....*....|....*....|....*..
gi 1907203014 519 PY-WSKIGRLRRSNmpklGSRSGFGER 544
Cdd:cd05785 100 PLaIGRDGSIPRQR----PSRFRFAER 122
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
488-530 |
7.66e-06 |
|
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: 48.73 E-value: 7.66e-06
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 1907203014 488 VHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRLRRS 530
Cdd:cd05777 82 VQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNI 124
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
458-554 |
1.05e-04 |
|
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: 44.87 E-value: 1.05e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 458 CDFKEVI------SKKNMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYwsKIGRLRRSn 531
Cdd:cd05784 26 EGQERVLmvgdpeDDAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPL--RLGRGGSP- 102
|
90 100
....*....|....*....|....
gi 1907203014 532 mPKLGSRSGFGERNATC-GRMICD 554
Cdd:cd05784 103 -LNWRQSGKPGQGFLSLpGRVVLD 125
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
477-617 |
1.97e-03 |
|
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: 40.77 E-value: 1.97e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 477 ERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYwsKIGRlRRSNMPklgSRSGFGERNATcGRMICDVE 556
Cdd:cd05781 48 DRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKL--DVGR-RGGSEP---STGVYGHYSIT-GRLNVDLY 120
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907203014 557 ISAKELIHCKS---YHLSELVQQILKTERIVIPTENIRNMYSESSYLLYLLEHIWKDARFILQI 617
Cdd:cd05781 121 DFAEEIPEVKVktlENVAEYLGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGL 184
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
439-618 |
2.16e-03 |
|
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: 41.07 E-value: 2.16e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 439 PPFQTHFCVVSKPKDcifPCDFKEVISK-KNMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRIN-EC 516
Cdd:cd05778 45 DANKVGVIIVDELKS---NASNGRIRSGlSGIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAaLG 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 517 KVPYWSKIGRLRRSNMPKLGSRSgfGERNAT-------CGRMICDV------EISakeLIhckSYHLSELVQQILKtERI 583
Cdd:cd05778 122 IDDLLDEISRVPSDSNGKFGDRD--DEWGYThtsgikiVGRHILNVwrlmrsELA---LT---NYTLENVVYHVLH-QRI 192
|
170 180 190
....*....|....*....|....*....|....*...
gi 1907203014 584 -VIPTENIRNMYSES--SYLLYLLEHIWKDARFILQIM 618
Cdd:cd05778 193 pLYSNKTLTEWYKSGsaSERWRVLEYYLKRVRLNLEIL 230
|
|
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
785-868 |
4.94e-03 |
|
DNA polymerase type-B epsilon 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) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Pssm-ID: 99918 Cd Length: 621 Bit Score: 41.12 E-value: 4.94e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907203014 785 KQVKQLMKQQDL-----NPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKMN-- 857
Cdd:cd05535 247 KKLEAAKAAGDAaeikeAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELVEQIGrp 326
|
90
....*....|.
gi 1907203014 858 LEViygDTDSI 868
Cdd:cd05535 327 LEL---DTDGI 334
|
|
| |
