|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1-1089 |
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: 1496.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1 MFIACAGKKTADKAVDLSKDGLLGDILQDLN-TETPQ--ITPPPVMILKKKRSIGAS---PNPFSVHTATAVPSGKIASP 74
Cdd:TIGR00592 85 VRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVVDIVKKAIP 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 75 VSRK---EPPLTPVPLKRAEFAGDDVQVE-STEEEQESGAME--FEDGDF----DE-PMEVEEVDL-EPMAAKAWDKESE 142
Cdd:TIGR00592 165 VSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDEnPADEEIMIStTPVIAKQWDYESE 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 143 PAEEVKQEADSGKGTV-SYLGSFLPDVSC----WD-IDQEGDSsfsvQEVQVDSSHLPLVKGADEeQVFHFYWlDAYEDQ 216
Cdd:TIGR00592 245 PEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD----VEITVNGDNFDLVYLADR-QVFQFYW-DAYEDP 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 217 YNQPGVVFLFGKvwieSAEtHVSCCVMVKNIERTLYFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKS 296
Cdd:TIGR00592 319 AEKLGVVLLFGR----DVD-HVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRA 393
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 297 KPVEKNYAFEIP--DVPEKSEYLEVKYS-----AEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQ 369
Cdd:TIGR00592 394 KPIAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPD 473
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 370 LLNQPV-SWCKVEAMALKPDLVNVIKDVSPPPLVVMAFSMKtMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFC 448
Cdd:TIGR00592 474 ELEYPRrSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPC 552
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 449 VVSKPKDCIFPYAFK-EVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIG 527
Cdd:TIGR00592 553 VGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIG 632
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 528 RLKRSnmPKLGGRsgFGERnaTCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLE 607
Cdd:TIGR00592 633 RLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLE 706
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 608 HTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQKLGDEDEEI 687
Cdd:TIGR00592 707 HTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKLGDEDEEI 785
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 688 DGdtnkYKKGrKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvaseaQKVTEDgeqeQIPELPD 767
Cdd:TIGR00592 786 DG----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDED----ELPELPD 850
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 768 PSLEMGILPREIRKLVERRKQVKQLMKQqDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREI 847
Cdd:TIGR00592 851 SELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREI 929
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 848 LMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPT 927
Cdd:TIGR00592 930 LEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYAAIKVEGD 1009
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 928 SDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDP 1007
Cdd:TIGR00592 1010 SDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVINKQLTRDP 1089
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1008 QDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQ-KQDNLTIDTQYYLAQQIHPVVAR 1086
Cdd:TIGR00592 1090 KDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEHQIHPVVLR 1169
|
...
gi 2462629845 1087 ICE 1089
Cdd:TIGR00592 1170 ILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
696-1106 |
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: 734.00 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 696 KGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAseaqkvtEDGEQEQIPELPDPSLEMGIL 775
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRAD-------PDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 776 PREIRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMV 855
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 856 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPtsDGNYVTK 935
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 936 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKS 1015
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1016 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGID 1095
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 2462629845 1096 AVLIATWLGLD 1106
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 ... |
638-1091 |
2.00e-172 |
|
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.
Pssm-ID: 395085 Cd Length: 439 Bit Score: 519.48 E-value: 2.00e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 638 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKLGDEDeeidgdtnkykkgrkkaAYAGGLVLDPKVGFYD 717
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 718 KFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPD------PSLEMGILPREIRKLVERRKQVKQ 791
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 792 LMKQqDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM---NLEVIYGDTD 868
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 869 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyvtKQELKGLDIVRR 946
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 947 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWIN 1026
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462629845 1027 SQGGRKVKAGDTVSYVICQDGS---NLTASQRAYAPEqLQKQDNLTIDTQYYLAQQIHPVVARICEPI 1091
Cdd:pfam00136 373 KRNGEAPEVGDRIPYVIVKAAKglkNLLIYERAEDPE-YVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
351-1092 |
2.62e-113 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 374.55 E-value: 2.62e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 351 FLMNRKIKGPCWLEVkspqllnQPVSWCKVEAMALKPDLVNVIKDVsPPPLVVMAF----SMKTMQNAKNHQNEIIAMAa 426
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 427 lVHHSFALDKAapkppfqshFCVVSKPKDcifpyafkeviekknVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGF 506
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 507 ELEVLLQRINVCKAPhwSKIGRLKRSnmPKLGGRSGFGERNATcGRMICDV-EISAKELIRCKSYHLSELVQQILKTERV 585
Cdd:COG0417 244 DLPYLQKRAERLGIP--LDLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 586 VIPMENIQNMYSESsqLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 665
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 666 IVPDKqifrkpqqklgdedEEIDGDtnkykkgrkkaAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQR 745
Cdd:COG0417 397 LAPNK--------------GEIKGE-----------AYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETLVE 450
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 746 VASEaqkvtEDGEQEQIPELP-----DPSlemGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSM 820
Cdd:COG0417 451 GGEE-----PCGDEDVAPGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 821 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KLYKL 899
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 900 LEIDIDGVFKSllllkkkkyaalVVEPTSDGNY--VTKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 974
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 975 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVIcqdgsnLTASQ 1054
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI------TKGGG 738
|
730 740 750
....*....|....*....|....*....|....*...
