|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
56-1229 |
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: 1560.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 56 EVEDLTSVYEEVDEEQYSKLVQARQDDDWIVDDDGIGYVEDGREIFDDDLEDDAldTCGK-GSDGKAHRKDRKDVKKpsV 134
Cdd:TIGR00592 1 MVEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILD--LDKDdGSAAEAKKKDKENHKK--V 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 135 TKPNNIKAMFIASAGKKTTDKAVDLSKDDLLGDILQDLN-TETAQ--ITPPPVLIPKKKRSTGAL---LNPFSVHTPKAI 208
Cdd:TIGR00592 77 TKPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVV 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 209 PSGKPASPVLRN---EPLLTPIPLKRAELAGELAQPE-CPEDEQELGVME--FEDGDF----DES-MDTEKVDEK-PVTA 276
Cdd:TIGR00592 157 DIVKKAIPVSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDENpADEEIMISTtPVIA 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 277 KTWDQETEPVERVEHEADPERGTT-SYLENFLPDVSC----WD-IDQDDESipQEVQVDSSNLPLVKGADdEQVFQFYWl 350
Cdd:TIGR00592 237 KQWDYESEPEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD--VEITVNGDNFDLVYLAD-RQVFQFYW- 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 351 DAYEDPYNQPGVVFLFGKVwiesvKTHVSCCVMVKNIERTLYFLPREMKFDLNTGKETAIPVTMKDVYEEFDSKISAKYK 430
Cdd:TIGR00592 313 DAYEDPAEKLGVVLLFGRD-----VDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYK 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 431 IMKFKSKIVEKNYAFEIP--DVPEKSEYLEVRYS-----AEVPQLPQNLKGETFSHVFGTNTSSLELFLMNRKIKGPCWL 503
Cdd:TIGR00592 388 KEKFRAKPIAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWL 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 504 EVKNPQLLNQP-ISWCKFEVMALKPDLVNVIKDVSPPPLVVMSFSMKtMQNVQNHQHEIIAMAALVHHSFALDKAPPEPP 582
Cdd:TIGR00592 468 AVKGPDELEYPrRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEPP 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 583 FQTHFCVVSKPKDCIFPCDFK-EVISKKNMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVP 661
Cdd:TIGR00592 547 YDVHPCVGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIP 626
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 662 YWSKIGRLRRSnmPKLGSRsgFGERnaTCGRMICDVEISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSY 741
Cdd:TIGR00592 627 TWSKIGRLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSS 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 742 LLYLLEHIWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQKLG 821
Cdd:TIGR00592 701 LTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKLG 779
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 822 DEDEEIDGdtnkYKKGrKKATYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvtsevQKATEDEeqeq 901
Cdd:TIGR00592 780 DEDEEIDG----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDEDE---- 844
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 902 IPELPDPNLEMGILPREIRKLVERRKQVKQLMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVT 981
Cdd:TIGR00592 845 LPELPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVT 923
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 982 YKGREILMHTKDMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDAVFKSLLLLKKKKYAA 1061
Cdd:TIGR00592 924 AKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYAA 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1062 LVVEPTSDGNYITKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINK 1141
Cdd:TIGR00592 1004 IKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVINK 1083
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1142 ALTKDPQDYPDRKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTATQRAYAPEQLQKLDN-LAIDTQYYLAQQI 1220
Cdd:TIGR00592 1084 QLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQRKHNnLIYDTQYYLEHQI 1163
|
....*....
gi 569009877 1221 HPVVARICE 1229
Cdd:TIGR00592 1164 HPVVLRILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
836-1246 |
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: 718.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 836 KGRKKATYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRvtsevqkATEDEEQEQIPELPDPNLEMGIL 915
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDR-------ADPDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 916 PREIRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMV 995
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 996 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDAVFKSLLLLKKKKYAALVVEPtsDGNYITK 1075
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1076 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDRKS 1155
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1156 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTATQRAYAPEQLQKLDNLAIDTQYYLAQQIHPVVARICEPIDGID 1235
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 569009877 1236 AVLIALWLGLD 1246
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 ... |
778-1231 |
1.87e-166 |
|
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: 505.22 E-value: 1.87e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 778 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKLGDEDeeidgdtnkykkgrkkaTYAGGLVLDPKVGFYD 857
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 858 KFILLLDFNSLYPSIIQEFNICFTTVQRVTSEVQKATEDEEQEQIPELPD------PNLEMGILPREIRKLVERRKQVKQ 931
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 932 LMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKM---NLEVIYGDTD 1008
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1009 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDAVFKSLLLLKKKKYAALVVEPTSDGNyitKQELKGLDIVRR 1086
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1087 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDRKSLPHVHVALWIN 1166
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 569009877 1167 SQGGRKVKAGDTVSYVICQDGS---NLTATQRAYAPE-QLQKldNLAIDTQYYLAQQIHPVVARICEPI 1231
Cdd:pfam00136 373 KRNGEAPEVGDRIPYVIVKAAKglkNLLIYERAEDPEyVLEN--NLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
491-1232 |
2.24e-109 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 364.92 E-value: 2.24e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 491 FLMNRKIKGPCWLEVknpqllnQPISWCKFEVMALKPDLVNVIKDVsPPPLVVMSF----SMKTMQNVQNHQHEIIAMAa 566
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 567 lVHHSFALDKAppeppfqthFCVVSKPKDcifpcdfkeviskknMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSF 646
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 647 ELEVLLQRINECKVPywSKIGRLRRSnmPKLGSRSGFGERNATcGRMICDV-EISAKELIHCKSYHLSELVQQILKTERI 725
Cdd:COG0417 244 DLPYLQKRAERLGIP--LDLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 726 VIPTENIRNMYSESsyLLYLLEHIWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 805
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 806 IVPDKqifrkpqqklgdedEEIDGDTnkykkgrkkatYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqr 885
Cdd:COG0417 397 LAPNK--------------GEIKGEA-----------YPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETL-- 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 886 vtSEVQKATEDEEQEqIPELP-----DPNlemGILPREIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSM 960
Cdd:COG0417 449 --VEGGEEPCGDEDV-APGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 961 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KLYKL 1039
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1040 LEIDIDAVFKSllllkkkkyaalVVEPTSDGNY--ITKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 1114
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1115 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDRKSLPHVHVALWINSQgGRKVKAGDTVSYVIcqdgsnLTATQ 1194
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI------TKGGG 738
|
730 740 750
....*....|....*....|....*....|....*...
