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Conserved domains on  [gi|379030588|ref|NP_001243778|]
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DNA polymerase delta catalytic subunit isoform 1 [Homo sapiens]

Protein Classification

DNA polymerase delta catalytic subunit( domain architecture ID 1001542)

DNA polymerase delta catalytic subunit acts as the catalytic component of the trimeric (Pol-delta3 complex) and tetrameric DNA polymerase delta complexes (Pol-delta4 complex), and plays a crucial role in high fidelity genome replication, including in lagging strand synthesis and repair

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PTZ00166 super family cl36522
DNA polymerase delta catalytic subunit; Provisional
81-1100 0e+00

DNA polymerase delta catalytic subunit; Provisional


The actual alignment was detected with superfamily member PTZ00166:

Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 1489.13  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   81 RPTPPalDPQTEPLIFQQLEIDHYVG----PAQPVPGGPPPSRGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPPGF 156
Cdd:PTZ00166   31 RPLPP--ISLQKDLVFFQLDADYTEKddksQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNF 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  157 GPEHMGDLQRELNLAISRDSRGGRelTGPAVLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRV--- 233
Cdd:PTZ00166  109 LPEDSQKLKRELNAQLSEQSQFKK--YQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVcgg 186
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  234 AGLGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALR-LKEKATQCQLEADVLWSDVVSHPPEGPWQRIAPLRV 312
Cdd:PTZ00166  187 GWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRpPKKKTSTCQIEVDCSYEDLIPLPPEGEYLTIAPLRI 266
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  313 LSFDIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIRIMDP 390
Cdd:PTZ00166  267 LSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDP 346
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  391 DVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLR 470
Cdd:PTZ00166  347 DFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLK 426
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  471 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRG 550
Cdd:PTZ00166  427 SYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRG 506
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  551 QQVKVVSQLLRQAMHEGLLMPVVKSEGG---EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTA 627
Cdd:PTZ00166  507 QQIKVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDA 586
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  628 QKlgLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQ 707
Cdd:PTZ00166  587 NN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQ 664
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  708 V-GKLPCLEISQSVTGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHF 786
Cdd:PTZ00166  665 VgGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKF 744
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  787 PSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQD 866
Cdd:PTZ00166  745 LKPIKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKG 823
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  867 VISDLLCNRIDISQLVITKELTRaaSDYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVL 946
Cdd:PTZ00166  824 KISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL 901
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  947 EHSLPIDTQYYLEqQLAKPLLRIFEPILGEgraEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLShQGAVC 1026
Cdd:PTZ00166  902 ENNIPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIK-EGALC 976
                         970       980       990      1000      1010      1020      1030
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 379030588 1027 EFC-QPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQEQLLRRFG 1100
Cdd:PTZ00166  977 DNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
 
Name Accession Description Interval E-value
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
81-1100 0e+00

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 1489.13  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   81 RPTPPalDPQTEPLIFQQLEIDHYVG----PAQPVPGGPPPSRGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPPGF 156
Cdd:PTZ00166   31 RPLPP--ISLQKDLVFFQLDADYTEKddksQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNF 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  157 GPEHMGDLQRELNLAISRDSRGGRelTGPAVLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRV--- 233
Cdd:PTZ00166  109 LPEDSQKLKRELNAQLSEQSQFKK--YQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVcgg 186
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  234 AGLGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALR-LKEKATQCQLEADVLWSDVVSHPPEGPWQRIAPLRV 312
Cdd:PTZ00166  187 GWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRpPKKKTSTCQIEVDCSYEDLIPLPPEGEYLTIAPLRI 266
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  313 LSFDIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIRIMDP 390
Cdd:PTZ00166  267 LSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDP 346
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  391 DVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLR 470
Cdd:PTZ00166  347 DFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLK 426
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  471 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRG 550
Cdd:PTZ00166  427 SYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRG 506
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  551 QQVKVVSQLLRQAMHEGLLMPVVKSEGG---EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTA 627
Cdd:PTZ00166  507 QQIKVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDA 586
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  628 QKlgLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQ 707
Cdd:PTZ00166  587 NN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQ 664
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  708 V-GKLPCLEISQSVTGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHF 786
Cdd:PTZ00166  665 VgGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKF 744
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  787 PSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQD 866
Cdd:PTZ00166  745 LKPIKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKG 823
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  867 VISDLLCNRIDISQLVITKELTRaaSDYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVL 946
Cdd:PTZ00166  824 KISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL 901
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  947 EHSLPIDTQYYLEqQLAKPLLRIFEPILGEgraEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLShQGAVC 1026
Cdd:PTZ00166  902 ENNIPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIK-EGALC 976
                         970       980       990      1000      1010      1020      1030
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 379030588 1027 EFC-QPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQEQLLRRFG 1100
Cdd:PTZ00166  977 DNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
579-974 0e+00

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: 829.99  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  579 EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGltEDQFIRTPTGDEFVKTSVRKGLLPQ 658
Cdd:cd05533     1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLP--PEDYIKTPNGDYFVKSSVRKGLLPE 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  659 ILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESK 738
Cdd:cd05533    79 ILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEK 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  739 YTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRP 818
Cdd:cd05533   159 YTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLW-TNP 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  819 DAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYAGKQ 898
Cdd:cd05533   238 DKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADDYAGKQ 317
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 379030588  899 AHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPIL 974
Cdd:cd05533   318 AHVELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLENNIPIDTQYYLENQLSKPLLRIFEPIL 393
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
541-973 0e+00

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: 576.87  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   541 VPLSYLLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGG--EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 618
Cdd:pfam00136    1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGdeDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   619 TTLLRPGTA---QKLGLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKV 695
Cdd:pfam00136   81 TTLVRSVDEannLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLALKI 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   696 SANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTvengysTSAKVVYGDTDSVMCRFGVSSVAEAMALG 775
Cdd:pfam00136  161 TANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT------YNFRVIYGDTDSVFIEFGGKDVEEAMKIG 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   776 REAADWVSGH-FPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLID 854
Cdd:pfam00136  235 DELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKY-TAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSD 313
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   855 RDPEGAVAHAQDVI----SDLLCNRIDISQLVITKELTRAASDYAGKQ-AHVELAERMRKRDpGSAPSLGDRVPYVIISA 929
Cdd:pfam00136  314 RGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEVALRMNKRN-GEAPEVGDRIPYVIVKA 392
                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*..
gi 379030588   930 AK---GVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 973
Cdd:pfam00136  393 AKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
119-973 0e+00

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


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 548.66  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  119 RGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPpgfgpehmgdlQRELNLAISRDSRGgreltgpaVLAVELCSRESM 198
Cdd:COG0417    15 EDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLP-----------DEEKLEELLRDIKE--------ITEVEPVKLKSF 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  199 FGyhghGPSPFLRITVALPRLVAPAR-RLLEQGIRVaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRL 277
Cdd:COG0417    76 FG----EPVPVLKIYTRDPRDVRELRdRLKEGGIDV----------YEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKL 141
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  278 KEKatqcqleadvlwsdVVSHPPEGPWQRIAPLRVLSFDIECAGRKGiFPEPERD-PVIQICSlglrwgEPEPFLRLALT 356
Cdd:COG0417   142 DYE--------------VKENPRLKPEDYRPKLKVLSFDIEVSTPRG-FPDPERDgPIISIGL------AGSDGEKKVLM 200
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  357 LRpcAPILGAKVQSYEKEEDLLQAwstFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRVAGLCSnIR 432
Cdd:COG0417   201 LG--REGVDFEVEYFDDEKALLEA---FFEIIreyDPDIIIGWNVDNFDLPYLQKRAERLGI---PLdLGRDGSEPS-WR 271
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  433 DSSFQSKqtgrrdtkvVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQngnDQTRRRLAVY 511
Cdd:COG0417   272 EHGGQGF---------ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKLIVDGGEIERLW---DDDKPALAEY 339
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  512 CLKDAYLPLRLLERLMVLVNAVEMARVTGVPLsYLLSRGQQVKVVSQL-LRQAMHEGLLMPVVKSEGGEDYTGATVIEPL 590
Cdd:COG0417   340 NLRDAELTLRIFEKTLLLPFLIELSRITGLPL-DDVGRAGSSAAFENLlLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPK 418
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  591 KGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQklgltEDQFIRTPT-GDEFVKTsvRKGLLPQILENLLSARKR 669
Cdd:COG0417   419 PGLYE-NVLVLDFKSLYPSIIRTFNISPETLVEGGEEP-----CGDEDVAPGfGHRFCRE--PKGILPSILEELWDERDE 490
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  670 AKAELAK-ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKytvenGYsts 748
Cdd:COG0417   491 AKKKMKKaKPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEEL-----GY--- 562
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  749 aKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLI-SKKRYAGLLfssrPDahDRMDCK 827
Cdd:COG0417   563 -KVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPgSKKRYAGLT----ED--GKIDIK 635
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  828 GLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDY-AGKQAHVELAER 906
Cdd:COG0417   636 GLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYeKNVPPHVRAARK 715
                         810       820       830       840       850       860
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 379030588  907 MRKRdpGSAPSLGDRVPYVIISAAKGVaaymksEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 973
Cdd:COG0417   716 LDER--GRPYQRGDKISYVITKGGGRV------EPVELAKERESEIDYDYYIEKQLKPTADRILEAF 774
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
309-764 8.07e-149