gi 2462629845 1055 RAYaPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPID 1092
Cdd:COG0417 739 RVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
399-875 |
2.78e-113 |
|
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: 364.16 E-value: 2.78e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 399 PPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQsHFCVVSKPKDCIfpyafkeviekKNVKVEVAAT 478
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 479 ERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRS----NMPKLGGRSGFGERNAT---CG 551
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripNKKPLFGSKSFGLSDIKvyiKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 552 RMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSES-SQLLYLLEHTWKDAKFILQIMCELNVLPLAL 630
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNyEERDELLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 631 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqklgdedEEIDGDTNKYKKgRKKAAYAGGLVLD 710
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSK--------------ELYDFKGSEPDL-KKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 711 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKV-TEDGEQEQIPELPDP--------SLEMGILPREIRK 781
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGdLIIPEDLLTIKYEKGnkyrfvkkNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 782 LVERRKQVKQLMKQ-QDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM-- 858
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 2462629845 859 ---NLEVIYGDTDSIMINTN 875
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
473-1105 |
7.77e-77 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 271.73 E-value: 7.77e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 473 VEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRLKRSNMPKL-GGRSGFGERNATcG 551
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIP--LRLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 552 RMICD-VEISAKELIRCKSYHLSELVQQIL----KTERVVIPMENIQNMYSESSQLLylLEHTWKDAKFILQIMCELNVL 626
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSLEYVSQRLLgegkAIDDPYDRMDEIDRRFAEDKPAL--ARYNLKDCELVTRIFEKTKLL 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 627 PLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDkqifrkpqqkLGDEDEEidgdtnkykkgrkkaAYAGG 706
Cdd:PRK05762 352 PFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPN----------LGERPGE---------------ASPGG 404
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 707 LVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTvqRVASEAQKvtedgEQEQIPELPDP--SLEMGILPREIRKLVE 784
Cdd:PRK05762 405 YVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDG--LVEGLAQP-----PEESVAGFLGArfSREKHFLPEIVERLWE 476
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 785 RRKQVKQLMKQqdlnpdlilqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIY 864
Cdd:PRK05762 477 GRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIY 544
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 865 GDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDGVFK--------SLLLLKKKKYAALVV 924
Cdd:PRK05762 545 GDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSKKRYAGLIQ 624
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 925 EPTSDGNYVtkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQFEINKALT 1004
Cdd:PRK05762 625 EGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EKLVYRKRLR 692
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1005 KDPQDYpDKKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGSnltasqrayapeqlQKQDNLT--IDTQYYLA 1077
Cdd:PRK05762 693 RPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNGP--------------EPLEYRKspIDYDYYIE 757
|
650 660
....*....|....*....|....*...
gi 2462629845 1078 QQIHPVVARICEPIDGIDAVLIATWLGL 1105
Cdd:PRK05762 758 KQLQPVADRILPFFGDDFATLKTGQLGL 785
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1129-1319 |
1.85e-74 |
|
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: 245.21 E-value: 1.85e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1129 AQLTDEEKYRDCERFKCPCPTCGTENIYDNVFDGS-GTDMEPSLYRCSNidCKASPLTFtvQLSNKLIMDIRRFIKKYYD 1207
Cdd:pfam08996 1 SQISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1208 GWLICEEPTCRNRTRHLPLQFSRTgpLCPACmKATLQPEYSDKSLYTQLCFYRYIFDAECALEKLTTDHEKDKLKKQFFT 1287
Cdd:pfam08996 77 GWLVCDDPTCGNRTRQMSVYGKRC--LGPGC-KGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLALAE 153
|
170 180 190
....*....|....*....|....*....|..
gi 2462629845 1288 pKVLQDYRKLKNTAEQFLSRSGYSEVNLSKLF 1319
Cdd:pfam08996 154 -QNRELFKTLKSVVDKYLDKCGRRWVNLSSLF 184
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1-1089 |
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: 1496.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1 MFIACAGKKTADKAVDLSKDGLLGDILQDLN-TETPQ--ITPPPVMILKKKRSIGAS---PNPFSVHTATAVPSGKIASP 74
Cdd:TIGR00592 85 VRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVVDIVKKAIP 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 75 VSRK---EPPLTPVPLKRAEFAGDDVQVE-STEEEQESGAME--FEDGDF----DE-PMEVEEVDL-EPMAAKAWDKESE 142
Cdd:TIGR00592 165 VSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDEnPADEEIMIStTPVIAKQWDYESE 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 143 PAEEVKQEADSGKGTV-SYLGSFLPDVSC----WD-IDQEGDSsfsvQEVQVDSSHLPLVKGADEeQVFHFYWlDAYEDQ 216
Cdd:TIGR00592 245 PEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD----VEITVNGDNFDLVYLADR-QVFQFYW-DAYEDP 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 217 YNQPGVVFLFGKvwieSAEtHVSCCVMVKNIERTLYFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKS 296
Cdd:TIGR00592 319 AEKLGVVLLFGR----DVD-HVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRA 393
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 297 KPVEKNYAFEIP--DVPEKSEYLEVKYS-----AEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQ 369
Cdd:TIGR00592 394 KPIAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPD 473
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 370 LLNQPV-SWCKVEAMALKPDLVNVIKDVSPPPLVVMAFSMKtMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFC 448
Cdd:TIGR00592 474 ELEYPRrSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPC 552
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 449 VVSKPKDCIFPYAFK-EVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIG 527
Cdd:TIGR00592 553 VGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIG 632
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 528 RLKRSnmPKLGGRsgFGERnaTCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLE 607
Cdd:TIGR00592 633 RLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLE 706
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 608 HTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQKLGDEDEEI 687
Cdd:TIGR00592 707 HTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKLGDEDEEI 785
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 688 DGdtnkYKKGrKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvaseaQKVTEDgeqeQIPELPD 767
Cdd:TIGR00592 786 DG----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDED----ELPELPD 850
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 768 PSLEMGILPREIRKLVERRKQVKQLMKQqDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREI 847
Cdd:TIGR00592 851 SELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREI 929
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 848 LMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPT 927
Cdd:TIGR00592 930 LEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYAAIKVEGD 1009
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 928 SDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDP 1007
Cdd:TIGR00592 1010 SDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVINKQLTRDP 1089
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1008 QDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQ-KQDNLTIDTQYYLAQQIHPVVAR 1086
Cdd:TIGR00592 1090 KDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEHQIHPVVLR 1169
|
...
