|
Name |
Accession |
Description |
Interval |
E-value |
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
56-1187 |
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 1370518488 56 EVEDFTGVYEEVDEEQYSKLVQARQDDDWIVDDDGIGYVEDGREIFDDDLEDDALDADeKGKDGKARNKDKRNVKKlaVT 135
Cdd:TIGR00592 1 MVEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILDLDKD-DGSAAEAKKKDKENHKK--VT 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 136 KPNNIKSMFIACAGKKTADKAVDLSKDGLLGDILQDLN-TETPQ--ITPPPVMILKKKRSIGAS---PNPFSVHTATAVP 209
Cdd:TIGR00592 78 KPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNkTETAQrkITPRLVSVPKLKFSSPADvpaINDFSNHHPAVVD 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 210 SGKIASPVSRK---EPPLTPVPLKRAEFAGDDVQVE-STEEEQESGAME--FEDGDF----DE-PMEVEEVDL-EPMAAK 277
Cdd:TIGR00592 158 IVKKAIPVSTRyllEKILIPVPLKRAEFAGGDVQMEgDPELKLASFDIEtyFHDGKDffpgDEnPADEEIMIStTPVIAK 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 278 AWDKESEPAEEVKQEADSGKGTV-SYLGSFLPDVSC----WD-IDQEGDSsfsvQEVQVDSSHLPLVKGADEeQVFHFYW 351
Cdd:TIGR00592 238 QWDYESEPEARVVTWKKPDKPTTgSYVESVSEEISMikrfWDvIDQEDTD----VEITVNGDNFDLVYLADR-QVFQFYW 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 352 lDAYEDQYNQPGVVFLFGKvwieSAEtHVSCCVMVKNIERTLYFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKY 431
Cdd:TIGR00592 313 -DAYEDPAEKLGVVLLFGR----DVD-HVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGY 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 432 KIMKFKSKPVEKNYAFEIP--DVPEKSEYLEVKYS-----AEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCW 504
Cdd:TIGR00592 387 KKEKFRAKPIAKKYEFEAPdiDAPYSSEYLEVTYElgkefAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCW 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 505 LEVKSPQLLNQPV-SWCKVEAMALKPDLVNVIKDVSPPPLVVMAFSMKtMQNAKNHQNEIIAMAALVHHSFALDKAAPKP 583
Cdd:TIGR00592 467 LAVKGPDELEYPRrSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-SLNPSIIRNEIVSIPDTLHREFALDKPPPEP 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 584 PFQSHFCVVSKPKDCIFPYAFK-EVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKA 662
Cdd:TIGR00592 546 PYDVHPCVGTRPKDCSFPLDLKgEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKI 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 663 PHWSKIGRLKRSnmPKLGGRsgFGERnaTCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESS 742
Cdd:TIGR00592 626 PTWSKIGRLRRS--PKFGRR--FGER--TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESS 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 743 QLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKpQQKL 822
Cdd:TIGR00592 700 SLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRK-QQKL 778
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 823 GDEDEEIDGdtnkYKKGrKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQrvaseaQKVTEDgeqe 902
Cdd:TIGR00592 779 GDEDEEIDG----YKKG-KKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ------QKVDED---- 843
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 903 QIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQqDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALV 982
Cdd:TIGR00592 844 ELPELPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALV 922
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 983 TYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYA 1062
Cdd:TIGR00592 923 TAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYA 1002
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1063 ALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEIN 1142
Cdd:TIGR00592 1003 AIKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVIN 1082
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|....*
gi 1370518488 1143 KALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQ 1187
Cdd:TIGR00592 1083 KQLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICK 1127
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
838-1188 |
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: 627.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 838 KGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAseaqkvtEDGEQEQIPELPDPSLEMGIL 917
Cdd:cd05532 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRAD-------PDDEDDEEPPLPPSDQEKGIL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 918 PREIRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMV 997
Cdd:cd05532 74 PRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 998 QKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPtsDGNYVTK 1077
Cdd:cd05532 153 EKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVD--DDKGKLK 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1078 QELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKS 1157
Cdd:cd05532 231 KEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKS 310
|
330 340 350
....*....|....*....|....*....|.