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: 453.53  E-value: 8.07e-149
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588    309 PLRVLSFDIECAGRKGIFPEPE--RDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIR 386
Cdd:smart00486    2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588    387 IMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRV-AGLCSNIRDSSFQSKQTGRRDTKVVsMVGRVQMDMLQVLLR 465
Cdd:smart00486   82 KYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLkIGLRIPNKKPLFGSKSFGLSDIKVY-IKGRLVIDLYRLYKN 160
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588    466 EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSY 545
Cdd:smart00486  161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588    546 LLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGG----------EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHN 615
Cdd:smart00486  241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588    616 LCYTTLLRPGTAQKLGLT----EDQFIRTPTG--DEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPL--RRQVLD 687
Cdd:smart00486  321 LCYSTLVGVGEVVIKGDLiipeDLLTIKYEKGnkYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESeeLKKLLD 400
                           410       420       430       440       450       460       470
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 379030588    688 GRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTVENGYstsaKVVYGDTDSVMCRFG 764
Cdd:smart00486  401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPKPGF----KVIYGDTDSIFVTKP 473
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
253-971 3.75e-87

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: 306.21  E-value: 3.75e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   253 RFMVDTDIVGCNWLELpaGKYALRLKEKATQCQLEADVLWSDVVShppEGPWQRIAPLRVLSFDIECAGRKGIFPEPERD 332
Cdd:TIGR00592  454 RFLLLRKIKGPCWLAV--KGPDELEYPRRSWCKYEGGYVKPPNVE---KGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSI 528
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   333 PVIQICSLGLRWGEPEPFLRLALTL--RP--CAPILG----------AKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNI 398
Cdd:TIGR00592  529 PDTLHREFALDKPPPEPPYDVHPCVgtRPkdCSFPLDlkgefpgkkpSLVEDLATERALIKKFMAKVKKIDPDEIVGHDY 608
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   399 QNFDLPYLISRAQTLKVQTFPFLGRVAglcsnirdssfQSKQTGRRdtKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVS 478
Cdd:TIGR00592  609 QQRALKVLANRINDLKIPTWSKIGRLR-----------RSPKFGRR--FGERTCGRMICDVEISAKELIRCKSYDLSELV 675
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   479 FHFLG-EQKEDVQHSIITDLQNGNDQTRrrLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRGQQVKVVS 557
Cdd:TIGR00592  676 QQILKtERKVIPIDNINNMYSESSSLTY--LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEF 753
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   558 QLLRQAMHEGLLMP----VVKSEGGED---------------YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 618
Cdd:TIGR00592  754 LLLHAFYENNYIVPdkqiFRKQQKLGDedeeidgykkgkkaaYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICF 833
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   619 TTLLRPgtaqklgLTEDQFIRTPtgdefvKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSAN 698
Cdd:TIGR00592  834 TTVQQK-------VDEDELPELP------DSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTAN 900
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   699 SVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTvengystsaKVVYGDTDSVMCRFGVSSVAEAMALGREA 778
Cdd:TIGR00592  901 SMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMNL---------EVIYGDTDSIMINTPGTKYEEVFKIGKEF 971
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   779 ADWVSGHFPsPIRLEFEKVYFPYLLISKKRYAGLLFS--SRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRD 856
Cdd:TIGR00592  972 KSEVNKLYK-LLELDIDGVFKRLLLLKKKKYAAIKVEgdSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKD 1050
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   857 PEGAVAHAQDVISDL----LCNRIDISQLVITKELTRAASDYAGK--QAHVELAERMRKRDPGSAPSlGDRVPYVIISAA 930
Cdd:TIGR00592 1051 VEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLTRDPKDYPDGasLPHVHVALRINARGGRKVKA-GDVVSYVICKDG 1129
                          730       740       750       760
                   ....*....|....*....|....*....|....*....|....
gi 379030588   931 KGVAAYMKS---EDPLFvLEHSLPIDTQYYLEQQLAKPLLRIFE 971
Cdd:TIGR00592 1130 GNLSARQRAyalEELQR-KHNNLIYDTQYYLEHQIHPVVLRILE 1172
 
Name Accession Description Interval E-value
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
81-1100 0e+00

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 1489.13  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   81 RPTPPalDPQTEPLIFQQLEIDHYVG----PAQPVPGGPPPSRGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPPGF 156
Cdd:PTZ00166   31 RPLPP--ISLQKDLVFFQLDADYTEKddksQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNF 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  157 GPEHMGDLQRELNLAISRDSRGGRelTGPAVLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRV--- 233
Cdd:PTZ00166  109 LPEDSQKLKRELNAQLSEQSQFKK--YQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVcgg 186
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  234 AGLGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALR-LKEKATQCQLEADVLWSDVVSHPPEGPWQRIAPLRV 312
Cdd:PTZ00166  187 GWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRpPKKKTSTCQIEVDCSYEDLIPLPPEGEYLTIAPLRI 266
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  313 LSFDIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIRIMDP 390
Cdd:PTZ00166  267 LSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDP 346
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  391 DVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLR 470
Cdd:PTZ00166  347 DFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLK 426
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  471 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRG 550
Cdd:PTZ00166  427 SYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRG 506
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  551 QQVKVVSQLLRQAMHEGLLMPVVKSEGG---EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTA 627
Cdd:PTZ00166  507 QQIKVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDA 586
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  628 QKlgLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQ 707
Cdd:PTZ00166  587 NN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQ 664
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  708 V-GKLPCLEISQSVTGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHF 786
Cdd:PTZ00166  665 VgGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKF 744
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  787 PSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQD 866
Cdd:PTZ00166  745 LKPIKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKG 823
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  867 VISDLLCNRIDISQLVITKELTRaaSDYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVL 946
Cdd:PTZ00166  824 KISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL 901
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  947 EHSLPIDTQYYLEqQLAKPLLRIFEPILGEgraEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLShQGAVC 1026
Cdd:PTZ00166  902 ENNIPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIK-EGALC 976
                         970       980       990      1000      1010      1020      1030
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 379030588 1027 EFC-QPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQEQLLRRFG 1100
Cdd:PTZ00166  977 DNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
579-974 0e+00

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: 829.99  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  579 EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGltEDQFIRTPTGDEFVKTSVRKGLLPQ 658
Cdd:cd05533     1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLP--PEDYIKTPNGDYFVKSSVRKGLLPE 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  659 ILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESK 738
Cdd:cd05533    79 ILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEK 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  739 YTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRP 818
Cdd:cd05533   159 YTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLW-TNP 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  819 DAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYAGKQ 898
Cdd:cd05533   238 DKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADDYAGKQ 317
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 379030588  899 AHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPIL 974
Cdd:cd05533   318 AHVELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLENNIPIDTQYYLENQLSKPLLRIFEPIL 393
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
541-973 0e+00

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: 576.87  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   541 VPLSYLLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGG--EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 618
Cdd:pfam00136    1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGdeDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   619 TTLLRPGTA---QKLGLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKV 695
Cdd:pfam00136   81 TTLVRSVDEannLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLALKI 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   696 SANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTvengysTSAKVVYGDTDSVMCRFGVSSVAEAMALG 775
Cdd:pfam00136  161 TANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT------YNFRVIYGDTDSVFIEFGGKDVEEAMKIG 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   776 REAADWVSGH-FPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLID 854
Cdd:pfam00136  235 DELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKY-TAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSD 313
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   855 RDPEGAVAHAQDVI----SDLLCNRIDISQLVITKELTRAASDYAGKQ-AHVELAERMRKRDpGSAPSLGDRVPYVIISA 929
Cdd:pfam00136  314 RGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEVALRMNKRN-GEAPEVGDRIPYVIVKA 392
                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*..
gi 379030588   930 AK---GVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 973
Cdd:pfam00136  393 AKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
119-973 0e+00

