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Conserved domains on  [gi|392896659|ref|NP_001255109|]
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DNA polymerase [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
pol2 super family cl36695
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
48-1190 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]


The actual alignment was detected with superfamily member TIGR00592:

Pssm-ID: 273159 [Multi-domain]  Cd Length: 1172  Bit Score: 694.88  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    48 ELDVEDVYDTVDDDEYEKIVAKRQKDNFIVDDDGMGYVDNGVDFEDDYEDDYA--PSSSKNSNSSKKGEKKPKKDKKKGG 125
Cdd:TIGR00592    2 VEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILDldKDDGSAAEAKKKDKENHKKVTKPNN 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   126 LHAFLSTTSTKKPIDesvVKAEFDDDEEVKNMLEQLGSSdEEAEEKPKATPANPFKRgrKFDSPsgsdslAPRPIAKKAK 205
Cdd:TIGR00592   82 IKAVRIACAPKKKKD---RKKSLGKDGLLGDILQELNKT-ETAQRKITPRLVSVPKL--KFSSP------ADVPAINDFS 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   206 REATGLAEHkfqrhVKVDED-------EDYGIPDDYPVASPVTSPVKTEKMaEVEAPTAPAIQKIEETVK---------M 269
Cdd:TIGR00592  150 NHHPAVVDI-----VKKAIPvstryllEKILIPVPLKRAEFAGGDVQMEGD-PELKLASFDIETYFHDGKdffpgdenpA 223
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   270 ETEHLEEVEDSLAKFRVIED----------------------------------WTggSSSQEDEDVKVEVKTGSEAFYT 315
Cdd:TIGR00592  224 DEEIMISTTPVIAKQWDYESepearvvtwkkpdkpttgsyvesvseeismikrfWD--VIDQEDTDVEITVNGDNFDLVY 301
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   316 MGGEDnttkAIRMYWiDAYEDVHKANGTVYLFGKVKTSgnawETCSIVVKNICRKVYFMPRTKNLS------TGEESSLA 389
Cdd:TIGR00592  302 LADRQ----VFQFYW-DAYEDPAEKLGVVLLFGRDVDH----VSPCVQVKGINRDLFFLPREGKIDfdlgkvTRRTINLP 372
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   390 ELHKEIGDVLRNKFNTHEFKCKMVEKelirdeSFGYGCGT-----KSPLMEVLYPAEKGK-----LPSDLKGDTFSNTFN 459
Cdd:TIGR00592  373 DYYLEFVSELALGYKKEKFRAKPIAK------KYEFEAPDidapySSEYLEVTYELGKEFapmeaLPSDLKGQTFWHVFG 446
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   460 TSVTPLERLLIEKKFMGPGWIELYNYSD-PKAKTSNCKYEFEVDMEKMRNIkyleSSDAPPPTIKLLALNVVTTLNDRKD 538
Cdd:TIGR00592  447 SNTGNLERFLLLRKIKGPCWLAVKGPDElEYPRRSWCKYEGGYVKPPNVEK----GLDKTPPPLVVLDFSMKSLNPSIIR 522
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   539 NEICMISMLFNPKCDLAHPSGDSKDLKPKCLVTKPPGGSLPYDIqKRLETEKLSKFVKSVANEKALLTLFLAMINEDEPD 618
Cdd:TIGR00592  523 NEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPLDL-KGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPD 601
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   619 MIVGHDL-SATIALLVSRLEKLKLPNWSRISRLKRSINIGKighsksGQWELTAGRMMLDSKLAAMELVKSRSFDLTELS 697
Cdd:TIGR00592  602 EIVGHDYqQRALKVLANRINDLKIPTWSKIGRLRRSPKFGR------RFGERTCGRMICDVEISAKELIRCKSYDLSELV 675
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   698 QQILGAERREIYANEIPQLYVDSKDLISLINWSWNDLLLSLRIVVRLNALPLYIQISQIVGGIASRTMMGGRAERNEYLL 777
Cdd:TIGR00592  676 QQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLL 755
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   778 LHAFEKADLIAPDKYNSSESKKKKEESQEGD-EKKSGKAQYSGGLVLEPKKGLYETLILLLDFNSLYPSIIQEYNICYTT 856
Cdd:TIGR00592  756 LHAFYENNYIVPDKQIFRKQQKLGDEDEEIDgYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTT 835
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   857 LEYSKDSDEQLSVPQSTDIEGVLPREIRKLVECRRDVKSLMKSERNEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYA 936
Cdd:TIGR00592  836 VQQKVDEDELPELPDSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYA 915
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   937 KPLAALVTAKGREILMHSKDLVEKMGYSVVYGDTDSIMINTNSVDLVAAKKLGNEIKKAVNKCHRLLELDLDGVFKRMLL 1016
Cdd:TIGR00592  916 KPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLL 995
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1017 LKKKKYAALTINPDTK---VEAKELKGLDIVRRDWSQLAKETGTAVVDKILDASlTRDEMVSSIDDLLREIRAKLDSGTV 1093
Cdd:TIGR00592  996 LKKKKYAAIKVEGDSDgnyTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDK-DVEEAVEEVQEVLEKIGKNVLNGEV 1074
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1094 PLEMFQISKQLTRNPEQYADVKAQCHAAVAQRLNKSGKFNLRHNDIVEYVICEDGTDNPATQRAYHRTE-MAENSALKID 1172
Cdd:TIGR00592 1075 PLEKFVINKQLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEElQRKHNNLIYD 1154
                         1210
                   ....*....|....*...
gi 392896659  1173 LLYYLAQQIHPVVSRLVE 1190
Cdd:TIGR00592 1155 TQYYLEHQIHPVVLRILE 1172
zf-DNA_Pol pfam08996
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ...
1232-1421 2.30e-49

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: 173.56  E-value: 2.30e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1232 QENYDLCEGIHVICPldGCGHSNVIRETFDCvTDASSPRLLFSGCAQCQGSWdlqeHQAVIGNQVDRQMSEFVARHHLAA 1311
Cdd:pfam08996    6 EERFKDCEPLELRCP--SCGTEFEFEGVFAS-ADGYSVTPSGLRCPNCDASL----SPASLVNQLELQIRAHISRYYEGW 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1312 FKCDEPTCEFKTRVQTMKWCRegleCIR--CsTGVLRREYTSKQLFDQQMFFRTILDVDAAVRKLSDAQKKAAKVRVEYN 1389
Cdd:pfam08996   79 LVCDDPTCGNRTRQMSVYGKR----CLGpgC-KGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLALAE 153
                          170       180       190
                   ....*....|....*....|....*....|..
gi 392896659  1390 GCKIDSMMLADRInEKYLEKNAYNRVDLSYIF 1421
Cdd:pfam08996  154 QNRELFKTLKSVV-DKYLDKCGRRWVNLSSLF 184
 
