|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
56-1232 |
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: 1546.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 56 EVEDLTSVYEEVDEEQYSKLVQARQDDDWIVDDDGIGYVEDGREIFDDDLEDDAldTCGE-GSDGKAHRKDRKDVKKpsV 134
Cdd:TIGR00592 1 MVEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILD--LDKDdGSAAEAKKKDKENHKK--V 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 135 TKPNNIKAMFIASAGKKTTDKTVDLSKDDLLGDILQDLN-TETPQ--IAPPPVLIPKKKRSTGAS---PNPFSVHTATAV 208
Cdd:TIGR00592 77 TKPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVV 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 209 PSGKIASPVSRK---EPPLTPVPLKRAEFAGDLAQPE-CPEDEQESGVIE--FEDGDF----DE-PMDTEEVDEEEPVTA 277
Cdd:TIGR00592 157 DIVKKAIPVSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDEnPADEEIMISTTPVIA 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 278 KIWDQESEPVEGVKHEADPETGTT-SFLDSFLPDVSC----WD-IDQKDENsfllQEVQVDSNHLPLVKGADdEQVFQFY 351
Cdd:TIGR00592 237 KQWDYESEPEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD----VEITVNGDNFDLVYLAD-RQVFQFY 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 352 WlDAYEDPYNQPGVVFLFGKvwvesAKTHVSCCVMVKNIERTLYFLPREMKIDLNTGKETATPITMKDVYEEFDSKISAK 431
Cdd:TIGR00592 312 W-DAYEDPAEKLGVVLLFGR-----DVDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALG 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 432 YKIMKFKSKIVEKNYAFEIP--DVPEKSEYLEVRYS-----AEVPQLPQNLKGETFSHVFGTNTSSLELFLMNRKIKGPC 504
Cdd:TIGR00592 386 YKKEKFRAKPIAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPC 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 505 WLEVKNPQLLNQP-ISWCKFEAMALKPDLVNVIKDVSPPPLVVMSFSMKtMQNVQNHQHEIIAMAALVHHNFPLDKAPPK 583
Cdd:TIGR00592 466 WLAVKGPDELEYPrRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPE 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 584 PPFQTHFCVVSKPKDCIFPCAFK-EVIKKKNMEVEVAATERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECK 662
Cdd:TIGR00592 545 PPYDVHPCVGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLK 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 663 VPFWSKIGRLRRSnmPKLGSRsgFGERnaTCGRMICDVEISVKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSEP 742
Cdd:TIGR00592 625 IPTWSKIGRLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSES 698
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 743 SHLLYLLEHIWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQK 822
Cdd:TIGR00592 699 SSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQK 777
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 823 PGDEDEEIDGdtnkYKKGrKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRvasetlKATEDEeq 902
Cdd:TIGR00592 778 LGDEDEEIDG----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQ------KVDEDE-- 844
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 903 eqIPELPDPNLDMGILPREIRKLVERRKQVKQLMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAAL 982
Cdd:TIGR00592 845 --LPELPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAAL 921
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 983 VTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKNEVNKLYKLLEIDIDGVFKSLLLLKKKKY 1062
Cdd:TIGR00592 922 VTAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKY 1001
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1063 AALVVEPTSDGNYITKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEI 1142
Cdd:TIGR00592 1002 AAIKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVI 1081
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1143 NKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLPATQRAYAPEQLQ-KQDNLAIDTQYYLAQ 1221
Cdd:TIGR00592 1082 NKQLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEH 1161
|
1210
....*....|.
gi 281604221 1222 QIHPVVARICE 1232
Cdd:TIGR00592 1162 QIHPVVLRILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
839-1249 |
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: 727.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 839 KGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAsetlkatEDEEQEQIPELPDPNLDMGIL 918
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRAD-------PDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 919 PREIRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMV 998
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 999 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKNEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPtsDGNYITK 1078
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1079 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKS 1158
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1159 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLPATQRAYAPEQLQKQDNLAIDTQYYLAQQIHPVVARICEPIDGID 1238
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 281604221 1239 AVLIALWLGLD 1249
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 ... |
781-1234 |
6.05e-168 |
|
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: 511.00 E-value: 6.05e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 781 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKPGDEDeeidgdtnkykkgrkkaAYAGGLVLDPKVGFYD 860
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 861 KFILLLDFNSLYPSIIQEFNICFTTVQRVASETLKATEDEEQEQIPELPD------PNLDMGILPREIRKLVERRKQVKQ 934
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 935 LMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM---NLEVIYGDTD 1011
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1012 SIMINTNSTNLEEVFKLGNKVKNEVNK-LYKL-LEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyitKQELKGLDIVRR 1089
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1090 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWIN 1169
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 281604221 1170 SQGGRKVKAGDTVSYVICQDGS---NLPATQRAYAPEqLQKQDNLAIDTQYYLAQQIHPVVARICEPI 1234
Cdd:pfam00136 373 KRNGEAPEVGDRIPYVIVKAAKglkNLLIYERAEDPE-YVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
494-1235 |
1.12e-111 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 372.24 E-value: 1.12e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 494 FLMNRKIKGPCWLEVknpqllnQPISWCKFEAMALKPDLVNVIKDVsPPPLVVMSF----SMKTMQNVQNHQHEIIAMAa 569
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 570 lVHHNFPLDKAppkppfqthFCVVSKPKDcifpcafkevikkknMEVEVAATERTLLGFFLAKVHKLDPDILVGHNICGF 649
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 650 ELEVLLQRINECKVPFwsKIGRLRRSnmPKLGSRSGFGERNATcGRMICDVEISVKE-LIHCKSYHLSELVQQILKTERI 728
Cdd:COG0417 244 DLPYLQKRAERLGIPL--DLGRDGSE--PSWREHGGQGFASIP-GRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 729 VIPTENIRNMYSEPshLLYLLEHIWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 808
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 809 IVPDKqifrkpqqkpgdedEEIDGDtnkykkgrkkaAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqr 888
Cdd:COG0417 397 LAPNK--------------GEIKGE-----------AYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETL-- 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 889 vaSETLKATEDEEQEqIPELP-----DPNldmGILPREIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSM 963
Cdd:COG0417 449 --VEGGEEPCGDEDV-APGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 964 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKNEVN-KLYKL 1042
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1043 LEIDIDGVFKSllllkkkkyaalVVEPTSDGNY--ITKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 1117
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1118 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVICQDGsnlpatQ 1197
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVITKGG------G 738
|
730 740 750
....*....|....*....|....*....|....*...