gi 2462629845 1087 ICE 1089
Cdd:TIGR00592 1170 ILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
696-1106 |
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: 734.00 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 696 KGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAseaqkvtEDGEQEQIPELPDPSLEMGIL 775
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRAD-------PDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 776 PREIRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMV 855
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 856 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPtsDGNYVTK 935
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 936 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKS 1015
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1016 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGID 1095
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 2462629845 1096 AVLIATWLGLD 1106
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 ... |
638-1091 |
2.00e-172 |
|
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.
Pssm-ID: 395085 Cd Length: 439 Bit Score: 519.48 E-value: 2.00e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 638 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKLGDEDeeidgdtnkykkgrkkaAYAGGLVLDPKVGFYD 717
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 718 KFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPD------PSLEMGILPREIRKLVERRKQVKQ 791
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 792 LMKQqDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM---NLEVIYGDTD 868
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 869 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyvtKQELKGLDIVRR 946
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 947 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWIN 1026
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462629845 1027 SQGGRKVKAGDTVSYVICQDGS---NLTASQRAYAPEqLQKQDNLTIDTQYYLAQQIHPVVARICEPI 1091
Cdd:pfam00136 373 KRNGEAPEVGDRIPYVIVKAAKglkNLLIYERAEDPE-YVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
399-631 |
5.39e-118 |
|
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: 367.32 E-value: 5.39e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 399 PPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVSKPKDC-IFPYAFKEVIEKKNVKVEVAA 477
Cdd:cd05776 1 PPLTVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRsPPPDLFEKNAKKKKTKVRIFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 478 TERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDV 557
Cdd:cd05776 81 NERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDT 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462629845 558 EISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQIMCELNVLPLALQ 631
Cdd:cd05776 161 YLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLNILPLTKQ 234
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
351-1092 |
2.62e-113 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 374.55 E-value: 2.62e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 351 FLMNRKIKGPCWLEVkspqllnQPVSWCKVEAMALKPDLVNVIKDVsPPPLVVMAF----SMKTMQNAKNHQNEIIAMAa 426
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 427 lVHHSFALDKAapkppfqshFCVVSKPKDcifpyafkeviekknVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGF 506
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 507 ELEVLLQRINVCKAPhwSKIGRLKRSnmPKLGGRSGFGERNATcGRMICDV-EISAKELIRCKSYHLSELVQQILKTERV 585
Cdd:COG0417 244 DLPYLQKRAERLGIP--LDLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 586 VIPMENIQNMYSESsqLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 665
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 666 IVPDKqifrkpqqklgdedEEIDGDtnkykkgrkkaAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQR 745
Cdd:COG0417 397 LAPNK--------------GEIKGE-----------AYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETLVE 450
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 746 VASEaqkvtEDGEQEQIPELP-----DPSlemGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSM 820
Cdd:COG0417 451 GGEE-----PCGDEDVAPGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 821 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KLYKL 899
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 900 LEIDIDGVFKSllllkkkkyaalVVEPTSDGNY--VTKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 974
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 975 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVIcqdgsnLTASQ 1054
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI------TKGGG 738
|
730 740 750
....*....|....*....|....*....|....*...
gi 2462629845 1055 RAYaPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPID 1092
Cdd:COG0417 739 RVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
399-875 |
2.78e-113 |
|
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: 364.16 E-value: 2.78e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 399 PPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQsHFCVVSKPKDCIfpyafkeviekKNVKVEVAAT 478
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 479 ERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRS----NMPKLGGRSGFGERNAT---CG 551
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripNKKPLFGSKSFGLSDIKvyiKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 552 RMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSES-SQLLYLLEHTWKDAKFILQIMCELNVLPLAL 630
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNyEERDELLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 631 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqklgdedEEIDGDTNKYKKgRKKAAYAGGLVLD 710
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSK--------------ELYDFKGSEPDL-KKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 711 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKV-TEDGEQEQIPELPDP--------SLEMGILPREIRK 781
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGdLIIPEDLLTIKYEKGnkyrfvkkNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 782 LVERRKQVKQLMKQ-QDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM-- 858
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 2462629845 859 ---NLEVIYGDTDSIMINTN 875
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
473-1105 |
7.77e-77 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 271.73 E-value: 7.77e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 473 VEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRLKRSNMPKL-GGRSGFGERNATcG 551
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIP--LRLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 552 RMICD-VEISAKELIRCKSYHLSELVQQIL----KTERVVIPMENIQNMYSESSQLLylLEHTWKDAKFILQIMCELNVL 626
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSLEYVSQRLLgegkAIDDPYDRMDEIDRRFAEDKPAL--ARYNLKDCELVTRIFEKTKLL 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 627 PLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDkqifrkpqqkLGDEDEEidgdtnkykkgrkkaAYAGG 706
Cdd:PRK05762 352 PFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPN----------LGERPGE---------------ASPGG 404
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 707 LVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTvqRVASEAQKvtedgEQEQIPELPDP--SLEMGILPREIRKLVE 784
Cdd:PRK05762 405 YVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDG--LVEGLAQP-----PEESVAGFLGArfSREKHFLPEIVERLWE 476
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 785 RRKQVKQLMKQqdlnpdlilqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIY 864
Cdd:PRK05762 477 GRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIY 544
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 865 GDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDGVFK--------SLLLLKKKKYAALVV 924
Cdd:PRK05762 545 GDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSKKRYAGLIQ 624
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 925 EPTSDGNYVtkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQFEINKALT 1004
Cdd:PRK05762 625 EGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EKLVYRKRLR 692
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1005 KDPQDYpDKKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGSnltasqrayapeqlQKQDNLT--IDTQYYLA 1077
Cdd:PRK05762 693 RPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNGP--------------EPLEYRKspIDYDYYIE 757
|
650 660
....*....|....*....|....*...
