|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
56-1231 |
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: 1479.92 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 56 EVEDFTSVYEEVDEEQYSKLVQARQDDDWIVDDDGIGYVEDGREIFDDDLEDDALDShEKGKDNKACNKDKRTVKRaaVT 135
Cdd:TIGR00592 1 MVEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILDLDK-DDGSAAEAKKKDKENHKK--VT 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 136 KPNNIKSMFIASAGRKTVDKAVDLSKDDLLGDILQDLN-TETPQ--ITPPPVIIPKKKRSSGAS---LNPFSVHTPKAAP 209
Cdd:TIGR00592 78 KPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVVD 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 210 SGKTTPPASRR---EPSLTPAPLTCAEFAGEPGPP-LCTDDKEESGAME--FEDGDF----DEPMEAEEVDV--EPVAAK 277
Cdd:TIGR00592 158 IVKKAIPVSTRyllEKILIPVPLKRAEFAGGDVQMeGDPELKLASFDIEtyFHDGKDffpgDENPADEEIMIstTPVIAK 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 278 TLCQEREPAEEAKHKADSGKGTTSSSA-SFLPDVSC----WDMDQEDDSSFsalEVQVDSSHLPLVKGADEeQVFQFYWl 352
Cdd:TIGR00592 238 QWDYESEPEARVVTWKKPDKPTTGSYVeSVSEEISMikrfWDVIDQEDTDV---EITVNGDNFDLVYLADR-QVFQFYW- 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 353 DAYEDPYSQPGVVFLFGKvwieSAEtHVSCCVMVKNIERSLCFLPREMKVDLNTGKESGTPVTMKDVYDEFDEKIAAKYK 432
Cdd:TIGR00592 313 DAYEDPAEKLGVVLLFGR----DVD-HVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYK 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 433 IMKFKSKVVEKNYAFEIP--DVPEKSEYLEVRYS-----AEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWL 505
Cdd:TIGR00592 388 KEKFRAKPIAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWL 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 506 EVKNPQLLNQP-ISWCKVEAMVLKPDLVNVIKDVGPPPVVVMSLSMKtMQNAKTHENEIIAVSALVHHSFALDKAPPQPP 584
Cdd:TIGR00592 468 AVKGPDELEYPrRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEPP 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 585 FQSHFCVVSKPKDCIFPYDFK-ESIKEKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVP 663
Cdd:TIGR00592 547 YDVHPCVGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIP 626
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 664 FWSKIGRLKRSnmPKLGGRsgFGEKnaTCGRMICDVEISAKELIRCKSYHLSELVQQILKTERIVIPIETIRNMYSDSSH 743
Cdd:TIGR00592 627 TWSKIGRLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSS 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 744 LLYLLEHTWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQTFRKpQQKLG 823
Cdd:TIGR00592 701 LTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKLG 779
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 824 DEDEDIdgdtNKYKKGrKKAAYSGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvaseaQKVVEDgeqeQ 903
Cdd:TIGR00592 780 DEDEEI----DGYKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDED----E 844
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 904 IPELPDPSLEMGILPREIRKLVERRRQVKQLMKQqDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVT 983
Cdd:TIGR00592 845 LPELPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVT 923
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 984 YKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGIFKSLLLLKKKKYAA 1063
Cdd:TIGR00592 924 AKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYAA 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1064 LIVEPTSDGNYVTKQEVKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIQKRLIEIGENVLNGSVPVSQFEINK 1143
Cdd:TIGR00592 1004 IKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVINK 1083
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1144 ALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTAGQRAYAPEQLQ-KQDNLSIDTQYYLAQQI 1222
Cdd:TIGR00592 1084 QLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEHQI 1163
|
....*....
gi 1387294325 1223 HPVVARICE 1231
Cdd:TIGR00592 1164 HPVVLRILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
838-1248 |
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: 729.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 838 KGRKKAAYSGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAseaqkvvEDGEQEQIPELPDPSLEMGIL 917
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRAD-------PDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 918 PREIRKLVERRRQVKQLMKQQDlNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMV 997
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 998 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGIFKSLLLLKKKKYAALIVEPtsDGNYVTK 1077
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1078 QEVKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKS 1157
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1158 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTAGQRAYAPEQLQKQDNLSIDTQYYLAQQIHPVVARICEPIDGID 1237
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 1387294325 1238 AILIASWLGLD 1248
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 ... |
780-1233 |
8.70e-169 |
|
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: 511.39 E-value: 8.70e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 780 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQtfrkpqqklgdededidgdtnkyKKGRKKAAYSGGLVLDPKVGFYD 859
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP-----------------------SAKGDEDGYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 860 KFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVVEDGEQEQIPELPD------PSLEMGILPREIRKLVERRRQVKQ 933
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 934 LMKQqDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM---NLEVIYGDTD 1010
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1011 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDGIFKSLLLLKKKKYAALIVEPTSDGNyvtKQEVKGLDIVRR 1088
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1089 DWCDLAKDTGNFVIGQILSDQNRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWIN 1168
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1387294325 1169 SQGGRKVKAGDTVSYVICQDGS---NLTAGQRAYAPEqLQKQDNLSIDTQYYLAQQIHPVVARICEPI 1233
Cdd:pfam00136 373 KRNGEAPEVGDRIPYVIVKAAKglkNLLIYERAEDPE-YVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
493-1234 |
6.48e-114 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 377.25 E-value: 6.48e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 493 FLMNRKIKGPCWLEVknpqllnQPISWCKVEAMVLKPDLVNVIKDVgPPPVVVMSLSMKT-----MQNAKTHEnEIIAVS 567
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFDIEVstprgFPDPERDG-PIISIG 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 568 alVHHSFALDKAppqppfqshfCVVSKPkdcifpydfkesikEKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYG 647
Cdd:COG0417 189 --LAGSDGEKKV----------LMLGRE--------------GVDFEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDN 242
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 648 FELEVLLQRINVCKVPFwsKIGRLKRSnmPKLGGRSGFGEKNATcGRMICDV-EISAKELIRCKSYHLSELVQQILKTER 726
Cdd:COG0417 243 FDLPYLQKRAERLGIPL--DLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGK 317
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 727 IVIPIETIRNMYSDSshLLYLLEHTWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENN 806
Cdd:COG0417 318 LIVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRG 395
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 807 YIVPDKqtfrkpqqklgdededidgdtnkykKGRKKAAYSGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVq 886
Cdd:COG0417 396 YLAPNK-------------------------GEIKGEAYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETL- 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 887 rvaseaqkvVEDGEQEQIPELPDPSL-------EMGILPREIRKLVERRRQVKQLMKQQDLNPDLHLQYDIRQKALKLTA 959
Cdd:COG0417 449 ---------VEGGEEPCGDEDVAPGFghrfcrePKGILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILM 519
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 960 NSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KL 1038
Cdd:COG0417 520 NSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWW 599
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1039 YKLLEIDIDGIFKSllllkkkkyaalIVEPTSDGNY--VTKQE---VKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDT 1113
Cdd:COG0417 600 PSGLELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEK 667
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1114 IVENIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVIcqdgsnLT 1193
Cdd:COG0417 668 AVEYVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI------TK 735
|
730 740 750 760
....*....|....*....|....*....|....*....|.