Name Accession Description Interval E-value
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
48-1190 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: 694.88  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    48 ELDVEDVYDTVDDDEYEKIVAKRQKDNFIVDDDGMGYVDNGVDFEDDYEDDYA--PSSSKNSNSSKKGEKKPKKDKKKGG 125
Cdd:TIGR00592    2 VEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILDldKDDGSAAEAKKKDKENHKKVTKPNN 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   126 LHAFLSTTSTKKPIDesvVKAEFDDDEEVKNMLEQLGSSdEEAEEKPKATPANPFKRgrKFDSPsgsdslAPRPIAKKAK 205
Cdd:TIGR00592   82 IKAVRIACAPKKKKD---RKKSLGKDGLLGDILQELNKT-ETAQRKITPRLVSVPKL--KFSSP------ADVPAINDFS 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   206 REATGLAEHkfqrhVKVDED-------EDYGIPDDYPVASPVTSPVKTEKMaEVEAPTAPAIQKIEETVK---------M 269
Cdd:TIGR00592  150 NHHPAVVDI-----VKKAIPvstryllEKILIPVPLKRAEFAGGDVQMEGD-PELKLASFDIETYFHDGKdffpgdenpA 223
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   270 ETEHLEEVEDSLAKFRVIED----------------------------------WTggSSSQEDEDVKVEVKTGSEAFYT 315
Cdd:TIGR00592  224 DEEIMISTTPVIAKQWDYESepearvvtwkkpdkpttgsyvesvseeismikrfWD--VIDQEDTDVEITVNGDNFDLVY 301
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   316 MGGEDnttkAIRMYWiDAYEDVHKANGTVYLFGKVKTSgnawETCSIVVKNICRKVYFMPRTKNLS------TGEESSLA 389
Cdd:TIGR00592  302 LADRQ----VFQFYW-DAYEDPAEKLGVVLLFGRDVDH----VSPCVQVKGINRDLFFLPREGKIDfdlgkvTRRTINLP 372
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   390 ELHKEIGDVLRNKFNTHEFKCKMVEKelirdeSFGYGCGT-----KSPLMEVLYPAEKGK-----LPSDLKGDTFSNTFN 459
Cdd:TIGR00592  373 DYYLEFVSELALGYKKEKFRAKPIAK------KYEFEAPDidapySSEYLEVTYELGKEFapmeaLPSDLKGQTFWHVFG 446
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   460 TSVTPLERLLIEKKFMGPGWIELYNYSD-PKAKTSNCKYEFEVDMEKMRNIkyleSSDAPPPTIKLLALNVVTTLNDRKD 538
Cdd:TIGR00592  447 SNTGNLERFLLLRKIKGPCWLAVKGPDElEYPRRSWCKYEGGYVKPPNVEK----GLDKTPPPLVVLDFSMKSLNPSIIR 522
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   539 NEICMISMLFNPKCDLAHPSGDSKDLKPKCLVTKPPGGSLPYDIqKRLETEKLSKFVKSVANEKALLTLFLAMINEDEPD 618
Cdd:TIGR00592  523 NEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPLDL-KGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPD 601
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   619 MIVGHDL-SATIALLVSRLEKLKLPNWSRISRLKRSINIGKighsksGQWELTAGRMMLDSKLAAMELVKSRSFDLTELS 697
Cdd:TIGR00592  602 EIVGHDYqQRALKVLANRINDLKIPTWSKIGRLRRSPKFGR------RFGERTCGRMICDVEISAKELIRCKSYDLSELV 675
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   698 QQILGAERREIYANEIPQLYVDSKDLISLINWSWNDLLLSLRIVVRLNALPLYIQISQIVGGIASRTMMGGRAERNEYLL 777
Cdd:TIGR00592  676 QQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLL 755
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   778 LHAFEKADLIAPDKYNSSESKKKKEESQEGD-EKKSGKAQYSGGLVLEPKKGLYETLILLLDFNSLYPSIIQEYNICYTT 856
Cdd:TIGR00592  756 LHAFYENNYIVPDKQIFRKQQKLGDEDEEIDgYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTT 835
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   857 LEYSKDSDEQLSVPQSTDIEGVLPREIRKLVECRRDVKSLMKSERNEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYA 936
Cdd:TIGR00592  836 VQQKVDEDELPELPDSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYA 915
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   937 KPLAALVTAKGREILMHSKDLVEKMGYSVVYGDTDSIMINTNSVDLVAAKKLGNEIKKAVNKCHRLLELDLDGVFKRMLL 1016
Cdd:TIGR00592  916 KPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLL 995
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1017 LKKKKYAALTINPDTK---VEAKELKGLDIVRRDWSQLAKETGTAVVDKILDASlTRDEMVSSIDDLLREIRAKLDSGTV 1093
Cdd:TIGR00592  996 LKKKKYAAIKVEGDSDgnyTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDK-DVEEAVEEVQEVLEKIGKNVLNGEV 1074
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1094 PLEMFQISKQLTRNPEQYADVKAQCHAAVAQRLNKSGKFNLRHNDIVEYVICEDGTDNPATQRAYHRTE-MAENSALKID 1172
Cdd:TIGR00592 1075 PLEKFVINKQLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEElQRKHNNLIYD 1154
                         1210
                   ....*....|....*...
gi 392896659  1173 LLYYLAQQIHPVVSRLVE 1190
Cdd:TIGR00592 1155 TQYYLEHQIHPVVLRILE 1172
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
810-1207 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: 640.40  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  810 KKSGKAQYSGGLVLEPKKGLYETLILLLDFNSLYPSIIQEYNICYTTLEYSKDSDE---QLSVPQSTDIEGVLPREIRKL 886
Cdd:cd05532     1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEddeEPPLPPSDQEKGILPRIIRKL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  887 VECRRDVKSLMKSERNEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSVV 966
Cdd:cd05532    81 VERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMNLEVI 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  967 YGDTDSIMINTNSVDLVAAKKLGNEIKKAVNKCHRLLELDLDGVFKRMLLLKKKKYAALTINPD-TKVEAKELKGLDIVR 1045
Cdd:cd05532   161 YGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVDDdKGKLKKEVKGLDIVR 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1046 RDWSQLAKETGTAVVDKILDASLtRDEMVSSIDDLLREIRAKLDSGTVPLEMFQISKQLTRNPEQYADVKAQCHAAVAQR 1125
Cdd:cd05532   241 RDWCPLSKEIGNYVLDQILSDKS-REDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKSLPHVQVALR 319
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1126 LNKSGKfNLRHNDIVEYVICEDGTDNPATQRAYHRTEMAENSALKIDLLYYLAQQIHPVVSRLVEPIEETDAVRIAENLG 1205
Cdd:cd05532   320 MNKRGR-KVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTDAVRLAECLG 398

                  ..
gi 392896659 1206 LD 1207
Cdd:cd05532   399 LD 400
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
762-1192 4.08e-124

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: 393.52  E-value: 4.08e-124
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   762 SRTMMGGRAERNEYLLLHAFEKADLIAPDKynsseskkkkeesqegDEKKSGKAQYSGGLVLEPKKGLYETLILLLDFNS 841
Cdd:pfam00136    4 SRVLEGGQQIRVESCLLRLALEEGFILPDR----------------PSAKGDEDGYQGATVIEPKKGFYDKPVLVLDFNS 67
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   842 LYPSIIQEYNICYTTLEYSKD-------SDEQLSVP---------QSTDIEGVLPREIRKLVECRRDVKSLMKSERNEAK 905
Cdd:pfam00136   68 LYPSIIQAHNLCYTTLVRSVDeannlppEDNLITVEctprgvyfvKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFE 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   906 KKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKM---GYSVVYGDTDSIMINTNSVDL 982
Cdd:pfam00136  148 RAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTDSVFIEFGGKDV 227
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   983 VAAKKLGNEIKKAVNKcHRL---LELDLDGVFKRMLLLKKKKYAALTINPDTKVEAKELKGLDIVRRDWSQLAKETGTAV 1059
Cdd:pfam00136  228 EEAMKIGDELAEHVNQ-DLFkspIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKV 306
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1060 VDKILDASLtRDEMVSSIDDLLREIRAKLDSGTVPLEMFQISKQLTRNPEQYaDVKAQCHAAVAQRLNKSGKFNLRHNDI 1139
Cdd:pfam00136  307 LDLLLSDRG-LPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMNKRNGEAPEVGDR 384
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 392896659  1140 VEYVICEDGTDN---PATQRAYHRTEMAENSaLKIDLLYYLAQQIHPVVSRLVEPI 1192
Cdd:pfam00136  385 IPYVIVKAAKGLknlLIYERAEDPEYVLENN-LPIDYEYYFSNQLIPPVARLLEPI 439
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
464-1208 8.52e-104

DNA polymerase B elongation subunit [Replication, recombination and repair];


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 349.90  E-value: 8.52e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  464 PLERLLIEKkFMGPG-WIELYNYSDPKAKTSNCKYEFEvdmekmrnikylESSDAPPPTIKLLAL-----NVVTTLNDRK 537
Cdd:COG0417   114 FHDRYLIDR-FLTPGvWYEGEVEEDGGKLDYEVKENPR------------LKPEDYRPKLKVLSFdievsTPRGFPDPER 180
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  538 DNEICMISmlfnpkcdLAHPSGDSKDLkpkcLVTKPPggsLPYDIQkrleteklskfvkSVANEKALLTLFLAMINEDEP 617
Cdd:COG0417   181 DGPIISIG--------LAGSDGEKKVL----MLGREG---VDFEVE-------------YFDDEKALLEAFFEIIREYDP 232
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  618 DMIVGH-----DLsatiALLVSRLEKLKLPnwSRISRLKRSINIGKIGhsKSGQWELTaGRMMLDS-KLAAMELVKSRSF 691
Cdd:COG0417   233 DIIIGWnvdnfDL----PYLQKRAERLGIP--LDLGRDGSEPSWREHG--GQGFASIP-GRVVIDLyDALKSATYKFKSY 303
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  692 DLTELSQQILGAERREIYANEIPQLYVDSKDliSLINWSWNDLLLSLRIVVRLNALPLYIQISQIVGGIASRTMMGGRAE 771
Cdd:COG0417   304 SLDAVAEELLGEGKLIVDGGEIERLWDDDKP--ALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSA 381
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  772 RNEYLLLHAFEKADLIAPDKynsseskkkkeesqegdEKKSGKAqYSGGLVLEPKKGLYETlILLLDFNSLYPSIIQEYN 851
Cdd:COG0417   382 AFENLLLPEAHRRGYLAPNK-----------------GEIKGEA-YPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFN 442
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  852 ICYTTL--EYSKDSDEQLSVPQ-----STDIEGVLPREIRKLVECRRDVKSLMKS-ERNEAKKKQMDIRQMALKLTANSM 923
Cdd:COG0417   443 ISPETLveGGEEPCGDEDVAPGfghrfCREPKGILPSILEELWDERDEAKKKMKKaKPDSEEYRLYDALQQALKILMNSF 522
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  924 YGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSVVYGDTDSIMINTNSVDLVAAKKLGNEIKKAVNKCHRL- 1002
Cdd:COG0417   523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSg 602
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1003 LELDLDGVFKR--MlllkkkkyaaltinPDTK------VEAKEL--KGLDIVRRDWSQLAKETGTAVVDKILdasltRDE 1072
Cdd:COG0417   603 LELEFEKHYRRffF--------------PGSKkryaglTEDGKIdiKGLEAVRSDWTELAKEFQQEVYERIL-----KEE 663
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1073 MVSSIDDLLREIRAKLDSGTVPLEMFQISKQLTRNPEQYaDVKAQCHAAVAQRLNKSGKfNLRHNDIVEYVIcedgTDNP 1152
Cdd:COG0417   664 DVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDERGR-PYQRGDKISYVI----TKGG 737
                         730       740       750       760       770
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 392896659 1153 ATQRAYhrtEMAENSALKIDLLYYLAQQIHPVVSRLVEP--IEETDAVRIAENLGLDS 1208
Cdd:COG0417   738 GRVEPV---ELAKERESEIDYDYYIEKQLKPTADRILEAfgVSFDELKGGSKQLGLFD 792
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
520-978 6.04e-98

