|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
56-1206 |
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: 1522.29 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 56 EVEDFTGVYEEVDEEQYSKLVQARQDDDWIVDDDGIGYVEDGREIFDDDLEDDALDADeKGKDGKARNKDKRNVKKlaVT 135
Cdd:TIGR00592 1 MVEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILDLDKD-DGSAAEAKKKDKENHKK--VT 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 136 KPNNIKSMFIACAGKKTADKAVDLSKDGLLGDILQDLN-TETPQ--ITPPPVMILKKKRSIGAS---PNPFSVHTATAVP 209
Cdd:TIGR00592 78 KPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVVD 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 210 SGKIASPVSRK---EPPLTPVPLKRAEFAGDDVQVE-STEEEQESGAME--FEDGDF----DE-PMEVEEVDL-EPMAAK 277
Cdd:TIGR00592 158 IVKKAIPVSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDEnPADEEIMIStTPVIAK 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 278 AWDKESEPAEEVKQEADSGKGTV-SYLGSFLPDVSC----WD-IDQEGDSsfsvQEVQVDSSHLPLVKGADEeQVFHFYW 351
Cdd:TIGR00592 238 QWDYESEPEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD----VEITVNGDNFDLVYLADR-QVFQFYW 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 352 lDAYEDQYNQPGVVFLFGKvwieSAEtHVSCCVMVKNIERTLYFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKY 431
Cdd:TIGR00592 313 -DAYEDPAEKLGVVLLFGR----DVD-HVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGY 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 432 KIMKFKSK--------------------------------AEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCW 479
Cdd:TIGR00592 387 KKEKFRAKpiakkyefeapdidapysseylevtyelgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCW 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 480 LEVKSPQLLNQPV-SWCKVEAMALKPDLVNVIKDVSPPPLVVMAFSMKtMQNAKNHQNEIIAMAALVHHSFALDKAAPKP 558
Cdd:TIGR00592 467 LAVKGPDELEYPRrSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEP 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 559 PFQSHFCVVSKPKDCIFPYAFK-EVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKA 637
Cdd:TIGR00592 546 PYDVHPCVGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKI 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 638 PHWSKIGRLKRSnmPKLGGRsgFGERnaTCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESS 717
Cdd:TIGR00592 626 PTWSKIGRLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESS 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 718 QLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQKL 797
Cdd:TIGR00592 700 SLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKL 778
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 798 GDEDEEIDGdtnkYKKGrKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvaseaQKVTEDgeqe 877
Cdd:TIGR00592 779 GDEDEEIDG----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDED---- 843
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 878 QIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQqDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALV 957
Cdd:TIGR00592 844 ELPELPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALV 922
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 958 TYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYA 1037
Cdd:TIGR00592 923 TAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYA 1002
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1038 ALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEIN 1117
Cdd:TIGR00592 1003 AIKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVIN 1082
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1118 KALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQ-KQDNLTIDTQYYLAQQ 1196
Cdd:TIGR00592 1083 KQLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEHQ 1162
|
1210
....*....|
gi 1806646257 1197 IHPVVARICE 1206
Cdd:TIGR00592 1163 IHPVVLRILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
813-1223 |
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: 732.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 813 KGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAseaqkvtEDGEQEQIPELPDPSLEMGIL 892
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRAD-------PDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 893 PREIRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMV 972
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 973 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPtsDGNYVTK 1052
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1053 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKS 1132
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1133 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGID 1212
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 1806646257 1213 AVLIATWLGLD 1223
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 ... |
755-1208 |
2.77e-171 |
|
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: 519.09 E-value: 2.77e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 755 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKLGDEDeeidgdtnkykkgrkkaAYAGGLVLDPKVGFYD 834
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 835 KFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPD------PSLEMGILPREIRKLVERRKQVKQ 908
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 909 LMKQqDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM---NLEVIYGDTD 985
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 986 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyvtKQELKGLDIVRR 1063
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1064 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWIN 1143
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1806646257 1144 SQGGRKVKAGDTVSYVICQDGS---NLTASQRAYAPEqLQKQDNLTIDTQYYLAQQIHPVVARICEPI 1208
Cdd:pfam00136 373 KRNGEAPEVGDRIPYVIVKAAKglkNLLIYERAEDPE-YVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
516-992 |
3.34e-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: 365.31 E-value: 3.34e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 516 PPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQsHFCVVSKPKDCIfpyafkeviekKNVKVEVAAT 595
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 596 ERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRS----NMPKLGGRSGFGERNAT---CG 668
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripNKKPLFGSKSFGLSDIKvyiKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 669 RMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSES-SQLLYLLEHTWKDAKFILQIMCELNVLPLAL 747
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNyEERDELLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 748 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqklgdedEEIDGDTNKYKKgRKKAAYAGGLVLD 827
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSK--------------ELYDFKGSEPDL-KKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 828 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKV-TEDGEQEQIPELPDP--------SLEMGILPREIRK 898
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGdLIIPEDLLTIKYEKGnkyrfvkkNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 899 LVERRKQVKQLMKQ-QDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM-- 975
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 1806646257 976 ---NLEVIYGDTDSIMINTN 992
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
468-1209 |
2.24e-112 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 373.78 E-value: 2.24e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 468 FLMNRKIKGPCWLEVkspqllnQPVSWCKVEAMALKPDLVNVIKDVsPPPLVVMAF----SMKTMQNAKNHQNEIIAMAa 543
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 544 lVHHSFALDKAapkppfqshFCVVSKPKDcifpyafkeviekknVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGF 623
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 624 ELEVLLQRINVCKAPhwSKIGRLKRSnmPKLGGRSGFGERNATcGRMICDV-EISAKELIRCKSYHLSELVQQILKTERV 702
Cdd:COG0417 244 DLPYLQKRAERLGIP--LDLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 703 VIPMENIQNMYSESsqLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 782
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 783 IVPDKqifrkpqqklgdedEEIDGDtnkykkgrkkaAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQR 862
Cdd:COG0417 397 LAPNK--------------GEIKGE-----------AYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETLVE 450
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 863 VASEaqkvtEDGEQEQIPELP-----DPSlemGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSM 937
Cdd:COG0417 451 GGEE-----PCGDEDVAPGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 938 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KLYKL 1016
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1017 LEIDIDGVFKSllllkkkkyaalVVEPTSDGNY--VTKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 1091
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1092 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVIcqdgsnLTASQ 1171
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI------TKGGG 738
|
730 740 750
....*....|....*....|....*....|....*...