gi 569009877 1195 RAYaPEQLQKLDNLAIDTQYYLAQQIHPVVARICEPID 1232
Cdd:COG0417 739 RVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
539-1015 |
1.90e-107 |
|
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: 348.75 E-value: 1.90e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 539 PPLVVMSFSMKTMQNVQNHQHEIIAMAALVHHSFALDKAPPEPPFQtHFCVVSKPKDCIfpcdfkeviskKNMKVEIAAT 618
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 619 ERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRLRRS-----NMPKLGSRSG--FGERNATCG 691
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripnKKPLFGSKSFglSDIKVYIKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 692 RMICDVEISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSYLLY-LLEHIWKDARFILQIMCELNVLPLAL 770
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDeLLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 771 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqklgdedEEIDGDTNKYKKgRKKATYAGGLVLD 850
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSK--------------ELYDFKGSEPDL-KKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 851 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVTSEVQKA-TEDEEQEQIPELPDP--------NLEMGILPREIRK 921
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGdLIIPEDLLTIKYEKGnkyrfvkkNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 922 LVERRKQVKQLMKQ-QDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKM-- 998
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 569009877 999 ---NLEVIYGDTDSIMINTN 1015
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
613-1232 |
6.70e-75 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 266.34 E-value: 6.70e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 613 VEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYwsKIGRLRRSNMPKL-GSRSGFGERNATcG 691
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 692 RMICD-VEISAKELIHCKSYHLsELVQQilkteRIVIPTENIRNMYSESSYL--LY------LLEHIWKDARFILQIMCE 762
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSL-EYVSQ-----RLLGEGKAIDDPYDRMDEIdrRFaedkpaLARYNLKDCELVTRIFEK 347
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 763 LNVLPLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDkqifrkpqqkLGDEDEEidgdtnkykkgrkkaT 842
Cdd:PRK05762 348 TKLLPFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPN----------LGERPGE---------------A 400
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 843 YAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTvqRVtsevqKATEDEEQEQIPelpdPNL------EMGILP 916
Cdd:PRK05762 401 SPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDG--LV-----EGLAQPPEESVA----GFLgarfsrEKHFLP 468
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 917 REIRKLVERRKQVKQLMKQqdlnpdlvlqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQ 996
Cdd:PRK05762 469 EIVERLWEGRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIE 536
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 997 KMNLEVIYGDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDAVFK--------SLLLLKK 1056
Cdd:PRK05762 537 AQGYQVIYGDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSK 616
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1057 KKYAALVVEPTSDGNYItkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQ 1136
Cdd:PRK05762 617 KRYAGLIQEGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EK 684
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1137 FEINKALTKDPQDYpDRKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGSnltatqrayapeqlQKLDNL--A 1209
Cdd:PRK05762 685 LVYRKRLRRPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNGP--------------EPLEYRksP 749
|
650 660
....*....|....*....|...
gi 569009877 1210 IDTQYYLAQQIHPVVARICEPID 1232
Cdd:PRK05762 750 IDYDYYIEKQLQPVADRILPFFG 772
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1269-1386 |
2.21e-38 |
|
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: 141.97 E-value: 2.21e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1269 AQLTDEEKYKDCEKFKCLCPSCGTENIYDNVFEGS-GLDMEPSLYRCSNvdCKVSPLTFmvQLSNKLIMDIRRCIKKYYD 1347
Cdd:pfam08996 1 SQISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYE 76
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 569009877 1348 GWLICEEPTCCSRLRRLPLHFSRngplCP-VCMKAVLRPE 1386
Cdd:pfam08996 77 GWLVCDDPTCGNRTRQMSVYGKR----CLgPGCKGRMRYE 112
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
56-1229 |
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: 1560.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 56 EVEDLTSVYEEVDEEQYSKLVQARQDDDWIVDDDGIGYVEDGREIFDDDLEDDAldTCGK-GSDGKAHRKDRKDVKKpsV 134
Cdd:TIGR00592 1 MVEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILD--LDKDdGSAAEAKKKDKENHKK--V 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 135 TKPNNIKAMFIASAGKKTTDKAVDLSKDDLLGDILQDLN-TETAQ--ITPPPVLIPKKKRSTGAL---LNPFSVHTPKAI 208
Cdd:TIGR00592 77 TKPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVV 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 209 PSGKPASPVLRN---EPLLTPIPLKRAELAGELAQPE-CPEDEQELGVME--FEDGDF----DES-MDTEKVDEK-PVTA 276
Cdd:TIGR00592 157 DIVKKAIPVSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDENpADEEIMISTtPVIA 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 277 KTWDQETEPVERVEHEADPERGTT-SYLENFLPDVSC----WD-IDQDDESipQEVQVDSSNLPLVKGADdEQVFQFYWl 350
Cdd:TIGR00592 237 KQWDYESEPEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD--VEITVNGDNFDLVYLAD-RQVFQFYW- 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 351 DAYEDPYNQPGVVFLFGKVwiesvKTHVSCCVMVKNIERTLYFLPREMKFDLNTGKETAIPVTMKDVYEEFDSKISAKYK 430
Cdd:TIGR00592 313 DAYEDPAEKLGVVLLFGRD-----VDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYK 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 431 IMKFKSKIVEKNYAFEIP--DVPEKSEYLEVRYS-----AEVPQLPQNLKGETFSHVFGTNTSSLELFLMNRKIKGPCWL 503
Cdd:TIGR00592 388 KEKFRAKPIAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWL 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 504 EVKNPQLLNQP-ISWCKFEVMALKPDLVNVIKDVSPPPLVVMSFSMKtMQNVQNHQHEIIAMAALVHHSFALDKAPPEPP 582
Cdd:TIGR00592 468 AVKGPDELEYPrRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEPP 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 583 FQTHFCVVSKPKDCIFPCDFK-EVISKKNMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVP 661
Cdd:TIGR00592 547 YDVHPCVGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIP 626
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 662 YWSKIGRLRRSnmPKLGSRsgFGERnaTCGRMICDVEISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSY 741
Cdd:TIGR00592 627 TWSKIGRLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSS 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 742 LLYLLEHIWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQKLG 821
Cdd:TIGR00592 701 LTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKLG 779
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 822 DEDEEIDGdtnkYKKGrKKATYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvtsevQKATEDEeqeq 901
Cdd:TIGR00592 780 DEDEEIDG----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDEDE---- 844
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 902 IPELPDPNLEMGILPREIRKLVERRKQVKQLMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVT 981
Cdd:TIGR00592 845 LPELPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVT 923
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 982 YKGREILMHTKDMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDAVFKSLLLLKKKKYAA 1061
Cdd:TIGR00592 924 AKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYAA 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1062 LVVEPTSDGNYITKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINK 1141
Cdd:TIGR00592 1004 IKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVINK 1083
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1142 ALTKDPQDYPDRKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTATQRAYAPEQLQKLDN-LAIDTQYYLAQQI 1220
Cdd:TIGR00592 1084 QLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQRKHNnLIYDTQYYLEHQI 1163
|
....*....