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: 322.94  E-value: 6.04e-98
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    520 PTIKLLALNVVTTLNDRK-------DNEICMISMLFNpkcdlahpSGDSKDLKPKCLVTKPPGGSLPydiqkrleteklS 592
Cdd:smart00486    1 PPLKILSFDIETYTDGGNfpdaeifDDEIIQISLVIN--------DGDKKGANRRILFTLGTCKEID------------G 60
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    593 KFVKSVANEKALLTLFLAMINEDEPDMIVGHDLSA-TIALLVSRLEKLKLPNWSRISRLKRSINIGKIG-------HSKS 664
Cdd:smart00486   61 IEVYEFNNEKELLLAFFEFIKKYDPDIIYGHNISNfDLPYIISRLEKLKIDPLSKIGRLKIGLRIPNKKplfgsksFGLS 140
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    665 GQWELTAGRMMLDSKLAAMELVKSRSFDLTELSQQILGAERREIYANEIPQLYVDSKDLI-SLINWSWNDLLLSLRIVVR 743
Cdd:smart00486  141 DIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERdELLRYCIQDAVLTLKLFNK 220
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    744 LNALPLYIQISQIVGGIASRTMMGGRAERNEYLLLHAFEKADLIAPDKYnsseskkkKEESQEGDEKKSGKAQYSGGLVL 823
Cdd:smart00486  221 LNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKE--------LYDFKGSEPDLKKKVKYEGGKVL 292
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    824 EPKKGLYETLILLLDFNSLYPSIIQEYNICYTTLEYS-------------------KDSDEQLSVPQSTDIEGVLPREIR 884
Cdd:smart00486  293 EPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVgevvikgdliipedlltikYEKGNKYRFVKKNIRKGILPKLLK 372
                           410       420       430       440       450       460       470       480
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    885 KLVECRRDVKSLMKSERNEAK--KKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMG 962
Cdd:smart00486  373 KLLDKRKEIKKLMKKEKDESEelKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENG 452
                           490       500
                    ....*....|....*....|.
gi 392896659    963 YS-----VVYGDTDSIMINTN 978
Cdd:smart00486  453 YPkpgfkVIYGDTDSIFVTKP 473
PRK05762 PRK05762
DNA polymerase II; Reviewed
594-1206 8.32e-68

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 245.53  E-value: 8.32e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  594 FVKSVANEKALLTLFLAMINEDEPDMIVGH-----DLsatiALLVSRLEKLKLPnwSRISRLKRSINIGKIGhSKSGQ-- 666
Cdd:PRK05762  196 FLEYVADEKALLEKFNAWFAEHDPDVIIGWnvvqfDL----RLLQERAERYGIP--LRLGRDGSELEWREHP-FRSGYgf 268
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  667 WELtAGRMMLDsklaAMELVKS-----RSFDLTELSQQILGaERREI-----YANEIPQLYVDSKDliSLINWSWNDLLL 736
Cdd:PRK05762  269 ASV-PGRLVLD----GIDALKSatwvfDSFSLEYVSQRLLG-EGKAIddpydRMDEIDRRFAEDKP--ALARYNLKDCEL 340
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  737 SLRIVVRLNALPLYIQISQIVGGIASRTMMGGRAerNEYLLLHAFEKADLIAPDKynsseskkkkeesqeGDEKksGKAq 816
Cdd:PRK05762  341 VTRIFEKTKLLPFLLERATVTGLPLDRVGGSVAA--FEHLYLPRAHRAGYVAPNL---------------GERP--GEA- 400
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  817 YSGGLVLEPKKGLYETlILLLDFNSLYPSIIQEYNICYTTLeyskdsDEQLSVPQSTDIEG-----------VLPREIRK 885
Cdd:PRK05762  401 SPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGL------VEGLAQPPEESVAGflgarfsrekhFLPEIVER 473
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  886 LVECRRDVKSLMKSERneakkkqmdirQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSV 965
Cdd:PRK05762  474 LWEGRDEAKREMNKPL-----------SQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQV 542
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  966 VYGDTDSIMINTNS-VDLVAAKKLGNEIKKAVNKCHRL-----------LELDLDGVFKR--MlllkkkkyaalTINPDT 1031
Cdd:PRK05762  543 IYGDTDSTFVWLGGaHDEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRRffM-----------PTIRGA 611
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1032 KVEAK--------------EL--KGLDIVRRDWSQLAKETGTAVVDKILDasltRDEMVSSIDDLLREIRA-KLDSGTVp 1094
Cdd:PRK05762  612 EEGSKkryagliqegdgdgRIvfKGLETVRTDWTPLAKEFQQELYERIFR----GEPYVDYVREVIDKLRAgELDEKLV- 686
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1095 lemfqISKQLTRNPEQYADVKAQcHAAVAQRLNKSG-----KFNLRHNDIVEYVICEDGtdnpatqrayhrTEMAENSAL 1169
Cdd:PRK05762  687 -----YRKRLRRPLDEYQRNVPP-HVRAARLADEMGykvgrPLQYQNGGKIGYVITVNG------------PEPLEYRKS 748
                         650       660       670
                  ....*....|....*....|....*....|....*..
gi 392896659 1170 KIDLLYYLAQQIHPVVSRLVEPIEETDAVRIAENLGL 1206
Cdd:PRK05762  749 PIDYDYYIEKQLQPVADRILPFFGDDFATLKTGQLGL 785
zf-DNA_Pol pfam08996
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ...
1232-1421 2.30e-49

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: 173.56  E-value: 2.30e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1232 QENYDLCEGIHVICPldGCGHSNVIRETFDCvTDASSPRLLFSGCAQCQGSWdlqeHQAVIGNQVDRQMSEFVARHHLAA 1311
Cdd:pfam08996    6 EERFKDCEPLELRCP--SCGTEFEFEGVFAS-ADGYSVTPSGLRCPNCDASL----SPASLVNQLELQIRAHISRYYEGW 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1312 FKCDEPTCEFKTRVQTMKWCRegleCIR--CsTGVLRREYTSKQLFDQQMFFRTILDVDAAVRKLSDAQKKAAKVRVEYN 1389
Cdd:pfam08996   79 LVCDDPTCGNRTRQMSVYGKR----CLGpgC-KGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLALAE 153
                          170       180       190
                   ....*....|....*....|....*....|..
gi 392896659  1390 GCKIDSMMLADRInEKYLEKNAYNRVDLSYIF 1421
Cdd:pfam08996  154 QNRELFKTLKSVV-DKYLDKCGRRWVNLSSLF 184
 