gi 2462629845 1078 QQIHPVVARICEPIDGIDAVLIATWLGL 1105
Cdd:PRK05762 758 KQLQPVADRILPFFGDDFATLKTGQLGL 785
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1129-1319 |
1.85e-74 |
|
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: 245.21 E-value: 1.85e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1129 AQLTDEEKYRDCERFKCPCPTCGTENIYDNVFDGS-GTDMEPSLYRCSNidCKASPLTFtvQLSNKLIMDIRRFIKKYYD 1207
Cdd:pfam08996 1 SQISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1208 GWLICEEPTCRNRTRHLPLQFSRTgpLCPACmKATLQPEYSDKSLYTQLCFYRYIFDAECALEKLTTDHEKDKLKKQFFT 1287
Cdd:pfam08996 77 GWLVCDDPTCGNRTRQMSVYGKRC--LGPGC-KGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLALAE 153
|
170 180 190
....*....|....*....|....*....|..
gi 2462629845 1288 pKVLQDYRKLKNTAEQFLSRSGYSEVNLSKLF 1319
Cdd:pfam08996 154 -QNRELFKTLKSVVDKYLDKCGRRWVNLSSLF 184
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
701-1087 |
1.66e-72 |
|
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: 244.97 E-value: 1.66e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 701 AAYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPDpslemGILPREIR 780
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVGFRSPKDRK-----GLLPRILE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 781 KLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNL 860
Cdd:cd00145 75 ELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGA 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 861 EVIYGDTDSIMINTN-STNLEEVFKLGNKVKSEVNKlYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyvtKQELK 939
Cdd:cd00145 155 RVIYGDTDSIFVSLPkMGTKEDAIKEGREILQELAD-EHLLELEFEKVYLPFFLGKKKRYAGLDIWKGQDEG---KIDIK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 940 GLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigenvlngsvpvsqfeinkaltkdpqdypdkkslphv 1019
Cdd:cd00145 231 GLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL--------------------------------------- 271
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462629845 1020 hvalwinsqggrkvkagDTVSYVICQDGSNLTASQRAYAPEQLQkQDNLTIDTQYYLAQQIHPVVARI 1087
Cdd:cd00145 272 -----------------DKVKYVVTRGGKGVPDYERADPPLEDL-DKRHRIDYEYYLERLLQPPLERI 321
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
235-575 |
2.55e-70 |
|
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: 239.24 E-value: 2.55e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 235 ETHVSCCVMVKNIERTLYFLPREmkidlntGKETgtpismKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPekS 314
Cdd:pfam03104 3 DEGVSVCVNVFGFKPYFYCLAPD-------GKEL------EEVIEEIKELYEGLDKIEKIELKLKKSLYGYEEDPVP--Y 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 315 EYLEVKYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVK-SPQLLNQPVSWCKVEAMALKPDLVNVI 393
Cdd:pfam03104 68 LKVSFANPRPLLKIRKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKvYPFRAEGRISNCDVEIDCDSPDLISVP 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 394 KDVSPPPLVVMAFSMKTMQ------NAKNHQNEIIAMAALVHhsfalDKAAPKPPFQSHFCVVSKPKDCIFPYAFKEVIE 467
Cdd:pfam03104 148 FEKEWPPLRVLSFDIECTSlpgkfpDAENVKDPIIQISCMLD-----GQGEPEPEPRFLFTLRECDSEDIEDFEYTPKPI 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 468 KKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRsNMPKLGGRSGFG--- 544
Cdd:pfam03104 223 YPGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNR-GGRSKVREIGFGtrs 301
|
330 340 350
....*....|....*....|....*....|..