gi 569009877 1221 HPVVARICE 1229
Cdd:TIGR00592 1164 HPVVLRILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
836-1246 |
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: 718.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 836 KGRKKATYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRvtsevqkATEDEEQEQIPELPDPNLEMGIL 915
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDR-------ADPDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 916 PREIRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMV 995
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 996 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDAVFKSLLLLKKKKYAALVVEPtsDGNYITK 1075
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1076 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDRKS 1155
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1156 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTATQRAYAPEQLQKLDNLAIDTQYYLAQQIHPVVARICEPIDGID 1235
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 569009877 1236 AVLIALWLGLD 1246
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 ... |
778-1231 |
1.87e-166 |
|
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: 505.22 E-value: 1.87e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 778 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKLGDEDeeidgdtnkykkgrkkaTYAGGLVLDPKVGFYD 857
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 858 KFILLLDFNSLYPSIIQEFNICFTTVQRVTSEVQKATEDEEQEQIPELPD------PNLEMGILPREIRKLVERRKQVKQ 931
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 932 LMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKM---NLEVIYGDTD 1008
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1009 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDAVFKSLLLLKKKKYAALVVEPTSDGNyitKQELKGLDIVRR 1086
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1087 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDRKSLPHVHVALWIN 1166
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 569009877 1167 SQGGRKVKAGDTVSYVICQDGS---NLTATQRAYAPE-QLQKldNLAIDTQYYLAQQIHPVVARICEPI 1231
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 ... |
539-771 |
2.51e-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: 355.38 E-value: 2.51e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 539 PPLVVMSFSMKTMQNVQNHQHEIIAMAALVHHSFALDKAPPEPPFQTHFCVVSKPKDC-IFPCDFKEVISKKNMKVEIAA 617
Cdd:cd05776 1 PPLTVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRsPPPDLFEKNAKKKKTKVRIFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 618 TERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRLRRSNMPKLGSRSGFGERNATCGRMICDV 697
Cdd:cd05776 81 NERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDT 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 569009877 698 EISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSYLLYLLEHIWKDARFILQIMCELNVLPLALQ 771
Cdd:cd05776 161 YLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLNILPLTKQ 234
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
491-1232 |
2.24e-109 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 364.92 E-value: 2.24e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 491 FLMNRKIKGPCWLEVknpqllnQPISWCKFEVMALKPDLVNVIKDVsPPPLVVMSF----SMKTMQNVQNHQHEIIAMAa 566
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 567 lVHHSFALDKAppeppfqthFCVVSKPKDcifpcdfkeviskknMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSF 646
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 647 ELEVLLQRINECKVPywSKIGRLRRSnmPKLGSRSGFGERNATcGRMICDV-EISAKELIHCKSYHLSELVQQILKTERI 725
Cdd:COG0417 244 DLPYLQKRAERLGIP--LDLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 726 VIPTENIRNMYSESsyLLYLLEHIWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 805
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 806 IVPDKqifrkpqqklgdedEEIDGDTnkykkgrkkatYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqr 885
Cdd:COG0417 397 LAPNK--------------GEIKGEA-----------YPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETL-- 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 886 vtSEVQKATEDEEQEqIPELP-----DPNlemGILPREIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSM 960
Cdd:COG0417 449 --VEGGEEPCGDEDV-APGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 961 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KLYKL 1039
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1040 LEIDIDAVFKSllllkkkkyaalVVEPTSDGNY--ITKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 1114
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1115 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDRKSLPHVHVALWINSQgGRKVKAGDTVSYVIcqdgsnLTATQ 1194
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI------TKGGG 738
|
730 740 750
....*....|....*....|....*....|....*...