gi 1806646257 1172 RAYaPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPID 1209
Cdd:COG0417 739 RVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
590-1222 |
1.74e-76 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 271.34 E-value: 1.74e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 590 VEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRLKRSNMPKL-GGRSGFGERNATcG 668
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIP--LRLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 669 RMICD-VEISAKELIRCKSYHLSELVQQIL----KTERVVIPMENIQNMYSESSQLLylLEHTWKDAKFILQIMCELNVL 743
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSLEYVSQRLLgegkAIDDPYDRMDEIDRRFAEDKPAL--ARYNLKDCELVTRIFEKTKLL 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 744 PLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDkqifrkpqqkLGDEDEEidgdtnkykkgrkkaAYAGG 823
Cdd:PRK05762 352 PFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPN----------LGERPGE---------------ASPGG 404
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 824 LVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTvqRVASEAQKvtedgEQEQIPELPDP--SLEMGILPREIRKLVE 901
Cdd:PRK05762 405 YVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDG--LVEGLAQP-----PEESVAGFLGArfSREKHFLPEIVERLWE 476
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 902 RRKQVKQLMKQqdlnpdlilqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIY 981
Cdd:PRK05762 477 GRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIY 544
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 982 GDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDGVFK--------SLLLLKKKKYAALVV 1041
Cdd:PRK05762 545 GDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSKKRYAGLIQ 624
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1042 EPTSDGNYVtkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQFEINKALT 1121
Cdd:PRK05762 625 EGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EKLVYRKRLR 692
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1122 KDPQDYpDKKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGSnltasqrayapeqlQKQDNLT--IDTQYYLA 1194
Cdd:PRK05762 693 RPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNGP--------------EPLEYRKspIDYDYYIE 757
|
650 660
....*....|....*....|....*...
gi 1806646257 1195 QQIHPVVARICEPIDGIDAVLIATWLGL 1222
Cdd:PRK05762 758 KQLQPVADRILPFFGDDFATLKTGQLGL 785
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1246-1436 |
2.55e-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: 244.82 E-value: 2.55e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1246 AQLTDEEKYRDCERFKCPCPTCGTENIYDNVFDGS-GTDMEPSLYRCSNidCKASPLTFtvQLSNKLIMDIRRFIKKYYD 1324
Cdd:pfam08996 1 SQISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1325 GWLICEEPTCRNRTRHLPLQFSRTgpLCPACmKATLQPEYSDKSLYTQLCFYRYIFDAECALEKLTTDHEKDKLKKQFFT 1404
Cdd:pfam08996 77 GWLVCDDPTCGNRTRQMSVYGKRC--LGPGC-KGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLALAE 153
|
170 180 190
....*....|....*....|....*....|..
gi 1806646257 1405 pKVLQDYRKLKNTAEQFLSRSGYSEVNLSKLF 1436
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 ... |
56-1206 |
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: 1522.29 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 56 EVEDFTGVYEEVDEEQYSKLVQARQDDDWIVDDDGIGYVEDGREIFDDDLEDDALDADeKGKDGKARNKDKRNVKKlaVT 135
Cdd:TIGR00592 1 MVEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILDLDKD-DGSAAEAKKKDKENHKK--VT 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 136 KPNNIKSMFIACAGKKTADKAVDLSKDGLLGDILQDLN-TETPQ--ITPPPVMILKKKRSIGAS---PNPFSVHTATAVP 209
Cdd:TIGR00592 78 KPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVVD 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 210 SGKIASPVSRK---EPPLTPVPLKRAEFAGDDVQVE-STEEEQESGAME--FEDGDF----DE-PMEVEEVDL-EPMAAK 277
Cdd:TIGR00592 158 IVKKAIPVSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDEnPADEEIMIStTPVIAK 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 278 AWDKESEPAEEVKQEADSGKGTV-SYLGSFLPDVSC----WD-IDQEGDSsfsvQEVQVDSSHLPLVKGADEeQVFHFYW 351
Cdd:TIGR00592 238 QWDYESEPEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD----VEITVNGDNFDLVYLADR-QVFQFYW 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 352 lDAYEDQYNQPGVVFLFGKvwieSAEtHVSCCVMVKNIERTLYFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKY 431
Cdd:TIGR00592 313 -DAYEDPAEKLGVVLLFGR----DVD-HVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGY 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 432 KIMKFKSK--------------------------------AEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCW 479
Cdd:TIGR00592 387 KKEKFRAKpiakkyefeapdidapysseylevtyelgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCW 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 480 LEVKSPQLLNQPV-SWCKVEAMALKPDLVNVIKDVSPPPLVVMAFSMKtMQNAKNHQNEIIAMAALVHHSFALDKAAPKP 558
Cdd:TIGR00592 467 LAVKGPDELEYPRrSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEP 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 559 PFQSHFCVVSKPKDCIFPYAFK-EVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKA 637
Cdd:TIGR00592 546 PYDVHPCVGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKI 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 638 PHWSKIGRLKRSnmPKLGGRsgFGERnaTCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESS 717
Cdd:TIGR00592 626 PTWSKIGRLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESS 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 718 QLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQKL 797
Cdd:TIGR00592 700 SLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKL 778
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 798 GDEDEEIDGdtnkYKKGrKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvaseaQKVTEDgeqe 877
Cdd:TIGR00592 779 GDEDEEIDG----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDED---- 843
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 878 QIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQqDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALV 957
Cdd:TIGR00592 844 ELPELPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALV 922
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 958 TYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYA 1037
Cdd:TIGR00592 923 TAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYA 1002
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1038 ALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEIN 1117