gi 1387294325 1194 AGQRAYaPEQLQKQDNLSIDTQYYLAQQIHPVVARICEPID 1234
Cdd:COG0417 736 GGGRVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
541-1017 |
6.07e-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: 363.77 E-value: 6.07e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 541 PPVVVMSLSMKTMQNAKTHENEIIAVSALVHHSFALDKAPPQPPFQsHFCVVSKPKDCIfpydfkesikeKNVKVEVAAT 620
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 621 ERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFWSKIGRLKRS-NMPKLGGRSGF------GEKNATCG 693
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlRIPNKKPLFGSksfglsDIKVYIKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 694 RMICDVEISAKELIRCKSYHLSELVQQILKTERIVIPIETIRNMYSDSSHLLY-LLEHTWKDARFILQIMCELNVLPLAL 772
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDeLLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 773 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQTFRKPQQKlgdededidgdtnkyKKGRKKAAYSGGLVLD 852
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSE---------------PDLKKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 853 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQK----VVEDGEQEQIPE-----LPDPSLEMGILPREIRK 923
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKgdliIPEDLLTIKYEKgnkyrFVKKNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 924 LVERRRQVKQLMKQ-QDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM-- 1000
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 1387294325 1001 ---NLEVIYGDTDSIMINTN 1017
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
615-1247 |
4.64e-76 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 269.80 E-value: 4.64e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 615 VEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFwsKIGRLKRSNMPKL-GGRSGFGEKNATcG 693
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 694 RMICD-VEISAKELIRCKSYHLSELVQQIL-KTERIVIP---IETIRNMYSDSSHLLylLEHTWKDARFILQIMCELNVL 768
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSLEYVSQRLLgEGKAIDDPydrMDEIDRRFAEDKPAL--ARYNLKDCELVTRIFEKTKLL 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 769 PLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDKQTfrkpqqklgdededidgdtnkykkgRKKAAYSGG 848
Cdd:PRK05762 352 PFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPNLGE-------------------------RPGEASPGG 404
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 849 LVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvaseaqkvVEDGEQEQIPELPDP-----SLEMGILPREIRK 923
Cdd:PRK05762 405 YVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGL----------VEGLAQPPEESVAGFlgarfSREKHFLPEIVER 473
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 924 LVERRRQVKQLMKQqdlnpdlhlqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLE 1003
Cdd:PRK05762 474 LWEGRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQ 541
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1004 VIYGDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDGIFK--------SLLLLKKKKYAA 1063
Cdd:PRK05762 542 VIYGDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSKKRYAG 621
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1064 LIVEPTSDGNYVtkqeVKGLDIVRRDWCDLAKDTGNFVIGQILSDQnrdtiveNIQKRLIEIGENVLNGSVPvSQFEINK 1143
Cdd:PRK05762 622 LIQEGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EKLVYRK 689
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1144 ALTKDPQDYpDKKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGsnltagqrayaPEQLQKQDNLsIDTQYYL 1218
Cdd:PRK05762 690 RLRRPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNG-----------PEPLEYRKSP-IDYDYYI 756
|
650 660
....*....|....*....|....*....
gi 1387294325 1219 AQQIHPVVARICEPIDGIDAILIASWLGL 1247
Cdd:PRK05762 757 EKQLQPVADRILPFFGDDFATLKTGQLGL 785
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1273-1388 |
3.68e-39 |
|
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: 144.28 E-value: 3.68e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1273 LTDEEKYKDCERFKCPCPTCGTENIYDSVLDGS-GTDMEPSLYRCSNinCKASPLTFmvQLSNKLIMDIRRCIKKYYEGW 1351
Cdd:pfam08996 3 ISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYEGW 78
|
90 100 110
....*....|....*....|....*....|....*...