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


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 548.66  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  119 RGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPpgfgpehmgdlQRELNLAISRDSRGgreltgpaVLAVELCSRESM 198
Cdd:COG0417    15 EDGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLP-----------DEEKLEELLRDIKE--------ITEVEPVKLKSF 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  199 FGyhghGPSPFLRITVALPRLVAPAR-RLLEQGIRVaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRL 277
Cdd:COG0417    76 FG----EPVPVLKIYTRDPRDVRELRdRLKEGGIDV----------YEADIRFHDRYLIDRFLTPGVWYEGEVEEDGGKL 141
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  278 KEKatqcqleadvlwsdVVSHPPEGPWQRIAPLRVLSFDIECAGRKGiFPEPERD-PVIQICSlglrwgEPEPFLRLALT 356
Cdd:COG0417   142 DYE--------------VKENPRLKPEDYRPKLKVLSFDIEVSTPRG-FPDPERDgPIISIGL------AGSDGEKKVLM 200
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  357 LRpcAPILGAKVQSYEKEEDLLQAwstFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRVAGLCSnIR 432
Cdd:COG0417   201 LG--REGVDFEVEYFDDEKALLEA---FFEIIreyDPDIIIGWNVDNFDLPYLQKRAERLGI---PLdLGRDGSEPS-WR 271
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  433 DSSFQSKqtgrrdtkvVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQngnDQTRRRLAVY 511
Cdd:COG0417   272 EHGGQGF---------ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKLIVDGGEIERLW---DDDKPALAEY 339
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  512 CLKDAYLPLRLLERLMVLVNAVEMARVTGVPLsYLLSRGQQVKVVSQL-LRQAMHEGLLMPVVKSEGGEDYTGATVIEPL 590
Cdd:COG0417   340 NLRDAELTLRIFEKTLLLPFLIELSRITGLPL-DDVGRAGSSAAFENLlLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPK 418
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  591 KGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQklgltEDQFIRTPT-GDEFVKTsvRKGLLPQILENLLSARKR 669
Cdd:COG0417   419 PGLYE-NVLVLDFKSLYPSIIRTFNISPETLVEGGEEP-----CGDEDVAPGfGHRFCRE--PKGILPSILEELWDERDE 490
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  670 AKAELAK-ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKytvenGYsts 748
Cdd:COG0417   491 AKKKMKKaKPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAEEL-----GY--- 562
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  749 aKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLI-SKKRYAGLLfssrPDahDRMDCK 827
Cdd:COG0417   563 -KVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPgSKKRYAGLT----ED--GKIDIK 635
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  828 GLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDY-AGKQAHVELAER 906
Cdd:COG0417   636 GLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYeKNVPPHVRAARK 715
                         810       820       830       840       850       860
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 379030588  907 MRKRdpGSAPSLGDRVPYVIISAAKGVaaymksEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 973
Cdd:COG0417   716 LDER--GRPYQRGDKISYVITKGGGRV------EPVELAKERESEIDYDYYIEKQLKPTADRILEAF 774
DNA_polB_delta_exo cd05777
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ...
304-533 1.14e-152

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: 453.96  E-value: 1.14e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  304 WQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWST 383
Cdd:cd05777     1 WSKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  384 FIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVL 463
Cdd:cd05777    81 FVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVI 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  464 LREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAV 533
Cdd:cd05777   161 QRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLVNYI 230
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
309-764 8.07e-149

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: 453.53  E-value: 8.07e-149
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588    309 PLRVLSFDIECAGRKGIFPEPE--RDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIR 386
Cdd:smart00486    2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588    387 IMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRV-AGLCSNIRDSSFQSKQTGRRDTKVVsMVGRVQMDMLQVLLR 465
Cdd:smart00486   82 KYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLkIGLRIPNKKPLFGSKSFGLSDIKVY-IKGRLVIDLYRLYKN 160
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588    466 EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSY 545
Cdd:smart00486  161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588    546 LLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGG----------EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHN 615
Cdd:smart00486  241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588    616 LCYTTLLRPGTAQKLGLT----EDQFIRTPTG--DEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPL--RRQVLD 687
Cdd:smart00486  321 LCYSTLVGVGEVVIKGDLiipeDLLTIKYEKGnkYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESeeLKKLLD 400
                           410       420       430       440       450       460       470
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 379030588    688 GRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTVENGYstsaKVVYGDTDSVMCRFG 764
Cdd:smart00486  401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPKPGF----KVIYGDTDSIFVTKP 473
PRK05762 PRK05762
DNA polymerase II; Reviewed
119-975 4.22e-113

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 369.57  E-value: 4.22e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  119 RGSVPVLRAFGVTDEGFSVCCHIHGFAPYFYtPAppgfgpEHMGDLQRELNLAISRDSRggreltgpavlAVELCS--RE 196
Cdd:PRK05762   16 TPGGPEVELWLATDEGPRVVLLDPQFRPYFI-PA------EQDERAESLLAGEIGVRLS-----------PLALKDfhRR 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  197 SMFGYhghgPSPFLRITVALPRlvaparRLLEQGIRVaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLElpaGKYALR 276
Cdd:PRK05762   78 PVLGL----YCRQHRQLTRLPK------RLREGGVDV----------YEADIRFPERYLMERFITPCVWFS---GEVEQY 134
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  277 LKE-KATQCQLEADVLWsdvvshPPegpwqriaPLRVLSFDIECAgRKGI-----FPEPERDPVIQIcslglrwGEPEPf 350
Cdd:PRK05762  135 TTDgVLRNARLKPAPDY------RP--------PLKVVSLDIETS-NKGElysigLEGCGQRPVIML-------GPPNG- 191
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  351 lrlaltlrpCAPILGAKVQSyekEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRvAGLCS 429
Cdd:PRK05762  192 ---------EALDFLEYVAD---EKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGI---PLrLGR-DGSEL 255
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  430 NIRDSSFQSkqtgrrDTKVVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEdvqhsIITDLQNGNDQTRR-- 506
Cdd:PRK05762  256 EWREHPFRS------GYGFASVPGRLVLDGIDALKSaTWVFDSFSLEYVSQRLLGEGKA-----IDDPYDRMDEIDRRfa 324
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  507 ----RLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPlsylLSR--GQQVKVVSQLLRQAMHEGLLMPVVKSEGGED 580
Cdd:PRK05762  325 edkpALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLP----LDRvgGSVAAFEHLYLPRAHRAGYVAPNLGERPGEA 400
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  581 YTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPgtaqkLGLTEDQFIRTPTGDEFVKTsvrKGLLPQIL 660
Cdd:PRK05762  401 SPGGYVMDSKPGLYD-SVLVLDFKSLYPSIIRTFNIDPDGLVEG-----LAQPPEESVAGFLGARFSRE---KHFLPEIV 471
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  661 ENLLSARKRAKAELAKEtdplrrqvldgRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKyt 740
Cdd:PRK05762  472 ERLWEGRDEAKREMNKP-----------LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQ-- 538
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  741 venGYstsaKVVYGDTDSVMCRFGVS-SVAEAMALGREAADWVSGHFPSPIR----------LEFEKVY----FPYLLI- 804
Cdd:PRK05762  539 ---GY----QVIYGDTDSTFVWLGGAhDEEDAAKIGRALVQEINQWWQEHLQqefglesaleLEFEKHYrrffMPTIRGa 611
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  805 ---SKKRYAGLLfsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVahaQDVISDLLCNRIDiSQL 881
Cdd:PRK05762  612 eegSKKRYAGLI--QEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEPYVDYV---REVIDKLRAGELD-EKL 685
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  882 VITKELTRAASDYAGKQA-HV----ELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSedplfvlehslPIDTQY 956
Cdd:PRK05762  686 VYRKRLRRPLDEYQRNVPpHVraarLADEMGYKVGRPLQYQNGGKIGYVITVNGPEPLEYRKS-----------PIDYDY 754
                         890
                  ....*....|....*....
gi 379030588  957 YLEQQLaKPLLRIFEPILG 975
Cdd:PRK05762  755 YIEKQL-QPVADRILPFFG 772
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
550-973 3.73e-101