Name Accession Description Interval E-value
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
48-1190 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: 694.88  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    48 ELDVEDVYDTVDDDEYEKIVAKRQKDNFIVDDDGMGYVDNGVDFEDDYEDDYA--PSSSKNSNSSKKGEKKPKKDKKKGG 125
Cdd:TIGR00592    2 VEDTDYIYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILDldKDDGSAAEAKKKDKENHKKVTKPNN 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   126 LHAFLSTTSTKKPIDesvVKAEFDDDEEVKNMLEQLGSSdEEAEEKPKATPANPFKRgrKFDSPsgsdslAPRPIAKKAK 205
Cdd:TIGR00592   82 IKAVRIACAPKKKKD---RKKSLGKDGLLGDILQELNKT-ETAQRKITPRLVSVPKL--KFSSP------ADVPAINDFS 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   206 REATGLAEHkfqrhVKVDED-------EDYGIPDDYPVASPVTSPVKTEKMaEVEAPTAPAIQKIEETVK---------M 269
Cdd:TIGR00592  150 NHHPAVVDI-----VKKAIPvstryllEKILIPVPLKRAEFAGGDVQMEGD-PELKLASFDIETYFHDGKdffpgdenpA 223
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   270 ETEHLEEVEDSLAKFRVIED----------------------------------WTggSSSQEDEDVKVEVKTGSEAFYT 315
Cdd:TIGR00592  224 DEEIMISTTPVIAKQWDYESepearvvtwkkpdkpttgsyvesvseeismikrfWD--VIDQEDTDVEITVNGDNFDLVY 301
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   316 MGGEDnttkAIRMYWiDAYEDVHKANGTVYLFGKVKTSgnawETCSIVVKNICRKVYFMPRTKNLS------TGEESSLA 389
Cdd:TIGR00592  302 LADRQ----VFQFYW-DAYEDPAEKLGVVLLFGRDVDH----VSPCVQVKGINRDLFFLPREGKIDfdlgkvTRRTINLP 372
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   390 ELHKEIGDVLRNKFNTHEFKCKMVEKelirdeSFGYGCGT-----KSPLMEVLYPAEKGK-----LPSDLKGDTFSNTFN 459
Cdd:TIGR00592  373 DYYLEFVSELALGYKKEKFRAKPIAK------KYEFEAPDidapySSEYLEVTYELGKEFapmeaLPSDLKGQTFWHVFG 446
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   460 TSVTPLERLLIEKKFMGPGWIELYNYSD-PKAKTSNCKYEFEVDMEKMRNIkyleSSDAPPPTIKLLALNVVTTLNDRKD 538
Cdd:TIGR00592  447 SNTGNLERFLLLRKIKGPCWLAVKGPDElEYPRRSWCKYEGGYVKPPNVEK----GLDKTPPPLVVLDFSMKSLNPSIIR 522
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   539 NEICMISMLFNPKCDLAHPSGDSKDLKPKCLVTKPPGGSLPYDIqKRLETEKLSKFVKSVANEKALLTLFLAMINEDEPD 618
Cdd:TIGR00592  523 NEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPLDL-KGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPD 601
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   619 MIVGHDL-SATIALLVSRLEKLKLPNWSRISRLKRSINIGKighsksGQWELTAGRMMLDSKLAAMELVKSRSFDLTELS 697
Cdd:TIGR00592  602 EIVGHDYqQRALKVLANRINDLKIPTWSKIGRLRRSPKFGR------RFGERTCGRMICDVEISAKELIRCKSYDLSELV 675
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   698 QQILGAERREIYANEIPQLYVDSKDLISLINWSWNDLLLSLRIVVRLNALPLYIQISQIVGGIASRTMMGGRAERNEYLL 777
Cdd:TIGR00592  676 QQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLL 755
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   778 LHAFEKADLIAPDKYNSSESKKKKEESQEGD-EKKSGKAQYSGGLVLEPKKGLYETLILLLDFNSLYPSIIQEYNICYTT 856
Cdd:TIGR00592  756 LHAFYENNYIVPDKQIFRKQQKLGDEDEEIDgYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTT 835
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   857 LEYSKDSDEQLSVPQSTDIEGVLPREIRKLVECRRDVKSLMKSERNEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYA 936
Cdd:TIGR00592  836 VQQKVDEDELPELPDSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYA 915
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   937 KPLAALVTAKGREILMHSKDLVEKMGYSVVYGDTDSIMINTNSVDLVAAKKLGNEIKKAVNKCHRLLELDLDGVFKRMLL 1016
Cdd:TIGR00592  916 KPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLL 995
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1017 LKKKKYAALTINPDTK---VEAKELKGLDIVRRDWSQLAKETGTAVVDKILDASlTRDEMVSSIDDLLREIRAKLDSGTV 1093
Cdd:TIGR00592  996 LKKKKYAAIKVEGDSDgnyTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDK-DVEEAVEEVQEVLEKIGKNVLNGEV 1074
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1094 PLEMFQISKQLTRNPEQYADVKAQCHAAVAQRLNKSGKFNLRHNDIVEYVICEDGTDNPATQRAYHRTE-MAENSALKID 1172
Cdd:TIGR00592 1075 PLEKFVINKQLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRAYALEElQRKHNNLIYD 1154
                         1210
                   ....*....|....*...
gi 392896659  1173 LLYYLAQQIHPVVSRLVE 1190
Cdd:TIGR00592 1155 TQYYLEHQIHPVVLRILE 1172
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
810-1207 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: 640.40  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  810 KKSGKAQYSGGLVLEPKKGLYETLILLLDFNSLYPSIIQEYNICYTTLEYSKDSDE---QLSVPQSTDIEGVLPREIRKL 886
Cdd:cd05532     1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEddeEPPLPPSDQEKGILPRIIRKL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  887 VECRRDVKSLMKSERNEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSVV 966
Cdd:cd05532    81 VERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMNLEVI 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  967 YGDTDSIMINTNSVDLVAAKKLGNEIKKAVNKCHRLLELDLDGVFKRMLLLKKKKYAALTINPD-TKVEAKELKGLDIVR 1045
Cdd:cd05532   161 YGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVDDdKGKLKKEVKGLDIVR 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1046 RDWSQLAKETGTAVVDKILDASLtRDEMVSSIDDLLREIRAKLDSGTVPLEMFQISKQLTRNPEQYADVKAQCHAAVAQR 1125
Cdd:cd05532   241 RDWCPLSKEIGNYVLDQILSDKS-REDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKSLPHVQVALR 319
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1126 LNKSGKfNLRHNDIVEYVICEDGTDNPATQRAYHRTEMAENSALKIDLLYYLAQQIHPVVSRLVEPIEETDAVRIAENLG 1205
Cdd:cd05532   320 MNKRGR-KVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTDAVRLAECLG 398

                  ..
gi 392896659 1206 LD 1207
Cdd:cd05532   399 LD 400
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
762-1192 4.08e-124

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: 393.52  E-value: 4.08e-124
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   762 SRTMMGGRAERNEYLLLHAFEKADLIAPDKynsseskkkkeesqegDEKKSGKAQYSGGLVLEPKKGLYETLILLLDFNS 841
Cdd:pfam00136    4 SRVLEGGQQIRVESCLLRLALEEGFILPDR----------------PSAKGDEDGYQGATVIEPKKGFYDKPVLVLDFNS 67
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   842 LYPSIIQEYNICYTTLEYSKD-------SDEQLSVP---------QSTDIEGVLPREIRKLVECRRDVKSLMKSERNEAK 905
Cdd:pfam00136   68 LYPSIIQAHNLCYTTLVRSVDeannlppEDNLITVEctprgvyfvKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFE 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   906 KKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKM---GYSVVYGDTDSIMINTNSVDL 982
Cdd:pfam00136  148 RAILDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMytyNFRVIYGDTDSVFIEFGGKDV 227
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   983 VAAKKLGNEIKKAVNKcHRL---LELDLDGVFKRMLLLKKKKYAALTINPDTKVEAKELKGLDIVRRDWSQLAKETGTAV 1059
Cdd:pfam00136  228 EEAMKIGDELAEHVNQ-DLFkspIKLEFEKVYKPLLLISKKKYAGLKYTAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKV 306
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1060 VDKILDASLtRDEMVSSIDDLLREIRAKLDSGTVPLEMFQISKQLTRNPEQYaDVKAQCHAAVAQRLNKSGKFNLRHNDI 1139
Cdd:pfam00136  307 LDLLLSDRG-LPVGLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNY-KSKNLPHVEVALRMNKRNGEAPEVGDR 384
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 392896659  1140 VEYVICEDGTDN---PATQRAYHRTEMAENSaLKIDLLYYLAQQIHPVVSRLVEPI 1192
Cdd:pfam00136  385 IPYVIVKAAKGLknlLIYERAEDPEYVLENN-LPIDYEYYFSNQLIPPVARLLEPI 439
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
464-1208 8.52e-104

DNA polymerase B elongation subunit [Replication, recombination and repair];


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 349.90  E-value: 8.52e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  464 PLERLLIEKkFMGPG-WIELYNYSDPKAKTSNCKYEFEvdmekmrnikylESSDAPPPTIKLLAL-----NVVTTLNDRK 537
Cdd:COG0417   114 FHDRYLIDR-FLTPGvWYEGEVEEDGGKLDYEVKENPR------------LKPEDYRPKLKVLSFdievsTPRGFPDPER 180
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  538 DNEICMISmlfnpkcdLAHPSGDSKDLkpkcLVTKPPggsLPYDIQkrleteklskfvkSVANEKALLTLFLAMINEDEP 617
Cdd:COG0417   181 DGPIISIG--------LAGSDGEKKVL----MLGREG---VDFEVE-------------YFDDEKALLEAFFEIIREYDP 232
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  618 DMIVGH-----DLsatiALLVSRLEKLKLPnwSRISRLKRSINIGKIGhsKSGQWELTaGRMMLDS-KLAAMELVKSRSF 691
Cdd:COG0417   233 DIIIGWnvdnfDL----PYLQKRAERLGIP--LDLGRDGSEPSWREHG--GQGFASIP-GRVVIDLyDALKSATYKFKSY 303
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  692 DLTELSQQILGAERREIYANEIPQLYVDSKDliSLINWSWNDLLLSLRIVVRLNALPLYIQISQIVGGIASRTMMGGRAE 771
Cdd:COG0417   304 SLDAVAEELLGEGKLIVDGGEIERLWDDDKP--ALAEYNLRDAELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSA 381
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  772 RNEYLLLHAFEKADLIAPDKynsseskkkkeesqegdEKKSGKAqYSGGLVLEPKKGLYETlILLLDFNSLYPSIIQEYN 851
Cdd:COG0417   382 AFENLLLPEAHRRGYLAPNK-----------------GEIKGEA-YPGGYVLDPKPGLYEN-VLVLDFKSLYPSIIRTFN 442
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  852 ICYTTL--EYSKDSDEQLSVPQ-----STDIEGVLPREIRKLVECRRDVKSLMKS-ERNEAKKKQMDIRQMALKLTANSM 923
Cdd:COG0417   443 ISPETLveGGEEPCGDEDVAPGfghrfCREPKGILPSILEELWDERDEAKKKMKKaKPDSEEYRLYDALQQALKILMNSF 522
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  924 YGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSVVYGDTDSIMINTNSVDLVAAKKLGNEIKKAVNKCHRL- 1002
Cdd:COG0417   523 YGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEELGYKVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSg 602
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1003 LELDLDGVFKR--MlllkkkkyaaltinPDTK------VEAKEL--KGLDIVRRDWSQLAKETGTAVVDKILdasltRDE 1072
Cdd:COG0417   603 LELEFEKHYRRffF--------------PGSKkryaglTEDGKIdiKGLEAVRSDWTELAKEFQQEVYERIL-----KEE 663
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1073 MVSSIDDLLREIRAKLDSGTVPLEMFQISKQLTRNPEQYaDVKAQCHAAVAQRLNKSGKfNLRHNDIVEYVIcedgTDNP 1152
Cdd:COG0417   664 DVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEY-EKNVPPHVRAARKLDERGR-PYQRGDKISYVI----TKGG 737
                         730       740       750       760       770
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 392896659 1153 ATQRAYhrtEMAENSALKIDLLYYLAQQIHPVVSRLVEP--IEETDAVRIAENLGLDS 1208
Cdd:COG0417   738 GRVEPV---ELAKERESEIDYDYYIEKQLKPTADRILEAfgVSFDELKGGSKQLGLFD 792
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
520-978 6.04e-98