gi 1387294325 1352 LICEEPTCRNRTRHLPLQFSR-NGPLCqvcmKATLRLE 1388
Cdd:pfam08996 79 LVCDDPTCGNRTRQMSVYGKRcLGPGC----KGRMRYE 112
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
56-1231 |
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: 1479.92 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 56 EVEDFTSVYEEVDEEQYSKLVQARQDDDWIVDDDGIGYVEDGREIFDDDLEDDALDShEKGKDNKACNKDKRTVKRaaVT 135
Cdd:TIGR00592 1 MVEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILDLDK-DDGSAAEAKKKDKENHKK--VT 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 136 KPNNIKSMFIASAGRKTVDKAVDLSKDDLLGDILQDLN-TETPQ--ITPPPVIIPKKKRSSGAS---LNPFSVHTPKAAP 209
Cdd:TIGR00592 78 KPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVVD 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 210 SGKTTPPASRR---EPSLTPAPLTCAEFAGEPGPP-LCTDDKEESGAME--FEDGDF----DEPMEAEEVDV--EPVAAK 277
Cdd:TIGR00592 158 IVKKAIPVSTRyllEKILIPVPLKRAEFAGGDVQMeGDPELKLASFDIEtyFHDGKDffpgDENPADEEIMIstTPVIAK 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 278 TLCQEREPAEEAKHKADSGKGTTSSSA-SFLPDVSC----WDMDQEDDSSFsalEVQVDSSHLPLVKGADEeQVFQFYWl 352
Cdd:TIGR00592 238 QWDYESEPEARVVTWKKPDKPTTGSYVeSVSEEISMikrfWDVIDQEDTDV---EITVNGDNFDLVYLADR-QVFQFYW- 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 353 DAYEDPYSQPGVVFLFGKvwieSAEtHVSCCVMVKNIERSLCFLPREMKVDLNTGKESGTPVTMKDVYDEFDEKIAAKYK 432
Cdd:TIGR00592 313 DAYEDPAEKLGVVLLFGR----DVD-HVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYK 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 433 IMKFKSKVVEKNYAFEIP--DVPEKSEYLEVRYS-----AEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWL 505
Cdd:TIGR00592 388 KEKFRAKPIAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWL 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 506 EVKNPQLLNQP-ISWCKVEAMVLKPDLVNVIKDVGPPPVVVMSLSMKtMQNAKTHENEIIAVSALVHHSFALDKAPPQPP 584
Cdd:TIGR00592 468 AVKGPDELEYPrRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEPP 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 585 FQSHFCVVSKPKDCIFPYDFK-ESIKEKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVP 663
Cdd:TIGR00592 547 YDVHPCVGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIP 626
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 664 FWSKIGRLKRSnmPKLGGRsgFGEKnaTCGRMICDVEISAKELIRCKSYHLSELVQQILKTERIVIPIETIRNMYSDSSH 743
Cdd:TIGR00592 627 TWSKIGRLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSS 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 744 LLYLLEHTWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQTFRKpQQKLG 823
Cdd:TIGR00592 701 LTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKLG 779
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 824 DEDEDIdgdtNKYKKGrKKAAYSGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvaseaQKVVEDgeqeQ 903
Cdd:TIGR00592 780 DEDEEI----DGYKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDED----E 844
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 904 IPELPDPSLEMGILPREIRKLVERRRQVKQLMKQqDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVT 983
Cdd:TIGR00592 845 LPELPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVT 923
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 984 YKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGIFKSLLLLKKKKYAA 1063
Cdd:TIGR00592 924 AKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYAA 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1064 LIVEPTSDGNYVTKQEVKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIQKRLIEIGENVLNGSVPVSQFEINK 1143
Cdd:TIGR00592 1004 IKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVINK 1083
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1144 ALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTAGQRAYAPEQLQ-KQDNLSIDTQYYLAQQI 1222
Cdd:TIGR00592 1084 QLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEELQrKHNNLIYDTQYYLEHQI 1163
|
....*....
gi 1387294325 1223 HPVVARICE 1231
Cdd:TIGR00592 1164 HPVVLRILE 1172
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
838-1248 |
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: 729.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 838 KGRKKAAYSGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAseaqkvvEDGEQEQIPELPDPSLEMGIL 917
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRAD-------PDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 918 PREIRKLVERRRQVKQLMKQQDlNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMV 997
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 998 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGIFKSLLLLKKKKYAALIVEPtsDGNYVTK 1077
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1078 QEVKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKS 1157
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1158 LPHVHVALWINSQgGRKVKAGDTVSYVICQDGSNLTAGQRAYAPEQLQKQDNLSIDTQYYLAQQIHPVVARICEPIDGID 1237
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTD 389
|
410
....*....|.
gi 1387294325 1238 AILIASWLGLD 1248
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 ... |
780-1233 |
8.70e-169 |
|
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: 511.39 E-value: 8.70e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 780 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQtfrkpqqklgdededidgdtnkyKKGRKKAAYSGGLVLDPKVGFYD 859
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP-----------------------SAKGDEDGYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 860 KFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVVEDGEQEQIPELPD------PSLEMGILPREIRKLVERRRQVKQ 933
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 934 LMKQqDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM---NLEVIYGDTD 1010
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1011 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDGIFKSLLLLKKKKYAALIVEPTSDGNyvtKQEVKGLDIVRR 1088
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1089 DWCDLAKDTGNFVIGQILSDQNRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWIN 1168
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1387294325 1169 SQGGRKVKAGDTVSYVICQDGS---NLTAGQRAYAPEqLQKQDNLSIDTQYYLAQQIHPVVARICEPI 1233
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 ... |
541-773 |
6.15e-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: 368.09 E-value: 6.15e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 541 PPVVVMSLSMKTMQNAKTHENEIIAVSALVHHSFALDKAPPQPPFQSHFCVVSKPKDC-IFPYDFKESIKEKNVKVEVAA 619
Cdd:cd05776 1 PPLTVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRsPPPDLFEKNAKKKKTKVRIFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 620 TERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFWSKIGRLKRSNMPKLGGRSGFGEKNATCGRMICDV 699
Cdd:cd05776 81 NERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDT 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1387294325 700 EISAKELIRCKSYHLSELVQQILKTERIVIPIETIRNMYSDSSHLLYLLEHTWKDARFILQIMCELNVLPLALQ 773
Cdd:cd05776 161 YLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLNILPLTKQ 234
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
493-1234 |
6.48e-114 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 377.25 E-value: 6.48e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 493 FLMNRKIKGPCWLEVknpqllnQPISWCKVEAMVLKPDLVNVIKDVgPPPVVVMSLSMKT-----MQNAKTHEnEIIAVS 567
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFDIEVstprgFPDPERDG-PIISIG 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 568 alVHHSFALDKAppqppfqshfCVVSKPkdcifpydfkesikEKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYG 647
Cdd:COG0417 189 --LAGSDGEKKV----------LMLGRE--------------GVDFEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDN 242
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 648 FELEVLLQRINVCKVPFwsKIGRLKRSnmPKLGGRSGFGEKNATcGRMICDV-EISAKELIRCKSYHLSELVQQILKTER 726
Cdd:COG0417 243 FDLPYLQKRAERLGIPL--DLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGK 317
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 727 IVIPIETIRNMYSDSshLLYLLEHTWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENN 806
Cdd:COG0417 318 LIVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRG 395
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 807 YIVPDKqtfrkpqqklgdededidgdtnkykKGRKKAAYSGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVq 886
Cdd:COG0417 396 YLAPNK-------------------------GEIKGEAYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETL- 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 887 rvaseaqkvVEDGEQEQIPELPDPSL-------EMGILPREIRKLVERRRQVKQLMKQQDLNPDLHLQYDIRQKALKLTA 959
Cdd:COG0417 449 ---------VEGGEEPCGDEDVAPGFghrfcrePKGILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILM 519
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 960 NSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KL 1038
Cdd:COG0417 520 NSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWW 599
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1039 YKLLEIDIDGIFKSllllkkkkyaalIVEPTSDGNY--VTKQE---VKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDT 1113
Cdd:COG0417 600 PSGLELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEK 667
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1114 IVENIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVIcqdgsnLT 1193
Cdd:COG0417 668 AVEYVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI------TK 735
|
730 740 750 760
....*....|....*....|....*....|....*....|.