Cdd:TIGR00592 1003 AIKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVIN 1082
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1118 KALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQ-KQDNLTIDTQYYLAQQ 1196
Cdd:TIGR00592 1083 KQLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEHQ 1162
|
1210
....*....|
gi 1806646257 1197 IHPVVARICE 1206
Cdd:TIGR00592 1163 IHPVVLRILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
813-1223 |
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: 732.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 813 KGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAseaqkvtEDGEQEQIPELPDPSLEMGIL 892
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRAD-------PDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 893 PREIRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMV 972
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 973 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPtsDGNYVTK 1052
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1053 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKS 1132
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1133 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGID 1212
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 1806646257 1213 AVLIATWLGLD 1223
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 ... |
755-1208 |
2.77e-171 |
|
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: 519.09 E-value: 2.77e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 755 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKLGDEDeeidgdtnkykkgrkkaAYAGGLVLDPKVGFYD 834
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 835 KFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPD------PSLEMGILPREIRKLVERRKQVKQ 908
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 909 LMKQqDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM---NLEVIYGDTD 985
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 986 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyvtKQELKGLDIVRR 1063
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1064 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWIN 1143
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1806646257 1144 SQGGRKVKAGDTVSYVICQDGS---NLTASQRAYAPEqLQKQDNLTIDTQYYLAQQIHPVVARICEPI 1208
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 ... |
516-748 |
5.58e-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: 368.86 E-value: 5.58e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 516 PPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVSKPKDC-IFPYAFKEVIEKKNVKVEVAA 594
Cdd:cd05776 1 PPLTVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRsPPPDLFEKNAKKKKTKVRIFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 595 TERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDV 674
Cdd:cd05776 81 NERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDT 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1806646257 675 EISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQIMCELNVLPLALQ 748
Cdd:cd05776 161 YLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLNILPLTKQ 234
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
516-992 |
3.34e-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: 365.31 E-value: 3.34e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 516 PPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQsHFCVVSKPKDCIfpyafkeviekKNVKVEVAAT 595
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 596 ERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRS----NMPKLGGRSGFGERNAT---CG 668
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripNKKPLFGSKSFGLSDIKvyiKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 669 RMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSES-SQLLYLLEHTWKDAKFILQIMCELNVLPLAL 747
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNyEERDELLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 748 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqklgdedEEIDGDTNKYKKgRKKAAYAGGLVLD 827
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSK--------------ELYDFKGSEPDL-KKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 828 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKV-TEDGEQEQIPELPDP--------SLEMGILPREIRK 898
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGdLIIPEDLLTIKYEKGnkyrfvkkNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 899 LVERRKQVKQLMKQ-QDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM-- 975
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 1806646257 976 ---NLEVIYGDTDSIMINTN 992
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
468-1209 |
2.24e-112 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 373.78 E-value: 2.24e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 468 FLMNRKIKGPCWLEVkspqllnQPVSWCKVEAMALKPDLVNVIKDVsPPPLVVMAF----SMKTMQNAKNHQNEIIAMAa 543
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 544 lVHHSFALDKAapkppfqshFCVVSKPKDcifpyafkeviekknVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGF 623
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 624 ELEVLLQRINVCKAPhwSKIGRLKRSnmPKLGGRSGFGERNATcGRMICDV-EISAKELIRCKSYHLSELVQQILKTERV 702
Cdd:COG0417 244 DLPYLQKRAERLGIP--LDLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 703 VIPMENIQNMYSESsqLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 782
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 783 IVPDKqifrkpqqklgdedEEIDGDtnkykkgrkkaAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQR 862
Cdd:COG0417 397 LAPNK--------------GEIKGE-----------AYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETLVE 450
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 863 VASEaqkvtEDGEQEQIPELP-----DPSlemGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSM 937
Cdd:COG0417 451 GGEE-----PCGDEDVAPGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 938 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KLYKL 1016
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1017 LEIDIDGVFKSllllkkkkyaalVVEPTSDGNY--VTKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 1091
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1092 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVIcqdgsnLTASQ 1171
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI------TKGGG 738
|
730 740 750
....*....|....*....|....*....|....*...