gi 1370518488 1158 LPHVHVALWINSQgGRKVKAGDTVSYVICQQ 1188
Cdd:cd05532 311 LPHVQVALRMNKR-GRKVKAGDTIPYIICKD 340
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
780-1188 |
6.20e-154 |
|
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: 467.47 E-value: 6.20e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 780 NIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQifrkpqQKLGDEDeeidgdtnkykkgrkkaAYAGGLVLDPKVGFYD 859
Cdd:pfam00136 1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRP------SAKGDED-----------------GYQGATVIEPKKGFYD 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 860 KFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPD------PSLEMGILPREIRKLVERRKQVKQ 933
Cdd:pfam00136 58 KPVLVLDFNSLYPSIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRgvyfvkDHVREGLLPKLLKDLLAKRKAIKK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 934 LMKQqDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM---NLEVIYGDTD 1010
Cdd:pfam00136 138 LLKE-ETDPFERAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTD 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1011 SIMINTNSTNLEEVFKLGNKVKSEVNK-LYKL-LEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyvtKQELKGLDIVRR 1088
Cdd:pfam00136 217 SVFIEFGGKDVEEAMKIGDELAEHVNQdLFKSpIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFN---KLDMKGVDLVRR 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1089 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWIN 1168
Cdd:pfam00136 294 DNCPLVKEVIKKVLDLLLSDRGLPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMN 372
|
410 420
....*....|....*....|
gi 1370518488 1169 SQGGRKVKAGDTVSYVICQQ 1188
Cdd:pfam00136 373 KRNGEAPEVGDRIPYVIVKA 392
|
|
| DNA_polB_alpha_exo |
cd05776 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ... |
541-773 |
1.32e-119 |
|
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: 369.25 E-value: 1.32e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 541 PPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVSKPKDC-IFPYAFKEVIEKKNVKVEVAA 619
Cdd:cd05776 1 PPLTVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRsPPPDLFEKNAKKKKTKVRIFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 620 TERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDV 699
Cdd:cd05776 81 NERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDT 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1370518488 700 EISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQIMCELNVLPLALQ 773
Cdd:cd05776 161 YLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLNILPLTKQ 234
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
541-1017 |
6.09e-114 |
|
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: 363.39 E-value: 6.09e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 541 PPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQsHFCVVSKPKDCIfpyafkeviekKNVKVEVAAT 620
Cdd:smart00486 1 PPLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANR-RILFTLGTCKEI-----------DGIEVYEFNN 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 621 ERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRS----NMPKLGGRSGFGERNAT---CG 693
Cdd:smart00486 69 EKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIGlripNKKPLFGSKSFGLSDIKvyiKG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 694 RMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSES-SQLLYLLEHTWKDAKFILQIMCELNVLPLAL 772
Cdd:smart00486 149 RLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNyEERDELLRYCIQDAVLTLKLFNKLNVIPLII 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 773 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKqifrkpqqklgdedEEIDGDTNKYKKgRKKAAYAGGLVLD 852
Cdd:smart00486 229 ELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSK--------------ELYDFKGSEPDL-KKKVKYEGGKVLE 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 853 PKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKV-TEDGEQEQIPELPDP--------SLEMGILPREIRK 923
Cdd:smart00486 294 PKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGdLIIPEDLLTIKYEKGnkyrfvkkNIRKGILPKLLKK 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 924 LVERRKQVKQLMKQ-QDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM-- 1000
Cdd:smart00486 374 LLDKRKEIKKLMKKeKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENgy 453
|
490 500
....*....|....*....|
gi 1370518488 1001 ---NLEVIYGDTDSIMINTN 1017
Cdd:smart00486 454 pkpGFKVIYGDTDSIFVTKP 473
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
493-1185 |
4.61e-104 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 347.20 E-value: 4.61e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 493 FLMNRKIKGPCWLEVkspqllnQPVSWCKVEAMALKPDLVNVIKDVsPPPLVVMAF----SMKTMQNAKNHQNEIIAMAa 568
Cdd:COG0417 118 YLIDRFLTPGVWYEG-------EVEEDGGKLDYEVKENPRLKPEDY-RPKLKVLSFdievSTPRGFPDPERDGPIISIG- 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 569 lVHHSFALDKAapkppfqshFCVVSKPKDcifpyafkeviekknVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGF 648
Cdd:COG0417 189 -LAGSDGEKKV---------LMLGREGVD---------------FEVEYFDDEKALLEAFFEIIREYDPDIIIGWNVDNF 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 649 ELEVLLQRINVCKAPhwSKIGRLKRSnmPKLGGRSGFGERNATcGRMICDV-EISAKELIRCKSYHLSELVQQILKTERV 727
Cdd:COG0417 244 DLPYLQKRAERLGIP--LDLGRDGSE--PSWREHGGQGFASIP-GRVVIDLyDALKSATYKFKSYSLDAVAEELLGEGKL 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 728 VIPMENIQNMYSESsqLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNY 807
Cdd:COG0417 319 IVDGGEIERLWDDD--KPALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGY 396
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 808 IVPDKqifrkpqqklgdedEEIDGDtnkykkgrkkaAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQR 887
Cdd:COG0417 397 LAPNK--------------GEIKGE-----------AYPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFNISPETLVE 450
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 888 VASEaqkvtEDGEQEQIPELP-----DPSlemGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSM 962
Cdd:COG0417 451 GGEE-----PCGDEDVAPGFGhrfcrEPK---GILPSILEELWDERDEAKKKMKKAKPDSEEYRLYDALQQALKILMNSF 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 963 YGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVN-KLYKL 1041
Cdd:COG0417 523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINaWWPSG 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1042 LEIDIDGVFKSllllkkkkyaalVVEPTSDGNY--VTKQE---LKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVE 1116
Cdd:COG0417 603 LELEFEKHYRR------------FFFPGSKKRYagLTEDGkidIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVE 670
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370518488 1117 NIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYVI 1185
Cdd:COG0417 671 YVR----DVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDER-GRPYQRGDKISYVI 733
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
377-717 |
1.39e-70 |
|
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.