gi 569009877 1195 RAYaPEQLQKLDNLAIDTQYYLAQQIHPVVARICEPID 1232
Cdd:COG0417 739 RVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
539-1015 |
1.90e-107 |
|
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: 348.75 E-value: 1.90e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 539 PPLVVMSFSMKTMQNVQNHQHEIIAMAALVHHSFALDKAPPEPPFQtHFCVVSKPKDCIfpcdfkeviskKNMKVEIAAT 618
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 619 ERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRLRRS-----NMPKLGSRSG--FGERNATCG 691
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripnKKPLFGSKSFglSDIKVYIKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 692 RMICDVEISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSYLLY-LLEHIWKDARFILQIMCELNVLPLAL 770
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDeLLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 771 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqklgdedEEIDGDTNKYKKgRKKATYAGGLVLD 850
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSK--------------ELYDFKGSEPDL-KKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 851 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVTSEVQKA-TEDEEQEQIPELPDP--------NLEMGILPREIRK 921
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGdLIIPEDLLTIKYEKGnkyrfvkkNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 922 LVERRKQVKQLMKQ-QDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKM-- 998
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 569009877 999 ---NLEVIYGDTDSIMINTN 1015
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
374-715 |
2.88e-75 |
|
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: 253.49 E-value: 2.88e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 374 VKTHVSCCVMVKNIERTLYFLPREmkfdlnTGKETAIPVTMKDVYEEFdskisakYKIMKFKSKIVEKNYAFEIPDVPek 453
Cdd:pfam03104 2 TDEGVSVCVNVFGFKPYFYCLAPD------GKELEEVIEEIKELYEGL-------DKIEKIELKLKKSLYGYEEDPVP-- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 454 SEYLEVRYSAEVPQLPQNLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVK-NPQLLNQPISWCKFEVMALKPDLVNV 532
Cdd:pfam03104 67 YLKVSFANPRPLLKIRKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKvYPFRAEGRISNCDVEIDCDSPDLISV 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 533 IKDVSPPPLVVMSFSMKTMQ------NVQNHQHEIIAMAALVHhsfalDKAPPEPPFQthfcVVSKPKDCIFPCDFKEVI 606
Cdd:pfam03104 147 PFEKEWPPLRVLSFDIECTSlpgkfpDAENVKDPIIQISCMLD-----GQGEPEPEPR----FLFTLRECDSEDIEDFEY 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 607 SKKNM----KVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRLRRsNMPKLGSRSG 682
Cdd:pfam03104 218 TPKPIypgvKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNR-GGRSKVREIG 296
|
330 340 350
....*....|....*....|....*....|....*..
gi 569009877 683 FG----ERNATCGRMICDVEISAKELIHCKSYHLSEL 715
Cdd:pfam03104 297 FGtrsyEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
613-1232 |
6.70e-75 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 266.34 E-value: 6.70e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 613 VEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYwsKIGRLRRSNMPKL-GSRSGFGERNATcG 691
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 692 RMICD-VEISAKELIHCKSYHLsELVQQilkteRIVIPTENIRNMYSESSYL--LY------LLEHIWKDARFILQIMCE 762
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSL-EYVSQ-----RLLGEGKAIDDPYDRMDEIdrRFaedkpaLARYNLKDCELVTRIFEK 347
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 763 LNVLPLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDkqifrkpqqkLGDEDEEidgdtnkykkgrkkaT 842
Cdd:PRK05762 348 TKLLPFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPN----------LGERPGE---------------A 400
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 843 YAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTvqRVtsevqKATEDEEQEQIPelpdPNL------EMGILP 916
Cdd:PRK05762 401 SPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDG--LV-----EGLAQPPEESVA----GFLgarfsrEKHFLP 468
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 917 REIRKLVERRKQVKQLMKQqdlnpdlvlqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQ 996
Cdd:PRK05762 469 EIVERLWEGRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIE 536
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 997 KMNLEVIYGDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDAVFK--------SLLLLKK 1056
Cdd:PRK05762 537 AQGYQVIYGDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSK 616
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1057 KKYAALVVEPTSDGNYItkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQ 1136
Cdd:PRK05762 617 KRYAGLIQEGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EK 684
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1137 FEINKALTKDPQDYpDRKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGSnltatqrayapeqlQKLDNL--A 1209
Cdd:PRK05762 685 LVYRKRLRRPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNGP--------------EPLEYRksP 749
|
650 660
....*....|....*....|...
gi 569009877 1210 IDTQYYLAQQIHPVVARICEPID 1232
Cdd:PRK05762 750 IDYDYYIEKQLQPVADRILPFFG 772
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
841-1227 |
4.41e-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: 238.42 E-value: 4.41e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 841 ATYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQRvtSEVQKATEDEEQEQIPELPDPNlemGILPREIR 920
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVG--NGEIAAPEDYIGVGFRSPKDRK---GLLPRILE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 921 KLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKMNL 1000
Cdd:cd00145 75 ELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGA 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1001 EVIYGDTDSIMINTN-STNLEEVFKLGNKVKSEVNKlYKLLEIDIDAVFKSLLLLKKKKYAALVVEPTSDGNyitKQELK 1079
Cdd:cd00145 155 RVIYGDTDSIFVSLPkMGTKEDAIKEGREILQELAD-EHLLELEFEKVYLPFFLGKKKRYAGLDIWKGQDEG---KIDIK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1080 GLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigenvlngsvpvsqfeinkaltkdpqdypdrkslphv 1159
Cdd:cd00145 231 GLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL--------------------------------------- 271
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 569009877 1160 hvalwinsqggrkvkagDTVSYVICQDGSNLTATQRAYAPEQLQKlDNLAIDTQYYLAQQIHPVVARI 1227
Cdd:cd00145 272 -----------------DKVKYVVTRGGKGVPDYERADPPLEDLD-KRHRIDYEYYLERLLQPPLERI 321
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
842-1229 |
1.39e-64 |
|
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: 224.13 E-value: 1.39e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 842 TYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQRvtsevqkateDEEQEQIPELP-------DPnleMGI 914
Cdd:cd05536 3 SYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVR----------EGCEDCDVEPQvghkfrkDP---PGF 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 915 LPREIRKLVERRKQVKQLMKQ-QDLNPDLVLqYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKD 993
Cdd:cd05536 69 IPSVLEDLLEERRRIKEKMKKlDPESEEYKL-LDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIK 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 994 MVQKMNLEVIYGDTDSIM--INTNSTNLEEVFKLGNKVKSEVNklyklLEIDIDAVFKSLLLLKKKKYAALvvepTSDGN 1071