gi 1806646257 1172 RAYaPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPID 1209
Cdd:COG0417 739 RVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
590-1222 |
1.74e-76 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 271.34 E-value: 1.74e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 590 VEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRLKRSNMPKL-GGRSGFGERNATcG 668
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIP--LRLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 669 RMICD-VEISAKELIRCKSYHLSELVQQIL----KTERVVIPMENIQNMYSESSQLLylLEHTWKDAKFILQIMCELNVL 743
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSLEYVSQRLLgegkAIDDPYDRMDEIDRRFAEDKPAL--ARYNLKDCELVTRIFEKTKLL 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 744 PLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDkqifrkpqqkLGDEDEEidgdtnkykkgrkkaAYAGG 823
Cdd:PRK05762 352 PFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPN----------LGERPGE---------------ASPGG 404
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 824 LVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTvqRVASEAQKvtedgEQEQIPELPDP--SLEMGILPREIRKLVE 901
Cdd:PRK05762 405 YVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDG--LVEGLAQP-----PEESVAGFLGArfSREKHFLPEIVERLWE 476
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 902 RRKQVKQLMKQqdlnpdlilqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIY 981
Cdd:PRK05762 477 GRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIY 544
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 982 GDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDGVFK--------SLLLLKKKKYAALVV 1041
Cdd:PRK05762 545 GDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSKKRYAGLIQ 624
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1042 EPTSDGNYVtkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQFEINKALT 1121
Cdd:PRK05762 625 EGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EKLVYRKRLR 692
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1122 KDPQDYpDKKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGSnltasqrayapeqlQKQDNLT--IDTQYYLA 1194
Cdd:PRK05762 693 RPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNGP--------------EPLEYRKspIDYDYYIE 757
|
650 660
....*....|....*....|....*...
gi 1806646257 1195 QQIHPVVARICEPIDGIDAVLIATWLGL 1222
Cdd:PRK05762 758 KQLQPVADRILPFFGDDFATLKTGQLGL 785
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1246-1436 |
2.55e-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: 244.82 E-value: 2.55e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1246 AQLTDEEKYRDCERFKCPCPTCGTENIYDNVFDGS-GTDMEPSLYRCSNidCKASPLTFtvQLSNKLIMDIRRFIKKYYD 1324
Cdd:pfam08996 1 SQISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1325 GWLICEEPTCRNRTRHLPLQFSRTgpLCPACmKATLQPEYSDKSLYTQLCFYRYIFDAECALEKLTTDHEKDKLKKQFFT 1404
Cdd:pfam08996 77 GWLVCDDPTCGNRTRQMSVYGKRC--LGPGC-KGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLALAE 153
|
170 180 190
....*....|....*....|....*....|..
gi 1806646257 1405 pKVLQDYRKLKNTAEQFLSRSGYSEVNLSKLF 1436
Cdd:pfam08996 154 -QNRELFKTLKSVVDKYLDKCGRRWVNLSSLF 184
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
818-1204 |
3.69e-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: 244.20 E-value: 3.69e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 818 AAYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPDpslemGILPREIR 897
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVGFRSPKDRK-----GLLPRILE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 898 KLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNL 977
Cdd:cd00145 75 ELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGA 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 978 EVIYGDTDSIMINTN-STNLEEVFKLGNKVKSEVNKlYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyvtKQELK 1056
Cdd:cd00145 155 RVIYGDTDSIFVSLPkMGTKEDAIKEGREILQELAD-EHLLELEFEKVYLPFFLGKKKRYAGLDIWKGQDEG---KIDIK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1057 GLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigenvlngsvpvsqfeinkaltkdpqdypdkkslphv 1136
Cdd:cd00145 231 GLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL--------------------------------------- 271
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1806646257 1137 hvalwinsqggrkvkagDTVSYVICQDGSNLTASQRAYAPEQLQkQDNLTIDTQYYLAQQIHPVVARI 1204
Cdd:cd00145 272 -----------------DKVKYVVTRGGKGVPDYERADPPLEDL-DKRHRIDYEYYLERLLQPPLERI 321
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
819-1206 |
3.84e-68 |
|
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: 234.53 E-value: 3.84e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 819 AYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQRvaseaqkvteDGEQEQIPELP-------DPSlemGI 891
Cdd:cd05536 3 SYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVR----------EGCEDCDVEPQvghkfrkDPP---GF 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 892 LPREIRKLVERRKQVKQLMKQ-QDLNPDLILqYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKE 970
Cdd:cd05536 69 IPSVLEDLLEERRRIKEKMKKlDPESEEYKL-LDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIK 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 971 MVQKMNLEVIYGDTDSIM--INTNSTNLEEVFKLGNKVKSEVNklyklLEIDIDGVFKSLLLLKKKKYAALvvepTSDGN 1048
Cdd:cd05536 148 IAEEKGFKVIYGDTDSLFvkIDGADAVKKKVKKLLKYINEELP-----LELEIEKFYKRGFFVTKKRYAGL----TEDGK 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1049 YVTkqelKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYp 1128
Cdd:cd05536 219 IDV----VGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVK----EVIEKLKRGEVPPEKLVIWKQLTKDLSEY- 289
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1806646257 1129 dKKSLPHVHVALWInSQGGRKVKAGDTVSYVICQDGSNLtaSQRAYAPEQLQKQDNltIDTQYYLAQQIHPVVARICE 1206
Cdd:cd05536 290 -KATGPHVAAAKKL-AKRGYKVRPGTKIGYVIVKGSGKI--SDRAYPYDMVDEKHK--YDAEYYIDNQVLPAVLRILE 361
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
820-1208 |
1.31e-62 |
|
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: 219.44 E-value: 1.31e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 820 YAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRvASEAQKVTEdgeqEQIPELPD------PSLEMGILP 893
Cdd:cd05533 3 YEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLN-KNTAKKLPP----EDYIKTPNgdyfvkSSVRKGLLP 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 894 REIRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQ 973