Pssm-ID: 397292 Cd Length: 333 Bit Score: 239.63 E-value: 1.39e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 377 ETHVSCCVMVKNIERTLYFLPREmkidlntGKETgtpismKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPekS 456
Cdd:pfam03104 3 DEGVSVCVNVFGFKPYFYCLAPD-------GKEL------EEVIEEIKELYEGLDKIEKIELKLKKSLYGYEEDPVP--Y 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 457 EYLEVKYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVK-SPQLLNQPVSWCKVEAMALKPDLVNVI 535
Cdd:pfam03104 68 LKVSFANPRPLLKIRKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKvYPFRAEGRISNCDVEIDCDSPDLISVP 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 536 KDVSPPPLVVMAFSMKTMQ------NAKNHQNEIIAMAALVHhsfalDKAAPKPPFQSHFCVVSKPKDCIFPYAFKEVIE 609
Cdd:pfam03104 148 FEKEWPPLRVLSFDIECTSlpgkfpDAENVKDPIIQISCMLD-----GQGEPEPEPRFLFTLRECDSEDIEDFEYTPKPI 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 610 KKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRsNMPKLGGRSGFG--- 686
Cdd:pfam03104 223 YPGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNR-GGRSKVREIGFGtrs 301
|
330 340 350
....*....|....*....|....*....|..
gi 1370518488 687 -ERNATCGRMICDVEISAKELIRCKSYHLSEL 717
Cdd:pfam03104 302 yEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
843-1157 |
2.31e-70 |
|
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.
Pssm-ID: 99912 [Multi-domain] Cd Length: 323 Bit Score: 238.42 E-value: 2.31e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 843 AAYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPDpslemGILPREIR 922
Cdd:cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVGFRSPKDRK-----GLLPRILE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 923 KLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNL 1002
Cdd:cd00145 75 ELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGA 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1003 EVIYGDTDSIMINTN-STNLEEVFKLGNKVKSEVNKlYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNyvtKQELK 1081
Cdd:cd00145 155 RVIYGDTDSIFVSLPkMGTKEDAIKEGREILQELAD-EHLLELEFEKVYLPFFLGKKKRYAGLDIWKGQDEG---KIDIK 230
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1370518488 1082 GLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEInkalTKDPQDYPDKKS 1157
Cdd:cd00145 231 GLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDELDKVKYVVTRGGKGVPDYER----ADPPLEDLDKRH 302
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
615-1185 |
4.39e-70 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 251.31 E-value: 4.39e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 615 VEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRLKRSNMPKL-GGRSGFGERNATcG 693
Cdd:PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIP--LRLGRDGSELEWREhPFRSGYGFASVP-G 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 694 RMICD-VEISAKELIRCKSYHLSELVQQIL----KTERVVIPMENIQNMYSESSQLLylLEHTWKDAKFILQIMCELNVL 768
Cdd:PRK05762 274 RLVLDgIDALKSATWVFDSFSLEYVSQRLLgegkAIDDPYDRMDEIDRRFAEDKPAL--ARYNLKDCELVTRIFEKTKLL 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 769 PLALQITNIAGNIMSRtlMGGRSERNEFLLLHAFYENNYIVPDkqifrkpqqkLGDEDEEidgdtnkykkgrkkaAYAGG 848
Cdd:PRK05762 352 PFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPN----------LGERPGE---------------ASPGG 404
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 849 LVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTvqRVASEAQKvtedgEQEQIPELPDP--SLEMGILPREIRKLVE 926
Cdd:PRK05762 405 YVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDG--LVEGLAQP-----PEESVAGFLGArfSREKHFLPEIVERLWE 476
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 927 RRKQVKQLMKQqdlnpdlilqydIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIY 1006
Cdd:PRK05762 477 GRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIY 544
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1007 GDTDSIMINTNSTN-LEEVFKLGNKVKSEVNKLYKL-----------LEIDIDGVFK--------SLLLLKKKKYAALVV 1066
Cdd:PRK05762 545 GDTDSTFVWLGGAHdEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRrffmptirGAEEGSKKRYAGLIQ 624
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1067 EPTSDGNYVtkqeLKGLDIVRRDWCDLAKDTGNFVIGQILSDQsrdtiveNIQKRLIEIGENVLNGSVPvSQFEINKALT 1146
Cdd:PRK05762 625 EGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGE-------PYVDYVREVIDKLRAGELD-EKLVYRKRLR 692
|
570 580 590 600
....*....|....*....|....*....|....*....|....