Cdd:cd05536 148 IAEEKGFKVIYGDTDSLFvkIDGADAVKKKVKKLLKYINEELP-----LELEIEKFYKRGFFVTKKRYAGL----TEDGK 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1072 YITkqelKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYp 1151
Cdd:cd05536 219 IDV----VGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVK----EVIEKLKRGEVPPEKLVIWKQLTKDLSEY- 289
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 569009877 1152 dRKSLPHVHVALWInSQGGRKVKAGDTVSYVICQDGSNLtaTQRAYAPEQLQKLDNlaIDTQYYLAQQIHPVVARICE 1229
Cdd:cd05536 290 -KATGPHVAAAKKL-AKRGYKVRPGTKIGYVIVKGSGKI--SDRAYPYDMVDEKHK--YDAEYYIDNQVLPAVLRILE 361
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
842-1231 |
1.40e-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: 1.40e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 842 TYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVqrVTSEVQKATEDEEQEQIP---ELPDPNLEMGILPRE 918
Cdd:cd05533 2 QYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTL--LNKNTAKKLPPEDYIKTPngdYFVKSSVRKGLLPEI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 919 IRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQ-- 996
Cdd:cd05533 80 LEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEek 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 997 -------KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDAVFKSLLLLKKKKYAALVVepTS 1068
Cdd:cd05533 159 ytkangySHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFiKPIKLEFEKVYFPYLLINKKRYAGLLW--TN 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1069 DGNYiTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIqKRLIeigENVLNGSVPVSQFEINKALTKDPQ 1148
Cdd:cd05533 237 PDKH-DKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFV-KGVI---SDLLQNKIDISLLVITKALTKTAD 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1149 DYPDRksLPHVHVALWINSQG-GRKVKAGDTVSYVICQDGSNLTATQRAYAPeqLQKLD-NLAIDTQYYLAQQIHPVVAR 1226
Cdd:cd05533 312 DYAGK--QAHVELAERMRKRDpGSAPNVGDRVPYVIIKGAKGAKAYEKAEDP--IYVLEnNIPIDTQYYLENQLSKPLLR 387
|
....*
gi 569009877 1227 ICEPI 1231
Cdd:cd05533 388 IFEPI 392
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
491-1231 |
2.31e-63 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 236.08 E-value: 2.31e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 491 FLMNRKIKGPCWLEVKNPQ----LLNQPISWCKFEVmALKPDLVNVIKDV----SPPPLVVMSFSMKTMQNV-----QNH 557
Cdd:PTZ00166 207 FLIDNNITGGSWLTLPKGKykirPPKKKTSTCQIEV-DCSYEDLIPLPPEgeylTIAPLRILSFDIECIKLKglgfpEAE 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 558 QHEIIAMAALVHhsfaLDKAPPEPPFQTHFCVvskpKDC--IFPCdfkEVISKKNMKVEIAATERTLIgfflakvhKIDP 635
Cdd:PTZ00166 286 NDPVIQISSVVT----NQGDEEEPLTKFIFTL----KECasIAGA---NVLSFETEKELLLAWAEFVI--------AVDP 346
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 636 DILVGHNICSFELEVLLQRINECKVP---YWSKIGRLRRSNMPKLGSRSGFGERNATC----GRMICDVeisaKELIH-- 706
Cdd:PTZ00166 347 DFLTGYNIINFDLPYLLNRAKALKLNdfkYLGRIKSTRSVIKDSKFSSKQMGTRESKEinieGRIQFDV----MDLIRrd 422
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 707 --CKSYHLSELVQQILKTERIVIPTENIRNMYSES--------SYLLyllehiwKDARFILQIMCELNVLPLALQITNIA 776
Cdd:PTZ00166 423 ykLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSpetrrriaVYCL-------KDAILPLRLLDKLLLIYNYVEMARVT 495
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 777 GNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqifrkpqqklgdedeeidgdTNKYKKGRKKATYAGGLVLDPKVGFY 856
Cdd:PTZ00166 496 GTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIP----------------------TVKYSGGGSEEKYEGATVLEPKKGFY 553
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 857 DKFILLLDFNSLYPSIIQEFNICFTTVqrVTSEVQKATEDEEQEQIP---ELPDPNLEMGILPREIRKLVERRKQVKQLM 933
Cdd:PTZ00166 554 DEPIATLDFASLYPSIMIAHNLCYSTL--VPPNDANNYPEDTYVTTPtgdKFVKKEVRKGILPLIVEELIAARKKAKKEM 631
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 934 KQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYakP---LAALVTYKGREILMHTKDMVQKM---------NLE 1001
Cdd:PTZ00166 632 KDEK-DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQL--PcleVSTSITSFGRQMIDKTKELVEKHytkangykhDAT 708
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1002 VIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDAVFKSLLLLKKKKYAALVVepTSDGNYiTKQELKG 1080
Cdd:PTZ00166 709 VIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFlKPIKLEFEKVYCPYLLMNKKRYAGLLY--TNPEKY-DKIDCKG 785
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1081 LDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNgsvpVSQFEINKALTKDpqDYPDRksLPHVH 1160
Cdd:PTZ00166 786 IETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRID----ISLLVITKSLGKD--DYEGR--LAHVE 857
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1161 VAlwinsqggRKVKA---------GDTVSYVICQDGSNLTATQRAYAPeqLQKLDN-LAIDTQYYLaQQIHPVVARICEP 1230
Cdd:PTZ00166 858 LA--------KKLRQrdpgsapnvGDRVSYVIVKGAKGAPQYERAEDP--LYVLENnIPIDTQYYL-DQIKNPLLRIFEG 926
|
.
gi 569009877 1231 I 1231
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 ... |
543-761 |
3.93e-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: 181.78 E-value: 3.93e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 543 VMSFSMKTMQNVQ---NHQHEIIAMAALVhhSFALDKAPPEPPFQTHFCVVSKpkdcifpcdfkevisKKNMKVEIAATE 619
Cdd:cd05160 1 VLSFDIETTPPVGgpePDRDPIICITYAD--SFDGVKVVFLLKTSTVGDDIEF---------------IDGIEVEYFADE 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 620 RTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYWskIGRLRRSNMPKlgsRSGFGERNATCGRMICDVEI 699
Cdd:cd05160 64 KELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLT--DGIYRRSGGEK---SSGSTERIAVKGRVVFDLLA 138
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 569009877 700 SAKELIHCKSYHLSELVQQILK-TERIVIPTENIRNMysESSYLLYLLEHIWKDARFILQIMC 761
Cdd:cd05160 139 AYKRDFKLKSYTLDAVAEELLGeGKEKVDGEIIEDAE--WEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
847-1235 |
3.24e-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: 3.24e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 847 LVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTT-VQRVTSEVQKATEDEEQEQIPELPDPNLEM------------- 912
Cdd:cd05534 40 LVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTcLGRVEELNGGGKFGFLGVKLYLPPPPLDLLllkddvtispngv 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 913 ---------GILPREIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYS-RFYAKPLAALVTY 982
Cdd:cd05534 120 mfvkksvrkGILPKMLEEILDTRIMVKKAMKKYKDDKKLQRILDARQLALKLLANVTYGYTAASFSgRMPCVEIADSIVQ 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 983 KGREILMHTKDMVQ---KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDAVFKSLLLLKKKK 1058
Cdd:cd05534 200 TGRETLERAIELIEstpKWGAKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVTAANpSPIKLKFEKVYHPCVLVTKKR 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1059 YAALVVE------PTSDGnyitkqelKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigENVLNGSV 1132
Cdd:cd05534 280 YVGYKYEspdqtePTFDA--------KGIETVRRDGCPAVQKILEKSLRILFETKDLSTVKSYLQRQW----SKLLQGRV 347
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1133 PVSQFEINKALTKDpQDYPDRKSLPHVHVAL-WINSQGGRKVKAGDTVSYVICQDGSNLTATQRAYAPEQLQKLDNLAID 1211
Cdd:cd05534 348 SIQDFIFAKEVRLG-TYKEGATLPAGAIVALrRMEKDPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLADPSLRLD 426
|
410 420
....*....|....*....|....