gi 281604221 1198 RAYaPEQLQKQDNLAIDTQYYLAQQIHPVVARICEPID 1235
Cdd:COG0417 739 RVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
542-1018 |
9.85e-108 |
|
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: 350.68 E-value: 9.85e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 542 PPLVVMSFSMKTMQNVQNHQHEIIAMAALVHHNFPLDKAPPKPPFQtHFCVVSKPKDCIfpcafkevikkKNMEVEVAAT 621
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 622 ERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFWSKIGRLRRS-----NMPKLGSRSG--FGERNATCG 694
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripnKKPLFGSKSFglSDIKVYIKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 695 RMICDVEISVKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSEPSHLLY-LLEHIWKDARFILQIMCELNVLPLAL 773
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDeLLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 774 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQKPgdedeeidgdtnkykKGRKKAAYAGGLVLD 853
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEP---------------DLKKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 854 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASE-TLKATEDEEQEQIPELPDPNLDM--------GILPREIRK 924
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVvIKGDLIIPEDLLTIKYEKGNKYRfvkknirkGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 925 LVERRKQVKQLMKQ-QDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM-- 1001
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 281604221 1002 ---NLEVIYGDTDSIMINTN 1018
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
616-1235 |
2.80e-77 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 273.65 E-value: 2.80e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 616 VEVAATERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFwsKIGRLRRSNMPKL-GSRSGFGERNATcG 694
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 695 RMICDVEISVKELI-HCKSYHLsELVQQilkteRIVIPTENIRNMY---SEPSHLLY-----LLEHIWKDARFILQIMCE 765
Cdd:PRK05762 274 RLVLDGIDALKSATwVFDSFSL-EYVSQ-----RLLGEGKAIDDPYdrmDEIDRRFAedkpaLARYNLKDCELVTRIFEK 347
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 766 LNVLPLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqkpGDEDEEidgdtnkykkgrkkaA 845
Cdd:PRK05762 348 TKLLPFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPNL----------GERPGE---------------A 400
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 846 YAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvasetLKATEDEEQEQIPelpdPNL------DMGILP 919
Cdd:PRK05762 401 SPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGL-------VEGLAQPPEESVA----GFLgarfsrEKHFLP 468
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 920 REIRKLVERRKQVKQLMKQqdlnpdlvlqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQ 999
Cdd:PRK05762 469 EIVERLWEGRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIE 536
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1000 KMNLEVIYGDTDSIMINTNSTN-LEEVFKLGNKVKNEVNKLYKL-----------LEIDIDGVFK--------SLLLLKK 1059
Cdd:PRK05762 537 AQGYQVIYGDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSK 616
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1060 KKYAALVVEPTSDGNYItkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQ 1139
Cdd:PRK05762 617 KRYAGLIQEGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EK 684
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1140 FEINKALTKDPQDYpDKKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGsnlpatqrayaPEQLQKQdNLAID 1214
Cdd:PRK05762 685 LVYRKRLRRPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNG-----------PEPLEYR-KSPID 751
|
650 660
....*....|....*....|.
gi 281604221 1215 TQYYLAQQIHPVVARICEPID 1235
Cdd:PRK05762 752 YDYYIEKQLQPVADRILPFFG 772
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1272-1461 |
6.60e-71 |
|
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: 235.19 E-value: 6.60e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1272 AQLTDEEKYKDCEKFKCLCPSCGTENIYDNVFEGS-GMDMEPSLNRCSNidCKASPATFmvQLSNKLIMDIRRCIKKYYD 1350
Cdd:pfam08996 1 SQISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1351 GWLICEEPTCRNRIRRLPLHFSRngplCPA--CmKAVLRPEYSDKSLYTQLCFYRYIFDADCALEKLPEHEKDKLKKQFF 1428
Cdd:pfam08996 77 GWLVCDDPTCGNRTRQMSVYGKR----CLGpgC-KGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLAL 151
|
170 180 190
....*....|....*....|....*....|...
gi 281604221 1429 TPRVLQDYRKVKNIAEHFLSWSGYSEVNLSKLF 1461
Cdd:pfam08996 152 AEQNRELFKTLKSVVDKYLDKCGRRWVNLSSLF 184
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
56-1232 |
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: 1546.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 56 EVEDLTSVYEEVDEEQYSKLVQARQDDDWIVDDDGIGYVEDGREIFDDDLEDDAldTCGE-GSDGKAHRKDRKDVKKpsV 134
Cdd:TIGR00592 1 MVEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILD--LDKDdGSAAEAKKKDKENHKK--V 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 135 TKPNNIKAMFIASAGKKTTDKTVDLSKDDLLGDILQDLN-TETPQ--IAPPPVLIPKKKRSTGAS---PNPFSVHTATAV 208
Cdd:TIGR00592 77 TKPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVV 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 209 PSGKIASPVSRK---EPPLTPVPLKRAEFAGDLAQPE-CPEDEQESGVIE--FEDGDF----DE-PMDTEEVDEEEPVTA 277
Cdd:TIGR00592 157 DIVKKAIPVSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDEnPADEEIMISTTPVIA 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 278 KIWDQESEPVEGVKHEADPETGTT-SFLDSFLPDVSC----WD-IDQKDENsfllQEVQVDSNHLPLVKGADdEQVFQFY 351
Cdd:TIGR00592 237 KQWDYESEPEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD----VEITVNGDNFDLVYLAD-RQVFQFY 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 352 WlDAYEDPYNQPGVVFLFGKvwvesAKTHVSCCVMVKNIERTLYFLPREMKIDLNTGKETATPITMKDVYEEFDSKISAK 431
Cdd:TIGR00592 312 W-DAYEDPAEKLGVVLLFGR-----DVDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALG 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 432 YKIMKFKSKIVEKNYAFEIP--DVPEKSEYLEVRYS-----AEVPQLPQNLKGETFSHVFGTNTSSLELFLMNRKIKGPC 504
Cdd:TIGR00592 386 YKKEKFRAKPIAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPC 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 505 WLEVKNPQLLNQP-ISWCKFEAMALKPDLVNVIKDVSPPPLVVMSFSMKtMQNVQNHQHEIIAMAALVHHNFPLDKAPPK 583
Cdd:TIGR00592 466 WLAVKGPDELEYPrRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPE 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 584 PPFQTHFCVVSKPKDCIFPCAFK-EVIKKKNMEVEVAATERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECK 662
Cdd:TIGR00592 545 PPYDVHPCVGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLK 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 663 VPFWSKIGRLRRSnmPKLGSRsgFGERnaTCGRMICDVEISVKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSEP 742
Cdd:TIGR00592 625 IPTWSKIGRLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSES 698
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 743 SHLLYLLEHIWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQK 822
Cdd:TIGR00592 699 SSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQK 777
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 823 PGDEDEEIDGdtnkYKKGrKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRvasetlKATEDEeq 902
Cdd:TIGR00592 778 LGDEDEEIDG----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQ------KVDEDE-- 844
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 903 eqIPELPDPNLDMGILPREIRKLVERRKQVKQLMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAAL 982
Cdd:TIGR00592 845 --LPELPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAAL 921
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 983 VTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKNEVNKLYKLLEIDIDGVFKSLLLLKKKKY 1062
Cdd:TIGR00592 922 VTAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKY 1001
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1063 AALVVEPTSDGNYITKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEI 1142
Cdd:TIGR00592 1002 AAIKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVI 1081
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1143 NKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLPATQRAYAPEQLQ-KQDNLAIDTQYYLAQ 1221
Cdd:TIGR00592 1082 NKQLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEH 1161
|
1210
....*....|.