gi 1370518488 1147 KDPQDYpDKKSLPHVHVALWINSQGGRKVKA-----GDTVSYVI 1185
Cdd:PRK05762 693 RPLDEY-QRNVPPHVRAARLADEMGYKVGRPlqyqnGGKIGYVI 735
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
844-1185 |
1.97e-59 |
|
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: 209.10 E-value: 1.97e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 844 AYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQRvaseaqkvteDGEQEQIPELP-------DPSlemGI 916
Cdd:cd05536 3 SYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVR----------EGCEDCDVEPQvghkfrkDPP---GF 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 917 LPREIRKLVERRKQVKQLMKQ-QDLNPDLILqYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKE 995
Cdd:cd05536 69 IPSVLEDLLEERRRIKEKMKKlDPESEEYKL-LDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIK 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 996 MVQKMNLEVIYGDTDSIM--INTNSTNLEEVFKLGNKVKSEVNklyklLEIDIDGVFKSLLLLKKKKYAALvvepTSDGN 1073
Cdd:cd05536 148 IAEEKGFKVIYGDTDSLFvkIDGADAVKKKVKKLLKYINEELP-----LELEIEKFYKRGFFVTKKRYAGL----TEDGK 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1074 YVTkqelKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQkrliEIGENVLNGSVPVSQFEINKALTKDPQDYp 1153
Cdd:cd05536 219 IDV----VGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVK----EVIEKLKRGEVPPEKLVIWKQLTKDLSEY- 289
|
330 340 350
....*....|....*....|....*....|..
gi 1370518488 1154 dKKSLPHVHVALWInSQGGRKVKAGDTVSYVI 1185
Cdd:cd05536 290 -KATGPHVAAAKKL-AKRGYKVRPGTKIGYVI 319
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
493-1187 |
2.16e-54 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 207.19 E-value: 2.16e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 493 FLMNRKIKGPCWLEVKSPQ----LLNQPVSWCKVEaMALKPDLVNVIKDV----SPPPLVVMAFSmktmqnaknhqneiI 564
Cdd:PTZ00166 207 FLIDNNITGGSWLTLPKGKykirPPKKKTSTCQIE-VDCSYEDLIPLPPEgeylTIAPLRILSFD--------------I 271
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 565 AMAALVHHSFALDKAAPKPPFQSHFCVVSKPKDCI--FPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVG 642
Cdd:PTZ00166 272 ECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLtkFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDPDFLTG 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 643 HNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSG---FGERNATC----GRMICDVeisaKELIR----CKS 711
Cdd:PTZ00166 352 YNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSskqMGTRESKEinieGRIQFDV----MDLIRrdykLKS 427
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 712 YHLSELVQQILKTERVVI---PMENIQNMYSESSQLL--YLLehtwKDAKFILQIMCELNVLPLALQITNIAGNIMSRTL 786
Cdd:PTZ00166 428 YSLNYVSFEFLKEQKEDVhysIISDLQNGSPETRRRIavYCL----KDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLL 503
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 787 MGGRSERNEFLLLHAFYENNYIVPdkqifrkpqqklgdedeeidgdTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLD 866
Cdd:PTZ00166 504 TRGQQIKVTSQLLRKCKKLNYVIP----------------------TVKYSGGGSEEKYEGATVLEPKKGFYDEPIATLD 561
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 867 FNSLYPSIIQEFNICFTTVQRvASEAQKVTEDgeqEQIPELPD-----PSLEMGILPREIRKLVERRKQVKQLMKQQDlN 941
Cdd:PTZ00166 562 FASLYPSIMIAHNLCYSTLVP-PNDANNYPED---TYVTTPTGdkfvkKEVRKGILPLIVEELIAARKKAKKEMKDEK-D 636
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 942 PDLILQYDIRQKALKLTANSMYGCLGFSYSRFYakP---LAALVTYKGREILMHTKEMVQKM---------NLEVIYGDT 1009
Cdd:PTZ00166 637 PLLKKVLNGRQLALKISANSVYGYTGAQVGGQL--PcleVSTSITSFGRQMIDKTKELVEKHytkangykhDATVIYGDT 714
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1010 DSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGVFKSLLLLKKKKYAALVVepTSDGNYvTKQELKGLDIVRR 1088
Cdd:PTZ00166 715 DSVMVKFGTDDIQEAMDLGKEAAERISKKFlKPIKLEFEKVYCPYLLMNKKRYAGLLY--TNPEKY-DKIDCKGIETVRR 791
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1089 DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNgsvpVSQFEINKALTKDpqDYpdKKSLPHVHVAlwin 1168
Cdd:PTZ00166 792 DNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRID----ISLLVITKSLGKD--DY--EGRLAHVELA---- 859
|
730 740
....*....|....*....|....*...