gi 2462629845 545 -ERNATCGRMICDVEISAKELIRCKSYHLSEL 575
Cdd:pfam03104 302 yEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
702-1089 |
9.33e-69 |
|
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: 236.07 E-value: 9.33e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 702 AYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQRvaseaqkvteDGEQEQIPELP-------DPSlemGI 774
Cdd:cd05536 3 SYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVR----------EGCEDCDVEPQvghkfrkDPP---GF 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 775 LPREIRKLVERRKQVKQLMKQ-QDLNPDLILqYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKE 853
Cdd:cd05536 69 IPSVLEDLLEERRRIKEKMKKlDPESEEYKL-LDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIK 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 854 MVQKMNLEVIYGDTDSIM--INTNSTNLEEVFKLGNKVKSEVNklyklLEIDIDGVFKSLLLLKKKKYAALvvepTSDGN 931
Cdd:cd05536 148 IAEEKGFKVIYGDTDSLFvkIDGADAVKKKVKKLLKYINEELP-----LELEIEKFYKRGFFVTKKRYAGL----TEDGK 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 932 YVTkqelKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYp 1011
Cdd:cd05536 219 IDV----VGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVK----EVIEKLKRGEVPPEKLVIWKQLTKDLSEY- 289
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462629845 1012 dKKSLPHVHVALWInSQGGRKVKAGDTVSYVICQDGSNLtaSQRAYAPEQLQKQDNltIDTQYYLAQQIHPVVARICE 1089
Cdd:cd05536 290 -KATGPHVAAAKKL-AKRGYKVRPGTKIGYVIVKGSGKI--SDRAYPYDMVDEKHK--YDAEYYIDNQVLPAVLRILE 361
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
703-1091 |
8.37e-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: 219.83 E-value: 8.37e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 703 YAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRvASEAQKVTEdgeqEQIPELPD------PSLEMGILP 776
Cdd:cd05533 3 YEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLN-KNTAKKLPP----EDYIKTPNgdyfvkSSVRKGLLP 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 777 REIRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQ 856
Cdd:cd05533 78 EILEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVE 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 857 ---------KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGVFKSLLLLKKKKYAALVVep 926
Cdd:cd05533 157 ekytkangySHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFiKPIKLEFEKVYFPYLLINKKRYAGLLW-- 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 927 TSDGNYvTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIqKRLIeigENVLNGSVPVSQFEINKALTKD 1006
Cdd:cd05533 235 TNPDKH-DKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFV-KGVI---SDLLQNKIDISLLVITKALTKT 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1007 PQDYPDKksLPHVHVALWINSQG-GRKVKAGDTVSYVICQDGSNLTASQRA----YAPEqlqkqDNLTIDTQYYLAQQIH 1081
Cdd:cd05533 310 ADDYAGK--QAHVELAERMRKRDpGSAPNVGDRVPYVIIKGAKGAKAYEKAedpiYVLE-----NNIPIDTQYYLENQLS 382
|
410
....*....|
gi 2462629845 1082 PVVARICEPI 1091
Cdd:cd05533 383 KPLLRIFEPI 392
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
351-1091 |
1.64e-61 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 229.91 E-value: 1.64e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 351 FLMNRKIKGPCWLEVKSPQ----LLNQPVSWCKVEaMALKPDLVNVIKDV----SPPPLVVMAFSM-------KTMQNAK 415
Cdd:PTZ00166 207 FLIDNNITGGSWLTLPKGKykirPPKKKTSTCQIE-VDCSYEDLIPLPPEgeylTIAPLRILSFDIeciklkgLGFPEAE 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 416 NhqNEIIAMAALVHhsfaldkaapkppfqshfcVVSKPKDCI--FPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKI 493
Cdd:PTZ00166 286 N--DPVIQISSVVT-------------------NQGDEEEPLtkFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAV 344
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 494 DPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSG---FGERNATC----GRMICDVeisaKELIR 566
Cdd:PTZ00166 345 DPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSskqMGTRESKEinieGRIQFDV----MDLIR 420
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 567 ----CKSYHLSELVQQILKTERVVI---PMENIQNMYSESSQLL--YLLehtwKDAKFILQIMCELNVLPLALQITNIAG 637
Cdd:PTZ00166 421 rdykLKSYSLNYVSFEFLKEQKEDVhysIISDLQNGSPETRRRIavYCL----KDAILPLRLLDKLLLIYNYVEMARVTG 496
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 638 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqifrkpqqklgdedeeidgdTNKYKKGRKKAAYAGGLVLDPKVGFYD 717
Cdd:PTZ00166 497 TPIGWLLTRGQQIKVTSQLLRKCKKLNYVIP----------------------TVKYSGGGSEEKYEGATVLEPKKGFYD 554
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 718 KFILLLDFNSLYPSIIQEFNICFTTVQRvASEAQKVTEDgeqEQIPELPD-----PSLEMGILPREIRKLVERRKQVKQL 792
Cdd:PTZ00166 555 EPIATLDFASLYPSIMIAHNLCYSTLVP-PNDANNYPED---TYVTTPTGdkfvkKEVRKGILPLIVEELIAARKKAKKE 630
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 793 MKQQDlNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYakP---LAALVTYKGREILMHTKEMVQKM---------NL 860
Cdd:PTZ00166 631 MKDEK-DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQL--PcleVSTSITSFGRQMIDKTKELVEKHytkangykhDA 707
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 861 EVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGVFKSLLLLKKKKYAALVVepTSDGNYvTKQELK 939
Cdd:PTZ00166 708 TVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFlKPIKLEFEKVYCPYLLMNKKRYAGLLY--TNPEKY-DKIDCK 784
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 940 GLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNgsvpVSQFEINKALTKDpqDYpdKKSLPHV 1019
Cdd:PTZ00166 785 GIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRID----ISLLVITKSLGKD--DY--EGRLAHV 856
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1020 HVAlwinsqggRKVKA---------GDTVSYVICQDGSNLTASQRA----YAPEqlqkqDNLTIDTQYYLaQQIHPVVAR 1086
Cdd:PTZ00166 857 ELA--------KKLRQrdpgsapnvGDRVSYVIVKGAKGAPQYERAedplYVLE-----NNIPIDTQYYL-DQIKNPLLR 922
|
....*
gi 2462629845 1087 ICEPI 1091
Cdd:PTZ00166 923 IFEGV 927
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
707-1095 |
2.56e-45 |
|
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: 170.47 E-value: 2.56e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 707 LVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTT-VQRVASEAQKVTEDGEQEQIPELPDPSLEM------------- 772
Cdd:cd05534 40 LVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTcLGRVEELNGGGKFGFLGVKLYLPPPPLDLLllkddvtispngv 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 773 ---------GILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYS-RFYAKPLAALVTY 842
Cdd:cd05534 120 mfvkksvrkGILPKMLEEILDTRIMVKKAMKKYKDDKKLQRILDARQLALKLLANVTYGYTAASFSgRMPCVEIADSIVQ 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 843 KGREILMHTKEMVQ---KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGVFKSLLLLKKKK 918
Cdd:cd05534 200 TGRETLERAIELIEstpKWGAKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVTAANpSPIKLKFEKVYHPCVLVTKKR 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 919 YAALVVEPTSDGnyVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigENVLNGSVPVSQFE 998
Cdd:cd05534 280 YVGYKYESPDQT--EPTFDAKGIETVRRDGCPAVQKILEKSLRILFETKDLSTVKSYLQRQW----SKLLQGRVSIQDFI 353
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 999 INKALTKDpqDYPDKKSLP-HVHVAL-WINSQGGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYL 1076
Cdd:cd05534 354 FAKEVRLG--TYKEGATLPaGAIVALrRMEKDPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLADPSLRLDAEYYI 431
|
410
....*....|....*....