gi 281604221 1222 QIHPVVARICE 1232
Cdd:TIGR00592 1162 QIHPVVLRILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
839-1249 |
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: 727.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 839 KGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAsetlkatEDEEQEQIPELPDPNLDMGIL 918
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRAD-------PDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 919 PREIRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMV 998
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 999 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKNEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPtsDGNYITK 1078
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1079 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKS 1158
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1159 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLPATQRAYAPEQLQKQDNLAIDTQYYLAQQIHPVVARICEPIDGID 1238
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 281604221 1239 AVLIALWLGLD 1249
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 ... |
781-1234 |
6.05e-168 |
|
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: 511.00 E-value: 6.05e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 781 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKPGDEDeeidgdtnkykkgrkkaAYAGGLVLDPKVGFYD 860
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 861 KFILLLDFNSLYPSIIQEFNICFTTVQRVASETLKATEDEEQEQIPELPD------PNLDMGILPREIRKLVERRKQVKQ 934
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 935 LMKQqDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM---NLEVIYGDTD 1011
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1012 SIMINTNSTNLEEVFKLGNKVKNEVNK-LYKL-LEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyitKQELKGLDIVRR 1089
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1090 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWIN 1169
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 281604221 1170 SQGGRKVKAGDTVSYVICQDGS---NLPATQRAYAPEqLQKQDNLAIDTQYYLAQQIHPVVARICEPI 1234
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 ... |
542-774 |
2.68e-114 |
|
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: 358.85 E-value: 2.68e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 542 PPLVVMSFSMKTMQNVQNHQHEIIAMAALVHHNFPLDKAPPKPPFQTHFCVVSKPKDC-IFPCAFKEVIKKKNMEVEVAA 620
Cdd:cd05776 1 PPLTVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRsPPPDLFEKNAKKKKTKVRIFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 621 TERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFWSKIGRLRRSNMPKLGSRSGFGERNATCGRMICDV 700
Cdd:cd05776 81 NERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDT 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281604221 701 EISVKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSEPSHLLYLLEHIWKDARFILQIMCELNVLPLALQ 774
Cdd:cd05776 161 YLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLNILPLTKQ 234
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
494-1235 |
1.12e-111 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 372.24 E-value: 1.12e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 494 FLMNRKIKGPCWLEVknpqllnQPISWCKFEAMALKPDLVNVIKDVsPPPLVVMSF----SMKTMQNVQNHQHEIIAMAa 569
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 570 lVHHNFPLDKAppkppfqthFCVVSKPKDcifpcafkevikkknMEVEVAATERTLLGFFLAKVHKLDPDILVGHNICGF 649
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 650 ELEVLLQRINECKVPFwsKIGRLRRSnmPKLGSRSGFGERNATcGRMICDVEISVKE-LIHCKSYHLSELVQQILKTERI 728
Cdd:COG0417 244 DLPYLQKRAERLGIPL--DLGRDGSE--PSWREHGGQGFASIP-GRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 729 VIPTENIRNMYSEPshLLYLLEHIWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 808
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 809 IVPDKqifrkpqqkpgdedEEIDGDtnkykkgrkkaAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqr 888
Cdd:COG0417 397 LAPNK--------------GEIKGE-----------AYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETL-- 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 889 vaSETLKATEDEEQEqIPELP-----DPNldmGILPREIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSM 963
Cdd:COG0417 449 --VEGGEEPCGDEDV-APGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 964 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKNEVN-KLYKL 1042
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1043 LEIDIDGVFKSllllkkkkyaalVVEPTSDGNY--ITKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 1117
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1118 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVICQDGsnlpatQ 1197
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVITKGG------G 738
|
730 740 750
....*....|....*....|....*....|....*...