gi 1370518488 1169 sqggRKVKA---------GDTVSYVICQ 1187
Cdd:PTZ00166 860 ----KKLRQrdpgsapnvGDRVSYVIVK 883
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
845-1187 |
1.20e-51 |
|
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: 187.09 E-value: 1.20e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 845 YAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRvASEAQKVTEdgeqEQIPELPD------PSLEMGILP 918
Cdd:cd05533 3 YEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLN-KNTAKKLPP----EDYIKTPNgdyfvkSSVRKGLLP 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 919 REIRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQ 998
Cdd:cd05533 78 EILEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVE 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 999 ---------KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGVFKSLLLLKKKKYAALVVep 1068
Cdd:cd05533 157 ekytkangySHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFiKPIKLEFEKVYFPYLLINKKRYAGLLW-- 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1069 TSDGNYvTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIqKRLIeigENVLNGSVPVSQFEINKALTKD 1148
Cdd:cd05533 235 TNPDKH-DKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFV-KGVI---SDLLQNKIDISLLVITKALTKT 309
|
330 340 350 360
....*....|....*....|....*....|....*....|
gi 1370518488 1149 PQDYPDKksLPHVHVALWINSQG-GRKVKAGDTVSYVICQ 1187
Cdd:cd05533 310 ADDYAGK--QAHVELAERMRKRDpGSAPNVGDRVPYVIIK 347
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
545-763 |
3.09e-44 |
|
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 176646 [Multi-domain] Cd Length: 199 Bit Score: 159.06 E-value: 3.09e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 545 VMAFSMKTMQNAK---NHQNEIIAMAALVhhSFALDKAAPKPPFQSHFCVVSKpkdcifpyafkevieKKNVKVEVAATE 621
Cdd:cd05160 1 VLSFDIETTPPVGgpePDRDPIICITYAD--SFDGVKVVFLLKTSTVGDDIEF---------------IDGIEVEYFADE 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 622 RTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRlkRSNMPKlggRSGFGERNATCGRMICDVEI 701
Cdd:cd05160 64 KELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYR--RSGGEK---SSGSTERIAVKGRVVFDLLA 138
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1370518488 702 SAKELIRCKSYHLSELVQQILKTERV-VIPMENIQNMysESSQLLYLLEHTWKDAKFILQIMC 763
Cdd:cd05160 139 AYKRDFKLKSYTLDAVAEELLGEGKEkVDGEIIEDAE--WEEDPERLIEYNLKDAELTLQILE 199
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
838-1184 |
2.86e-40 |
|
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: 153.28 E-value: 2.86e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 838 KGRKkaaYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQrvaseaqKVTEDGEQEQIPELPD-------- 909
Cdd:cd05530 9 KGKK---YRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVN-------CPHCECKTNEVPEVGHwvckkrpg 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 910 -PSLEMGILpreiRKLveRRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGRE 988
Cdd:cd05530 78 iTSQIIGLL----RDL--RVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRY 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 989 ILMHTKEMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDGVFKsllllkkkkyaaLVVE 1067
Cdd:cd05530 152 IITSTIKKARELGLKVLYGDTDSLFLwNPPQEQLEDLVE---WVEKELG-----LDLELDKEYR------------YVVF 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1068 PTSDGNY--VTKQ---ELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRD---TIVENIQKRLIEIGENVLNGSVPVSQF 1139
Cdd:cd05530 212 SGLKKNYlgVTKDgsvDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPEdfeKAREKIRDIVKGVYKRLKKKEYTLDQL 291
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 1370518488 1140 EINKALTKDPQDYpDKKSLPHVHVALWINSQgGRKVKAGDTVSYV 1184
Cdd:cd05530 292 AFKVMLSKPPEEY-TKNTPQHVKAARQLEKY-GRNVEAGDIISYV 334
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
825-1184 |
5.63e-39 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 156.77 E-value: 5.63e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 825 EDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVqrvaseaqkvtEDGEQEQI 904
Cdd:PRK05761 387 EDILRLDHEVYKKAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETV-----------RIPECKCH 454
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 905 PELPDPSL------EMGILPREIRKLV--ERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAK 976
Cdd:PRK05761 455 YDDEVPELghsvcdDRPGLTSVLVGLLrdFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRI 534
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 977 PLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMI-NTNSTNLEEVFKlgnKVKSEVNklyklLEIDIDGVFKslll 1055