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: 326.86  E-value: 3.73e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  550 GQQVKVVSQLLRQAMHEGLLMP-----VVKSEGGEDYTgATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLL-- 622
Cdd:cd05534     1 GSQFRVESMLLRLAKPENYILPspsrqQVAQQRALECL-PLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLgr 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  623 -----------RPGTAQK-------LGLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSAR---KRAKAELAKETDPL 681
Cdd:cd05534    80 veelngggkfgFLGVKLYlppppldLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRimvKKAMKKYKDDKKLQ 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  682 RRqvLDGRQLALKVSANSVYGFTGAQV-GKLPCLEISQSVTGFGRQMIEKTKQLVESkyTVENGystsAKVVYGDTDSVM 760
Cdd:cd05534   160 RI--LDARQLALKLLANVTYGYTAASFsGRMPCVEIADSIVQTGRETLERAIELIES--TPKWG----AKVVYGDTDSLF 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  761 CRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLV 840
Cdd:cd05534   232 VLLPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAV 311
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  841 ANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYAGK-QAHVELAERMRKRDPGSAPSLG 919
Cdd:cd05534   312 QKILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGATlPAGAIVALRRMEKDPRAEPQYG 391
                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 379030588  920 DRVPYVIISAAKGVAAYMKSEDP-LFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 973
Cdd:cd05534   392 ERVPYVVVRGEPGSRLIDLVVSPeEFLADPSLRLDAEYYITKQIIPALDRLFNLV 446
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
130-477 1.55e-96

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: 310.12  E-value: 1.55e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   130 VTDEGFSVCCHIHGFAPYFYTPAPPGFGPEHMGDLQRELNLAISRdsrggreltgpaVLAVELCSRESMFGYHGHgPSPF 209
Cdd:pfam03104    1 KTDEGVSVCVNVFGFKPYFYCLAPDGKELEEVIEEIKELYEGLDK------------IEKIELKLKKSLYGYEED-PVPY 67
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   210 LRITVALPRLVAPARRLLEQGirvaglgtPSFAPYEANVDFEIRFMVDTDIVGCNWLELPagKYALRLKEKATQCQLEAD 289
Cdd:pfam03104   68 LKVSFANPRPLLKIRKYLSPE--------NISDVYEYDVDYLERFLIDNDIVGFGWYKVK--VYPFRAEGRISNCDVEID 137
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   290 VLWSDVVSHPPEGPWqriAPLRVLSFDIECAGRKGIFPEPER--DPVIQICSLGLRWGEPEPFLRLALTLRPCAPI---- 363
Cdd:pfam03104  138 CDSPDLISVPFEKEW---PPLRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEPRFLFTLRECDSEdied 214
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   364 ---------LGAKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVA-GLCSNIRD 433
Cdd:pfam03104  215 feytpkpiyPGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLNrGGRSKVRE 294
                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....
gi 379030588   434 SSFqskqtGRRDTKVVSMVGRVQMDMLQVLLREYKLRSYTLNAV 477
Cdd:pfam03104  295 IGF-----GTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
253-971 3.75e-87

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: 306.21  E-value: 3.75e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   253 RFMVDTDIVGCNWLELpaGKYALRLKEKATQCQLEADVLWSDVVShppEGPWQRIAPLRVLSFDIECAGRKGIFPEPERD 332
Cdd:TIGR00592  454 RFLLLRKIKGPCWLAV--KGPDELEYPRRSWCKYEGGYVKPPNVE---KGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSI 528
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   333 PVIQICSLGLRWGEPEPFLRLALTL--RP--CAPILG----------AKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNI 398
Cdd:TIGR00592  529 PDTLHREFALDKPPPEPPYDVHPCVgtRPkdCSFPLDlkgefpgkkpSLVEDLATERALIKKFMAKVKKIDPDEIVGHDY 608
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   399 QNFDLPYLISRAQTLKVQTFPFLGRVAglcsnirdssfQSKQTGRRdtKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVS 478
Cdd:TIGR00592  609 QQRALKVLANRINDLKIPTWSKIGRLR-----------RSPKFGRR--FGERTCGRMICDVEISAKELIRCKSYDLSELV 675
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   479 FHFLG-EQKEDVQHSIITDLQNGNDQTRrrLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRGQQVKVVS 557
Cdd:TIGR00592  676 QQILKtERKVIPIDNINNMYSESSSLTY--LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEF 753
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   558 QLLRQAMHEGLLMP----VVKSEGGED---------------YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 618
Cdd:TIGR00592  754 LLLHAFYENNYIVPdkqiFRKQQKLGDedeeidgykkgkkaaYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICF 833
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   619 TTLLRPgtaqklgLTEDQFIRTPtgdefvKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSAN 698
Cdd:TIGR00592  834 TTVQQK-------VDEDELPELP------DSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTAN 900
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   699 SVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTvengystsaKVVYGDTDSVMCRFGVSSVAEAMALGREA 778
Cdd:TIGR00592  901 SMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMNL---------EVIYGDTDSIMINTPGTKYEEVFKIGKEF 971
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   779 ADWVSGHFPsPIRLEFEKVYFPYLLISKKRYAGLLFS--SRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRD 856
Cdd:TIGR00592  972 KSEVNKLYK-LLELDIDGVFKRLLLLKKKKYAAIKVEgdSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKD 1050
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   857 PEGAVAHAQDVISDL----LCNRIDISQLVITKELTRAASDYAGK--QAHVELAERMRKRDPGSAPSlGDRVPYVIISAA 930
Cdd:TIGR00592 1051 VEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQLTRDPKDYPDGasLPHVHVALRINARGGRKVKA-GDVVSYVICKDG 1129
                          730       740       750       760
                   ....*....|....*....|....*....|....*....|....
gi 379030588   931 KGVAAYMKS---EDPLFvLEHSLPIDTQYYLEQQLAKPLLRIFE 971
Cdd:TIGR00592 1130 GNLSARQRAyalEELQR-KHNNLIYDTQYYLEHQIHPVVLRILE 1172
POLBc cd00145
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
579-971 2.61e-86

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: 281.95  E-value: 2.61e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  579 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLgltEDqfirtPTGDEFVKTSVRKGLLPQ 658
Cdd:cd00145     1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAP---ED-----YIGVGFRSPKDRKGLLPR 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  659 ILENLLSARKRAKAELAK-ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVES 737
Cdd:cd00145    72 ILEELLNFRDEAKKRMKAaKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEE 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  738 KytvenGYstsaKVVYGDTDSVMCRFGVS-SVAEAMALGREAADWVsgHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsS 816
Cdd:cd00145   152 H-----GA----RVIYGDTDSIFVSLPKMgTKEDAIKEGREILQEL--ADEHLLELEFEKVYLPFFLGKKKRYAGLDI-W 219
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  817 RPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVIsdllcnridisqlvitkeltraasdyag 896
Cdd:cd00145   220 KGQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL---------------------------- 271
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 379030588  897 kqahvelaermrkrdpgsapslgDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 971
Cdd:cd00145   272 -----------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
581-975 3.53e-84

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: 279.08  E-value: 3.53e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  581 YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQfirtptgdefVKTSVRKGLLPQIL 660
Cdd:cd05532     8 YAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPPL----------PPSDQEKGILPRII 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  661 ENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKyt 740
Cdd:cd05532    78 RKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKM-- 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  741 venGYStsakVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSpIRLEFEKVYFPYLLISKKRYAGLLFSSRPDA 820
Cdd:cd05532   156 ---NLE----VIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKK-LEIDIDGVFKRLLLLKKKKYAALKVVDDDKG 227
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  821 HDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAV----AHAQDVISDLLCNRIDISQLVITKELTRAASDYAG 896
Cdd:cd05532   228 KLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVenihEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPD 307
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  897 K--QAHVELAERMRKRDPGSAPslGDRVPYVIIS--AAKGVA--AYMKSEdplFVLEHSLPIDTQYYLEQQLAKPLLRIF 970
Cdd:cd05532   308 KksLPHVQVALRMNKRGRKVKA--GDTIPYIICKdgSSKSLAdrAYHPDE---VKKNENLKIDIEYYLSQQILPPISRLC 382

                  ....*
gi 379030588  971 EPILG 975
Cdd:cd05532   383 EPIEG 387
POLBc_B3 cd05536
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ...
579-971 1.38e-76