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: 322.94  E-value: 6.04e-98
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    520 PTIKLLALNVVTTLNDRK-------DNEICMISMLFNpkcdlahpSGDSKDLKPKCLVTKPPGGSLPydiqkrleteklS 592
Cdd:smart00486    1 PPLKILSFDIETYTDGGNfpdaeifDDEIIQISLVIN--------DGDKKGANRRILFTLGTCKEID------------G 60
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    593 KFVKSVANEKALLTLFLAMINEDEPDMIVGHDLSA-TIALLVSRLEKLKLPNWSRISRLKRSINIGKIG-------HSKS 664
Cdd:smart00486   61 IEVYEFNNEKELLLAFFEFIKKYDPDIIYGHNISNfDLPYIISRLEKLKIDPLSKIGRLKIGLRIPNKKplfgsksFGLS 140
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    665 GQWELTAGRMMLDSKLAAMELVKSRSFDLTELSQQILGAERREIYANEIPQLYVDSKDLI-SLINWSWNDLLLSLRIVVR 743
Cdd:smart00486  141 DIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERdELLRYCIQDAVLTLKLFNK 220
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    744 LNALPLYIQISQIVGGIASRTMMGGRAERNEYLLLHAFEKADLIAPDKYnsseskkkKEESQEGDEKKSGKAQYSGGLVL 823
Cdd:smart00486  221 LNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKE--------LYDFKGSEPDLKKKVKYEGGKVL 292
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    824 EPKKGLYETLILLLDFNSLYPSIIQEYNICYTTLEYS-------------------KDSDEQLSVPQSTDIEGVLPREIR 884
Cdd:smart00486  293 EPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVgevvikgdliipedlltikYEKGNKYRFVKKNIRKGILPKLLK 372
                           410       420       430       440       450       460       470       480
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659    885 KLVECRRDVKSLMKSERNEAK--KKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMG 962
Cdd:smart00486  373 KLLDKRKEIKKLMKKEKDESEelKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENG 452
                           490       500
                    ....*....|....*....|.
gi 392896659    963 YS-----VVYGDTDSIMINTN 978
Cdd:smart00486  453 YPkpgfkVIYGDTDSIFVTKP 473
DNA_polB_alpha_exo cd05776
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ...
520-752 5.67e-79

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: 260.24  E-value: 5.67e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  520 PTIKLLALNVVTTLNDRK-DNEICMISMLFNPKCDLAHPSGDSKDLKPKCLVTKPPGGSLPyDIQKRLETEKLSKFVKSV 598
Cdd:cd05776     1 PPLTVMSLSIKTVLNSKTnKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPP-PDLFEKNAKKKKTKVRIF 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  599 ANEKALLTLFLAMINEDEPDMIVGHDLSA-TIALLVSRLEKLKLPNWSRISRLKRSINIGKIGHSKSGQWELTAGRMMLD 677
Cdd:cd05776    80 ENERALLNFFLAKLQKIDPDVLVGHDLEGfDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCD 159
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 392896659  678 SKLAAMELVKSRSFDLTELSQQILGAERREIYANEIPQLYVDSKDLISLINWSWNDLLLSLRIVVRLNALPLYIQ 752
Cdd:cd05776   160 TYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLNILPLTKQ 234
PRK05762 PRK05762
DNA polymerase II; Reviewed
594-1206 8.32e-68

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 245.53  E-value: 8.32e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  594 FVKSVANEKALLTLFLAMINEDEPDMIVGH-----DLsatiALLVSRLEKLKLPnwSRISRLKRSINIGKIGhSKSGQ-- 666
Cdd:PRK05762  196 FLEYVADEKALLEKFNAWFAEHDPDVIIGWnvvqfDL----RLLQERAERYGIP--LRLGRDGSELEWREHP-FRSGYgf 268
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  667 WELtAGRMMLDsklaAMELVKS-----RSFDLTELSQQILGaERREI-----YANEIPQLYVDSKDliSLINWSWNDLLL 736
Cdd:PRK05762  269 ASV-PGRLVLD----GIDALKSatwvfDSFSLEYVSQRLLG-EGKAIddpydRMDEIDRRFAEDKP--ALARYNLKDCEL 340
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  737 SLRIVVRLNALPLYIQISQIVGGIASRTMMGGRAerNEYLLLHAFEKADLIAPDKynsseskkkkeesqeGDEKksGKAq 816
Cdd:PRK05762  341 VTRIFEKTKLLPFLLERATVTGLPLDRVGGSVAA--FEHLYLPRAHRAGYVAPNL---------------GERP--GEA- 400
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  817 YSGGLVLEPKKGLYETlILLLDFNSLYPSIIQEYNICYTTLeyskdsDEQLSVPQSTDIEG-----------VLPREIRK 885
Cdd:PRK05762  401 SPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGL------VEGLAQPPEESVAGflgarfsrekhFLPEIVER 473
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  886 LVECRRDVKSLMKSERneakkkqmdirQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSV 965
Cdd:PRK05762  474 LWEGRDEAKREMNKPL-----------SQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQV 542
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  966 VYGDTDSIMINTNS-VDLVAAKKLGNEIKKAVNKCHRL-----------LELDLDGVFKR--MlllkkkkyaalTINPDT 1031
Cdd:PRK05762  543 IYGDTDSTFVWLGGaHDEEDAAKIGRALVQEINQWWQEhlqqefglesaLELEFEKHYRRffM-----------PTIRGA 611
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1032 KVEAK--------------EL--KGLDIVRRDWSQLAKETGTAVVDKILDasltRDEMVSSIDDLLREIRA-KLDSGTVp 1094
Cdd:PRK05762  612 EEGSKkryagliqegdgdgRIvfKGLETVRTDWTPLAKEFQQELYERIFR----GEPYVDYVREVIDKLRAgELDEKLV- 686
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1095 lemfqISKQLTRNPEQYADVKAQcHAAVAQRLNKSG-----KFNLRHNDIVEYVICEDGtdnpatqrayhrTEMAENSAL 1169
Cdd:PRK05762  687 -----YRKRLRRPLDEYQRNVPP-HVRAARLADEMGykvgrPLQYQNGGKIGYVITVNG------------PEPLEYRKS 748
                         650       660       670
                  ....*....|....*....|....*....|....*..
gi 392896659 1170 KIDLLYYLAQQIHPVVSRLVEPIEETDAVRIAENLGL 1206
Cdd:PRK05762  749 PIDYDYYIEKQLQPVADRILPFFGDDFATLKTGQLGL 785
POLBc_B3 cd05536
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ...
817-1190 1.17e-64

DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.


Pssm-ID: 99919  Cd Length: 371  Bit Score: 224.51  E-value: 1.17e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  817 YSGGLVLEPKKGLYETlILLLDFNSLYPSIIQEYNICYTTLEYSKDSDEQLSVPQS----TDIEGVLPREIRKLVECRRD 892
Cdd:cd05536     4 YEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVREGCEDCDVEPQVGhkfrKDPPGFIPSVLEDLLEERRR 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  893 VKSLMKS-ERNEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSVVYGDTD 971
Cdd:cd05536    83 IKEKMKKlDPESEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEKGFKVIYGDTD 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  972 SIMINTNSVDLVA--AKKLGNEIKKavnkchRL-LELDLDGVFKRMLLLKKKKYAAltINPDTKVeakELKGLDIVRRDW 1048
Cdd:cd05536   163 SLFVKIDGADAVKkkVKKLLKYINE------ELpLELEIEKFYKRGFFVTKKRYAG--LTEDGKI---DVVGLEVVRRDW 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1049 SQLAKETGTAVVDKILdasltRDEMVSSIDDLLREIRAKLDSGTVPLEMFQISKQLTRNPEQYadVKAQCHAAVAQRLNK 1128
Cdd:cd05536   232 SEIAKETQARVLEAIL-----KEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEY--KATGPHVAAAKKLAK 304
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 392896659 1129 SGkFNLRHNDIVEYVICEDGtdNPATQRAYHRTEMAENSalKIDLLYYLAQQIHPVVSRLVE 1190
Cdd:cd05536   305 RG-YKVRPGTKIGYVIVKGS--GKISDRAYPYDMVDEKH--KYDAEYYIDNQVLPAVLRILE 361
POLBc cd00145
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
815-1117 6.18e-64