Cdd:PRK05761 535 EVAESITALGREILLSTKKKAEELGLKVLYGDTDSLFVwGPTKESLEELIK---EIEERTG-----IDLEVDKTYD---- 602
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1056 lkkkkyaaLVVEPTSDGNY--VTKQ---ELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQK---RLIEIGE 1127
Cdd:PRK05761 603 --------WVAFSGLKKNYfgVLKDgkvKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEKVKDEiedVLKRYYE 674
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 1370518488 1128 NVLNGSVPVSQFEINKALTKDPQDYpDKKSLPHVHVALWINSQGGrKVKAGDTVSYV 1184
Cdd:PRK05761 675 KLRAKDYPLDELAIRVRLSKPLDEY-TKNTPQHVKAALQLRDYGV-EVSPGDIISYV 729
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
846-1188 |
5.14e-36 |
|
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: 140.87 E-value: 5.14e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 846 AGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNIcfTTVQRVasEAQKvtEDGEQEQIPELPDP--SLEMGILPREIRK 923
Cdd:cd05537 4 PGGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLI--DPLGLI--EGLK--APDPEDLIPGFLGArfSREKHILPDLIAR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 924 LVERRKQVKQlmkqqdlNPDLILQYdirqkALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLE 1003
Cdd:cd05537 77 LWAARDEAKR-------EKNAPLSQ-----AIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQ 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1004 VIYGDTDSIMINTNST-NLEEVFKLGNKVKSEVN--------KLYKL---LEIDIDGVF--------KSLLLLKKKKYAA 1063
Cdd:cd05537 145 VIYGDTDSTFVWLGEElDAAEAQAIGKELASQINqwwaqklkEEFGLesfLEIEFETHYsrffmptiRGSDEGSKKRYAG 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1064 LVVEPTSDgnyvtKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEiGEnvLNgsvpvSQFEINK 1143
Cdd:cd05537 225 LKSTDGGD-----ELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFIKETVEELLA-GE--LD-----ELLVYRK 291
|
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 1370518488 1144 ALTKDPQDYpDKKSLPHVHVALW---INSQGGRKvKAGDTVSYVICQQ 1188
Cdd:cd05537 292 RLRRPLSEY-TKNVPPHVQAARLadqINRELGRP-RQYQWIEYVITVN 337
|
|
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
849-1185 |
2.09e-35 |
|
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: 141.20 E-value: 2.09e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 849 LVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTT-VQRVASEAQKVTEDGEQEQIPELPDPSLEM------------- 914
Cdd:cd05534 40 LVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTcLGRVEELNGGGKFGFLGVKLYLPPPPLDLLllkddvtispngv 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 915 ---------GILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYS-RFYAKPLAALVTY 984
Cdd:cd05534 120 mfvkksvrkGILPKMLEEILDTRIMVKKAMKKYKDDKKLQRILDARQLALKLLANVTYGYTAASFSgRMPCVEIADSIVQ 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 985 KGREILMHTKEMVQ---KMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLY-KLLEIDIDGVFKSLLLLKKKK 1060
Cdd:cd05534 200 TGRETLERAIELIEstpKWGAKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVTAANpSPIKLKFEKVYHPCVLVTKKR 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1061 YAALVVEPTSDGnyVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLieigENVLNGSVPVSQFE 1140
Cdd:cd05534 280 YVGYKYESPDQT--EPTFDAKGIETVRRDGCPAVQKILEKSLRILFETKDLSTVKSYLQRQW----SKLLQGRVSIQDFI 353
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 1370518488 1141 INKALTKDpQDYPDKKSLPHVHVAL-WINSQGGRKVKAGDTVSYVI 1185
Cdd:cd05534 354 FAKEVRLG-TYKEGATLPAGAIVALrRMEKDPRAEPQYGERVPYVV 398
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
843-1185 |
1.22e-28 |
|
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: 118.60 E-value: 1.22e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 843 AAYAGGLVLDPKVGFYDKfILLLDFNSLYPSIIQEFNICFTTVQrvaseaqkvTEDGEQEQIPELPDPSL--EMGILPRE 920
Cdd:cd05531 3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETIN---------CRCCECRDHVYLGHRIClkRRGFLPEV 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 921 IRKLVERRKQVKQLMKQQDlnpdlilQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM 1000
Cdd:cd05531 73 LEPLLERRLEYKRLKKEED-------PYAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEM 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1001 NLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKsevnklyklLEIDIDGVFKsllllkkkkyaALVVEPTSDG-----NYV 1075
Cdd:cd05531 146 GFRVLHGIVDSLWIQGRGDIEELAREIEERTG---------IPLKLEGHYD-----------WIVFLPERDGlgapnRYF 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1076 TKQE-----LKGLDIVRRDWCDLAKDTGNFVIgQILSdQSRDtiVENIQKRLIEIgENVLNGSV------PVSQFEINKA 1144