Cdd:cd05533 78 EILEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVE 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 974 ---------KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGVFKSLLLLKKKKYAALVVep 1043
Cdd:cd05533 157 ekytkangySHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFiKPIKLEFEKVYFPYLLINKKRYAGLLW-- 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1044 TSDGNYvTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIqKRLIeigENVLNGSVPVSQFEINKALTKD 1123
Cdd:cd05533 235 TNPDKH-DKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFV-KGVI---SDLLQNKIDISLLVITKALTKT 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1124 PQDYPDKksLPHVHVALWINSQG-GRKVKAGDTVSYVICQDGSNLTASQRA----YAPEqlqkqDNLTIDTQYYLAQQIH 1198
Cdd:cd05533 310 ADDYAGK--QAHVELAERMRKRDpGSAPNVGDRVPYVIIKGAKGAKAYEKAedpiYVLE-----NNIPIDTQYYLENQLS 382
|
410
....*....|
gi 1806646257 1199 PVVARICEPI 1208
Cdd:cd05533 383 KPLLRIFEPI 392
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
377-692 |
1.21e-61 |
|
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: 214.59 E-value: 1.21e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 377 ETHVSCCVMVKNIERTLYFLPREmkidlntGKETGTPIS-MKDVYEEFD----EKIATKYKIMKFKSKA----------- 440
Cdd:pfam03104 3 DEGVSVCVNVFGFKPYFYCLAPD-------GKELEEVIEeIKELYEGLDkiekIELKLKKSLYGYEEDPvpylkvsfanp 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 441 -EMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVK-SPQLLNQPVSWCKVEAMALKPDLVNVIKDVSPPPL 518
Cdd:pfam03104 76 rPLLKIRKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKvYPFRAEGRISNCDVEIDCDSPDLISVPFEKEWPPL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 519 VVMAFSMKTMQ------NAKNHQNEIIAMAALVHhsfalDKAAPKPPFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEV 592
Cdd:pfam03104 156 RVLSFDIECTSlpgkfpDAENVKDPIIQISCMLD-----GQGEPEPEPRFLFTLRECDSEDIEDFEYTPKPIYPGVKVFE 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 593 AATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRsNMPKLGGRSGFG----ERNATCG 668
Cdd:pfam03104 231 FPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNR-GGRSKVREIGFGtrsyEKVKISG 309
|
330 340
....*....|....*....|....
gi 1806646257 669 RMICDVEISAKELIRCKSYHLSEL 692
Cdd:pfam03104 310 RLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
468-1208 |
1.73e-61 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 230.30 E-value: 1.73e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 468 FLMNRKIKGPCWLEVKSPQ----LLNQPVSWCKVEaMALKPDLVNVIKDV----SPPPLVVMAFSM-------KTMQNAK 532
Cdd:PTZ00166 207 FLIDNNITGGSWLTLPKGKykirPPKKKTSTCQIE-VDCSYEDLIPLPPEgeylTIAPLRILSFDIeciklkgLGFPEAE 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 533 NhqNEIIAMAALVHhsfaldkaapkppfqshfcVVSKPKDCI--FPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKI 610
Cdd:PTZ00166 286 N--DPVIQISSVVT-------------------NQGDEEEPLtkFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAV 344
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 611 DPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSG---FGERNATC----GRMICDVeisaKELIR 683
Cdd:PTZ00166 345 DPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSskqMGTRESKEinieGRIQFDV----MDLIR 420
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 684 ----CKSYHLSELVQQILKTERVVIP---MENIQNMYSESSQLL--YLLehtwKDAKFILQIMCELNVLPLALQITNIAG 754
Cdd:PTZ00166 421 rdykLKSYSLNYVSFEFLKEQKEDVHysiISDLQNGSPETRRRIavYCL----KDAILPLRLLDKLLLIYNYVEMARVTG 496
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 755 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqifrkpqqklgdedeeidgdTNKYKKGRKKAAYAGGLVLDPKVGFYD 834
Cdd:PTZ00166 497 TPIGWLLTRGQQIKVTSQLLRKCKKLNYVIP----------------------TVKYSGGGSEEKYEGATVLEPKKGFYD 554
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 835 KFILLLDFNSLYPSIIQEFNICFTTVQRvASEAQKVTEDgeqEQIPELPD-----PSLEMGILPREIRKLVERRKQVKQL 909
Cdd:PTZ00166 555 EPIATLDFASLYPSIMIAHNLCYSTLVP-PNDANNYPED---TYVTTPTGdkfvkKEVRKGILPLIVEELIAARKKAKKE 630
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 910 MKQQDlNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYakP---LAALVTYKGREILMHTKEMVQKM---------NL 977
Cdd:PTZ00166 631 MKDEK-DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQL--PcleVSTSITSFGRQMIDKTKELVEKHytkangykhDA 707
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 978 EVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGVFKSLLLLKKKKYAALVVepTSDGNYvTKQELK 1056
Cdd:PTZ00166 708 TVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFlKPIKLEFEKVYCPYLLMNKKRYAGLLY--TNPEKY-DKIDCK 784
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1057 GLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNgsvpVSQFEINKALTKDpqDYpdKKSLPHV 1136
Cdd:PTZ00166 785 GIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRID----ISLLVITKSLGKD--DY--EGRLAHV 856
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1137 HVAlwinsqggRKVKA---------GDTVSYVICQDGSNLTASQRA----YAPEqlqkqDNLTIDTQYYLaQQIHPVVAR 1203
Cdd:PTZ00166 857 ELA--------KKLRQrdpgsapnvGDRVSYVIVKGAKGAPQYERAedplYVLE-----NNIPIDTQYYL-DQIKNPLLR 922
|
....*
gi 1806646257 1204 ICEPI 1208
Cdd:PTZ00166 923 IFEGV 927
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
824-1212 |
2.71e-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: 2.71e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 824 LVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTT-VQRVASEAQKVTEDGEQEQIPELPDPSLEM------------- 889
Cdd:cd05534 40 LVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTcLGRVEELNGGGKFGFLGVKLYLPPPPLDLLllkddvtispngv 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 890 ---------GILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYS-RFYAKPLAALVTY 959
Cdd:cd05534 120 mfvkksvrkGILPKMLEEILDTRIMVKKAMKKYKDDKKLQRILDARQLALKLLANVTYGYTAASFSgRMPCVEIADSIVQ 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 960 KGREILMHTKEMVQ---KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGVFKSLLLLKKKK 1035
Cdd:cd05534 200 TGRETLERAIELIEstpKWGAKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVTAANpSPIKLKFEKVYHPCVLVTKKR 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1036 YAALVVEPTSDGnyVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigENVLNGSVPVSQFE 1115
Cdd:cd05534 280 YVGYKYESPDQT--EPTFDAKGIETVRRDGCPAVQKILEKSLRILFETKDLSTVKSYLQRQW----SKLLQGRVSIQDFI 353
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1116 INKALTKDpqDYPDKKSLP-HVHVAL-WINSQGGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYL 1193
Cdd:cd05534 354 FAKEVRLG--TYKEGATLPaGAIVALrRMEKDPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLADPSLRLDAEYYI 431
|
410
....*....|....*....