gi 1387294325 1194 AGQRAYaPEQLQKQDNLSIDTQYYLAQQIHPVVARICEPID 1234
Cdd:COG0417 736 GGGRVE-PVELAKERESEIDYDYYIEKQLKPTADRILEAFG 775
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
541-1017 |
6.07e-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: 363.77 E-value: 6.07e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 541 PPVVVMSLSMKTMQNAKTHENEIIAVSALVHHSFALDKAPPQPPFQsHFCVVSKPKDCIfpydfkesikeKNVKVEVAAT 620
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 621 ERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFWSKIGRLKRS-NMPKLGGRSGF------GEKNATCG 693
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlRIPNKKPLFGSksfglsDIKVYIKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 694 RMICDVEISAKELIRCKSYHLSELVQQILKTERIVIPIETIRNMYSDSSHLLY-LLEHTWKDARFILQIMCELNVLPLAL 772
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDeLLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 773 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQTFRKPQQKlgdededidgdtnkyKKGRKKAAYSGGLVLD 852
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSE---------------PDLKKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 853 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQK----VVEDGEQEQIPE-----LPDPSLEMGILPREIRK 923
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKgdliIPEDLLTIKYEKgnkyrFVKKNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 924 LVERRRQVKQLMKQ-QDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM-- 1000
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 1387294325 1001 ---NLEVIYGDTDSIMINTN 1017
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
615-1247 |
4.64e-76 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 269.80 E-value: 4.64e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 615 VEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFwsKIGRLKRSNMPKL-GGRSGFGEKNATcG 693
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 694 RMICD-VEISAKELIRCKSYHLSELVQQIL-KTERIVIP---IETIRNMYSDSSHLLylLEHTWKDARFILQIMCELNVL 768
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSLEYVSQRLLgEGKAIDDPydrMDEIDRRFAEDKPAL--ARYNLKDCELVTRIFEKTKLL 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 769 PLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDKQTfrkpqqklgdededidgdtnkykkgRKKAAYSGG 848
Cdd:PRK05762 352 PFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPNLGE-------------------------RPGEASPGG 404
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 849 LVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvaseaqkvVEDGEQEQIPELPDP-----SLEMGILPREIRK 923
Cdd:PRK05762 405 YVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGL----------VEGLAQPPEESVAGFlgarfSREKHFLPEIVER 473
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 924 LVERRRQVKQLMKQqdlnpdlhlqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLE 1003
Cdd:PRK05762 474 LWEGRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQ 541
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1004 VIYGDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDGIFK--------SLLLLKKKKYAA 1063
Cdd:PRK05762 542 VIYGDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSKKRYAG 621
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1064 LIVEPTSDGNYVtkqeVKGLDIVRRDWCDLAKDTGNFVIGQILSDQnrdtiveNIQKRLIEIGENVLNGSVPvSQFEINK 1143
Cdd:PRK05762 622 LIQEGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EKLVYRK 689
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1144 ALTKDPQDYpDKKSLPHVHVALWINSQGGRKVKA-----GDTVSYVICQDGsnltagqrayaPEQLQKQDNLsIDTQYYL 1218
Cdd:PRK05762 690 RLRRPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVITVNG-----------PEPLEYRKSP-IDYDYYI 756
|
650 660
....*....|....*....|....*....
gi 1387294325 1219 AQQIHPVVARICEPIDGIDAILIASWLGL 1247
Cdd:PRK05762 757 EKQLQPVADRILPFFGDDFATLKTGQLGL 785
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
843-1229 |
1.59e-71 |
|
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: 242.28 E-value: 1.59e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 843 AAYSGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVVEDGEQEQIPELPDpslemGILPREIR 922
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVGFRSPKDRK-----GLLPRILE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 923 KLVERRRQVKQLMKQQDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNL 1002
Cdd:cd00145 75 ELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGA 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1003 EVIYGDTDSIMINTN-STNLEEVFKLGNKVKSEVNKlYKLLEIDIDGIFKSLLLLKKKKYAALIVEPTSDGNyvtKQEVK 1081
Cdd:cd00145 155 RVIYGDTDSIFVSLPkMGTKEDAIKEGREILQELAD-EHLLELEFEKVYLPFFLGKKKRYAGLDIWKGQDEG---KIDIK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1082 GLDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIQKRLieigenvlngsvpvsqfeinkaltkdpqdypdkkslphv 1161
Cdd:cd00145 231 GLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL--------------------------------------- 271
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1387294325 1162 hvalwinsqggrkvkagDTVSYVICQDGSNLTAGQRAYAPEQLQkQDNLSIDTQYYLAQQIHPVVARI 1229
Cdd:cd00145 272 -----------------DKVKYVVTRGGKGVPDYERADPPLEDL-DKRHRIDYEYYLERLLQPPLERI 321
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
844-1231 |
5.12e-69 |
|
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Pssm-ID: 99919 Cd Length: 371 Bit Score: 236.84 E-value: 5.12e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 844 AYSGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvaseaqkvVEDGEQEQIPELP-------DPSlemGI 916
Cdd:cd05536 3 SYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTL----------VREGCEDCDVEPQvghkfrkDPP---GF 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 917 LPREIRKLVERRRQVKQLMKQQDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEM 996
Cdd:cd05536 69 IPSVLEDLLEERRRIKEKMKKLDPESEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKI 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 997 VQKMNLEVIYGDTDSIM--INTNSTNLEEVFKLGNKVKSEVNklyklLEIDIDGIFKSLLLLKKKKYAALivepTSDGny 1074
Cdd:cd05536 149 AEEKGFKVIYGDTDSLFvkIDGADAVKKKVKKLLKYINEELP-----LELEIEKFYKRGFFVTKKRYAGL----TEDG-- 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1075 vtKQEVKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpd 1154
Cdd:cd05536 218 --KIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVK----EVIEKLKRGEVPPEKLVIWKQLTKDLSEY-- 289
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1387294325 1155 KKSLPHVHVALWInSQGGRKVKAGDTVSYVICQDGSNLtaGQRAYAPEQLQKQDNlsIDTQYYLAQQIHPVVARICE 1231
Cdd:cd05536 290 KATGPHVAAAKKL-AKRGYKVRPGTKIGYVIVKGSGKI--SDRAYPYDMVDEKHK--YDAEYYIDNQVLPAVLRILE 361
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
377-717 |
1.02e-67 |
|
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: 231.92 E-value: 1.02e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 377 ETHVSCCVMVKNIERSLCFLPREmkvdlntgkesgtPVTMKDVYDEFDEKIAAKYKIMKFKSKVVEKNYAFEIPDVPekS 456
Cdd:pfam03104 3 DEGVSVCVNVFGFKPYFYCLAPD-------------GKELEEVIEEIKELYEGLDKIEKIELKLKKSLYGYEEDPVP--Y 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 457 EYLEVRYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVK-NPQLLNQPISWCKVEAMVLKPDLVNVI 535
Cdd:pfam03104 68 LKVSFANPRPLLKIRKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKvYPFRAEGRISNCDVEIDCDSPDLISVP 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 536 KDVGPPPVVVMSLSMKTMQ------NAKTHENEIIAVSALvhhsfaLDKAPPQPPFQSHfcvVSKPKDCIFPYDFKESIK 609
Cdd:pfam03104 148 FEKEWPPLRVLSFDIECTSlpgkfpDAENVKDPIIQISCM------LDGQGEPEPEPRF---LFTLRECDSEDIEDFEYT 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 610 EKN----VKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFWSKIGRLKRsNMPKLGGRSGF 685
Cdd:pfam03104 219 PKPiypgVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNR-GGRSKVREIGF 297
|
330 340 350
....*....|....*....|....*....|....*.