Cdd:cd05531 206 GRLSdgemkVRGIELRRRDTPPFVKKFQEEAL-DILA-SAKT--PEELLKLREEA-LDLFRRYLqrlregDLEDLIIEKK 280
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 1370518488 1145 LTKDPQDYpdkKSLPHvHVALWINSQgGRKVKAGDTVSYVI 1185
Cdd:cd05531 281 ISKRSSEY---KVLAS-TALKALRAK-GVSVVPGMKIEYIV 316
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
836-1159 |
4.46e-21 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 100.09 E-value: 4.46e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 836 YKKGRKKAA--YAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVAS-----EAQKVTEDGEQ------- 901
Cdd:PHA03036 519 LVRSETKNKfpYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVndnrlEAEINKQELRRkypypry 598
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 902 ---EQIPELPDPSLEM--------GILPREIRKLVERRKQVKQLMKQQDLNPDLILqYDIRQKALKLTANSMYGCLGFSY 970
Cdd:PHA03036 599 iyvHCEPRSPDLVSEIavfdrrieGIIPKLLKTFLEERARYKKLLKEATSSVEKAI-YDSMQYTYKIVANSVYGLMGFRN 677
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 971 SRFYAKPLAALVTYKGREILMHTKEMV--------------------------------------QKMNLEVIYGDTDSI 1012
Cdd:PHA03036 678 SALYSYASAKSCTAIGRNMIKYLNSVLngsklingklilancpinpffkddrsidtnydtnlpveYNFTFRSVYGDTDSV 757
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1013 MINTNSTNLEEVFKLGNKVKSEVNK--LYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRRDW 1090
Cdd:PHA03036 758 FLEINTKDVDKSIKIAKELERIINEkvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVPERVNKGTSETRRDV 837
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370518488 1091 CDLAKdtgnfvigqilsdqsrdTIVENIQKRLIEIGENVLNGSVPVSqFEINKALTKDPQDYPDKKSLP 1159
Cdd:PHA03036 838 SKFHK-----------------YMIKIYKTRLLDMLSEGNMNSNQVC-IDILRSLEKDLIIEFDSRSAP 888
|
|
| 43 |
PHA02528 |
DNA polymerase; Provisional |
837-1015 |
4.70e-14 |
|
DNA polymerase; Provisional
Pssm-ID: 177369 [Multi-domain] Cd Length: 881 Bit Score: 77.04 E-value: 4.70e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 837 KKGRKKAAYAGGLVLDPKVGFYDkFILLLDFNSLYPSIIQEFNICFTTVQ---RVASEAQKVTEdgeqeqipELPDPSLE 913
Cdd:PHA02528 369 NKSHKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAgtfHVAPVHEYINK--------TAPRPSDE 439
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 914 M--------------GILPREIRKLVERRKQVKQLMKQQDLNPDLI---------------------------------- 945
Cdd:PHA02528 440 YscspngwmyrkdirGVIPTEIKKVFDQRKIYKKKMLAAERNAELIktiledlndsvdtpidvdyyfdfsdefkaelktl 519
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 946 ----------------LQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGR-EILMHTKEMVQKMNL------ 1002
Cdd:PHA02528 520 tksslkalleecekeiALCNTIQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQlAIQWIERKMNEYLNKlckted 599
|
250
....*....|....*
gi 1370518488 1003 --EVIYGDTDSIMIN 1015
Cdd:PHA02528 600 edYVIYGDTDSIYVN 614
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
866-1183 |
4.95e-14 |
|
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99921 Cd Length: 347 Bit Score: 74.83 E-value: 4.95e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 866 DFNSLYPSIIQEFNICfttvqrVASEaqkvtedgeqeqipelpdpslEMGILPREIRKLVERRKQVKQLMKQQDLnPDLI 945
Cdd:cd05538 23 DVASLYPSIMLAYRIC------PARD---------------------SLGIFLALLKYLVELRLAAKESARAAAR-PAER 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 946 LQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMI---NTNSTNLE 1022
Cdd:cd05538 75 DAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFippNGVDTEDE 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1023 EvfklgNKVKSEVNK-LYKLLEIDIDGVFKSLLLLKKKKYAALvveptsdgNYVTKQELKGLDIVRRDWCDLAKDTGNFV 1101
Cdd:cd05538 155 E-----EELVRELSStLPKGITVEFDGRYRAMFSYKIKNYALL--------DYDGKLIVKGSAFRSRGIEPFLREFLREA 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 1102 IGQILSDQSrdtivENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDK----KSLPhvHVALWINSQGGRKVKA 1177
Cdd:cd05538 222 VRLLLQGDG-----AGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYLQKvragKRNP--AAAYEIALARPREWRA 294
|
....*.
gi 1370518488 1178 GDTVSY 1183
Cdd:cd05538 295 GDRVTY 300
|
|
| DNA_pol_alpha_N |
pfam12254 |
DNA polymerase alpha subunit p180 N terminal; This domain family is found in eukaryotes, and ... |
41-101 |
6.92e-13 |
|
DNA polymerase alpha subunit p180 N terminal; This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam00136, pfam08996, pfam03104. This family is the N terminal of DNA polymerase alpha subunit p180 protein. The N terminal contains the catalytic region of the alpha subunit.