gi 569009877 1212 TQYYLAQQIHPVVARICEPIdGID 1235
Cdd:cd05534 427 AEYYITKQIIPALDRLFNLV-GVD 449
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
836-1216 |
7.14e-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: 158.28 E-value: 7.14e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 836 KGRKkatYAGGLVLDPKVG-FYDkfILLLDFNSLYPSIIQEFNICFTTVQRVTsevqkatEDEEQEQIPELP-----DPN 909
Cdd:cd05530 9 KGKK---YRGAIVLEPPPGiFFN--VVVLDFASLYPSIIKVWNLSYETVNCPH-------CECKTNEVPEVGhwvckKRP 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 910 LEMGILPREIRKLveRRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILM 989
Cdd:cd05530 77 GITSQIIGLLRDL--RVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIIT 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 990 HTKDMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDAVFKsllllkkkkyaaLVVEPTS 1068
Cdd:cd05530 155 STIKKARELGLKVLYGDTDSLFLwNPPQEQLEDLVE---WVEKELG-----LDLELDKEYR------------YVVFSGL 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1069 DGNYI-----TKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRD---TIVENIQKRLIEIGENVLNGSVPVSQFEIN 1140
Cdd:cd05530 215 KKNYLgvtkdGSVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPEdfeKAREKIRDIVKGVYKRLKKKEYTLDQLAFK 294
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 569009877 1141 KALTKDPQDYpdRKSLP-HVHVALWINSQgGRKVKAGDTVSYVicqdgsnLTATQRAYAPEQLQKLDNlaIDTQYYL 1216
Cdd:cd05530 295 VMLSKPPEEY--TKNTPqHVKAARQLEKY-GRNVEAGDIISYV-------KVKGKEGVKPVQLARLDE--VDVEKYV 359
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
823-1216 |
1.97e-40 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 161.78 E-value: 1.97e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 823 EDEEIDGDTNKYKKGRKKATYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvtsevqkatEDEEQEQI 902
Cdd:PRK05761 387 EDILRLDHEVYKKAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETV-----------RIPECKCH 454
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 903 PELPDPNL------EMGILPREIRKLV--ERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAK 974
Cdd:PRK05761 455 YDDEVPELghsvcdDRPGLTSVLVGLLrdFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRI 534
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 975 PLAALVTYKGREILMHTKDMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDAVFKslll 1053
Cdd:PRK05761 535 EVAESITALGREILLSTKKKAEELGLKVLYGDTDSLFVwGPTKESLEELIK---EIEERTG-----IDLEVDKTYD---- 602
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1054 lkkkkyaaLVVEPTSDGNYITKQ-----ELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQK---RLIEIGE 1125
Cdd:PRK05761 603 --------WVAFSGLKKNYFGVLkdgkvKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEKVKDEiedVLKRYYE 674
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1126 NVLNGSVPVSQFEINKALTKDPQDYpDRKSLPHVHVALWINSQGGrKVKAGDTVSYVICQDgsnltatQRAYAPEQLQKL 1205
Cdd:PRK05761 675 KLRAKDYPLDELAIRVRLSKPLDEY-TKNTPQHVKAALQLRDYGV-EVSPGDIISYVKVDD-------KRGVKPVQLAKL 745
|
410
....*....|.
gi 569009877 1206 DNlaIDTQYYL 1216
Cdd:PRK05761 746 SE--IDVEKYI 754
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
844-1231 |
7.73e-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: 152.42 E-value: 7.73e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 844 AGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNIcfTTVQRVtsEVQKAteDEEQEQIPELPDPNL--EMGILPREIRK 921
Cdd:cd05537 4 PGGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI--DPLGLI--EGLKA--PDPEDLIPGFLGARFsrEKHILPDLIAR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 922 LVERRKQVKQlmkqqDLNPDLvlqydirQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKMNLE 1001
Cdd:cd05537 77 LWAARDEAKR-----EKNAPL-------SQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQ 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1002 VIYGDTDSIMINTNST-NLEEVFKLGNKVKSEVN--------KLYKL---LEIDIDAVF--------KSLLLLKKKKYAA 1061
Cdd:cd05537 145 VIYGDTDSTFVWLGEElDAAEAQAIGKELASQINqwwaqklkEEFGLesfLEIEFETHYsrffmptiRGSDEGSKKRYAG 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1062 LVVEPTSDgnyitKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEiGEnvLNgsvpvSQFEINK 1141
Cdd:cd05537 225 LKSTDGGD-----ELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLA-GE--LD-----ELLVYRK 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1142 ALTKDPQDYpDRKSLPHVHVALW---INSQGGRKvKAGDTVSYVICQDGsnltatqrayaPEQLQKlDNLAIDTQYYLAQ 1218
Cdd:cd05537 292 RLRRPLSEY-TKNVPPHVQAARLadqINRELGRP-RQYQWIEYVITVNG-----------PEPLEY-RTSPLDYQHYIDK 357
|
410
....*....|...