gi 2462629845 1077 AQQIHPVVARICEPIdGID 1095
Cdd:cd05534 432 TKQIIPALDRLFNLV-GVD 449
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
403-621 |
3.14e-44 |
|
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: 159.06 E-value: 3.14e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 403 VMAFSMKTMQNAK---NHQNEIIAMAALVhhSFALDKAAPKPPFQSHFCVVSKpkdcifpyafkevieKKNVKVEVAATE 479
Cdd:cd05160 1 VLSFDIETTPPVGgpePDRDPIICITYAD--SFDGVKVVFLLKTSTVGDDIEF---------------IDGIEVEYFADE 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 480 RTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRlkRSNMPKlggRSGFGERNATCGRMICDVEI 559
Cdd:cd05160 64 KELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYR--RSGGEK---SSGSTERIAVKGRVVFDLLA 138
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462629845 560 SAKELIRCKSYHLSELVQQILKTERV-VIPMENIQNMysESSQLLYLLEHTWKDAKFILQIMC 621
Cdd:cd05160 139 AYKRDFKLKSYTLDAVAEELLGEGKEkVDGEIIEDAE--WEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
704-1091 |
1.18e-42 |
|
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: 160.51 E-value: 1.18e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 704 AGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNIcfTTVQRVasEAQKvtEDGEQEQIPELPDP--SLEMGILPREIRK 781
Cdd:cd05537 4 PGGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI--DPLGLI--EGLK--APDPEDLIPGFLGArfSREKHILPDLIAR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 782 LVERRKQVKQlmkqqdlNPDLILQYdirqkALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLE 861
Cdd:cd05537 77 LWAARDEAKR-------EKNAPLSQ-----AIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQ 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 862 VIYGDTDSIMINTNST-NLEEVFKLGNKVKSEVN--------KLYKL---LEIDIDGVF--------KSLLLLKKKKYAA 921
Cdd:cd05537 145 VIYGDTDSTFVWLGEElDAAEAQAIGKELASQINqwwaqklkEEFGLesfLEIEFETHYsrffmptiRGSDEGSKKRYAG 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 922 LVVEPTSDgnyvtKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEiGEnvLNgsvpvSQFEINK 1001
Cdd:cd05537 225 LKSTDGGD-----ELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLA-GE--LD-----ELLVYRK 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1002 ALTKDPQDYpDKKSLPHVHVALW---INSQGGRKvKAGDTVSYVICQDGsnltasqrayaPEQLQkQDNLTIDTQYYLAQ 1078
Cdd:cd05537 292 RLRRPLSEY-TKNVPPHVQAARLadqINRELGRP-RQYQWIEYVITVNG-----------PEPLE-YRTSPLDYQHYIDK 357
|
410
....*....|...
gi 2462629845 1079 QIHPvvarICEPI 1091
Cdd:cd05537 358 QLKP----IADSI 366
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
696-1076 |
4.39e-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: 4.39e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 696 KGRKkaaYAGGLVLDPKVG-FYDkfILLLDFNSLYPSIIQEFNICFTTVQrvaseaqKVTEDGEQEQIPELPD------- 767
Cdd:cd05530 9 KGKK---YRGAIVLEPPPGiFFN--VVVLDFASLYPSIIKVWNLSYETVN-------CPHCECKTNEVPEVGHwvckkrp 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 768 --PSLEMGILpreiRKLveRRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGR 845
Cdd:cd05530 77 giTSQIIGLL----RDL--RVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGR 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 846 EILMHTKEMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDGVFKsllllkkkkyaaLVV 924
Cdd:cd05530 151 YIITSTIKKARELGLKVLYGDTDSLFLwNPPQEQLEDLVE---WVEKELG-----LDLELDKEYR------------YVV 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 925 EPTSDGNY--VTKQ---ELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRD---TIVENIQKRLIEIGENVLNGSVPVSQ 996
Cdd:cd05530 211 FSGLKKNYlgVTKDgsvDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPEdfeKAREKIRDIVKGVYKRLKKKEYTLDQ 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 997 FEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTASQRAYAPEqlqkqdnltIDTQYYL 1076
Cdd:cd05530 291 LAFKVMLSKPPEEY-TKNTPQHVKAARQLEKY-GRNVEAGDIISYVKVKGKEGVKPVQLARLDE---------VDVEKYV 359
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
683-1076 |
6.74e-42 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 166.40 E-value: 6.74e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 683 EDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvaseaqkvtEDGEQEQI 762
Cdd:PRK05761 387 EDILRLDHEVYKKAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETV-----------RIPECKCH 454
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 763 PELPDPSL------EMGILPREIRKLV--ERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAK 834
Cdd:PRK05761 455 YDDEVPELghsvcdDRPGLTSVLVGLLrdFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRI 534
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 835 PLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDGVFKslll 913
Cdd:PRK05761 535 EVAESITALGREILLSTKKKAEELGLKVLYGDTDSLFVwGPTKESLEELIK---EIEERTG-----IDLEVDKTYD---- 602
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 914 lkkkkyaaLVVEPTSDGNY--VTKQ---ELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQK---RLIEIGE 985
Cdd:PRK05761 603 --------WVAFSGLKKNYfgVLKDgkvKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEKVKDEiedVLKRYYE 674
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 986 NVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQGGrKVKAGDTVSYVIcqdgsnlTASQRAYAPEQLQKQ 1065
Cdd:PRK05761 675 KLRAKDYPLDELAIRVRLSKPLDEY-TKNTPQHVKAALQLRDYGV-EVSPGDIISYVK-------VDDKRGVKPVQLAKL 745
|
410
....*....|.