gi 281604221 1198 RAYaPEQLQKQDNLAIDTQYYLAQQIHPVVARICEPID 1235
Cdd:COG0417 739 RVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
542-1018 |
9.85e-108 |
|
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: 350.68 E-value: 9.85e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 542 PPLVVMSFSMKTMQNVQNHQHEIIAMAALVHHNFPLDKAPPKPPFQtHFCVVSKPKDCIfpcafkevikkKNMEVEVAAT 621
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 622 ERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFWSKIGRLRRS-----NMPKLGSRSG--FGERNATCG 694
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripnKKPLFGSKSFglSDIKVYIKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 695 RMICDVEISVKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSEPSHLLY-LLEHIWKDARFILQIMCELNVLPLAL 773
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDeLLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 774 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQKPgdedeeidgdtnkykKGRKKAAYAGGLVLD 853
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEP---------------DLKKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 854 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASE-TLKATEDEEQEQIPELPDPNLDM--------GILPREIRK 924
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVvIKGDLIIPEDLLTIKYEKGNKYRfvkknirkGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 925 LVERRKQVKQLMKQ-QDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM-- 1001
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 281604221 1002 ---NLEVIYGDTDSIMINTN 1018
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
616-1235 |
2.80e-77 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 273.65 E-value: 2.80e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 616 VEVAATERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFwsKIGRLRRSNMPKL-GSRSGFGERNATcG 694
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 695 RMICDVEISVKELI-HCKSYHLsELVQQilkteRIVIPTENIRNMY---SEPSHLLY-----LLEHIWKDARFILQIMCE 765
Cdd:PRK05762 274 RLVLDGIDALKSATwVFDSFSL-EYVSQ-----RLLGEGKAIDDPYdrmDEIDRRFAedkpaLARYNLKDCELVTRIFEK 347
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 766 LNVLPLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqkpGDEDEEidgdtnkykkgrkkaA 845
Cdd:PRK05762 348 TKLLPFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPNL----------GERPGE---------------A 400
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 846 YAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvasetLKATEDEEQEQIPelpdPNL------DMGILP 919
Cdd:PRK05762 401 SPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGL-------VEGLAQPPEESVA----GFLgarfsrEKHFLP 468
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 920 REIRKLVERRKQVKQLMKQqdlnpdlvlqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQ 999
Cdd:PRK05762 469 EIVERLWEGRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIE 536
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1000 KMNLEVIYGDTDSIMINTNSTN-LEEVFKLGNKVKNEVNKLYKL-----------LEIDIDGVFK--------SLLLLKK 1059
Cdd:PRK05762 537 AQGYQVIYGDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSK 616
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1060 KKYAALVVEPTSDGNYItkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQ 1139
Cdd:PRK05762 617 KRYAGLIQEGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EK 684
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1140 FEINKALTKDPQDYpDKKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGsnlpatqrayaPEQLQKQdNLAID 1214
Cdd:PRK05762 685 LVYRKRLRRPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNG-----------PEPLEYR-KSPID 751
|
650 660
....*....|....*....|.
gi 281604221 1215 TQYYLAQQIHPVVARICEPID 1235
Cdd:PRK05762 752 YDYYIEKQLQPVADRILPFFG 772
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
378-718 |
3.43e-72 |
|
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: 245.02 E-value: 3.43e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 378 KTHVSCCVMVKNIERTLYFLPREmkidlnTGKETATPITMKDVYEEFdskisakYKIMKFKSKIVEKNYAFEIPDVPekS 457
Cdd:pfam03104 3 DEGVSVCVNVFGFKPYFYCLAPD------GKELEEVIEEIKELYEGL-------DKIEKIELKLKKSLYGYEEDPVP--Y 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 458 EYLEVRYSAEVPQLPQNLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVK-NPQLLNQPISWCKFEAMALKPDLVNVI 536
Cdd:pfam03104 68 LKVSFANPRPLLKIRKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKvYPFRAEGRISNCDVEIDCDSPDLISVP 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 537 KDVSPPPLVVMSFSMKTMQ------NVQNHQHEIIAMAALVHhnfplDKAPPKPPFQthfcVVSKPKDCIFPCAFKEVIK 610
Cdd:pfam03104 148 FEKEWPPLRVLSFDIECTSlpgkfpDAENVKDPIIQISCMLD-----GQGEPEPEPR----FLFTLRECDSEDIEDFEYT 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 611 KKNM----EVEVAATERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFWSKIGRLRRsNMPKLGSRSGF 686
Cdd:pfam03104 219 PKPIypgvKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNR-GGRSKVREIGF 297
|
330 340 350
....*....|....*....|....*....|....*.
gi 281604221 687 G----ERNATCGRMICDVEISVKELIHCKSYHLSEL 718
Cdd:pfam03104 298 GtrsyEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
844-1230 |
7.83e-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: 243.43 E-value: 7.83e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 844 AAYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQRvaSETLKATEDEEQEQIPELPDPNldmGILPREIR 923
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVG--NGEIAAPEDYIGVGFRSPKDRK---GLLPRILE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 924 KLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNL 1003
Cdd:cd00145 75 ELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGA 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1004 EVIYGDTDSIMINTN-STNLEEVFKLGNKVKNEVNKlYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyitKQELK 1082
Cdd:cd00145 155 RVIYGDTDSIFVSLPkMGTKEDAIKEGREILQELAD-EHLLELEFEKVYLPFFLGKKKRYAGLDIWKGQDEG---KIDIK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1083 GLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigenvlngsvpvsqfeinkaltkdpqdypdkkslphv 1162
Cdd:cd00145 231 GLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL--------------------------------------- 271
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 281604221 1163 hvalwinsqggrkvkagDTVSYVICQDGSNLPATQRAYAPEQLQkQDNLAIDTQYYLAQQIHPVVARI 1230
Cdd:cd00145 272 -----------------DKVKYVVTRGGKGVPDYERADPPLEDL-DKRHRIDYEYYLERLLQPPLERI 321
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1272-1461 |
6.60e-71 |
|
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: 235.19 E-value: 6.60e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1272 AQLTDEEKYKDCEKFKCLCPSCGTENIYDNVFEGS-GMDMEPSLNRCSNidCKASPATFmvQLSNKLIMDIRRCIKKYYD 1350
Cdd:pfam08996 1 SQISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1351 GWLICEEPTCRNRIRRLPLHFSRngplCPA--CmKAVLRPEYSDKSLYTQLCFYRYIFDADCALEKLPEHEKDKLKKQFF 1428
Cdd:pfam08996 77 GWLVCDDPTCGNRTRQMSVYGKR----CLGpgC-KGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLAL 151
|
170 180 190
....*....|....*....|....*....|...