gi 1806646257 1194 AQQIHPVVARICEPIdGID 1212
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 ... |
520-738 |
2.73e-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: 159.44 E-value: 2.73e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 520 VMAFSMKTMQNAK---NHQNEIIAMAALVhhSFALDKAAPKPPFQSHFCVVSKpkdcifpyafkevieKKNVKVEVAATE 596
Cdd:cd05160 1 VLSFDIETTPPVGgpePDRDPIICITYAD--SFDGVKVVFLLKTSTVGDDIEF---------------IDGIEVEYFADE 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 597 RTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRlkRSNMPKlggRSGFGERNATCGRMICDVEI 676
Cdd:cd05160 64 KELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYR--RSGGEK---SSGSTERIAVKGRVVFDLLA 138
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1806646257 677 SAKELIRCKSYHLSELVQQILKTERV-VIPMENIQNMysESSQLLYLLEHTWKDAKFILQIMC 738
Cdd:cd05160 139 AYKRDFKLKSYTLDAVAEELLGEGKEkVDGEIIEDAE--WEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
821-1208 |
1.35e-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: 1.35e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 821 AGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNIcfTTVQRVasEAQKvtEDGEQEQIPELPDP--SLEMGILPREIRK 898
Cdd:cd05537 4 PGGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI--DPLGLI--EGLK--APDPEDLIPGFLGArfSREKHILPDLIAR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 899 LVERRKQVKQlmkqqdlNPDLILQYdirqkALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLE 978
Cdd:cd05537 77 LWAARDEAKR-------EKNAPLSQ-----AIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQ 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 979 VIYGDTDSIMINTNST-NLEEVFKLGNKVKSEVN--------KLYKL---LEIDIDGVF--------KSLLLLKKKKYAA 1038
Cdd:cd05537 145 VIYGDTDSTFVWLGEElDAAEAQAIGKELASQINqwwaqklkEEFGLesfLEIEFETHYsrffmptiRGSDEGSKKRYAG 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1039 LVVEPTSDgnyvtKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEiGEnvLNgsvpvSQFEINK 1118
Cdd:cd05537 225 LKSTDGGD-----ELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLA-GE--LD-----ELLVYRK 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1119 ALTKDPQDYpDKKSLPHVHVALW---INSQGGRKvKAGDTVSYVICQDGsnltasqrayaPEQLQkQDNLTIDTQYYLAQ 1195
Cdd:cd05537 292 RLRRPLSEY-TKNVPPHVQAARLadqINRELGRP-RQYQWIEYVITVNG-----------PEPLE-YRTSPLDYQHYIDK 357
|
410
....*....|...
gi 1806646257 1196 QIHPvvarICEPI 1208
Cdd:cd05537 358 QLKP----IADSI 366
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
813-1193 |
8.98e-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: 8.98e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 813 KGRKkaaYAGGLVLDPKVG-FYDkfILLLDFNSLYPSIIQEFNICFTTVQrvaseaqKVTEDGEQEQIPELPD------- 884
Cdd:cd05530 9 KGKK---YRGAIVLEPPPGiFFN--VVVLDFASLYPSIIKVWNLSYETVN-------CPHCECKTNEVPEVGHwvckkrp 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 885 --PSLEMGILpreiRKLveRRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGR 962
Cdd:cd05530 77 giTSQIIGLL----RDL--RVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGR 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 963 EILMHTKEMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDGVFKsllllkkkkyaaLVV 1041
Cdd:cd05530 151 YIITSTIKKARELGLKVLYGDTDSLFLwNPPQEQLEDLVE---WVEKELG-----LDLELDKEYR------------YVV 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1042 EPTSDGNY--VTKQ---ELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRD---TIVENIQKRLIEIGENVLNGSVPVSQ 1113
Cdd:cd05530 211 FSGLKKNYlgVTKDgsvDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPEdfeKAREKIRDIVKGVYKRLKKKEYTLDQ 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1114 FEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTASQRAYAPEqlqkqdnltIDTQYYL 1193
Cdd:cd05530 291 LAFKVMLSKPPEEY-TKNTPQHVKAARQLEKY-GRNVEAGDIISYVKVKGKEGVKPVQLARLDE---------VDVEKYV 359
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
800-1193 |
1.09e-41 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 165.63 E-value: 1.09e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 800 EDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvaseaqkvtEDGEQEQI 879
Cdd:PRK05761 387 EDILRLDHEVYKKAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETV-----------RIPECKCH 454
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 880 PELPDPSL------EMGILPREIRKLV--ERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAK 951
Cdd:PRK05761 455 YDDEVPELghsvcdDRPGLTSVLVGLLrdFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRI 534
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 952 PLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDGVFKslll 1030
Cdd:PRK05761 535 EVAESITALGREILLSTKKKAEELGLKVLYGDTDSLFVwGPTKESLEELIK---EIEERTG-----IDLEVDKTYD---- 602
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1031 lkkkkyaaLVVEPTSDGNY--VTKQ---ELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQK---RLIEIGE 1102
Cdd:PRK05761 603 --------WVAFSGLKKNYfgVLKDgkvKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEKVKDEiedVLKRYYE 674
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1103 NVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQGGrKVKAGDTVSYVIcqdgsnlTASQRAYAPEQLQKQ 1182
Cdd:PRK05761 675 KLRAKDYPLDELAIRVRLSKPLDEY-TKNTPQHVKAALQLRDYGV-EVSPGDIISYVK-------VDDKRGVKPVQLAKL 745
|
410
....*....|.