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: 220.70  E-value: 6.18e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  815 AQYSGGLVLEPKKGLYEtLILLLDFNSLYPSIIQEYNICYTTLEYSKDSDEQLSVPQSTDIE-----GVLPREIRKLVEC 889
Cdd:cd00145     1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVGFRSpkdrkGLLPRILEELLNF 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  890 RRDVKSLMKSERN-EAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSVVYG 968
Cdd:cd00145    80 RDEAKKRMKAAKLaPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYG 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  969 DTDSIMINTNSV-DLVAAKKLGNEIKKAVNKCHrLLELDLDGVFKRMLLLKKKKYAALTINPDTKVEAKELKGLDIVRRD 1047
Cdd:cd00145   160 DTDSIFVSLPKMgTKEDAIKEGREILQELADEH-LLELEFEKVYLPFFLGKKKRYAGLDIWKGQDEGKIDIKGLETRRRD 238
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1048 WSQLAKETGTAVVDKILDASLTRDEMVSSIDDLLREIRAKLDSGTVPLEMfqiskQLTRNPEQYADVKAQ 1117
Cdd:cd00145   239 SPPLVKKFQKEVLELILEEERKVEAVKEYIDELDKVKYVVTRGGKGVPDY-----ERADPPLEDLDKRHR 303
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
816-1192 2.42e-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: 215.59  E-value: 2.42e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  816 QYSGGLVLEPKKGLYETLILLLDFNSLYPSIIQEYNICYTTL----EYSKDSDEQLSVPQSTDI-------EGVLPREIR 884
Cdd:cd05533     2 QYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLlnknTAKKLPPEDYIKTPNGDYfvkssvrKGLLPEILE 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  885 KLVECRRDVKSLMKSERNEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVE----- 959
Cdd:cd05533    82 ELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEekytk 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  960 KMGYS----VVYGDTDSIMINTNSVDLVAAKKLGNEIKKAVNKCH-RLLELDLDGVF--------KRMLLLKKKkyaalt 1026
Cdd:cd05533   162 ANGYShdakVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFiKPIKLEFEKVYfpyllinkKRYAGLLWT------ 235
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1027 iNPDT--KVEAkelKGLDIVRRDWSQLAKETGTAVVDKILdasLTRDemVSSIDDLLREIRAKLDSGTVPLEMFQISKQL 1104
Cdd:cd05533   236 -NPDKhdKMDT---KGIETVRRDNCLLVQNVVETCLNKIL---IERD--VEGAIEFVKGVISDLLQNKIDISLLVITKAL 306
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1105 TRNPEQYAdvKAQCHAAVAQRLNKSGKFNLRH-NDIVEYVICEDGTDNPATQRAYHRTEMAENSaLKIDLLYYLAQQIHP 1183
Cdd:cd05533   307 TKTADDYA--GKQAHVELAERMRKRDPGSAPNvGDRVPYVIIKGAKGAKAYEKAEDPIYVLENN-IPIDTQYYLENQLSK 383

                  ....*....
gi 392896659 1184 VVSRLVEPI 1192
Cdd:cd05533   384 PLLRIFEPI 392
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
467-1192 2.07e-58

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 220.67  E-value: 2.07e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  467 RLLIEKKFMGPGWIEL----YNYSDPKAKTSNCKYEFEVDMEKMRNIKYLESSDAPPP------TIKLLALNVVTTLNDR 536
Cdd:PTZ00166  206 RFLIDNNITGGSWLTLpkgkYKIRPPKKKTSTCQIEVDCSYEDLIPLPPEGEYLTIAPlrilsfDIECIKLKGLGFPEAE 285
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  537 KDNEICMISMLFNpkcdlahpSGDSKDLKPKCLVTKPPGGSLPydiqkrleteklSKFVKSVANEKALLTLFLAMINEDE 616
Cdd:PTZ00166  286 NDPVIQISSVVTN--------QGDEEEPLTKFIFTLKECASIA------------GANVLSFETEKELLLAWAEFVIAVD 345
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  617 PDMIVGHDLSA-TIALLVSRLEKLKLPNWSRISRLKRSINIGKIGHSKSGQW------ELT-AGRMMLDsklaAMELV-- 686
Cdd:PTZ00166  346 PDFLTGYNIINfDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMgtreskEINiEGRIQFD----VMDLIrr 421
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  687 --KSRSFDLTELSQQILGAERREIYANEIPQLYVDS-KDLISLINWSWNDLLLSLRIVVRLNALPLYIQISQIVGGIASR 763
Cdd:PTZ00166  422 dyKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSpETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGW 501
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  764 TMMGGRAERNEYLLLHAFEKADLIAPDKYNSseskkkkeesqegdeKKSGKAQYSGGLVLEPKKGLYETLILLLDFNSLY 843
Cdd:PTZ00166  502 LLTRGQQIKVTSQLLRKCKKLNYVIPTVKYS---------------GGGSEEKYEGATVLEPKKGFYDEPIATLDFASLY 566
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  844 PSIIQEYNICYTTLEYSKDSD---EQLSVPQSTDI--------EGVLPREIRKLVECRRDVKSLMKSERNEAKKKQMDIR 912
Cdd:PTZ00166  567 PSIMIAHNLCYSTLVPPNDANnypEDTYVTTPTGDkfvkkevrKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGR 646
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  913 QMALKLTANSMYGCLGFQYSRFYakP---LAALVTAKGREILMHSKDLVEKM-----GYS----VVYGDTDSIMINTNSV 980
Cdd:PTZ00166  647 QLALKISANSVYGYTGAQVGGQL--PcleVSTSITSFGRQMIDKTKELVEKHytkanGYKhdatVIYGDTDSVMVKFGTD 724
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  981 DLVAAKKLGNEIKKAVNKCH-RLLELDLDGVF--------KRMLLLKKKkyaaltiNPDtKVEAKELKGLDIVRRDWSQL 1051
Cdd:PTZ00166  725 DIQEAMDLGKEAAERISKKFlKPIKLEFEKVYcpyllmnkKRYAGLLYT-------NPE-KYDKIDCKGIETVRRDNCLL 796
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1052 AKETGTAVVDKIL-DASLTRD-EMV-SSIDDLLREiraKLDsgtvpLEMFQISKQLTRNpeQYAdvKAQCHAAVAQRLNK 1128
Cdd:PTZ00166  797 VQQMVETVLNKILiEKDVESAiEFTkGKISDLLQN---RID-----ISLLVITKSLGKD--DYE--GRLAHVELAKKLRQ 864
                         730       740       750       760       770       780       790
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 392896659 1129 --SGKF-NLrhNDIVEYVICEdGTDNpatQRAYHRTE----MAENSaLKIDLLYYLaQQIHPVVSRLVEPI 1192
Cdd:PTZ00166  865 rdPGSApNV--GDRVSYVIVK-GAKG---APQYERAEdplyVLENN-IPIDTQYYL-DQIKNPLLRIFEGV 927
zf-DNA_Pol pfam08996
DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an ...
1232-1421 2.30e-49

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: 173.56  E-value: 2.30e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1232 QENYDLCEGIHVICPldGCGHSNVIRETFDCvTDASSPRLLFSGCAQCQGSWdlqeHQAVIGNQVDRQMSEFVARHHLAA 1311
Cdd:pfam08996    6 EERFKDCEPLELRCP--SCGTEFEFEGVFAS-ADGYSVTPSGLRCPNCDASL----SPASLVNQLELQIRAHISRYYEGW 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  1312 FKCDEPTCEFKTRVQTMKWCRegleCIR--CsTGVLRREYTSKQLFDQQMFFRTILDVDAAVRKLSDAQKKAAKVRVEYN 1389
Cdd:pfam08996   79 LVCDDPTCGNRTRQMSVYGKR----CLGpgC-KGRMRYEYSDKQLYNQLLYFASLFDVDKAKKKLLKSEESREKVLALAE 153
                          170       180       190
                   ....*....|....*....|....*....|..
gi 392896659  1390 GCKIDSMMLADRInEKYLEKNAYNRVDLSYIF 1421
Cdd:pfam08996  154 QNRELFKTLKSVV-DKYLDKCGRRWVNLSSLF 184
POLBc_Pol_II cd05537
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
819-1185 7.36e-45

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: 167.06  E-value: 7.36e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  819 GGLVLEPKKGLYETlILLLDFNSLYPSIIQEYNI-CYTTLEYSKDSDEQLSVPQSTDI-----EGVLPREIRKLVEcrrd 892
Cdd:cd05537     5 GGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLIdPLGLIEGLKAPDPEDLIPGFLGArfsreKHILPDLIARLWA---- 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  893 vkslmksERNEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSVVYGDTDS 972
Cdd:cd05537    80 -------ARDEAKREKNAPLSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQVIYGDTDS 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  973 IMINTNS-VDLVAAKKLGNEIKKAVNK--CHRL---------LELDLDGVFKR--MlllkkkkyaaLTINPDTKVEAK-- 1036
Cdd:cd05537   153 TFVWLGEeLDAAEAQAIGKELASQINQwwAQKLkeefglesfLEIEFETHYSRffM----------PTIRGSDEGSKKry 222
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1037 ------------ELKGLDIVRRDWSQLAKETGTAVVDKILdasltRDEMVSS-IDDLLREIRA-KLDSGTVplemfqISK 1102
Cdd:cd05537   223 aglkstdggdelVFKGLETVRSDWTPLARQFQKELYERVF-----NDEPYEGfIKETVEELLAgELDELLV------YRK 291
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1103 QLTRNPEQYAD-----VKAqchAAVAQRLNKSGKFNLRHnDIVEYVICEDGtdnpatqrayhrTEMAENSALKIDLLYYL 1177
Cdd:cd05537   292 RLRRPLSEYTKnvpphVQA---ARLADQINRELGRPRQY-QWIEYVITVNG------------PEPLEYRTSPLDYQHYI 355

                  ....*...
gi 392896659 1178 AQQIHPVV 1185
Cdd:cd05537   356 DKQLKPIA 363
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
821-1192 9.77e-39