gi 281604221 1429 TPRVLQDYRKVKNIAEHFLSWSGYSEVNLSKLF 1461
Cdd:pfam08996 152 AEQNRELFKTLKSVVDKYLDKCGRRWVNLSSLF 184
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
845-1232 |
1.30e-66 |
|
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: 230.29 E-value: 1.30e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 845 AYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQRvasetlkateDEEQEQIPELP-------DPnldMGI 917
Cdd:cd05536 3 SYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVR----------EGCEDCDVEPQvghkfrkDP---PGF 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 918 LPREIRKLVERRKQVKQLMKQ-QDLNPDLVLqYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKE 996
Cdd:cd05536 69 IPSVLEDLLEERRRIKEKMKKlDPESEEYKL-LDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIK 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 997 MVQKMNLEVIYGDTDSIM--INTNSTNLEEVFKLGNKVKNEVNklyklLEIDIDGVFKSLLLLKKKKYAALvvepTSDGN 1074
Cdd:cd05536 148 IAEEKGFKVIYGDTDSLFvkIDGADAVKKKVKKLLKYINEELP-----LELEIEKFYKRGFFVTKKRYAGL----TEDGK 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1075 YITkqelKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYp 1154
Cdd:cd05536 219 IDV----VGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVK----EVIEKLKRGEVPPEKLVIWKQLTKDLSEY- 289
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 281604221 1155 dKKSLPHVHVALWInSQGGRKVKAGDTVSYVICQDGSNLpaTQRAYAPEQLQKQDNlaIDTQYYLAQQIHPVVARICE 1232
Cdd:cd05536 290 -KATGPHVAAAKKL-AKRGYKVRPGTKIGYVIVKGSGKI--SDRAYPYDMVDEKHK--YDAEYYIDNQVLPAVLRILE 361
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
846-1234 |
9.26e-65 |
|
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: 225.61 E-value: 9.26e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 846 YAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVqrVASETLKATEDEEQEQIP---ELPDPNLDMGILPREI 922
Cdd:cd05533 3 YEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTL--LNKNTAKKLPPEDYIKTPngdYFVKSSVRKGLLPEIL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 923 RKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQ--- 999
Cdd:cd05533 81 EELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEeky 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1000 ------KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKNEVNKLY-KLLEIDIDGVFKSLLLLKKKKYAALVVepTSD 1072
Cdd:cd05533 160 tkangySHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFiKPIKLEFEKVYFPYLLINKKRYAGLLW--TNP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1073 GNYiTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIqKRLIeigENVLNGSVPVSQFEINKALTKDPQD 1152
Cdd:cd05533 238 DKH-DKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFV-KGVI---SDLLQNKIDISLLVITKALTKTADD 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1153 YPDKksLPHVHVALWINSQG-GRKVKAGDTVSYVICQDGSNLPATQRA----YAPEqlqkqDNLAIDTQYYLAQQIHPVV 1227
Cdd:cd05533 313 YAGK--QAHVELAERMRKRDpGSAPNVGDRVPYVIIKGAKGAKAYEKAedpiYVLE-----NNIPIDTQYYLENQLSKPL 385
|
....*..
gi 281604221 1228 ARICEPI 1234
Cdd:cd05533 386 LRIFEPI 392
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
494-1234 |
1.74e-64 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 239.54 E-value: 1.74e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 494 FLMNRKIKGPCWLEVKNPQ----LLNQPISWCKFEaMALKPDLVNVIKDV----SPPPLVVMSFSmktmqnvqnhqheiI 565
Cdd:PTZ00166 207 FLIDNNITGGSWLTLPKGKykirPPKKKTSTCQIE-VDCSYEDLIPLPPEgeylTIAPLRILSFD--------------I 271
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 566 AMAALVHHNFPLDKAPPKPPFQTHFCVVSKPKDCI--FPCAFKEVIKKKNMEVEVAATERTLLGFFLAKVHKLDPDILVG 643
Cdd:PTZ00166 272 ECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLtkFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDPDFLTG 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 644 HNICGFELEVLLQRINECKVP---FWSKIGRLRRSNMPKLGSRSGFGERNATC----GRMICDVEISVKELIHCKSYHLS 716
Cdd:PTZ00166 352 YNIINFDLPYLLNRAKALKLNdfkYLGRIKSTRSVIKDSKFSSKQMGTRESKEinieGRIQFDVMDLIRRDYKLKSYSLN 431
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 717 ELVQQILKTERiviptENIRnmYSEPSHL------------LYLLehiwKDARFILQIMCELNVLPLALQITNIAGNIMS 784
Cdd:PTZ00166 432 YVSFEFLKEQK-----EDVH--YSIISDLqngspetrrriaVYCL----KDAILPLRLLDKLLLIYNYVEMARVTGTPIG 500
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 785 RTLMGGRSERNEFLLLHAFYENNYIVPdkqifrkpqqkpgdedeeidgdTNKYKKGRKKAAYAGGLVLDPKVGFYDKFIL 864
Cdd:PTZ00166 501 WLLTRGQQIKVTSQLLRKCKKLNYVIP----------------------TVKYSGGGSEEKYEGATVLEPKKGFYDEPIA 558
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 865 LLDFNSLYPSIIQEFNICFTTVqrVASETLKATEDEEQEQIP---ELPDPNLDMGILPREIRKLVERRKQVKQLMKQQDl 941
Cdd:PTZ00166 559 TLDFASLYPSIMIAHNLCYSTL--VPPNDANNYPEDTYVTTPtgdKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK- 635
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 942 NPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYakP---LAALVTYKGREILMHTKEMVQKM---------NLEVIYGD 1009
Cdd:PTZ00166 636 DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQL--PcleVSTSITSFGRQMIDKTKELVEKHytkangykhDATVIYGD 713
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1010 TDSIMINTNSTNLEEVFKLGNKVKNEVNKLY-KLLEIDIDGVFKSLLLLKKKKYAALVVepTSDGNYiTKQELKGLDIVR 1088
Cdd:PTZ00166 714 TDSVMVKFGTDDIQEAMDLGKEAAERISKKFlKPIKLEFEKVYCPYLLMNKKRYAGLLY--TNPEKY-DKIDCKGIETVR 790
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1089 RDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNgsvpVSQFEINKALTKDpqDYpdKKSLPHVHVAlwi 1168
Cdd:PTZ00166 791 RDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRID----ISLLVITKSLGKD--DY--EGRLAHVELA--- 859
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281604221 1169 nsqggRKVKA---------GDTVSYVICQDGSNLPATQRA----YAPEqlqkqDNLAIDTQYYLaQQIHPVVARICEPI 1234
Cdd:PTZ00166 860 -----KKLRQrdpgsapnvGDRVSYVIVKGAKGAPQYERAedplYVLE-----NNIPIDTQYYL-DQIKNPLLRIFEGV 927
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
546-764 |
1.01e-50 |
|
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 176646 [Multi-domain] Cd Length: 199 Bit Score: 177.93 E-value: 1.01e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 546 VMSFSMKTMQNVQ---NHQHEIIAMAALVHhnFPLDKAPPKPPFQTHFCVVSKpkdcifpcafkevikKKNMEVEVAATE 622
Cdd:cd05160 1 VLSFDIETTPPVGgpePDRDPIICITYADS--FDGVKVVFLLKTSTVGDDIEF---------------IDGIEVEYFADE 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 623 RTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFWskIGRLRRSNMPKlgsRSGFGERNATCGRMICDVEI 702