gi 1387294325 686 G----EKNATCGRMICDVEISAKELIRCKSYHLSEL 717
Cdd:pfam03104 298 GtrsyEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
845-1233 |
1.02e-61 |
|
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: 216.75 E-value: 1.02e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 845 YSGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRvASEAQKVVEdgeqEQIPELPD------PSLEMGILP 918
Cdd:cd05533 3 YEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLN-KNTAKKLPP----EDYIKTPNgdyfvkSSVRKGLLP 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 919 REIRKLVERRRQVKQLMKQQDlNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQ 998
Cdd:cd05533 78 EILEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVE 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 999 ---------KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGIFKSLLLLKKKKYAALIVep 1068
Cdd:cd05533 157 ekytkangySHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFiKPIKLEFEKVYFPYLLINKKRYAGLLW-- 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1069 TSDGNYvTKQEVKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIqKRLIeigENVLNGSVPVSQFEINKALTKD 1148
Cdd:cd05533 235 TNPDKH-DKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFV-KGVI---SDLLQNKIDISLLVITKALTKT 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1149 PQDYPDKksLPHVHVALWINSQG-GRKVKAGDTVSYVICQDGSNLTAGQRA----YAPEqlqkqDNLSIDTQYYLAQQIH 1223
Cdd:cd05533 310 ADDYAGK--QAHVELAERMRKRDpGSAPNVGDRVPYVIIKGAKGAKAYEKAedpiYVLE-----NNIPIDTQYYLENQLS 382
|
410
....*....|
gi 1387294325 1224 PVVARICEPI 1233
Cdd:cd05533 383 KPLLRIFEPI 392
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
493-1233 |
5.37e-60 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 225.29 E-value: 5.37e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 493 FLMNRKIKGPCWLEVKNPQ----LLNQPISWCKVEaMVLKPDLVNVIKDVG----PPPVVVMS-------LSMKTMQNAK 557
Cdd:PTZ00166 207 FLIDNNITGGSWLTLPKGKykirPPKKKTSTCQIE-VDCSYEDLIPLPPEGeyltIAPLRILSfdiecikLKGLGFPEAE 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 558 TheNEIIAVSALVHHsfaldKAPPQPPFQSH-FCVvskpKDCifpydfkESIKEKNVKVevAATERTLLGFFLAKVHKID 636
Cdd:PTZ00166 286 N--DPVIQISSVVTN-----QGDEEEPLTKFiFTL----KEC-------ASIAGANVLS--FETEKELLLAWAEFVIAVD 345
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 637 PDIIVGHNIYGFELEVLLQRINVCKVPFWSKIGRLK---------RSNMPKLGGRSGfGEKNaTCGRMICDVeisaKELI 707
Cdd:PTZ00166 346 PDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKstrsvikdsKFSSKQMGTRES-KEIN-IEGRIQFDV----MDLI 419
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 708 R----CKSYHLSELVQQILKTERIVIPIETIRNMY--SDSSH---LLYLLehtwKDARFILQIMCELNVLPLALQITNIA 778
Cdd:PTZ00166 420 RrdykLKSYSLNYVSFEFLKEQKEDVHYSIISDLQngSPETRrriAVYCL----KDAILPLRLLDKLLLIYNYVEMARVT 495
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 779 GNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqtfrkpqqklgdededidgdTNKYKKGRKKAAYSGGLVLDPKVGFY 858
Cdd:PTZ00166 496 GTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIP----------------------TVKYSGGGSEEKYEGATVLEPKKGFY 553
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 859 DKFILLLDFNSLYPSIIQEFNICFTTVqrVASEAQKVVEDGEQEQIP---ELPDPSLEMGILPREIRKLVERRRQVKQLM 935
Cdd:PTZ00166 554 DEPIATLDFASLYPSIMIAHNLCYSTL--VPPNDANNYPEDTYVTTPtgdKFVKKEVRKGILPLIVEELIAARKKAKKEM 631
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 936 KQQDlNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYakP---LAALVTYKGREILMHTKEMVQKM---------NLE 1003
Cdd:PTZ00166 632 KDEK-DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQL--PcleVSTSITSFGRQMIDKTKELVEKHytkangykhDAT 708
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1004 VIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGIFKSLLLLKKKKYAALIVepTSDGNYvTKQEVKG 1082
Cdd:PTZ00166 709 VIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFlKPIKLEFEKVYCPYLLMNKKRYAGLLY--TNPEKY-DKIDCKG 785
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1083 LDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIQKRLIEIGENVLNgsvpVSQFEINKALTKDpqDYpdKKSLPHVH 1162
Cdd:PTZ00166 786 IETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRID----ISLLVITKSLGKD--DY--EGRLAHVE 857
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1163 VAlwinsqggRKVKA---------GDTVSYVICQDgsnlTAGQRAY--APEQLQKQDN-LSIDTQYYLaQQIHPVVARIC 1230
Cdd:PTZ00166 858 LA--------KKLRQrdpgsapnvGDRVSYVIVKG----AKGAPQYerAEDPLYVLENnIPIDTQYYL-DQIKNPLLRIF 924
|
...