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: 256.87  E-value: 1.38e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  579 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGTaqklgltEDQFIRTPTGDEFVKTsvRKGLLPQ 658
Cdd:cd05536     2 ESYEGGIVLEPEKGLHE-NIVVLDFSSLYPSIMIKYNISPDTLVREGC-------EDCDVEPQVGHKFRKD--PPGFIPS 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  659 ILENLLSARKRAKAELaKETDP--LRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVE 736
Cdd:cd05536    72 VLEDLLEERRRIKEKM-KKLDPesEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAE 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  737 skytvENGYstsaKVVYGDTDSVmcrFGVSSVAEA-MALGREAADWVSGHFPspIRLEFEKVYFPYLLISKKRYAGLlfs 815
Cdd:cd05536   151 -----EKGF----KVIYGDTDSL---FVKIDGADAvKKKVKKLLKYINEELP--LELEIEKFYKRGFFVTKKRYAGL--- 213
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  816 srpDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYA 895
Cdd:cd05536   214 ---TEDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYK 290
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 379030588  896 GKQAHVELAERMRKRdpGSAPSLGDRVPYVIIsaaKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 971
Cdd:cd05536   291 ATGPHVAAAKKLAKR--GYKVRPGTKIGYVIV---KGSGKISDRAYPYDMVDEKHKYDAEYYIDNQVLPAVLRILE 361
PRK05761 PRK05761
DNA-directed DNA polymerase I;
143-975 4.85e-65

DNA-directed DNA polymerase I;


Pssm-ID: 235594 [Multi-domain]  Cd Length: 787  Bit Score: 235.74  E-value: 4.85e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  143 GFAPYFYTPAPPgfgpehmgDLQRELNLaISRDsrggreltgPAVLAVELCSRESmfGYHGHgPSPFLRITVALPRLVAP 222
Cdd:PRK05761   53 GHKPYFLTDLDP--------DEIDKIPK-ILRH---------PSFDHLEIVEKYD--GLRDK-KVKVTKIVVKDPLAVRR 111
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  223 ARRLLEQGIRVaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRLKE------KATQCQLEADVLWSDVV 296
Cdd:PRK05761  112 LRLSVRDIPRA----------WEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEIlveeikKAFKDERKLAEDWLPIF 181
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  297 SHPPegpwqriAPLRVLSFDIECAGrkgifPEPERDPViqicslglrwgepepflrlaltlrpcapilgakvqsyEKEED 376
Cdd:PRK05761  182 EAPI-------PKIKRIAIDIEVYT-----PAKGRIPD-------------------------------------DSEKE 212
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  377 LLQAWSTFIRIMDPDVItgYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSFQSKqtgrRDTKVVSMVGRvq 456
Cdd:PRK05761  213 LLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQN----KAVRSYAFYGK-- 284
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  457 mdmlqvllreYKLRSYTLNAVSFHFLGEQKEDVQHSIitdlqngNDQTRRRLAVYCLKDAYLPLRL--LERLMVLVNAVE 534
Cdd:PRK05761  285 ----------YRHREARLDAVGRALLGISKVELETNI-------SELDLEELAEYNFRDAEITLKLtfFNNELVLKLILL 347
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  535 MARVTGVPLSYLlSRGQQVKVVSQLL-RQAMHEGLLMP-----------VVKSEG--GEDYTGATVIEPLKG-YYDVpiA 599
Cdd:PRK05761  348 LSRISKLPIEEL-SRATISTWISNLEyWEHRKRGWLIPwkedilrldheVYKKAIikGKKYRGGLVFQPPPGiFFNV--Y 424
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  600 TLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLgltedqfIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKE-- 677
Cdd:PRK05761  425 VLDFASLYPSIIVKWNLSPETVRIPECKCHY-------DDEVPELGHSVCDDRPGLTSVLVGLLRDFRVKIYKKKAKDpn 497
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  678 TDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEskytvENGYstsaKVVYGDTD 757
Cdd:PRK05761  498 LDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAE-----ELGL----KVLYGDTD 568
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  758 SVMCRFGVSSVAEAMalgreaADWVSGHFpsPIRLEFEKVYfPYLLIS--KKRYAGLLFSsrpdahDRMDCKGLEAVRRD 835
Cdd:PRK05761  569 SLFVWGPTKESLEEL------IKEIEERT--GIDLEVDKTY-DWVAFSglKKNYFGVLKD------GKVKIKGIVAKKRN 633
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  836 NCPLVANLVTASLRRLLIDRDPEGAV-------AHAQDVISDLLCNRIDISQLVITKELTRAASDYA-GKQAHVELAERM 907
Cdd:PRK05761  634 TPEFVKELQREVLEVLKSIRSPEDVEkvkdeieDVLKRYYEKLRAKDYPLDELAIRVRLSKPLDEYTkNTPQHVKAALQL 713
                         810       820       830       840       850       860
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 379030588  908 RKRdpGSAPSLGDRVPYVIISAAKGVaaymkseDPLFVLEHSlPIDTQYYLEQqlakpLLRIFEPILG 975
Cdd:PRK05761  714 RDY--GVEVSPGDIISYVKVDDKRGV-------KPVQLAKLS-EIDVEKYIEL-----LRSALEQILS 766
DEDDy_DNA_polB_exo cd05160
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ...
312-524 2.06e-53

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: 185.25  E-value: 2.06e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  312 VLSFDIECAGRKGiFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAP-ILGAKVQSYEKEEDLLQAWSTFIRIMDP 390
Cdd:cd05160     1 VLSFDIETTPPVG-GPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEfIDGIEVEYFADEKELLKRFFDIIREYDP 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  391 DVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVaglcSNIRDSSfqskqtgrRDTKVVSMVGRVQMDMLQVLLREYKLR 470
Cdd:cd05160    80 DILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRR----SGGEKSS--------GSTERIAVKGRVVFDLLAAYKRDFKLK 147
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 379030588  471 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDqtRRRLAVYCLKDAYLPLRLLE 524
Cdd:cd05160   148 SYTLDAVAEELLGEGKEKVDGEIIEDAEWEED--PERLIEYNLKDAELTLQILE 199
POLBc_Pol_II cd05537
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
583-971 1.15e-44

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: 165.90  E-value: 1.15e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  583 GATVIEPLKGYYDvPIATLDFSSLYPSIMMahnlcyTTLLRP-GTAQKL-GLTEDQFIRTPTGDEFVKTsvrKGLLPQIL 660
Cdd:cd05537     5 GGYVMDSKPGLYK-NVLVLDFKSLYPSIIR------TFLIDPlGLIEGLkAPDPEDLIPGFLGARFSRE---KHILPDLI 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  661 ENLLSARKRAKaelaKETDPLRRQvldgrqlALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVEskyt 740
Cdd:cd05537    75 ARLWAARDEAK----REKNAPLSQ-------AIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIE---- 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  741 vENGYstsaKVVYGDTDSVMCRFG-VSSVAEAMALGREAAD----WVSGH------FPSPIRLEFEKVYFPYLLI----- 804
Cdd:cd05537   140 -QQGY----QVIYGDTDSTFVWLGeELDAAEAQAIGKELASqinqWWAQKlkeefgLESFLEIEFETHYSRFFMPtirgs 214
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  805 ---SKKRYAGLlfsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEGAVahaQDVISDLLCNRIDiSQL 881
Cdd:cd05537   215 degSKKRYAGL---KSTDGGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFI---KETVEELLAGELD-ELL 287
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  882 VITKELTRAASDY-AGKQAHVELAermRKRDPgSAPSLGDRVPYVIISaakgvaaYMKSEDPLFVLEH-SLPIDTQYYLE 959
Cdd:cd05537   288 VYRKRLRRPLSEYtKNVPPHVQAA---RLADQ-INRELGRPRQYQWIE-------YVITVNGPEPLEYrTSPLDYQHYID 356
                         410
                  ....*....|....*
gi 379030588  960 QQL---AKPLLRIFE 971
Cdd:cd05537   357 KQLkpiADSILPFLG 371
zf-C4pol pfam14260
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ...
1012-1082 2.69e-30

C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.


Pssm-ID: 464119  Cd Length: 68  Bit Score: 114.01  E-value: 2.69e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 379030588  1012 CIGCRTVlshQGAVCEFCQPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMR 1082
Cdd:pfam14260    1 CLGCGAP---EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYMR 68
POLBc_B2 cd05531
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ...
579-976 4.16e-30

DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.