Cdd:cd05160 64 KELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLT--DGIYRRSGGEK---SSGSTERIAVKGRVVFDLLA 138
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 281604221 703 SVKELIHCKSYHLSELVQQILK-TERIVIPTENIRNMYSEpsHLLYLLEHIWKDARFILQIMC 764
Cdd:cd05160 139 AYKRDFKLKSYTLDAVAEELLGeGKEKVDGEIIEDAEWEE--DPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
850-1238 |
4.00e-43 |
|
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: 164.31 E-value: 4.00e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 850 LVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTT-VQRVASETLKATEDEEQEQIPELPDPNLDM------------- 915
Cdd:cd05534 40 LVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTcLGRVEELNGGGKFGFLGVKLYLPPPPLDLLllkddvtispngv 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 916 ---------GILPREIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYS-RFYAKPLAALVTY 985
Cdd:cd05534 120 mfvkksvrkGILPKMLEEILDTRIMVKKAMKKYKDDKKLQRILDARQLALKLLANVTYGYTAASFSgRMPCVEIADSIVQ 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 986 KGREILMHTKEMVQ---KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKNEVNKLY-KLLEIDIDGVFKSLLLLKKKK 1061
Cdd:cd05534 200 TGRETLERAIELIEstpKWGAKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVTAANpSPIKLKFEKVYHPCVLVTKKR 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1062 YAALVVE------PTSDGnyitkqelKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigENVLNGSV 1135
Cdd:cd05534 280 YVGYKYEspdqtePTFDA--------KGIETVRRDGCPAVQKILEKSLRILFETKDLSTVKSYLQRQW----SKLLQGRV 347
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1136 PVSQFEINKALTKDpqDYPDKKSLP-HVHVAL-WINSQGGRKVKAGDTVSYVICQDGSNLPATQRAYAPEQLQKQDNLAI 1213
Cdd:cd05534 348 SIQDFIFAKEVRLG--TYKEGATLPaGAIVALrRMEKDPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLADPSLRL 425
|
410 420
....*....|....*....|....*
gi 281604221 1214 DTQYYLAQQIHPVVARICEPIdGID 1238
Cdd:cd05534 426 DAEYYITKQIIPALDRLFNLV-GVD 449
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
823-1219 |
1.37e-42 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 168.71 E-value: 1.37e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 823 PGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvasetlkatEDEEQ 902
Cdd:PRK05761 384 PWKEDILRLDHEVYKKAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETV-----------RIPEC 451
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 903 EQIPELPDPNL------DMGILPREIRKLV--ERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRF 974
Cdd:PRK05761 452 KCHYDDEVPELghsvcdDRPGLTSVLVGLLrdFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKL 531
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 975 YAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKNEVNklyklLEIDIDGVFKs 1053
Cdd:PRK05761 532 YRIEVAESITALGREILLSTKKKAEELGLKVLYGDTDSLFVwGPTKESLEELIK---EIEERTG-----IDLEVDKTYD- 602
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1054 llllkkkkyaaLVVEPTSDGNYITKQ-----ELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQK---RLIE 1125
Cdd:PRK05761 603 -----------WVAFSGLKKNYFGVLkdgkvKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEKVKDEiedVLKR 671
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1126 IGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQGGrKVKAGDTVSYVICQDgsnlpatQRAYAPEQL 1205
Cdd:PRK05761 672 YYEKLRAKDYPLDELAIRVRLSKPLDEY-TKNTPQHVKAALQLRDYGV-EVSPGDIISYVKVDD-------KRGVKPVQL 742
|
410
....*....|....
gi 281604221 1206 QKQDNlaIDTQYYL 1219
Cdd:PRK05761 743 AKLSE--IDVEKYI 754
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
839-1219 |
3.45e-42 |
|
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99913 Cd Length: 372 Bit Score: 159.44 E-value: 3.45e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 839 KGRKkaaYAGGLVLDPKVG-FYDkfILLLDFNSLYPSIIQEFNICFTTVQRVasetlkaTEDEEQEQIPELP-----DPN 912
Cdd:cd05530 9 KGKK---YRGAIVLEPPPGiFFN--VVVLDFASLYPSIIKVWNLSYETVNCP-------HCECKTNEVPEVGhwvckKRP 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 913 LDMGILPREIRKLveRRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILM 992
Cdd:cd05530 77 GITSQIIGLLRDL--RVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIIT 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 993 HTKEMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKNEVNklyklLEIDIDGVFKsllllkkkkyaaLVVEPTS 1071
Cdd:cd05530 155 STIKKARELGLKVLYGDTDSLFLwNPPQEQLEDLVE---WVEKELG-----LDLELDKEYR------------YVVFSGL 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1072 DGNYI-----TKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRD---TIVENIQKRLIEIGENVLNGSVPVSQFEIN 1143
Cdd:cd05530 215 KKNYLgvtkdGSVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPEdfeKAREKIRDIVKGVYKRLKKKEYTLDQLAFK 294
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 281604221 1144 KALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLPATQRAYAPEqlqkqdnlaIDTQYYL 1219
Cdd:cd05530 295 VMLSKPPEEY-TKNTPQHVKAARQLEKY-GRNVEAGDIISYVKVKGKEGVKPVQLARLDE---------VDVEKYV 359
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
847-1234 |
1.82e-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: 154.35 E-value: 1.82e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 847 AGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNIcfTTVQRVasETLKAteDEEQEQIPELPDPNL--DMGILPREIRK 924
Cdd:cd05537 4 PGGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI--DPLGLI--EGLKA--PDPEDLIPGFLGARFsrEKHILPDLIAR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 925 LVERRKQVKQlmkqqDLNPDLvlqydirQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLE 1004
Cdd:cd05537 77 LWAARDEAKR-----EKNAPL-------SQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQ 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1005 VIYGDTDSIMINTNST-NLEEVFKLGNKVKNEVN--------KLYKL---LEIDIDGVF--------KSLLLLKKKKYAA 1064
Cdd:cd05537 145 VIYGDTDSTFVWLGEElDAAEAQAIGKELASQINqwwaqklkEEFGLesfLEIEFETHYsrffmptiRGSDEGSKKRYAG 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1065 LVVEPTSDgnyitKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEiGEnvLNgsvpvSQFEINK 1144
Cdd:cd05537 225 LKSTDGGD-----ELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLA-GE--LD-----ELLVYRK 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1145 ALTKDPQDYpDKKSLPHVHVALW---INSQGGRKvKAGDTVSYVICQDGSNlPATQRayapeqlqkqdNLAIDTQYYLAQ 1221
Cdd:cd05537 292 RLRRPLSEY-TKNVPPHVQAARLadqINRELGRP-RQYQWIEYVITVNGPE-PLEYR-----------TSPLDYQHYIDK 357
|
410
....*....|...