gi 1387294325 1231 EPI 1233
Cdd:PTZ00166 925 EGV 927
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
849-1237 |
2.06e-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: 170.86 E-value: 2.06e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 849 LVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTT-VQRVASEAQKVVEDGEQEQIPELPDPSLEM------------- 914
Cdd:cd05534 40 LVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTcLGRVEELNGGGKFGFLGVKLYLPPPPLDLLllkddvtispngv 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 915 ---------GILPREIRKLVERRRQVKQLMKQQDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYS-RFYAKPLAALVTY 984
Cdd:cd05534 120 mfvkksvrkGILPKMLEEILDTRIMVKKAMKKYKDDKKLQRILDARQLALKLLANVTYGYTAASFSgRMPCVEIADSIVQ 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 985 KGREILMHTKEMVQ---KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGIFKSLLLLKKKK 1060
Cdd:cd05534 200 TGRETLERAIELIEstpKWGAKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVTAANpSPIKLKFEKVYHPCVLVTKKR 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1061 YAALIVEPTSDGnyVTKQEVKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIQKRLieigENVLNGSVPVSQFE 1140
Cdd:cd05534 280 YVGYKYESPDQT--EPTFDAKGIETVRRDGCPAVQKILEKSLRILFETKDLSTVKSYLQRQW----SKLLQGRVSIQDFI 353
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1141 INKALTKDpqDYPDKKSLP-HVHVAL-WINSQGGRKVKAGDTVSYVICQDGSNLTAGQRAYAPEQLQKQDNLSIDTQYYL 1218
Cdd:cd05534 354 FAKEVRLG--TYKEGATLPaGAIVALrRMEKDPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLADPSLRLDAEYYI 431
|
410
....*....|....*....
gi 1387294325 1219 AQQIHPVVARICEPIdGID 1237
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 ... |
545-763 |
5.14e-43 |
|
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: 155.59 E-value: 5.14e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 545 VMSLSMKTMQNAKTHEN---EIIAVSALVhhSFALDKAPPQPPFQSHFCVVSKpkdcifpydfkesikEKNVKVEVAATE 621
Cdd:cd05160 1 VLSFDIETTPPVGGPEPdrdPIICITYAD--SFDGVKVVFLLKTSTVGDDIEF---------------IDGIEVEYFADE 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 622 RTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFWSKIGRlkRSNMPKlggRSGFGEKNATCGRMICDVEI 701
Cdd:cd05160 64 KELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYR--RSGGEK---SSGSTERIAVKGRVVFDLLA 138
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1387294325 702 SAKELIRCKSYHLSELVQQILK-TERIVIPIETIRNMysDSSHLLYLLEHTWKDARFILQIMC 763
Cdd:cd05160 139 AYKRDFKLKSYTLDAVAEELLGeGKEKVDGEIIEDAE--WEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
838-1218 |
3.44e-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: 3.44e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 838 KGRKkaaYSGGLVLDPKVG-FYDkfILLLDFNSLYPSIIQEFNICFTTVQrvaseaqKVVEDGEQEQIPELPD------- 909
Cdd:cd05530 9 KGKK---YRGAIVLEPPPGiFFN--VVVLDFASLYPSIIKVWNLSYETVN-------CPHCECKTNEVPEVGHwvckkrp 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 910 --PSLEMGILpreiRKLveRRRQVKQLMKQQDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGR 987
Cdd:cd05530 77 giTSQIIGLL----RDL--RVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGR 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 988 EILMHTKEMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDGIFKsllllkkkkyaaLIV 1066
Cdd:cd05530 151 YIITSTIKKARELGLKVLYGDTDSLFLwNPPQEQLEDLVE---WVEKELG-----LDLELDKEYR------------YVV 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1067 EPTSDGNY--VTKQ---EVKGLDIVRRDWCDLAKDTGNFVIgQILSDQNRDTIVENIQKRLIEI----GENVLNGSVPVS 1137
Cdd:cd05530 211 FSGLKKNYlgVTKDgsvDIKGLLGKKRNTPEFVKELFYEVI-EILSAVNSPEDFEKAREKIRDIvkgvYKRLKKKEYTLD 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1138 QFEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVicqdgsnLTAGQRAYAPEQLQKQDNlsIDTQYY 1217
Cdd:cd05530 290 QLAFKVMLSKPPEEY-TKNTPQHVKAARQLEKY-GRNVEAGDIISYV-------KVKGKEGVKPVQLARLDE--VDVEKY 358
|
.
gi 1387294325 1218 L 1218
Cdd:cd05530 359 V 359
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
847-1233 |
5.81e-41 |
|
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: 155.50 E-value: 5.81e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 847 GGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNIcfTTVQRVasEAQKvvEDGEQEQIPELPDP--SLEMGILPREIRKL 924
Cdd:cd05537 5 GGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI--DPLGLI--EGLK--APDPEDLIPGFLGArfSREKHILPDLIARL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 925 VERRRQVKQlmkqqDLNPDLhlqydirQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEV 1004
Cdd:cd05537 78 WAARDEAKR-----EKNAPL-------SQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQV 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1005 IYGDTDSIMINTNST-NLEEVFKLGNKVKSEVN--------KLYKL---LEIDIDGIF--------KSLLLLKKKKYAAL 1064
Cdd:cd05537 146 IYGDTDSTFVWLGEElDAAEAQAIGKELASQINqwwaqklkEEFGLesfLEIEFETHYsrffmptiRGSDEGSKKRYAGL 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1065 IVEPTSDgnyvtKQEVKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIQKRLIEiGEnvLNgsvpvSQFEINKA 1144
Cdd:cd05537 226 KSTDGGD-----ELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLA-GE--LD-----ELLVYRKR 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1145 LTKDPQDYpDKKSLPHVHVALW---INSQGGRKvKAGDTVSYVICQDGsnltagqrayaPEQLQkQDNLSIDTQYYLAQQ 1221
Cdd:cd05537 293 LRRPLSEY-TKNVPPHVQAARLadqINRELGRP-RQYQWIEYVITVNG-----------PEPLE-YRTSPLDYQHYIDKQ 358
|
410
....*....|..