gi 1806646257 1183 DnlTIDTQYYL 1193
Cdd:PRK05761 746 S--EIDVEKYI 754
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
818-1211 |
1.26e-30 |
|
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: 124.76 E-value: 1.26e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 818 AAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQrvaseaqkvTEDGEQEQIPELPDPSL--EMGILPRE 895
Cdd:cd05531 3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETIN---------CRCCECRDHVYLGHRIClkRRGFLPEV 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 896 IRKLVERRKQVKQLMKQQDlnpdlilQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM 975
Cdd:cd05531 73 LEPLLERRLEYKRLKKEED-------PYAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEM 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 976 NLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKsevnklyklLEIDIDGVFKsllllkkkkyaALVVEPTSDG-----NYV 1050
Cdd:cd05531 146 GFRVLHGIVDSLWIQGRGDIEELAREIEERTG---------IPLKLEGHYD-----------WIVFLPERDGlgapnRYF 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1051 TKQE-----LKGLDIVRRDWCDLAKDTGNFVIgQILSdQSRDtiVENIQKRLIEIgENVLNGSV------PVSQFEINKA 1119
Cdd:cd05531 206 GRLSdgemkVRGIELRRRDTPPFVKKFQEEAL-DILA-SAKT--PEELLKLREEA-LDLFRRYLqrlregDLEDLIIEKK 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1120 LTKDPQDYpdkKSLPHvHVALWINSQgGRKVKAGDTVSYVIcQDGSNLTASqrayapeqlqKQDNLTIDTQYYLAQQIHP 1199
Cdd:cd05531 281 ISKRSSEY---KVLAS-TALKALRAK-GVSVVPGMKIEYIV-RDGKRPVPD----------LGNDEGYDTKYYRELLERA 344
|
410
....*....|..
gi 1806646257 1200 VvaricEPIDGI 1211
Cdd:cd05531 345 A-----EELLFP 351
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
811-1134 |
5.94e-21 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 100.09 E-value: 5.94e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 811 YKKGRKKAA--YAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAS-----EAQKVTEDGEQ------- 876
Cdd:PHA03036 519 LVRSETKNKfpYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVndnrlEAEINKQELRRkypypry 598
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 877 ---EQIPELPDPSLEM--------GILPREIRKLVERRKQVKQLMKQQDLNPDLILqYDIRQKALKLTANSMYGCLGFSY 945
Cdd:PHA03036 599 iyvHCEPRSPDLVSEIavfdrrieGIIPKLLKTFLEERARYKKLLKEATSSVEKAI-YDSMQYTYKIVANSVYGLMGFRN 677
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 946 SRFYAKPLAALVTYKGREILMHTKEMV--------------------------------------QKMNLEVIYGDTDSI 987
Cdd:PHA03036 678 SALYSYASAKSCTAIGRNMIKYLNSVLngsklingklilancpinpffkddrsidtnydtnlpveYNFTFRSVYGDTDSV 757
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 988 MINTNSTNLEEVFKLGNKVKSEVNK--LYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRRDW 1065
Cdd:PHA03036 758 FLEINTKDVDKSIKIAKELERIINEkvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVPERVNKGTSETRRDV 837
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1806646257 1066 CDLAKdtgnfvigqilsdqsrdTIVENIQKRLIEIGENVLNGSVPVSqFEINKALTKDPQDYPDKKSLP 1134
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, ... |
841-1203 |
1.01e-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: 77.53 E-value: 1.01e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 841 DFNSLYPSIIQEFNICfttvqrVASEaqkvtedgeqeqipelpdpslEMGILPREIRKLVERRKQVKQLMKQQDLnPDLI 920
Cdd:cd05538 23 DVASLYPSIMLAYRIC------PARD---------------------SLGIFLALLKYLVELRLAAKESARAAAR-PAER 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 921 LQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMI---NTNSTNLE 997
Cdd:cd05538 75 DAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFippNGVDTEDE 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 998 EvfklgNKVKSEVNK-LYKLLEIDIDGVFKSLLLLKKKKYAALvveptsdgNYVTKQELKGLDIVRRDWCDLAKDTGNFV 1076
Cdd:cd05538 155 E-----EELVRELSStLPKGITVEFDGRYRAMFSYKIKNYALL--------DYDGKLIVKGSAFRSRGIEPFLREFLREA 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 1077 IGQILSDQSrdtivENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDK----KSLPhvHVALWINSQGGRKVKA 1152
Cdd:cd05538 222 VRLLLQGDG-----AGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYLQKvragKRNP--AAAYEIALARPREWRA 294
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|.