Pssm-ID: 99914  Cd Length: 352  Bit Score: 122.84  E-value: 4.16e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  579 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTPtgdefvktsvRKGLLPQ 658
Cdd:cd05531     3 LADRGGLVFQPEPGLYE-NVAQIDFSSMYPSIIVKYNISPETINCRCCECRDHVYLGHRICLK----------RRGFLPE 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  659 ILENLLSARKRAKAELAKETDPlrrqvlDGRQLALKVSANSVYGFTG---AQVGKLPCLEisqSVTGFGRQMIEKTKQLV 735
Cdd:cd05531    72 VLEPLLERRLEYKRLKKEEDPY------AGRQKALKWILVTSFGYLGyknAKFGRIEVHE---AITAYGRKILLRAKEIA 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  736 EskytvENGYstsaKVVYGDTDSVMCRfgVSSVAEAMALGREAadwvsghfPSPIRLEFEKVY-FPYLLISK------KR 808
Cdd:cd05531   143 E-----EMGF----RVLHGIVDSLWIQ--GRGDIEELAREIEE--------RTGIPLKLEGHYdWIVFLPERdglgapNR 203
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  809 YAGLLFSsrpdahDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPE---GAVAHAQDVIS--DLLCNRIDISQLVI 883
Cdd:cd05531   204 YFGRLSD------GEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEellKLREEALDLFRryLQRLREGDLEDLII 277
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  884 TKELTRAASDYAGKQAHVelAERMRKRdpGSAPSLGDRVPYVIISAAKGVAaymksedplfVLEHSLPIDTQYYLEQqla 963
Cdd:cd05531   278 EKKISKRSSEYKVLASTA--LKALRAK--GVSVVPGMKIEYIVRDGKRPVP----------DLGNDEGYDTKYYREL--- 340
                         410
                  ....*....|...
gi 379030588  964 kpLLRIFEPILGE 976
Cdd:cd05531   341 --LERAAEELLFP 351
POLBc_B1 cd05530
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ...
578-933 8.73e-29

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: 119.38  E-value: 8.73e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  578 GEDYTGATVIEPLKG-YYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPGTaqklgltEDQFIRTPTGDEFVKTSvRKGLL 656
Cdd:cd05530    10 GKKYRGAIVLEPPPGiFFNV--VVLDFASLYPSIIKVWNLSYETVNCPHC-------ECKTNEVPEVGHWVCKK-RPGIT 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  657 PQILENLLSAR-----KRAKAelaKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKT 731
Cdd:cd05530    80 SQIIGLLRDLRvkiykKKAKD---KSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITST 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  732 kqlveSKYTVENGYstsaKVVYGDTDSVMCRFGVSSVAEamalgrEAADWVSGHFpsPIRLEFEKVYfPYLLIS--KKRY 809
Cdd:cd05530   157 -----IKKARELGL----KVLYGDTDSLFLWNPPQEQLE------DLVEWVEKEL--GLDLELDKEY-RYVVFSglKKNY 218
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  810 AGLLFSSrpdahdRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPEgAVAHAQDVISDL-------LCNR-IDISQL 881
Cdd:cd05530   219 LGVTKDG------SVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPE-DFEKAREKIRDIvkgvykrLKKKeYTLDQL 291
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 379030588  882 VITKELTRAASDYA-GKQAHVELAERMRKRdpGSAPSLGDRVPYVIISAAKGV 933
Cdd:cd05530   292 AFKVMLSKPPEEYTkNTPQHVKAARQLEKY--GRNVEAGDIISYVKVKGKEGV 342
43 PHA02528
DNA polymerase; Provisional
310-783 4.84e-26

DNA polymerase; Provisional


Pssm-ID: 177369 [Multi-domain]  Cd Length: 881  Bit Score: 115.94  E-value: 4.84e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  310 LRVLSFDIECAGRKGiFPEPERDPViQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQ----------SYEKEEDLLQ 379
Cdd:PHA02528  106 IRIANLDIEVTAEDG-FPDPEEAKY-EIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPqeildkvvymPFDTEREMLL 183
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  380 AWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLkvqtfpfLG-RVAGLCSNIRdsSFQSKQT----GRRDTKvVSMVGR 454
Cdd:PHA02528  184 EYINFWEENTPVIFTGWNVELFDVPYIINRIKNI-------LGeKTAKRLSPWG--KVKERTIenmyGREEIA-YDISGI 253
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  455 VQMDMLQVllreYK------LRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQtrrRLAVYCLKDAYLPLRLLERLMV 528
Cdd:PHA02528  254 SILDYLDL----YKkftftnQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQ---KYIEYNIIDVELVDRLDDKRKL 326
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  529 LVNAVEMARVTGVPLSYLLSrgqQVK-----VVSQLLRQamheGLLMPVVKSEGGEDYTGATVIEPLKGYYDVpIATLDF 603
Cdd:PHA02528  327 IELVLSMAYYAKINFEDVFS---PIKtwdaiIFNSLKEE----KIVIPENKSHKKQKYAGAFVKEPVPGAYRW-VVSFDL 398
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  604 SSLYPSIMMAHNLCYTTLLrpGT----------AQKLGLTEDQFIRTPTGDEFVKTsvRKGLLPQILENLLSARKRAK-- 671
Cdd:PHA02528  399 TSLYPSIIRQVNISPETIA--GTfhvapvheyiNKTAPRPSDEYSCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIYKkk 474
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  672 -------AELAKET----------------------------DPLRRQVLDGR--------------QLALKVSANSVYG 702
Cdd:PHA02528  475 mlaaernAELIKTIledlndsvdtpidvdyyfdfsdefkaelKTLTKSSLKALleecekeialcntiQMARKILINSLYG 554
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  703 FTGAQVGKLPCLEISQSVTGFGRQMIektkQLVESKYtveNGY-----STSAK--VVYGDTDSVMCRFGvsSVAEAMALG 775
Cdd:PHA02528  555 ALGNEHFRYYDLRNAEAITLFGQLAI----QWIERKM---NEYlnklcKTEDEdyVIYGDTDSIYVNLD--PLVEKVGED 625
                         570
                  ....*....|
gi 379030588  776 R--EAADWVS 783
Cdd:PHA02528  626 KfkDTNHWVD 635
PHA03036 PHA03036
DNA polymerase; Provisional
313-838 6.66e-26

DNA polymerase; Provisional


Pssm-ID: 222962 [Multi-domain]  Cd Length: 1004  Bit Score: 115.50  E-value: 6.66e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  313 LSFDIECAGRKGiFPEPERDPV--IQICSLGLRWGEpepfLRLALT---LRPCAPILGAKVQSYEKEEDLLQAWSTFIRI 387
Cdd:PHA03036  163 LFLDIECHFDKK-FPSVFINPVshISCCYIDLSGKE----KRFTLInedMLSEDEIEEAVKRGYYEIESLLDMDYSKELI 237
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  388 ----------------MDPDVITGYNIQNFDLPYLISRAQTLKVQTF----PFLGRVAGLCSNIRDSSFQSKQTGRRDT- 446
Cdd:PHA03036  238 lcseivllriakklleLEFDYVVTFNGHNFDLRYISNRLELLTGEKIifrsPDGKETVHLCIYERNLSSHKGVGGVANTt 317
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  447 -KVVSMVGRVQMDMLQVLLREYKLRSYTLNAVS---FH--------------FLGEQKEDVQ------------------ 490
Cdd:PHA03036  318 yHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISknaFNcnakvlsennnevtFIGDNTTDAKgkasifsevlstgnyvti 397
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  491 ------------------------------HSIIT--------DLQ----NGNDQTRRRLAVYCLKDAYLPLRLLERLMV 528
Cdd:PHA03036  398 ndddickildkdiiensftvkvicknnyipGDTYTlsfgkddvDLSdmykNYNLEIALEMARYCIHDACLCKYLWEYYGI 477
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  529 lvnaveMARVTGVPLSYLLSRGQQVKVVS------QLLRQAMHEGLLMPVVKSEGGEDYTGATVIEPLKGYYDVPIATLD 602
Cdd:PHA03036  478 ------ETKIDAGASTYLLPQSMVFEYRAstlikgPLLKLLLEEKTILVRSETKNKFPYEGGKVFAPKQKMFDNNVLIFD 551
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  603 FSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTE--DQFIR-------------TPTGDEFVKTSV-----RKGLLPQILEN 662
Cdd:PHA03036  552 YNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEinKQELRrkypypryiyvhcEPRSPDLVSEIAvfdrrIEGIIPKLLKT 631
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  663 LLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIE------------- 729
Cdd:PHA03036  632 FLEERARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKylnsvlngsklin 711
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  730 --------------KTKQLVESKY--TVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGH-FPSPIRL 792
Cdd:PHA03036  712 gklilancpinpffKDDRSIDTNYdtNLPVEYNFTFRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINEKvLFDNFKI 791
                         650       660       670       680
                  ....*....|....*....|....*....|....*....|....*...
gi 379030588  793 EFEKVYFPYLLISKKRYAGLLF--SSRPDAHDRMDCKGLEAVRRDNCP 838
Cdd:PHA03036  792 EFEAVYKNLIMQSKKKYTTLKYiaSSTDGSVPERVNKGTSETRRDVSK 839
DNA_polB_Kod1_like_exo cd05780
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ...
310-526 4.49e-24