gi 1387294325 1222 IHPvvarICEPI 1233
Cdd:cd05537 359 LKP----IADSI 366
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
837-1218 |
2.46e-40 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 161.40 E-value: 2.46e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 837 KKGRKKAAYSGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvaseaqkvvEDGEQEQIPELPDPSL---- 912
Cdd:PRK05761 399 KAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETV-----------RIPECKCHYDDEVPELghsv 466
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 913 --EMGILPREIRKLV--ERRRQVKQLMKQQDLNPDLHLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGRE 988
Cdd:PRK05761 467 cdDRPGLTSVLVGLLrdFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGRE 546
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 989 ILMHTKEMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDGIFKsllllkkkkYAALIVE 1067
Cdd:PRK05761 547 ILLSTKKKAEELGLKVLYGDTDSLFVwGPTKESLEELIK---EIEERTG-----IDLEVDKTYD---------WVAFSGL 609
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1068 P------TSDGNYvtkqEVKGLDIVRRDWCDLAKDTGNFVIGQILSDQNRDTIVENIQK---RLIEIGENVLNGSVPVSQ 1138
Cdd:PRK05761 610 KknyfgvLKDGKV----KIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEKVKDEiedVLKRYYEKLRAKDYPLDE 685
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1139 FEINKALTKDPQDYpDKKSLPHVHVALWINSQGGrKVKAGDTVSYVIcqdgsnlTAGQRAYAPEQLQKQDnlSIDTQYYL 1218
Cdd:PRK05761 686 LAIRVRLSKPLDEY-TKNTPQHVKAALQLRDYGV-EVSPGDIISYVK-------VDDKRGVKPVQLAKLS--EIDVEKYI 754
|
|
| zf-DNA_Pol |
pfam08996 |
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ... |
1273-1388 |
3.68e-39 |
|
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: 144.28 E-value: 3.68e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1273 LTDEEKYKDCERFKCPCPTCGTENIYDSVLDGS-GTDMEPSLYRCSNinCKASPLTFmvQLSNKLIMDIRRCIKKYYEGW 1351
Cdd:pfam08996 3 ISDEERFKDCEPLELRCPSCGTEFEFEGVFASAdGYSVTPSGLRCPN--CDASLSPA--SLVNQLELQIRAHISRYYEGW 78
|
90 100 110
....*....|....*....|....*....|....*...
gi 1387294325 1352 LICEEPTCRNRTRHLPLQFSR-NGPLCqvcmKATLRLE 1388
Cdd:pfam08996 79 LVCDDPTCGNRTRQMSVYGKRcLGPGC----KGRMRYE 112
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
843-1236 |
5.02e-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: 123.22 E-value: 5.02e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 843 AAYSGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVVEDGEQEQIPElpdpsleMGILPREIR 922
Cdd:cd05531 3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETINCRCCECRDHVYLGHRICLKR-------RGFLPEVLE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 923 KLVERRRQVKQLMKQQDlnpdlhlQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNL 1002
Cdd:cd05531 75 PLLERRLEYKRLKKEED-------PYAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEMGF 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1003 EVIYGDTDSIMINTNSTNLEEVFKLGNKVKsevnklyklLEIDIDGIFKsllllkkkkyaALIVEPTSDG-----NYVTK 1077
Cdd:cd05531 148 RVLHGIVDSLWIQGRGDIEELAREIEERTG---------IPLKLEGHYD-----------WIVFLPERDGlgapnRYFGR 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1078 QE-----VKGLDIVRRDWCDLAKDTGNFVIgQILSdQNRDtiVENIQKRLIEIgENVLNGSV------PVSQFEINKALT 1146
Cdd:cd05531 208 LSdgemkVRGIELRRRDTPPFVKKFQEEAL-DILA-SAKT--PEELLKLREEA-LDLFRRYLqrlregDLEDLIIEKKIS 282
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1147 KDPQDYpdkKSLPHvHVALWINSQgGRKVKAGDTVSYVIcqdgsnltAGQRAYAPEqlqKQDNLSIDTQYYLAQQIHPVv 1226
Cdd:cd05531 283 KRSSEY---KVLAS-TALKALRAK-GVSVVPGMKIEYIV--------RDGKRPVPD---LGNDEGYDTKYYRELLERAA- 345
|
410
....*....|
gi 1387294325 1227 aricEPIDGI 1236
Cdd:cd05531 346 ----EELLFP 351
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
836-1159 |
5.74e-20 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 96.63 E-value: 5.74e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 836 YKKGRKKAA--YSGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAS-----EAQKVVEDGEQ------- 901
Cdd:PHA03036 519 LVRSETKNKfpYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVndnrlEAEINKQELRRkypypry 598
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 902 ---EQIPELPDPSLEM--------GILPREIRKLVERRRQVKQLMKQQDLNPDLHLqYDIRQKALKLTANSMYGCLGFSY 970
Cdd:PHA03036 599 iyvHCEPRSPDLVSEIavfdrrieGIIPKLLKTFLEERARYKKLLKEATSSVEKAI-YDSMQYTYKIVANSVYGLMGFRN 677
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 971 SRFYAKPLAALVTYKGREILMHTKEMV--------------------------------------QKMNLEVIYGDTDSI 1012
Cdd:PHA03036 678 SALYSYASAKSCTAIGRNMIKYLNSVLngsklingklilancpinpffkddrsidtnydtnlpveYNFTFRSVYGDTDSV 757
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1013 MINTNSTNLEEVFKLGNKVKSEVNK--LYKLLEIDIDGIFKSLLLLKKKKYAALIVEPTSDGNYVTKQEVKGLDIVRRDW 1090
Cdd:PHA03036 758 FLEINTKDVDKSIKIAKELERIINEkvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVPERVNKGTSETRRDV 837
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1387294325 1091 CDLAKdtgnfvigqilsdqnrdTIVENIQKRLIEIGENVLNGSVPVSqFEINKALTKDPQDYPDKKSLP 1159
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, ... |
866-1194 |
1.92e-15 |
|
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99921 Cd Length: 347 Bit Score: 79.45 E-value: 1.92e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 866 DFNSLYPSIIQEFNICfttvqrVASEaqkvvedgeqeqipelpdpslEMGILPREIRKLVERRRQVKQLMKQQDLnPDLH 945
Cdd:cd05538 23 DVASLYPSIMLAYRIC------PARD---------------------SLGIFLALLKYLVELRLAAKESARAAAR-PAER 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 946 LQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMI---NTNSTNLE 1022
Cdd:cd05538 75 DAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFippNGVDTEDE 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1023 EvfklgNKVKSEVNK-LYKLLEIDIDGIFKSLLLLKKKKYAALiveptsdgNYVTKQEVKGLDIVRRDWCDLAKDTGNFV 1101
Cdd:cd05538 155 E-----EELVRELSStLPKGITVEFDGRYRAMFSYKIKNYALL--------DYDGKLIVKGSAFRSRGIEPFLREFLREA 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 1102 IGQILSDQnrdtiVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDK----KSLPhvHVALWINSQGGRKVKA 1177
Cdd:cd05538 222 VRLLLQGD-----GAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYLQKvragKRNP--AAAYEIALARPREWRA 294
|
330
....*....|....*..