gi 2462629845 1066 DnlTIDTQYYL 1076
Cdd:PRK05761 746 S--EIDVEKYI 754
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
701-1094 |
5.52e-31 |
|
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: 125.92 E-value: 5.52e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 701 AAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQrvaseaqkvTEDGEQEQIPELPDPSL--EMGILPRE 778
Cdd:cd05531 3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETIN---------CRCCECRDHVYLGHRIClkRRGFLPEV 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 779 IRKLVERRKQVKQLMKQQDlnpdlilQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM 858
Cdd:cd05531 73 LEPLLERRLEYKRLKKEED-------PYAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEM 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 859 NLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKsevnklyklLEIDIDGVFKsllllkkkkyaALVVEPTSDG-----NYV 933
Cdd:cd05531 146 GFRVLHGIVDSLWIQGRGDIEELAREIEERTG---------IPLKLEGHYD-----------WIVFLPERDGlgapnRYF 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 934 TKQE-----LKGLDIVRRDWCDLAKDTGNFVIgQILSdQSRDtiVENIQKRLIEIgENVLNGSV------PVSQFEINKA 1002
Cdd:cd05531 206 GRLSdgemkVRGIELRRRDTPPFVKKFQEEAL-DILA-SAKT--PEELLKLREEA-LDLFRRYLqrlregDLEDLIIEKK 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 1003 LTKDPQDYpdkKSLPHvHVALWINSQgGRKVKAGDTVSYVIcQDGSNLTASqrayapeqlqKQDNLTIDTQYYLAQQIHP 1082
Cdd:cd05531 281 ISKRSSEY---KVLAS-TALKALRAK-GVSVVPGMKIEYIV-RDGKRPVPD----------LGNDEGYDTKYYRELLERA 344
|
410
....*....|..
gi 2462629845 1083 VvaricEPIDGI 1094
Cdd:cd05531 345 A-----EELLFP 351
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
694-1017 |
6.84e-21 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 99.71 E-value: 6.84e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 694 YKKGRKKAA--YAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAS-----EAQKVTEDGEQ------- 759
Cdd:PHA03036 519 LVRSETKNKfpYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVndnrlEAEINKQELRRkypypry 598
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 760 ---EQIPELPDPSLEM--------GILPREIRKLVERRKQVKQLMKQQDLNPDLILqYDIRQKALKLTANSMYGCLGFSY 828
Cdd:PHA03036 599 iyvHCEPRSPDLVSEIavfdrrieGIIPKLLKTFLEERARYKKLLKEATSSVEKAI-YDSMQYTYKIVANSVYGLMGFRN 677
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 829 SRFYAKPLAALVTYKGREILMHTKEMV--------------------------------------QKMNLEVIYGDTDSI 870
Cdd:PHA03036 678 SALYSYASAKSCTAIGRNMIKYLNSVLngsklingklilancpinpffkddrsidtnydtnlpveYNFTFRSVYGDTDSV 757
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 871 MINTNSTNLEEVFKLGNKVKSEVNK--LYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRRDW 948
Cdd:PHA03036 758 FLEINTKDVDKSIKIAKELERIINEkvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVPERVNKGTSETRRDV 837
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462629845 949 CDLAKdtgnfvigqilsdqsrdTIVENIQKRLIEIGENVLNGSVPVSqFEINKALTKDPQDYPDKKSLP 1017
Cdd:PHA03036 838 SKFHK-----------------YMIKIYKTRLLDMLSEGNMNSNQVC-IDILRSLEKDLIIEFDSRSAP 888
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
724-1086 |
9.34e-15 |
|
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: 77.53 E-value: 9.34e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 724 DFNSLYPSIIQEFNICfttvqrVASEaqkvtedgeqeqipelpdpslEMGILPREIRKLVERRKQVKQLMKQQDLnPDLI 803
Cdd:cd05538 23 DVASLYPSIMLAYRIC------PARD---------------------SLGIFLALLKYLVELRLAAKESARAAAR-PAER 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 804 LQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMI---NTNSTNLE 880
Cdd:cd05538 75 DAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFippNGVDTEDE 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 881 EvfklgNKVKSEVNK-LYKLLEIDIDGVFKSLLLLKKKKYAALvveptsdgNYVTKQELKGLDIVRRDWCDLAKDTGNFV 959
Cdd:cd05538 155 E-----EELVRELSStLPKGITVEFDGRYRAMFSYKIKNYALL--------DYDGKLIVKGSAFRSRGIEPFLREFLREA 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 960 IGQILSDQSrdtivENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDK----KSLPhvHVALWINSQGGRKVKA 1035
Cdd:cd05538 222 VRLLLQGDG-----AGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYLQKvragKRNP--AAAYEIALARPREWRA 294
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|.