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: 100.89  E-value: 4.49e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  310 LRVLSFDIECAGRKGIfPEPERDPVIQI--CSLG----LRW-GEPEPFlrlaltlrpcapilgakVQSYEKEEDLLQaws 382
Cdd:cd05780     3 LKILSFDIEVLNHEGE-PNPEKDPIIMIsfADEGgnkvITWkKFDLPF-----------------VEVVKTEKEMIK--- 61
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  383 TFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVQtFPfLGRVAglcSNIrdssfqsKQTGRRDTKVVSMVGRVQMDM 459
Cdd:cd05780    62 RFIEIVkekDPDVIYTYNGDNFDFPYLKKRAEKLGIE-LD-LGRDG---SEI-------KIQRGGFNNASEIKGRIHVDL 129
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 379030588  460 LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNgNDQTRRRLAVYCLKDAYLPLRLLERL 526
Cdd:cd05780   130 YPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWD-SGENLERLFRYSMEDAKYTYEIGKEF 195
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
309-731 2.15e-23

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: 107.45  E-value: 2.15e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   309 PLRVLSFDIEC--AGRKGIFP--EPERDPVIQI----CSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQA 380
Cdd:TIGR00592  197 ELKLASFDIETyfHDGKDFFPgdENPADEEIMIsttpVIAKQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKR 276
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   381 WSTFIRIMDPDVITGYNIQNFDLPYLISRaqtlkvQTFPF-----------LGRVAGLCSNIRDSSFQSKQTG-RRDTKV 448
Cdd:TIGR00592  277 FWDVIDQEDTDVEITVNGDNFDLVYLADR------QVFQFywdayedpaekLGVVLLFGRDVDHVSPCVQVKGiNRDLFF 350
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   449 VSMVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITdlQNGNDQTRRRLAVYCLKDAYLPLRLLERLMV 528
Cdd:TIGR00592  351 LPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIA--KKYEFEAPDIDAPYSSEYLEVTYELGKEFAP 428
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   529 LVNAVEMARVTGVPLSYLLSRGQQVKVVsqLLRQAMHEGLLMPV------VKSEGGEDYTGATVIEPL--KGYY--DVPI 598
Cdd:TIGR00592  429 MEALPSDLKGQTFWHVFGSNTGNLERFL--LLRKIKGPCWLAVKgpdeleYPRRSWCKYEGGYVKPPNveKGLDktPPPL 506
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588   599 ATLDFS--SLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTP-TGDEFVKTSVR-------KGLLPQILENLLSARK 668
Cdd:TIGR00592  507 VVLDFSmkSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPcVGTRPKDCSFPldlkgefPGKKPSLVEDLATERA 586
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 379030588   669 RAKAELA--KETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSvtgFGRQMIEKT 731
Cdd:TIGR00592  587 LIKKFMAkvKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPK---FGRRFGERT 648
POLBc_Pol_II_B cd05538
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
597-968 2.29e-23

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: 102.95  E-value: 2.29e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  597 PIATLDFSSLYPSIMMAHNLCyttllrpgtaqklgltedqfirtPTGDEFvktsvrkGLLPQILENLLSARKRAKAELAK 676
Cdd:cd05538    18 PIVHADVASLYPSIMLAYRIC-----------------------PARDSL-------GIFLALLKYLVELRLAAKESARA 67
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  677 ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKytvengystSAKVVYGDT 756
Cdd:cd05538    68 AARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRR---------GATPVEVDT 138
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  757 DSV--MCRFGVSSVAEAMALGREaadwVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSsrpdahDRMDCKGLEAVRR 834
Cdd:cd05538   139 DGIyfIPPNGVDTEDEEEELVRE----LSSTLPKGITVEFDGRYRAMFSYKIKNYALLDYD------GKLIVKGSAFRSR 208
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  835 DNCPLVANLVTASLRRLLIDrDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDY-----AGKQAHVELAERMRK 909
Cdd:cd05538   209 GIEPFLREFLREAVRLLLQG-DGAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYlqkvrAGKRNPAAAYEIALA 287
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 379030588  910 RDPGSAPslGDRVPYVIISAAKGVAAYMK-SEDPLFVLEHSLpIDTQYYLEQ--QLAKPLLR 968
Cdd:cd05538   288 RPREWRA--GDRVTYYVSGTGKGVSVYENcRLVADYDPAHPD-ENTGFYAERllQLAARLLP 346
DNA_polB_zeta_exo cd05778
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ...
310-524 1.09e-22

inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.


Pssm-ID: 99821 [Multi-domain]  Cd Length: 231  Bit Score: 98.08  E-value: 1.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  310 LRVLSFDIECAGRKGIFPEPERDPVIQIC----------------SLGLRWGEPEPFLRLALTLRPCapiLGAKVQSYEK 373
Cdd:cd05778     4 LTILSLEVHVNTRGDLLPDPEFDPISAIFycidddvspfildankVGVIIVDELKSNASNGRIRSGL---SGIPVEVVES 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  374 EEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPF-LGRVaglcSNIRDSSFQSKQTGRRDTK--VVS 450
Cdd:cd05778    81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDeISRV----PSDSNGKFGDRDDEWGYTHtsGIK 156
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 379030588  451 MVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGND-QTRRRLAVYCLKDAYLPLRLLE 524
Cdd:cd05778   157 IVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSaSERWRVLEYYLKRVRLNLEILD 231
DNA_polB_II_exo cd05784
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ...
309-524 1.83e-18

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: 84.54  E-value: 1.83e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  309 PLRVLSFDIECagrkgifpeperDPVIQICSLGLrWGEPEpflRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIRIM 388
Cdd:cd05784     2 KLKVVSLDIET------------SMDGELYSIGL-YGEGQ---ERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQY 65
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  389 DPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRvAGLCSNIRDSSFQSKQTgrrdtkvVSMVGRVQMDMLQvLLRE- 466
Cdd:cd05784    66 DPDIIIGWNVINFDLRLLQRRAEAHGL---PLrLGR-GGSPLNWRQSGKPGQGF-------LSLPGRVVLDGID-ALKTa 133
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 379030588  467 -YKLRSYTLNAVSFHFLGEQKedvqhsIITDLQNGNDQTRRR-------LAVYCLKDAYLPLRLLE 524
Cdd:cd05784   134 tYHFESFSLENVAQELLGEGK------LIHDVDDRGAEIERLfredklaLARYNLQDCELVWRIFE 193
PHA03334 PHA03334
putative DNA polymerase catalytic subunit; Provisional
366-761 2.48e-16

putative DNA polymerase catalytic subunit; Provisional


Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 84.91  E-value: 2.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  366 AKVQSYEKEEDLLQAWSTFI----RIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPfLGRVAGLCSnIRDSSFQSKQT 441
Cdd:PHA03334  370 FKQRPHPLTKALMEAWEAFLskdpQLVPAQLLFGSDILNSNYLELLDVIESHKAQFKA-TCRKAAARK-EEIGSYMKTRD 447
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  442 GRRDTKVVSMV---------GRVQMDMLQVLLR---EYKLRSYTLNAVSFHFLGEQK-----------EDVQHSIITDLQ 498
Cdd:PHA03334  448 TVQDFNDNDKKylnstshgfGAHIIDLMRVCNTksiKAKCSSRKLDTVARLIISKSKphknppkigkmDDVKYTEMDGMF 527
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  499 NGNDQTRRRLAVYCLKDAYLPLRL----------LERLMVLVNA---------------VEMARVTGVPLSYllSRGQQV 553
Cdd:PHA03334  528 TAGGAALARYLIYNLVDSELLIRIaknldpviefLNRLRATYNIdyvahgrgvmnfcgfVQSTKSVEVPLLK--ARLRIG 605
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  554 KVVSQLlRQAmhEGLLMP-VVKSEGGEDYT--GATVIEPLKGY-----YDVPIATLDFSSLYPSIMMAHNLCYTTLLRPG 625
Cdd:PHA03334  606 IFVATG-RIA--ESLCMPeKYARDCRQKIKlkGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIVDPD 682
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  626 TA---------------QKLGLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQ 690
Cdd:PHA03334  683 CTarvrgwvvfdwkkidRGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQ 762
                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 379030588  691 LALKVSANSVYGftgaqVGKLPCleiSQSVTGFGRQMIektkQLVESKYTVENGYStsakVVYGDTDSVMC 761
Cdd:PHA03334  763 NEMKICANSHYG-----VAPHAC---QHLITTLGRHKI----KLVEEFIKKEPGMT----VNYGDTDSVMF 817
DNA_polB_B3_exo cd05781
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ...
309-483 9.61e-16

DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.