gi 569009877 1219 QIHPvvarICEPI 1231
Cdd:cd05537 358 QLKP----IADSI 366
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1269-1386 |
2.21e-38 |
|
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: 141.97 E-value: 2.21e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1269 AQLTDEEKYKDCEKFKCLCPSCGTENIYDNVFEGS-GLDMEPSLYRCSNvdCKVSPLTFmvQLSNKLIMDIRRCIKKYYD 1347
Cdd:pfam08996 1 SQISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYE 76
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 569009877 1348 GWLICEEPTCCSRLRRLPLHFSRngplCP-VCMKAVLRPE 1386
Cdd:pfam08996 77 GWLVCDDPTCGNRTRQMSVYGKR----CLgPGCKGRMRYE 112
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
841-1234 |
6.17e-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: 119.76 E-value: 6.17e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 841 ATYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQrvtsevqkaTEDEEQEQIPELPDP--NLEMGILPRE 918
Cdd:cd05531 3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETIN---------CRCCECRDHVYLGHRicLKRRGFLPEV 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 919 IRKLVERRKQVKQLMKQQDlnpdlvlQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKM 998
Cdd:cd05531 73 LEPLLERRLEYKRLKKEED-------PYAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEM 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 999 NLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKsevnklyklLEIDIDAVFKsllllkkkkyaALVVEPTSDG-----NYI 1073
Cdd:cd05531 146 GFRVLHGIVDSLWIQGRGDIEELAREIEERTG---------IPLKLEGHYD-----------WIVFLPERDGlgapnRYF 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1074 TKQE-----LKGLDIVRRDWCDLAKDTGNFVIgQILSdQSRDtiVENIQKRLIEIgENVLNGSV------PVSQFEINKA 1142
Cdd:cd05531 206 GRLSdgemkVRGIELRRRDTPPFVKKFQEEAL-DILA-SAKT--PEELLKLREEA-LDLFRRYLqrlregDLEDLIIEKK 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1143 LTKDPQDYpdrKSLPHvHVALWINSQgGRKVKAGDTVSYVICQDGSNLTATQrayapeqlqklDNLAIDTQYYLAQQIHP 1222
Cdd:cd05531 281 ISKRSSEY---KVLAS-TALKALRAK-GVSVVPGMKIEYIVRDGKRPVPDLG-----------NDEGYDTKYYRELLERA 344
|
410
....*....|..
gi 569009877 1223 VvaricEPIDGI 1234
Cdd:cd05531 345 A-----EELLFP 351
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
839-1157 |
2.16e-21 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 101.25 E-value: 2.16e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 839 KKATYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNIC-FTTVQRVTSEVQKATEDEEQEQIPELPDP--------- 908
Cdd:PHA03036 526 NKFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSpETLVGVVVNDNRLEAEINKQELRRKYPYPryiyvhcep 605
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 909 ---NL----------EMGILPREIRKLVERRKQVKQLMKQQDLNPDLVLqYDIRQKALKLTANSMYGCLGFSYSRFYAKP 975
Cdd:PHA03036 606 rspDLvseiavfdrrIEGIIPKLLKTFLEERARYKKLLKEATSSVEKAI-YDSMQYTYKIVANSVYGLMGFRNSALYSYA 684
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 976 LAALVTYKGREILMHTKDMV--------------------------------------QKMNLEVIYGDTDSIMINTNST 1017
Cdd:PHA03036 685 SAKSCTAIGRNMIKYLNSVLngsklingklilancpinpffkddrsidtnydtnlpveYNFTFRSVYGDTDSVFLEINTK 764
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1018 NLEEVFKLGNKVKSEVNK--LYKLLEIDIDAVFKSLLLLKKKKYAALVVEPTSDGNYITKQELKGLDIVRRDWCDLAKdt 1095
Cdd:PHA03036 765 DVDKSIKIAKELERIINEkvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVPERVNKGTSETRRDVSKFHK-- 842
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 569009877 1096 gnfvigqilsdqsrdTIVENIQKRLIEIGENVLNGSVPVSqFEINKALTKDPQDYPDRKSLP 1157
Cdd:PHA03036 843 ---------------YMIKIYKTRLLDMLSEGNMNSNQVC-IDILRSLEKDLIIEFDSRSAP 888
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
835-1013 |
1.79e-15 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 82.05 E-value: 1.79e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 835 KKGRKKATYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQRVTSEvqkATEDEEQEQIPELPD------P 908
Cdd:PHA02528 369 NKSHKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFHV---APVHEYINKTAPRPSdeyscsP 444
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 909 NLEM------GILPREIRKLVERRKQVKQLMKQQDLNPDL---------------------------------------- 942
Cdd:PHA02528 445 NGWMyrkdirGVIPTEIKKVFDQRKIYKKKMLAAERNAELiktiledlndsvdtpidvdyyfdfsdefkaelktltkssl 524
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 943 ----------VLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGR-EILMHTKDMVQKMNL--------EVI 1003
Cdd:PHA02528 525 kalleecekeIALCNTIQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQlAIQWIERKMNEYLNKlcktededYVI 604
|
250
....*....|
gi 569009877 1004 YGDTDSIMIN 1013
Cdd:PHA02528 605 YGDTDSIYVN 614
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
864-1192 |
6.71e-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: 6.71e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 864 DFNSLYPSIIQEFNICfttvqrvtsevqkATEDEEqeqipelpdpnlemGILPREIRKLVERRKQVKQLMKQQDLnPDLV 943
Cdd:cd05538 23 DVASLYPSIMLAYRIC-------------PARDSL--------------GIFLALLKYLVELRLAAKESARAAAR-PAER 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 944 LQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILmhtKDMVQKM---NLEVIYGDTDSIMI---NTNST 1017
Cdd:cd05538 75 DAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELL---KLMIRWLrrrGATPVEVDTDGIYFippNGVDT 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1018 NLEEvfklgNKVKSEVNK-LYKLLEIDIDAVFKSLLLLKKKKYAALvveptsdgNYITKQELKGLDIVRRDWCDLAKDTG 1096
Cdd:cd05538 152 EDEE-----EELVRELSStLPKGITVEFDGRYRAMFSYKIKNYALL--------DYDGKLIVKGSAFRSRGIEPFLREFL 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 1097 NFVIGQILSDQSrdtivENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPD----RKSLPhvHVALWINSQGGRK 1172
Cdd:cd05538 219 REAVRLLLQGDG-----AGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYLQkvraGKRNP--AAAYEIALARPRE 291
|
330 340
....*....|....*....|
gi 569009877 1173 VKAGDTVSYVICQDGSNLTA 1192
Cdd:cd05538 292 WRAGDRVTYYVSGTGKGVSV 311
|
|
| DNA_pol_alpha_N |
pfam12254 |
DNA polymerase alpha subunit p180 N terminal; This domain family is found in eukaryotes, and ... |
41-101 |
1.42e-13 |
|
DNA polymerase alpha subunit p180 N terminal; This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam00136, pfam08996, pfam03104. This family is the N terminal of DNA polymerase alpha subunit p180 protein. The N terminal contains the catalytic region of the alpha subunit.