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: 151.21  E-value: 9.77e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  821 LVLEPKKGLYETLILLLDFNSLYPSIIQEYNICYTT-------------------LEYSKDSDEQLSVpQSTDI------ 875
Cdd:cd05534    40 LVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTclgrveelngggkfgflgvKLYLPPPPLDLLL-LKDDVtispng 118
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  876 ---------EGVLPREIRKLVECRRDVKSLMKSERNEAK-KKQMDIRQMALKLTANSMYGCLGFQYS-RFYAKPLAALVT 944
Cdd:cd05534   119 vmfvkksvrKGILPKMLEEILDTRIMVKKAMKKYKDDKKlQRILDARQLALKLLANVTYGYTAASFSgRMPCVEIADSIV 198
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  945 AKGREILMHSKDLVE---KMGYSVVYGDTDSIMINTNSVDLVAAKKLGNEIKKAVNKCH-RLLELDLDGVF--------K 1012
Cdd:cd05534   199 QTGRETLERAIELIEstpKWGAKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVTAANpSPIKLKFEKVYhpcvlvtkK 278
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1013 RMLLLKKkkyaaltINPDTKVEAKELKGLDIVRRDwsqlaketGTAVVDKILDASL-----TRDemVSSIDDLLREIRAK 1087
Cdd:cd05534   279 RYVGYKY-------ESPDQTEPTFDAKGIETVRRD--------GCPAVQKILEKSLrilfeTKD--LSTVKSYLQRQWSK 341
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1088 LDSGTVPLEMFQISKQLtRNPEQYADVKAQCHAAVA-QRLNKSGKFNLRHNDIVEYVICEDGTDNPATQRAYHRTEMAEN 1166
Cdd:cd05534   342 LLQGRVSIQDFIFAKEV-RLGTYKEGATLPAGAIVAlRRMEKDPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLAD 420
                         410       420
                  ....*....|....*....|....*.
gi 392896659 1167 SALKIDLLYYLAQQIHPVVSRLVEPI 1192
Cdd:cd05534   421 PSLRLDAEYYITKQIIPALDRLFNLV 446
POLBc_B1 cd05530
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ...
813-1143 2.42e-37

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: 145.19  E-value: 2.42e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  813 GKaQYSGGLVLEPKKGLYETlILLLDFNSLYPSIIQEYNICYTTLEYSKDSDEQLSVPQS-----TDIEGVLPREIRKLV 887
Cdd:cd05530    10 GK-KYRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVNCPHCECKTNEVPEVghwvcKKRPGITSQIIGLLR 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  888 ECRRDV-KSLMKSER-NEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSV 965
Cdd:cd05530    88 DLRVKIyKKKAKDKSlDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKARELGLKV 167
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  966 VYGDTDSIMINTNSVDLVaakklgNEIKKAVNKCHRlLELDLDGVFkRMLLLKKKKYAALTINPDTKVeakELKGLDIVR 1045
Cdd:cd05530   168 LYGDTDSLFLWNPPQEQL------EDLVEWVEKELG-LDLELDKEY-RYVVFSGLKKNYLGVTKDGSV---DIKGLLGKK 236
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1046 RDWSQLAKETGTAVVDkILDASLTRDEMVSS---IDDLLREIRAKLDSGTVPLEMFQISKQLTRNPEQYADVKAQcHAAV 1122
Cdd:cd05530   237 RNTPEFVKELFYEVIE-ILSAVNSPEDFEKArekIRDIVKGVYKRLKKKEYTLDQLAFKVMLSKPPEEYTKNTPQ-HVKA 314
                         330       340
                  ....*....|....*....|.
gi 392896659 1123 AQRLNKSGKfNLRHNDIVEYV 1143
Cdd:cd05530   315 ARQLEKYGR-NVEAGDIISYV 334
PRK05761 PRK05761
DNA-directed DNA polymerase I;
813-1143 2.89e-34

DNA-directed DNA polymerase I;


Pssm-ID: 235594 [Multi-domain]  Cd Length: 787  Bit Score: 142.52  E-value: 2.89e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  813 GKAqYSGGLVLEPKKGLYETlILLLDFNSLYPSIIQEYNICYTTLEYSKDSDEQLSVPQSTD-------------IEGVL 879
Cdd:PRK05761  404 GKK-YRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETVRIPECKCHYDDEVPELGhsvcddrpgltsvLVGLL 481
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  880 pREIRKLVecrrdVKSLMKSERNEAKKKQM-DIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLV 958
Cdd:PRK05761  482 -RDFRVKI-----YKKKAKDPNLDEERRAWyDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKA 555
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  959 EKMGYSVVYGDTDSIMINTNSVDlvAAKKLGNEIKKAVNkchrlLELDLDGVFK-------------RMlllkkkkyaal 1025
Cdd:PRK05761  556 EELGLKVLYGDTDSLFVWGPTKE--SLEELIKEIEERTG-----IDLEVDKTYDwvafsglkknyfgVL----------- 617
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1026 tinPDTKVeakELKGLDIVRRDWSQLAKETGTAVVDkILDASLTRDEMVSSID---DLLREIRAKLDSGTVPLEMFQISK 1102
Cdd:PRK05761  618 ---KDGKV---KIKGIVAKKRNTPEFVKELQREVLE-VLKSIRSPEDVEKVKDeieDVLKRYYEKLRAKDYPLDELAIRV 690
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|.
gi 392896659 1103 QLTRNPEQYaDVKAQCHAAVAQRLNKSGKfNLRHNDIVEYV 1143
Cdd:PRK05761  691 RLSKPLDEY-TKNTPQHVKAALQLRDYGV-EVSPGDIISYV 729
POLBc_B2 cd05531
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ...
819-1199 2.62e-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: 118.21  E-value: 2.62e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  819 GGLVLEPKKGLYETlILLLDFNSLYPSIIQEYNICYTTLE---YSKDSDEQLSVPQSTDIEGVLPREIRKLVECRRDVKS 895
Cdd:cd05531     7 GGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETINcrcCECRDHVYLGHRICLKRRGFLPEVLEPLLERRLEYKR 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  896 LMKSERNEAKkkqmdiRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSVVYGDTDSIMI 975
Cdd:cd05531    86 LKKEEDPYAG------RQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEMGFRVLHGIVDSLWI 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  976 NTNSVDLVAAKKLGNEIKkavnkchrlLELDLDGVFK-------RMLLLKKKKYAALTINPDTKVeakelKGLDIVRRDW 1048
Cdd:cd05531   160 QGRGDIEELAREIEERTG---------IPLKLEGHYDwivflpeRDGLGAPNRYFGRLSDGEMKV-----RGIELRRRDT 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1049 SQLAKETGTAVVDkILDASLTRDE---MVSSIDDLLREIRAKLDSGtvPLEMFQISKQLTRNPEQYadvkaQCHAAVAQR 1125
Cdd:cd05531   226 PPFVKKFQEEALD-ILASAKTPEEllkLREEALDLFRRYLQRLREG--DLEDLIIEKKISKRSSEY-----KVLASTALK 297
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392896659 1126 LNKSGKFNLRHNDIVEYVICEDgtdnpatqraYHRTEMAENsALKIDLLYYLAQqihpvvsrLVEPIEETDAVR 1199
Cdd:cd05531   298 ALRAKGVSVVPGMKIEYIVRDG----------KRPVPDLGN-DEGYDTKYYREL--------LERAAEELLFPL 352
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
358-696 4.24e-24

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: 105.19  E-value: 4.24e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   358 ETCSIVVKNICRKVYFMPRtknlstgEESSLAELHKEIGDVlrnkfntHEFKCKMVEKELIRDES-FGYGcGTKSPLMEV 436
Cdd:pfam03104    6 VSVCVNVFGFKPYFYCLAP-------DGKELEEVIEEIKEL-------YEGLDKIEKIELKLKKSlYGYE-EDPVPYLKV 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   437 L--YPAEKGKLPSDLKGDTFSNTFNTSVTPLERLLIEKKFMGPGWIELYNYSDPKAKT-SNCKYEFEVDMEKmrNIKYLE 513
Cdd:pfam03104   71 SfaNPRPLLKIRKYLSPENISDVYEYDVDYLERFLIDNDIVGFGWYKVKVYPFRAEGRiSNCDVEIDCDSPD--LISVPF 148
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   514 SSDAPPPTIklLALNVVTTLNDRK-------DNEICMISMLFNpkcdlahpSGDSKDLKPK---CLVTKPPGGSLPYDIQ 583
Cdd:pfam03104  149 EKEWPPLRV--LSFDIECTSLPGKfpdaenvKDPIIQISCMLD--------GQGEPEPEPRflfTLRECDSEDIEDFEYT 218
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659   584 KRLETEKLSkfVKSVANEKALLTLFLAMINEDEPDMIVGHDL-SATIALLVSRLEKLKLPNWSRISRLKRS--INIGKIG 660
Cdd:pfam03104  219 PKPIYPGVK--VFEFPSEKELLRRFFEFIRQYDPDIITGYNGdNFDWPYILNRAKELYIVKLSSIGRLNRGgrSKVREIG 296
                          330       340       350
                   ....*....|....*....|....*....|....*..
gi 392896659   661 HSKSGQWEL-TAGRMMLDSKLAAMELVKSRSFDLTEL 696
Cdd:pfam03104  297 FGTRSYEKVkISGRLHLDLYRVIKRDYKLPSYKLNAV 333
PHA03036 PHA03036
DNA polymerase; Provisional
809-1107 8.30e-23

DNA polymerase; Provisional


Pssm-ID: 222962 [Multi-domain]  Cd Length: 1004  Bit Score: 106.26  E-value: 8.30e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  809 EKKSgKAQYSGGLVLEPKKGLYETLILLLDFNSLYPSIIQEYN------IC-------------------------YTTL 857
Cdd:PHA03036  523 ETKN-KFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNlspetlVGvvvndnrleaeinkqelrrkypyprYIYV 601
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  858 EYSKDSDEQLSVPQSTD--IEGVLPREIRKLVECRRDVKSLMKSERNEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFY 935
Cdd:PHA03036  602 HCEPRSPDLVSEIAVFDrrIEGIIPKLLKTFLEERARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALY 681
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  936 AKPLAALVTAKGREILMHSKDLV--------------------------------------EKMGYSVVYGDTDSIMINT 977
Cdd:PHA03036  682 SYASAKSCTAIGRNMIKYLNSVLngsklingklilancpinpffkddrsidtnydtnlpveYNFTFRSVYGDTDSVFLEI 761
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  978 NSVDLVAAKKLGNEIKKAVNK--CHRLLELDLDGVFKRMLLLKKKKYAALTINP---DTKVEAKELKGLDIVRRDWSQLA 1052
Cdd:PHA03036  762 NTKDVDKSIKIAKELERIINEkvLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIAsstDGSVPERVNKGTSETRRDVSKFH 841
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 392896659 1053 KETGTAVVDKILDaSLTRDEMVSS------IDDLLREIRAKLDSGTVPLEMFQISKQLTRN 1107
Cdd:PHA03036  842 KYMIKIYKTRLLD-MLSEGNMNSNqvcidiLRSLEKDLIIEFDSRSAPLEMFLLSRTHHCN 901
DNA_pol_alpha_N pfam12254
DNA polymerase alpha subunit p180 N terminal; This domain family is found in eukaryotes, and ...
33-89 2.92e-19