gi 281604221 1222 QIHPvvarICEPI 1234
Cdd:cd05537 358 QLKP----IADSI 366
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
844-1237 |
3.70e-32 |
|
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: 129.39 E-value: 3.70e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 844 AAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNIcfttvqrvASETLKATEDEEQEQIPELPDPNLD-MGILPREI 922
Cdd:cd05531 3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNI--------SPETINCRCCECRDHVYLGHRICLKrRGFLPEVL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 923 RKLVERRKQVKQLMKQQDlnpdlvlQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMN 1002
Cdd:cd05531 74 EPLLERRLEYKRLKKEED-------PYAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEMG 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1003 LEVIYGDTDSIMINTNSTNLEEVFKLGNKVKnevnklyklLEIDIDGVFKsllllkkkkyaALVVEPTSDG-----NYIT 1077
Cdd:cd05531 147 FRVLHGIVDSLWIQGRGDIEELAREIEERTG---------IPLKLEGHYD-----------WIVFLPERDGlgapnRYFG 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1078 KQE-----LKGLDIVRRDWCDLAKDTGNFVIgQILSdQSRDtiVENIQKRLIEIgENVLNGSV------PVSQFEINKAL 1146
Cdd:cd05531 207 RLSdgemkVRGIELRRRDTPPFVKKFQEEAL-DILA-SAKT--PEELLKLREEA-LDLFRRYLqrlregDLEDLIIEKKI 281
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1147 TKDPQDYpdkKSLPHvHVALWINSQgGRKVKAGDTVSYVICQDGSNLPATqrayapeqlqkQDNLAIDTQYYLAQQIHPV 1226
Cdd:cd05531 282 SKRSSEY---KVLAS-TALKALRAK-GVSVVPGMKIEYIVRDGKRPVPDL-----------GNDEGYDTKYYRELLERAA 345
|
410
....*....|.
gi 281604221 1227 varicEPIDGI 1237
Cdd:cd05531 346 -----EELLFP 351
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
837-1160 |
3.00e-21 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 101.25 E-value: 3.00e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 837 YKKGRKKAA--YAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRV--ASETLKAtEDEEQEQIPELPDP- 911
Cdd:PHA03036 519 LVRSETKNKfpYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVvvNDNRLEA-EINKQELRRKYPYPr 597
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 912 -----------NL----------DMGILPREIRKLVERRKQVKQLMKQQDLNPDLVLqYDIRQKALKLTANSMYGCLGFS 970
Cdd:PHA03036 598 yiyvhceprspDLvseiavfdrrIEGIIPKLLKTFLEERARYKKLLKEATSSVEKAI-YDSMQYTYKIVANSVYGLMGFR 676
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 971 YSRFYAKPLAALVTYKGREILMHTKEMV--------------------------------------QKMNLEVIYGDTDS 1012
Cdd:PHA03036 677 NSALYSYASAKSCTAIGRNMIKYLNSVLngsklingklilancpinpffkddrsidtnydtnlpveYNFTFRSVYGDTDS 756
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1013 IMINTNSTNLEEVFKLGNKVKNEVNK--LYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYITKQELKGLDIVRRD 1090
Cdd:PHA03036 757 VFLEINTKDVDKSIKIAKELERIINEkvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVPERVNKGTSETRRD 836
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1091 WCDLAKdtgnfvigqilsdqsrdTIVENIQKRLIEIGENVLNGSVPVSqFEINKALTKDPQDYPDKKSLP 1160
Cdd:PHA03036 837 VSKFHK-----------------YMIKIYKTRLLDMLSEGNMNSNQVC-IDILRSLEKDLIIEFDSRSAP 888
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
838-1041 |
3.98e-15 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 80.89 E-value: 3.98e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 838 KKGRKKAAYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQrvasETLK-ATEDEEQEQIPELPD------ 910
Cdd:PHA02528 369 NKSHKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIA----GTFHvAPVHEYINKTAPRPSdeyscs 443
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 911 PNLDM------GILPREIRKLVERRKQVKQLMKQQDLNPDL--------------------------------------- 945
Cdd:PHA02528 444 PNGWMyrkdirGVIPTEIKKVFDQRKIYKKKMLAAERNAELiktiledlndsvdtpidvdyyfdfsdefkaelktltkss 523
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 946 -----------VLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGR-EILMHTKEMVQKMNL--------EV 1005
Cdd:PHA02528 524 lkalleecekeIALCNTIQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQlAIQWIERKMNEYLNKlcktededYV 603
|
250 260 270
....*....|....*....|....*....|....*..
gi 281604221 1006 IYGDTDSIMINTNSTnLEEVFKLGNKVKNE-VNKLYK 1041
Cdd:PHA02528 604 IYGDTDSIYVNLDPL-VEKVGEDKFKDTNHwVDFLDK 639
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
867-1192 |
3.23e-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: 75.99 E-value: 3.23e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 867 DFNSLYPSIIQEFNICfttvqrVASETLkatedeeqeqipelpdpnldmGILPREIRKLVERRKQVKQLMKQQDLnPDLV 946
Cdd:cd05538 23 DVASLYPSIMLAYRIC------PARDSL---------------------GIFLALLKYLVELRLAAKESARAAAR-PAER 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 947 LQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMI---NTNSTNLE 1023
Cdd:cd05538 75 DAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFippNGVDTEDE 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1024 EvfklgNKVKNEVNK-LYKLLEIDIDGVFKSLLLLKKKKYAALvveptsdgNYITKQELKGLDIVRRDWCDLAKDTGNFV 1102
Cdd:cd05538 155 E-----EELVRELSStLPKGITVEFDGRYRAMFSYKIKNYALL--------DYDGKLIVKGSAFRSRGIEPFLREFLREA 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 1103 IGQILSDQSrdtivENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDK----KSLPhvHVALWINSQGGRKVKA 1178
Cdd:cd05538 222 VRLLLQGDG-----AGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYLQKvragKRNP--AAAYEIALARPREWRA 294
|
330
....*....|....