gi 1387294325 1178 GDTVSYVICQDGSNLTA 1194
Cdd:cd05538 295 GDRVTYYVSGTGKGVSV 311
|
|
| DNA_pol_alpha_N |
pfam12254 |
DNA polymerase alpha subunit p180 N terminal; This domain family is found in eukaryotes, and ... |
41-101 |
1.00e-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: 67.19 E-value: 1.00e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1387294325 41 LERLKRAKAGEK---YKYEVEDFTSVYEEVDEEQYSKLVQARQDDDW-IVDDDGIGYVEDGREIF 101
Cdd:pfam12254 1 LEKLKAARAGGKrrlDEYESEEDEDIYDEVDEEEYRKIVRKRLLDDDfVVDDDGEGYVDDGREDW 65
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
837-1015 |
1.90e-13 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 75.50 E-value: 1.90e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 837 KKGRKKAAYSGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQkvVEDGEQEQIPELPD-----PS 911
Cdd:PHA02528 369 NKSHKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFHVAP--VHEYINKTAPRPSDeyscsPN 445
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 912 LEM------GILPREIRKLVERRRQVKQLM---KQQ-----------------DLNPDLHL------------------- 946
Cdd:PHA02528 446 GWMyrkdirGVIPTEIKKVFDQRKIYKKKMlaaERNaeliktiledlndsvdtPIDVDYYFdfsdefkaelktltksslk 525
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 947 -----------QYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGR-EILMHTKEMVQKMNL--------EVIY 1006
Cdd:PHA02528 526 alleecekeiaLCNTIQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQlAIQWIERKMNEYLNKlcktededYVIY 605
|
....*....
gi 1387294325 1007 GDTDSIMIN 1015
Cdd:PHA02528 606 GDTDSIYVN 614
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
833-1013 |
3.69e-09 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 61.80 E-value: 3.69e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 833 TNKYKKG-RKKAAYSGGLVLDPKVGF-----YDKFILLLDFNSLYPSIIQEFNICFTTV---QRVASEAQKVVEDgeQEQ 903
Cdd:PHA03334 620 PEKYARDcRQKIKLKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIvdpDCTARVRGWVVFD--WKK 697
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 904 IPE-LPDPSLEMGIL---PRE-------------IRKLVERRRQVKQLMKQQDlNPDLHLQYDIRQKALKLTANSMYGcl 966
Cdd:PHA03334 698 IDRgFGKATLMYTILrtkPEEpswrrfttyttssLNHYLSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYG-- 774
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 1387294325 967 gfsysrfyAKPLAA--LVTYKGREILMHTKEMVQKM-NLEVIYGDTDSIM 1013
Cdd:PHA03334 775 --------VAPHACqhLITTLGRHKIKLVEEFIKKEpGMTVNYGDTDSVM 816
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
603-761 |
2.53e-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: 55.44 E-value: 2.53e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 603 DFKESIKEKNV---KVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFwsKIGRLKRSnmPKL 679
Cdd:cd05780 35 GGNKVITWKKFdlpFVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIEL--DLGRDGSE--IKI 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 680 gGRSGFGEKNATCGRMICDVEISAKELIRCKSYHLSELVQQILKTERIVIPIETIRNMYSDSSHLLYLLEHTWKDARFIL 759
Cdd:cd05780 111 -QRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTY 189
|
..
gi 1387294325 760 QI 761
Cdd:cd05780 190 EI 191
|
|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
589-674 |
2.93e-07 |
|
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 99828 [Multi-domain] Cd Length: 207 Bit Score: 52.80 E-value: 2.93e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 589 FCVVSKPKDCIFPYDFKESIKEKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPF-WSK 667
Cdd:cd05785 26 FSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLaIGR 105
|
....*..
gi 1387294325 668 IGRLKRS 674
Cdd:cd05785 106 DGSIPRQ 112
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
620-674 |
4.01e-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: 52.58 E-value: 4.01e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1387294325 620 TERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFWSKIGRLKRS 674
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 ... |
583-762 |
1.72e-06 |
|
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: 50.70 E-value: 1.72e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 583 PPFQSHFCVVSKPKDcifPYDFKESIK-EKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRIN-VC 660
Cdd:cd05778 45 DANKVGVIIVDELKS---NASNGRIRSgLSGIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAaLG 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 661 KVPFWSKIGRLKRSNMPKLGGRS-GFGEKNAT----CGRMICDV------EISakeLIrckSYHLSELVQQILKtERI-V 728
Cdd:cd05778 122 IDDLLDEISRVPSDSNGKFGDRDdEWGYTHTSgikiVGRHILNVwrlmrsELA---LT---NYTLENVVYHVLH-QRIpL 194
|
170 180 190
....*....|....*....|....*....|....*.
gi 1387294325 729 IPIETIRNMY--SDSSHLLYLLEHTWKDARFILQIM 762
Cdd:cd05778 195 YSNKTLTEWYksGSASERWRVLEYYLKRVRLNLEIL 230
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
610-670 |
2.24e-06 |
|
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: 49.87 E-value: 2.24e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1387294325 610 EKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFwsKIGR 670
Cdd:cd05784 40 DAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPL--RLGR 98
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
607-761 |
2.62e-05 |
|
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: 46.55 E-value: 2.62e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 607 SIKEKNVKVEVAATE----RTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKVPFwsKIGRlKRSNMPKlggR 682
Cdd:cd05781 30 SLATSNGDVEFILAEglddRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKL--DVGR-RGGSEPS---T 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387294325 683 SGFGEKNATcGRMICDVEISAKEL--IRCKS-YHLSELVQQILKTERIVIPIETIRNMYSDSSHLLYLLEHTWKDARFIL 759
Cdd:cd05781 104 GVYGHYSIT-GRLNVDLYDFAEEIpeVKVKTlENVAEYLGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTY 182
|
..
gi 1387294325 760 QI 761
Cdd:cd05781 183 GL 184
|
|
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
946-1012 |
8.85e-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: 40.35 E-value: 8.85e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1387294325 946 LQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMN--LEViygDTDSI 1012
Cdd:cd05535 269 VLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELVEQIGrpLEL---DTDGI 334
|
|
| |