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: 82.99  E-value: 2.92e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 392896659    33 EQLKLARSTGKAYRPEL---DVEDVYDTVDDDEYEKIVAKR-QKDNFIVDDDGMGYVDNGV 89
Cdd:pfam12254    2 EKLKAARAGGKRRLDEYeseEDEDIYDEVDEEEYRKIVRKRlLDDDFVVDDDGEGYVDDGR 62
POLBc_Pol_II_B cd05538
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
816-1154 3.28e-17

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: 84.85  E-value: 3.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  816 QYSGGLVLEPKKGLYETlILLLDFNSLYPSIIQEYNICyttleyskdsdeqlsvPQStDIEGVLPREIRKLVECRRDVKS 895
Cdd:cd05538     2 KFEGGYAYVFITGVLGP-IVHADVASLYPSIMLAYRIC----------------PAR-DSLGIFLALLKYLVELRLAAKE 63
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  896 LMKSERNEAKKKQMDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKGREILMHSKDLVEKMGYSVVYGDTDSI-M 974
Cdd:cd05538    64 SARAAARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIyF 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  975 INTNSVDLVaakklgNEIKKAVNKCHRLL----ELDLDGVFKRMLLLKKKKYAAltINPDTKVeakELKGLDIVRRDWSQ 1050
Cdd:cd05538   144 IPPNGVDTE------DEEEELVRELSSTLpkgiTVEFDGRYRAMFSYKIKNYAL--LDYDGKL---IVKGSAFRSRGIEP 212
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659 1051 LAKETGTAVVDKILDASltrdemVSSIDDLLREIRAKLDSGTVPLEMFQISKQLTRNPEQY-ADVKA-QCHAAVAQRLNK 1128
Cdd:cd05538   213 FLREFLREAVRLLLQGD------GAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYlQKVRAgKRNPAAAYEIAL 286
                         330       340
                  ....*....|....*....|....*.
gi 392896659 1129 SGKFNLRHNDIVEYVIceDGTDNPAT 1154
Cdd:cd05538   287 ARPREWRAGDRVTYYV--SGTGKGVS 310
43 PHA02528
DNA polymerase; Provisional
809-989 2.38e-15

DNA polymerase; Provisional


Pssm-ID: 177369 [Multi-domain]  Cd Length: 881  Bit Score: 81.66  E-value: 2.38e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  809 EKKSGKAQ-YSGGLVLEPKKGLYEtLILLLDFNSLYPSIIQEYNICYTTL---------------EYSKDSDEQLSVPQS 872
Cdd:PHA02528  368 ENKSHKKQkYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIagtfhvapvheyinkTAPRPSDEYSCSPNG 446
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  873 T----DIEGVLPREIRKLVECRRDVKSLM-KSERN-EAKKKQMDIR---------------------------------- 912
Cdd:PHA02528  447 WmyrkDIRGVIPTEIKKVFDQRKIYKKKMlAAERNaELIKTILEDLndsvdtpidvdyyfdfsdefkaelktltksslka 526
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  913 ---------------QMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKG--------REILMHSKDLVEKMGYS-VVYG 968
Cdd:PHA02528  527 lleecekeialcntiQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGqlaiqwieRKMNEYLNKLCKTEDEDyVIYG 606
                         250       260
                  ....*....|....*....|..
gi 392896659  969 DTDSIMINTNS-VDLVAAKKLG 989
Cdd:PHA02528  607 DTDSIYVNLDPlVEKVGEDKFK 628
DEDDy_DNA_polB_exo cd05160
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ...
595-740 4.33e-08

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: 55.05  E-value: 4.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  595 VKSVANEKALLTLFLAMINEDEPDMIVGHDL-SATIALLVSRLEKLKLPNWSRISRL-KRSINIGKIGHSKsgqwelTAG 672
Cdd:cd05160    57 VEYFADEKELLKRFFDIIREYDPDILTGYNIdDFDLPYLLKRAEALGIKLTDGIYRRsGGEKSSGSTERIA------VKG 130
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 392896659  673 RMMLDSKLAAMELVKSRSFDLTELSQQILGAERREIYANEIPQLYvDSKDLISLINWSWNDLLLSLRI 740
Cdd:cd05160   131 RVVFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDGEIIEDAE-WEEDPERLIEYNLKDAELTLQI 197
PHA03334 PHA03334
putative DNA polymerase catalytic subunit; Provisional
819-974 5.87e-08

putative DNA polymerase catalytic subunit; Provisional


Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 57.94  E-value: 5.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  819 GGLVLEPKKGL-----YETLILLLDFNSLYPSIIQEYNIC---------------YTTLEYSK----------------- 861
Cdd:PHA03334  635 GGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISpeaivdpdctarvrgWVVFDWKKidrgfgkatlmytilrt 714
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  862 DSDEQLSVPQSTDIEGVLPREIRklveCRRDVKSLMKSERNEAKKKQMDIRQMALKLTANSMYGclgfqysrfyAKPLAA 941
Cdd:PHA03334  715 KPEEPSWRRFTTYTTSSLNHYLS----MRTEYKGAMKQAKDPKLKSYHNQLQNEMKICANSHYG----------VAPHAC 780
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 392896659  942 --LVTAKGREILMHSKDLVEKM-GYSVVYGDTDSIM 974
Cdd:PHA03334  781 qhLITTLGRHKIKLVEEFIKKEpGMTVNYGDTDSVM 816
DNA_polB_Kod1_like_exo cd05780
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ...
581-740 2.74e-06

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: 49.66  E-value: 2.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  581 DIQKRLETEKLSK-FVKSVANEKALLTLFLAMINEDEPDMIVGH-----DLsatiALLVSRLEKLKLPnwSRISRLKRSI 654
Cdd:cd05780    35 GGNKVITWKKFDLpFVEVVKTEKEMIKRFIEIVKEKDPDVIYTYngdnfDF----PYLKKRAEKLGIE--LDLGRDGSEI 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  655 NIGKIGHSKSGqweLTAGRMMLDSKLAAMELVKSRSFDLTELSQQILGAERREIYANEIPQLYVDSKDLISLINWSWNDL 734
Cdd:cd05780   109 KIQRGGFNNAS---EIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDA 185

                  ....*.
gi 392896659  735 LLSLRI 740
Cdd:cd05780   186 KYTYEI 191
DNA_polB_II_exo cd05784
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ...
598-702 1.95e-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: 1.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  598 VANEKALLTLFLAMINEDEPDMIVG-----HDLsatiALLVSRLEKLKLPnwSRISRLKRSINIGKigHSKSGQWELT-A 671
Cdd:cd05784    48 FADEKSLLLALIAWFAQYDPDIIIGwnvinFDL----RLLQRRAEAHGLP--LRLGRGGSPLNWRQ--SGKPGQGFLSlP 119
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 392896659  672 GRMMLDsklaAMELVKS-----RSFDLTELSQQILG 702
Cdd:cd05784   120 GRVVLD----GIDALKTatyhfESFSLENVAQELLG 151
DNA_polB_delta_exo cd05777
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ...
595-716 7.25e-04

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: 42.95  E-value: 7.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  595 VKSVANEKALLTLFLAMINEDEPDMIVGHDLSA-TIALLVSRLEKLKLPNWSRISRLKRSINIGKIGHSKS---GQWELT 670
Cdd:cd05777    65 VFSFETEEELLLAWRDFVQEVDPDIITGYNICNfDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSkqmGTRETK 144
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 392896659  671 ----AGRMMLDsklaAMELV----KSRSFDLTELSQQILGAERREIYANEIPQL 716
Cdd:cd05777   145 einiEGRIQFD----LLQVIqrdyKLRSYSLNSVSAHFLGEQKEDVHYSIITDL 194
43B PHA02523
DNA polymerase subunit B; Provisional
894-1011 4.89e-03

DNA polymerase subunit B; Provisional


Pssm-ID: 164924  Cd Length: 391  Bit Score: 40.85  E-value: 4.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896659  894 KSLMKSERNEAKKkqmDIRQMALKLTANSMYGCLGFQYSRFYAKPLAALVTAKG--------REILMHSKDLVEKMGYS- 964
Cdd:PHA02523   27 QMIARCEKEEQKR---NTNQLNRKILINSLYGALGNNWFRYFDLRNAEAITTYGqlairwieRKLNEYINELVKTTGVDy 103
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392896659  965 VVYGDTDSIMINTNSV-------------------DLVAAKKLG-------NEIKKAVNKCHRLLELDLDGVF 1011
Cdd:PHA02523  104 VCYIDTDSVYLNMEAVvnrvgidkfrdtnhlidflDNLGSKKLEpfiddsyKELEEYMNHDHHLLLMDREAIF 176
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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