gi 2462629845 1036 GDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTiDTQYYlAQQIHPVVAR 1086
Cdd:cd05538 295 GDRVTYYVSGTGKGVSVYENCRLVADYDPAHPDE-NTGFY-AERLLQLAAR 343
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
695-873 |
2.50e-14 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 78.19 E-value: 2.50e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 695 KKGRKKAAYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQ---RVASEAQKVTEdgeqeqipELPDPSLE 771
Cdd:PHA02528 369 NKSHKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAgtfHVAPVHEYINK--------TAPRPSDE 439
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 772 M--------------GILPREIRKLVERRKQVKQLM----KQQDLNPDL------------------------------- 802
Cdd:PHA02528 440 YscspngwmyrkdirGVIPTEIKKVFDQRKIYKKKMlaaeRNAELIKTIledlndsvdtpidvdyyfdfsdefkaelktl 519
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 803 ---------------ILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGR-EILMHTKEMVQKMNL------ 860
Cdd:PHA02528 520 tksslkalleecekeIALCNTIQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQlAIQWIERKMNEYLNKlckted 599
|
250
....*....|....*
gi 2462629845 861 --EVIYGDTDSIMIN 873
Cdd:PHA02528 600 edYVIYGDTDSIYVN 614
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
462-619 |
3.78e-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: 57.75 E-value: 3.78e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 462 FKEVIEKKNV---KVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRLKRSnmPKLg 538
Cdd:cd05780 36 GNKVITWKKFdlpFVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIE--LDLGRDGSE--IKI- 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 539 GRSGFGERNATCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQ 618
Cdd:cd05780 111 QRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYE 190
|
.
gi 2462629845 619 I 619
Cdd:cd05780 191 I 191
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
691-871 |
1.07e-08 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 59.87 E-value: 1.07e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 691 TNKYKKG-RKKAAYAGGLVLDPKVGF-----YDKFILLLDFNSLYPSIIQEFNICFTTV---QRVASEAQKVTEDgeQEQ 761
Cdd:PHA03334 620 PEKYARDcRQKIKLKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIvdpDCTARVRGWVVFD--WKK 697
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 762 IPE-LPDPSLEMGIL---PRE-------------IRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGcl 824
Cdd:PHA03334 698 IDRgFGKATLMYTILrtkPEEpswrrfttyttssLNHYLSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYG-- 774
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 2462629845 825 gfsysrfyAKPLAA--LVTYKGREILMHTKEMVQKM-NLEVIYGDTDSIM 871
Cdd:PHA03334 775 --------VAPHACqhLITTLGRHKIKLVEEFIKKEpGMTVNYGDTDSVM 816
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
478-532 |
5.88e-07 |
|
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: 52.19 E-value: 5.88e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 2462629845 478 TERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRS 532
Cdd:cd05777 70 TEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNI 124
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
447-596 |
2.44e-06 |
|
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: 49.72 E-value: 2.44e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 447 FCVVSKPKDCIF------PYAFKEVIEKKNvkvevaATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKA 520
Cdd:cd05785 26 FSNPDRGDDRIIivalrdNRGWEEVLHAED------AAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGV 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 521 P-HWSKIGRLKRSNmpklGGRSGFGERNA------TCGRMICDV-------EISAKELircKSYHLSELVQQ--ILKTER 584
Cdd:cd05785 100 PlAIGRDGSIPRQR----PSRFRFAERLIdyprydIPGRHVIDTyflvqlfDVSSRDL---PSYGLKAVAKHfgLASPDR 172
|
170
....*....|..
gi 2462629845 585 VVIPMENIQNMY 596
Cdd:cd05785 173 TYIDGRQIAEVW 184
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
468-514 |
1.95e-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: 43.71 E-value: 1.95e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 2462629845 468 KKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQR 514
Cdd:cd05784 40 DAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRR 86
|
|
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
787-870 |
1.14e-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: 43.43 E-value: 1.14e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 787 KQVKQLMKQQDL-----NPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMN-- 859
Cdd:cd05535 247 KKLEAAKAAGDAaeikeAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELVEQIGrp 326
|
90
....*....|.
gi 2462629845 860 LEViygDTDSI 870
Cdd:cd05535 327 LEL---DTDGI 334
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
479-619 |
1.24e-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: 41.54 E-value: 1.24e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 479 ERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRlKRSNMPKlggRSGFGERNATcGRMICDVE 558
Cdd:cd05781 48 DRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVK--LDVGR-RGGSEPS---TGVYGHYSIT-GRLNVDLY 120
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462629845 559 ISAKEL--IRCKS-YHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQI 619
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 ... |
470-557 |
2.69e-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: 2.69e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462629845 470 NVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRinvCKAPH----WSKIGRLKRSNMPKLGGRSgfGE 545
Cdd:cd05778 72 GIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIER---AAALGiddlLDEISRVPSDSNGKFGDRD--DE 146
|
90
....*....|....*....
gi 2462629845 546 RNAT-------CGRMICDV 557
Cdd:cd05778 147 WGYThtsgikiVGRHILNV 165
|
|
| |