Pssm-ID: 463508 Cd Length: 65 Bit Score: 64.50 E-value: 6.92e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370518488 41 LERLKKAKAGEK---YKYEVEDFTGVYEEVDEEQYSKLVQARQDDDW-IVDDDGIGYVEDGREIF 101
Cdd:pfam12254 1 LEKLKAARAGGKrrlDEYESEEDEDIYDEVDEEEYRKIVRKRLLDDDfVVDDDGEGYVDDGREDW 65
|
|
| PHA03334 |
PHA03334 |
putative DNA polymerase catalytic subunit; Provisional |
833-1013 |
7.51e-09 |
|
putative DNA polymerase catalytic subunit; Provisional
Pssm-ID: 223049 [Multi-domain] Cd Length: 1545 Bit Score: 60.26 E-value: 7.51e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 833 TNKYKKG-RKKAAYAGGLVLDPKVGF-----YDKFILLLDFNSLYPSIIQEFNICFTTV---QRVASEAQKVTEDgeQEQ 903
Cdd:PHA03334 620 PEKYARDcRQKIKLKGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIvdpDCTARVRGWVVFD--WKK 697
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 904 IPE-LPDPSLEMGIL---PRE-------------IRKLVERRKQVKQLMKQQDlNPDLILQYDIRQKALKLTANSMYGcl 966
Cdd:PHA03334 698 IDRgFGKATLMYTILrtkPEEpswrrfttyttssLNHYLSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYG-- 774
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 1370518488 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 ... |
604-761 |
7.85e-09 |
|
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family-B DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99823 [Multi-domain] Cd Length: 195 Bit Score: 56.98 E-value: 7.85e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 604 FKEVIEKKNV---KVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRLKRSnmPKLg 680
Cdd:cd05780 36 GNKVITWKKFdlpFVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIE--LDLGRDGSE--IKI- 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 681 GRSGFGERNATCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQ 760
Cdd:cd05780 111 QRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYE 190
|
.
gi 1370518488 761 I 761
Cdd:cd05780 191 I 191
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
620-674 |
4.79e-07 |
|
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues necessary for metal binding and catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation.
Pssm-ID: 99820 [Multi-domain] Cd Length: 230 Bit Score: 52.19 E-value: 4.79e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1370518488 620 TERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRS 674
Cdd:cd05777 70 TEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNI 124
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|
| DNA_polB_like2_exo |
cd05785 |
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ... |
589-738 |
2.17e-06 |
|
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 99828 [Multi-domain] Cd Length: 207 Bit Score: 49.72 E-value: 2.17e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 589 FCVVSKPKDCIF------PYAFKEVIEKKNvkvevaATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKA 662
Cdd:cd05785 26 FSNPDRGDDRIIivalrdNRGWEEVLHAED------AAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGV 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 663 P-HWSKIGRLKRSNmpklGGRSGFGERNA------TCGRMICDV-------EISAKELircKSYHLSELVQQ--ILKTER 726
Cdd:cd05785 100 PlAIGRDGSIPRQR----PSRFRFAERLIdyprydIPGRHVIDTyflvqlfDVSSRDL---PSYGLKAVAKHfgLASPDR 172
|
170
....*....|..
gi 1370518488 727 VVIPMENIQNMY 738
Cdd:cd05785 173 TYIDGRQIAEVW 184
|
|
| DNA_polB_II_exo |
cd05784 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ... |
610-656 |
1.71e-04 |
|
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Pol II is also involved in lagging strand synthesis.
Pssm-ID: 99827 [Multi-domain] Cd Length: 193 Bit Score: 44.10 E-value: 1.71e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 1370518488 610 KKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQR 656
Cdd:cd05784 40 DAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRR 86
|
|
| POLBc_epsilon |
cd05535 |
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
929-1012 |
1.34e-03 |
|
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Pssm-ID: 99918 Cd Length: 621 Bit Score: 43.05 E-value: 1.34e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 929 KQVKQLMKQQDL-----NPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMN-- 1001
Cdd:cd05535 247 KKLEAAKAAGDAaeikeAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMARELVEQIGrp 326
|
90
....*....|.
gi 1370518488 1002 LEViygDTDSI 1012
Cdd:cd05535 327 LEL---DTDGI 334
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
612-699 |
2.01e-03 |
|
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Pssm-ID: 99821 [Multi-domain] Cd Length: 231 Bit Score: 41.07 E-value: 2.01e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 612 NVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRinvCKAPH----WSKIGRLKRSNMPKLGGRSgfGE 687
Cdd:cd05778 72 GIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIER---AAALGiddlLDEISRVPSDSNGKFGDRD--DE 146
|
90
....*....|....*....
gi 1370518488 688 RNAT-------CGRMICDV 699
Cdd:cd05778 147 WGYThtsgikiVGRHILNV 165
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
621-761 |
2.32e-03 |
|
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99824 [Multi-domain] Cd Length: 188 Bit Score: 40.39 E-value: 2.32e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370518488 621 ERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPhwSKIGRlKRSNMPKlggRSGFGERNATcGRMICDVE 700
Cdd:cd05781 48 DRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVK--LDVGR-RGGSEPS---TGVYGHYSIT-GRLNVDLY 120
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1370518488 701 ISAKEL--IRCKS-YHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQI 761
Cdd:cd05781 121 DFAEEIpeVKVKTlENVAEYLGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGL 184
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