Pssm-ID: 99824 [Multi-domain]  Cd Length: 188  Bit Score: 76.60  E-value: 9.61e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  309 PLRVLSFDIECAGRKGiFPEPERDPVIQIcSLGLRWGEPEPFLrlaltlrpcapilgakvQSYEKEEDLLQAWSTFIRIM 388
Cdd:cd05781     2 DLKTLAFDIEVYSKYG-TPNPRRDPIIVI-SLATSNGDVEFIL-----------------AEGLDDRKIIREFVKYVKEY 62
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  389 DPDVITGYNIQNFDLPYLISRAQTLKVQTfpFLGRVAGlcsnirDSSFQSKqTGRrdtkvVSMVGRVQMDMLQVLLREYK 468
Cdd:cd05781    63 DPDIIVGYNSNAFDWPYLVERARVLGVKL--DVGRRGG------SEPSTGV-YGH-----YSITGRLNVDLYDFAEEIPE 128
                         170
                  ....*....|....*
gi 379030588  469 LRSYTLNAVSfHFLG 483
Cdd:cd05781   129 VKVKTLENVA-EYLG 142
DNA_polB_B1_exo cd05783
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ...
307-522 2.39e-15

DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 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. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthesis. This is an additional safeguard mechanism against increased levels of deaminated bases during genome duplication at high temperatures. S. solfataricus B1 also interacts with DNA polymerase Y and may contribute to genome stability mechanisms.


Pssm-ID: 99826 [Multi-domain]  Cd Length: 204  Bit Score: 75.82  E-value: 2.39e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  307 IAPLRVLSFDIEC-AGRKGIFPEPERD--PVIQIC---SLGLRwgepepflRLALTLRPCAPIL------GAKVQSYEKE 374
Cdd:cd05783     2 IPKLKRIAIDIEVyTPIKGRIPDPKTAeyPVISVAlagSDGLK--------RVLVLKREGVEGLegllpeGAEVEFFDSE 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  375 EDLLQAwstFIRIMD--PDVITgYNIQNFDLPYLISRAQTLKV--QTFPFLGRvaglcsniRDSsfqskqtgrrdtkvVS 450
Cdd:cd05783    74 KELIRE---AFKIISeyPIVLT-FNGDNFDLPYLYNRALKLGIpkEEIPIYLK--------RDY--------------AT 127
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  451 MVGRVQMDM--------LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIitdlqngNDQTRRRLAVYCLKDAYLPLRL 522
Cdd:cd05783   128 LKHGIHIDLykffsnraIQVYAFGNKYREYTLDAVAKALLGEGKVELEKNI-------SELNLYELAEYNYRDAELTLEL 200
DNA_polB_like2_exo cd05785
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ...
310-515 2.95e-13

Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.


Pssm-ID: 99828 [Multi-domain]  Cd Length: 207  Bit Score: 69.75  E-value: 2.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  310 LRVLSFDIECAGRKGIF---PEPERDPVIQIcslGLRwgEPEPFlRLALTLRPCApilgakvqsyekEEDLLQAWSTFIR 386
Cdd:cd05785     9 LRRLQLDIETYSLPGFFfsnPDRGDDRIIIV---ALR--DNRGW-EEVLHAEDAA------------EKELLEELVAIIR 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  387 IMDPDVITGYNIQNFDLPYLISRAQTLKVqtfPF-LGRVaGLCSNIRDSSFQSKQtGRRDTKVVSMVGRVQMDMLQVLLR 465
Cdd:cd05785    71 ERDPDVIEGHNIFRFDLPYLRRRCRRHGV---PLaIGRD-GSIPRQRPSRFRFAE-RLIDYPRYDIPGRHVIDTYFLVQL 145
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 379030588  466 ----EYKLRSYTLNAVSFHF--LGEQKEDVQHSIITDLQNGNdqtRRRLAVYCLKD 515
Cdd:cd05785   146 fdvsSRDLPSYGLKAVAKHFglASPDRTYIDGRQIAEVWRSD---PARLLAYALDD 198
DNA_polB_alpha_exo cd05776
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ...
327-529 4.22e-13

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: 69.95  E-value: 4.22e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  327 PEPERDPVIQICSLGL---RWGEPEPFLRLALTLRPcapilgaKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDL 403
Cdd:cd05776    39 PTPPPPFQSHTCTLTRplgRSPPPDLFEKNAKKKKT-------KVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDL 111
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  404 PYLISRAQTLKVQTFPFLGRVaglcsnIRDSSFQSKQTGRRDTKVVsMVGRVQMDMlQVLLRE-YKLRSYTLNAVSFHFL 482
Cdd:cd05776   112 DVLLSRIQELKVPHWSRIGRL------KRSVWPKKKGGGKFGEREL-TAGRLLCDT-YLSAKElIRCKSYDLTELSQQVL 183
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 379030588  483 GEQKEDVqhsIITDLQNGNDQTRR--RLAVYCLKDAYLPLRLLERLMVL 529
Cdd:cd05776   184 GIERQDI---DPEEILNMYNDSESllKLLEHTEKDAYLILQLMFKLNIL 229
43A PHA02524
DNA polymerase subunit A; Provisional
371-671 1.10e-06

DNA polymerase subunit A; Provisional


Pssm-ID: 164925 [Multi-domain]  Cd Length: 498  Bit Score: 52.69  E-value: 1.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  371 YEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLkvqtfpfLG-RVAGLCSNIRDSSFQSKQTGRRDTKVV 449
Cdd:PHA02524  177 FEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNI-------LGeKAANQLSPYGKITSKTITNLYGEKIIY 249
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  450 SMVGRVQMDMLQVLlREYK---LRSYTLNAVSFHFLGEQKEDVQHSIiTDLQNGNDQtrrRLAVYCLKDAYLPLRLLERL 526
Cdd:PHA02524  250 KIHGIALMDYMDVF-KKFSftpMPDYKLGNVGYREVKADKLDYEGPI-NKFRKADHQ---RYVDYCVRDTDIILLIDGRR 324
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  527 MVLVNAVEMARVTGVPLSYLLSrgqQVKVVSQLLRQAMHE-GLLMPVVKSEGGEDYTGATVIEPLKGYYDVPIaTLDFSS 605
Cdd:PHA02524  325 CFIDLILSLSYYAKIRFDDVLG---TIKVWDSIIFNSLVEsNVVIPAMKASPKQSFPGAYVKEPVPGGYRYGL-SFDLTS 400
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 379030588  606 LYPSIMMAHNLC---YTTLLRP--------GTAQKlglTEDQFIRTPTGDEFVKTSVrkGLLPQILENLLSARKRAK 671
Cdd:PHA02524  401 LYPSILRLLNISpemIAGMFSParledyinKVAPK---PSDQFSCAPNGMMYKKGVV--GVLPNETEKVFLQRKSEK 472
DNA_polB_epsilon_exo cd05779
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ...
309-413 7.10e-06

DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon 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 delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal 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. DNA polymerase epsilon also carries a unique large C-terminal domain with an unknown function. Phylogenetic analyses indicate that it is orthologous to the archaeal DNA polymerase B3 rather than to the eukaryotic alpha, delta, or zeta polymerases. 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


Pssm-ID: 99822 [Multi-domain]  Cd Length: 204  Bit Score: 48.03  E-value: 7.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379030588  309 PLRVLSFDIECAGRKGIFPEPERDPVIQIcSLGLrwgEPEPFLrlaLTLRPcapILGAKVQSYE---------------- 372
Cdd:cd05779     1 DPRVLAFDIETTKLPLKFPDAETDQIMMI-SYMI---DGQGYL---IVNRE---IVSEDIEDFEytpkpeyegpfkvfne 70
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 379030588  373 -KEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTL 413
Cdd:cd05779    71 pDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIH 112
 
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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