Pssm-ID: 463508 Cd Length: 65 Bit Score: 66.81 E-value: 1.42e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 569009877 41 LERLKKAKAGEK---YKYEVEDLTSVYEEVDEEQYSKLVQARQDDDW-IVDDDGIGYVEDGREIF 101
Cdd:pfam12254 1 LEKLKAARAGGKrrlDEYESEEDEDIYDEVDEEEYRKIVRKRLLDDDfVVDDDGEGYVDDGREDW 65
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
601-759 |
1.31e-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: 1.31e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 601 DFKEVISKKNM---KVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPywSKIGRLRRSnmPKL 677
Cdd:cd05780 35 GGNKVITWKKFdlpFVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIE--LDLGRDGSE--IKI 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 678 gSRSGFGERNATCGRMICDVEISAKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSESSYLLYLLEHIWKDARFIL 757
Cdd:cd05780 111 -QRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTY 189
|
..
gi 569009877 758 QI 759
Cdd:cd05780 190 EI 191
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
831-1011 |
3.78e-08 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 58.33 E-value: 3.78e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 831 TNKYKKG-RKKATYAGGLVLDPKVGF-----YDKFILLLDFNSLYPSIIQEFNICFTTV--QRVTSEVQkATEDEEQEQI 902
Cdd:PHA03334 620 PEKYARDcRQKIKLKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIvdPDCTARVR-GWVVFDWKKI 698
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 903 PE-LPDPNLEMGIL---PRE-------------IRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGclg 965
Cdd:PHA03334 699 DRgFGKATLMYTILrtkPEEpswrrfttyttssLNHYLSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYG--- 774
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 569009877 966 fsysrfyAKPLAA--LVTYKGREILMHTKDMVQKM-NLEVIYGDTDSIM 1011
Cdd:PHA03334 775 -------VAPHACqhLITTLGRHKIKLVEEFIKKEpGMTVNYGDTDSVM 816
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
587-686 |
4.98e-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: 4.98e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 587 FCVVSKPKDCIF------PCDFKEVISKKNMkveiaaTERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKV 660
Cdd:cd05785 26 FSNPDRGDDRIIivalrdNRGWEEVLHAEDA------AEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGV 99
|
90 100
....*....|....*....|....*..
gi 569009877 661 PY-WSKIGRLRRSNmpklGSRSGFGER 686
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; ... |
630-672 |
6.97e-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: 6.97e-06
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 569009877 630 VHKIDPDILVGHNICSFELEVLLQRINECKVPYWSKIGRLRRS 672
Cdd:cd05777 82 VQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNI 124
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
600-696 |
9.23e-05 |
|
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: 9.23e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 600 CDFKEVI------SKKNMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYwsKIGRLRRSn 673
Cdd:cd05784 26 EGQERVLmvgdpeDDAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPL--RLGRGGSP- 102
|
90 100
....*....|....*....|....
gi 569009877 674 mPKLGSRSGFGERNATC-GRMICD 696
Cdd:cd05784 103 -LNWRQSGKPGQGFLSLpGRVVLD 125
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
581-760 |
1.61e-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: 41.84 E-value: 1.61e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 581 PPFQTHFCVVSKPKDcifPCDFKEVISK-KNMKVEIAATERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRIN-EC 658
Cdd:cd05778 45 DANKVGVIIVDELKS---NASNGRIRSGlSGIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAaLG 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 659 KVPYWSKIGRLRRSNMPKLGSRSgfGERNAT-------CGRMICDV------EISakeLIhckSYHLSELVQQILKtERI 725
Cdd:cd05778 122 IDDLLDEISRVPSDSNGKFGDRD--DEWGYThtsgikiVGRHILNVwrlmrsELA---LT---NYTLENVVYHVLH-QRI 192
|
170 180 190
....*....|....*....|....*....|....*...
gi 569009877 726 -VIPTENIRNMYSES--SYLLYLLEHIWKDARFILQIM 760
Cdd:cd05778 193 pLYSNKTLTEWYKSGsaSERWRVLEYYLKRVRLNLEIL 230
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
619-759 |
2.19e-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: 2.19e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 619 ERTLIGFFLAKVHKIDPDILVGHNICSFELEVLLQRINECKVPYwsKIGRlRRSNMPklgSRSGFGERNATcGRMICDVE 698
Cdd:cd05781 48 DRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKL--DVGR-RGGSEP---STGVYGHYSIT-GRLNVDLY 120
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 569009877 699 ISAKELIHCKS---YHLSELVQQILKTERIVIPTENIRNMYSESSYLLYLLEHIWKDARFILQI 759
Cdd:cd05781 121 DFAEEIPEVKVktlENVAEYLGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGL 184
|
|
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
927-1010 |
5.58e-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: 5.58e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569009877 927 KQVKQLMKQQDL-----NPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKDMVQKMN-- 999
Cdd:cd05535 247 KKLEAAKAAGDAaeikeAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELVEQIGrp 326
|
90
....*....|.
gi 569009877 1000 LEViygDTDSI 1010
Cdd:cd05535 327 LEL---DTDGI 334
|
|
| |