gi 281604221 1179 GDTVSYVICQDGSN 1192
Cdd:cd05538 295 GDRVTYYVSGTGKG 308
|
|
| DNA_pol_alpha_N |
pfam12254 |
DNA polymerase alpha subunit p180 N terminal; This domain family is found in eukaryotes, and ... |
41-101 |
1.31e-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: 1.31e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281604221 41 LERLKKAKAGEK---YKYEVEDLTSVYEEVDEEQYSKLVQARQDDDW-IVDDDGIGYVEDGREIF 101
Cdd:pfam12254 1 LEKLKAARAGGKrrlDEYESEEDEDIYDEVDEEEYRKIVRKRLLDDDfVVDDDGEGYVDDGREDW 65
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
590-750 |
6.23e-09 |
|
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: 57.81 E-value: 6.23e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 590 FCVVSKPKDCIF------PCAFKEVIKKKNMevevaaTERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKV 663
Cdd:cd05785 26 FSNPDRGDDRIIivalrdNRGWEEVLHAEDA------AEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGV 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 664 PF-WSKIGRLRRSNmpklGSRSGFGERNA------TCGRMICDV-------EISVKELihcKSYHLSELVQQ--ILKTER 727
Cdd:cd05785 100 PLaIGRDGSIPRQR----PSRFRFAERLIdyprydIPGRHVIDTyflvqlfDVSSRDL---PSYGLKAVAKHfgLASPDR 172
|
170 180
....*....|....*....|....*
gi 281604221 728 IVIPTENIRNMY-SEPSHLL-YLLE 750
Cdd:cd05785 173 TYIDGRQIAEVWrSDPARLLaYALD 197
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
605-762 |
1.46e-08 |
|
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: 56.21 E-value: 1.46e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 605 FKEVIKKKNME---VEVAATERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFwsKIGRLRRSnmPKLg 681
Cdd:cd05780 36 GNKVITWKKFDlpfVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIEL--DLGRDGSE--IKI- 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 682 SRSGFGERNATCGRMICDVEISVKELIHCKSYHLSELVQQILKTERIVIPTENIRNMYSEPSHLLYLLEHIWKDARFILQ 761
Cdd:cd05780 111 QRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYE 190
|
.
gi 281604221 762 I 762
Cdd:cd05780 191 I 191
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
834-1014 |
4.75e-07 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 54.86 E-value: 4.75e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 834 TNKYKKG-RKKAAYAGGLVLDPKVGF-----YDKFILLLDFNSLYPSIIQEFNICFTTVqrVASETLKATEDE---EQEQ 904
Cdd:PHA03334 620 PEKYARDcRQKIKLKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAI--VDPDCTARVRGWvvfDWKK 697
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 905 IPE-LPDPNLDMGIL---PRE-------------IRKLVERRKQVKQLMKQQDlNPDLVLQYDIRQKALKLTANSMYGcl 967
Cdd:PHA03334 698 IDRgFGKATLMYTILrtkPEEpswrrfttyttssLNHYLSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYG-- 774
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 281604221 968 gfsysrfyAKPLAA--LVTYKGREILMHTKEMVQKM-NLEVIYGDTDSIM 1014
Cdd:PHA03334 775 --------VAPHACqhLITTLGRHKIKLVEEFIKKEpGMTVNYGDTDSVM 816
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
611-699 |
7.21e-07 |
|
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: 51.41 E-value: 7.21e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 611 KKNMEVEVAATERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFwsKIGRLRRSnmPKLGSRSGFGERN 690
Cdd:cd05784 40 DAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPL--RLGRGGSP--LNWRQSGKPGQGF 115
|
90
....*....|
gi 281604221 691 ATC-GRMICD 699
Cdd:cd05784 116 LSLpGRVVLD 125
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
621-675 |
1.18e-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: 51.42 E-value: 1.18e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 281604221 621 TERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFWSKIGRLRRS 675
Cdd:cd05777 70 TEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNI 124
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
613-763 |
2.16e-04 |
|
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: 44.53 E-value: 2.16e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 613 NMEVEVAATERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRIN-ECKVPFWSKIGRLRRSNMPKLGSRSgfGERNA 691
Cdd:cd05778 72 GIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAaLGIDDLLDEISRVPSDSNGKFGDRD--DEWGY 149
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 692 T-------CGRMICDV------EISVkelihcKSYHLSELVQQILKtERI-VIPTENIRNMY--SEPSHLLYLLEHIWKD 755
Cdd:cd05778 150 ThtsgikiVGRHILNVwrlmrsELAL------TNYTLENVVYHVLH-QRIpLYSNKTLTEWYksGSASERWRVLEYYLKR 222
|
....*...
gi 281604221 756 ARFILQIM 763
Cdd:cd05778 223 VRLNLEIL 230
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
622-762 |
5.02e-04 |
|
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: 42.70 E-value: 5.02e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 622 ERTLLGFFLAKVHKLDPDILVGHNICGFELEVLLQRINECKVPFwsKIGRlRRSNMPklgSRSGFGERNATcGRMICDV- 700
Cdd:cd05781 48 DRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKL--DVGR-RGGSEP---STGVYGHYSIT-GRLNVDLy 120
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281604221 701 -------EISVKELihcksYHLSELVQQILKTERIVIPTENIRNMYSEPSHLLYLLEHIWKDARFILQI 762
Cdd:cd05781 121 dfaeeipEVKVKTL-----ENVAEYLGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGL 184
|
|
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
930-1013 |
1.23e-03 |
|
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Pssm-ID: 99918 Cd Length: 621 Bit Score: 43.43 E-value: 1.23e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281604221 930 KQVKQLMKQQDL-----NPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMN-- 1002
Cdd:cd05535 247 KKLEAAKAAGDAaeikeAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELVEQIGrp 326
|
90
....*....|.
gi 281604221 1003 LEViygDTDSI 1013
Cdd:cd05535 327 LEL---DTDGI 334
|
|
| |