gi 1806646257 1153 GDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTiDTQYYlAQQIHPVVAR 1203
Cdd:cd05538 295 GDRVTYYVSGTGKGVSVYENCRLVADYDPAHPDE-NTGFY-AERLLQLAAR 343
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
812-990 |
3.07e-14 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 78.19 E-value: 3.07e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 812 KKGRKKAAYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQ---RVASEAQKVTEdgeqeqipELPDPSLE 888
Cdd:PHA02528 369 NKSHKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAgtfHVAPVHEYINK--------TAPRPSDE 439
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 889 M--------------GILPREIRKLVERRKQVKQLMKQQDLNPDLI---------------------------------- 920
Cdd:PHA02528 440 YscspngwmyrkdirGVIPTEIKKVFDQRKIYKKKMLAAERNAELIktiledlndsvdtpidvdyyfdfsdefkaelktl 519
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 921 ----------------LQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGR-EILMHTKEMVQKMNL------ 977
Cdd:PHA02528 520 tksslkalleecekeiALCNTIQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQlAIQWIERKMNEYLNKlckted 599
|
250
....*....|....*
gi 1806646257 978 --EVIYGDTDSIMIN 990
Cdd:PHA02528 600 edYVIYGDTDSIYVN 614
|
|
| DNA_pol_alpha_N |
pfam12254 |
DNA polymerase alpha subunit p180 N terminal; This domain family is found in eukaryotes, and ... |
41-101 |
6.27e-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: 64.88 E-value: 6.27e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1806646257 41 LERLKKAKAGEK---YKYEVEDFTGVYEEVDEEQYSKLVQARQDDDW-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 ... |
579-736 |
5.10e-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: 5.10e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 579 FKEVIEKKNV---KVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRLKRSnmPKLg 655
Cdd:cd05780 36 GNKVITWKKFdlpFVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIE--LDLGRDGSE--IKI- 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 656 GRSGFGERNATCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQ 735
Cdd:cd05780 111 QRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYE 190
|
.
gi 1806646257 736 I 736
Cdd:cd05780 191 I 191
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
808-988 |
1.23e-08 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 59.87 E-value: 1.23e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 808 TNKYKKG-RKKAAYAGGLVLDPKVGF-----YDKFILLLDFNSLYPSIIQEFNICFTTV---QRVASEAQKVTEDgeQEQ 878
Cdd:PHA03334 620 PEKYARDcRQKIKLKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIvdpDCTARVRGWVVFD--WKK 697
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 879 IPE-LPDPSLEMGIL---PRE-------------IRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGcl 941
Cdd:PHA03334 698 IDRgFGKATLMYTILrtkPEEpswrrfttyttssLNHYLSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYG-- 774
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 1806646257 942 gfsysrfyAKPLAA--LVTYKGREILMHTKEMVQKM-NLEVIYGDTDSIM 988
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; ... |
595-649 |
6.05e-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: 6.05e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1806646257 595 TERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRS 649
Cdd:cd05777 70 TEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNI 124
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
564-713 |
2.68e-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: 2.68e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 564 FCVVSKPKDCIF------PYAFKEVIEKKNvkvevaATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKA 637
Cdd:cd05785 26 FSNPDRGDDRIIivalrdNRGWEEVLHAED------AAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGV 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 638 P-HWSKIGRLKRSNmpklGGRSGFGERNA------TCGRMICDV-------EISAKELircKSYHLSELVQQ--ILKTER 701
Cdd:cd05785 100 PlAIGRDGSIPRQR----PSRFRFAERLIdyprydIPGRHVIDTyflvqlfDVSSRDL---PSYGLKAVAKHfgLASPDR 172
|
170
....*....|..
gi 1806646257 702 VVIPMENIQNMY 713
Cdd:cd05785 173 TYIDGRQIAEVW 184
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
585-631 |
2.10e-04 |
|
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Pol II is also involved in lagging strand synthesis.
Pssm-ID: 99827 [Multi-domain] Cd Length: 193 Bit Score: 44.10 E-value: 2.10e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 1806646257 585 KKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQR 631
Cdd:cd05784 40 DAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRR 86
|
|
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
904-987 |
1.30e-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: 43.05 E-value: 1.30e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 904 KQVKQLMKQQDL-----NPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMN-- 976
Cdd:cd05535 247 KKLEAAKAAGDAaeikeAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELVEQIGrp 326
|
90
....*....|.
gi 1806646257 977 LEViygDTDSI 987
Cdd:cd05535 327 LEL---DTDGI 334
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
596-736 |
1.62e-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: 41.16 E-value: 1.62e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 596 ERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRlKRSNMPKlggRSGFGERNATcGRMICDVE 675
Cdd:cd05781 48 DRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVK--LDVGR-RGGSEPS---TGVYGHYSIT-GRLNVDLY 120
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1806646257 676 ISAKEL--IRCKS-YHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQI 736
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 ... |
587-674 |
2.48e-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: 2.48e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806646257 587 NVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRinvCKAPH----WSKIGRLKRSNMPKLGGRSgfGE 662
Cdd:cd05778 72 GIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIER---AAALGiddlLDEISRVPSDSNGKFGDRD--DE 146
|
90
....*....|....*....
gi 1806646257 663 RNAT-------CGRMICDV 674
Cdd:cd05778 147 WGYThtsgikiVGRHILNV 165
|
|
| |
