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Conserved domains on  [gi|27806073|ref|NP_776852|]
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DNA polymerase delta catalytic subunit [Bos taurus]

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
80-1099 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: 1480.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    80 RPAPPalDPQMEPLIFQQLEIDHYV----APARPLPGAPPPSQDSVPILRAFGVTNEGVSVCCHIHGFAPYFYTPAPPGF 155
Cdd:PTZ00166   31 RPLPP--ISLQKDLVFFQLDADYTEkddkSQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNF 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   156 GPEHLSELQRELSAAISRDQRGGKelTGPAVLAVELCSRESMFGYHGHGPSPFLRITLALPRLMAPARRLLEQGIRL--- 232
Cdd:PTZ00166  109 LPEDSQKLKRELNAQLSEQSQFKK--YQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVcgg 186
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   233 AGLGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYILRPEGKAT-LCQLEADVLWSDVISHPPEGEWQRIAPLRV 311
Cdd:PTZ00166  187 GWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKTsTCQIEVDCSYEDLIPLPPEGEYLTIAPLRI 266
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   312 LSFDIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEREEDLLQAWSTFIRIMDP 389
Cdd:PTZ00166  267 LSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDP 346
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   390 DVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVIGLRSNIRESSFQSRQTGRRDSKVVSMVGRVQMDMLQVLLREYKLR 469
Cdd:PTZ00166  347 DFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLK 426
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   470 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGYLLSRG 549
Cdd:PTZ00166  427 SYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRG 506
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   550 QQVKVVSQLLRQAMRQGLLMPVVKTEGG---EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAA 626
Cdd:PTZ00166  507 QQIKVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDA 586
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   627 QKlgLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQ 706
Cdd:PTZ00166  587 NN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQ 664
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   707 V-GRLPCLEISQSVTGFGRQMIEKTKQLVETKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHF 785
Cdd:PTZ00166  665 VgGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKF 744
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   786 PSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQD 865
Cdd:PTZ00166  745 LKPIKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKG 823
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   866 VISDLLCNRIDISQLVITKELTRaaADYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVL 945
Cdd:PTZ00166  824 KISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL 901
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   946 EHSLPIDTQYYLEqQLAKPLLRIFEPILGEgraEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLShQGAVC 1025
Cdd:PTZ00166  902 ENNIPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIK-EGALC 976
                         970       980       990      1000      1010      1020      1030
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27806073  1026 KFC-QPRESELYQKEVSHLSALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQERLLRRFG 1099
Cdd:PTZ00166  977 DNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
 
Name Accession Description Interval E-value
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
80-1099 0e+00

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 1480.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    80 RPAPPalDPQMEPLIFQQLEIDHYV----APARPLPGAPPPSQDSVPILRAFGVTNEGVSVCCHIHGFAPYFYTPAPPGF 155
Cdd:PTZ00166   31 RPLPP--ISLQKDLVFFQLDADYTEkddkSQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNF 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   156 GPEHLSELQRELSAAISRDQRGGKelTGPAVLAVELCSRESMFGYHGHGPSPFLRITLALPRLMAPARRLLEQGIRL--- 232
Cdd:PTZ00166  109 LPEDSQKLKRELNAQLSEQSQFKK--YQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVcgg 186
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   233 AGLGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYILRPEGKAT-LCQLEADVLWSDVISHPPEGEWQRIAPLRV 311
Cdd:PTZ00166  187 GWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKTsTCQIEVDCSYEDLIPLPPEGEYLTIAPLRI 266
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   312 LSFDIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEREEDLLQAWSTFIRIMDP 389
Cdd:PTZ00166  267 LSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDP 346
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   390 DVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVIGLRSNIRESSFQSRQTGRRDSKVVSMVGRVQMDMLQVLLREYKLR 469
Cdd:PTZ00166  347 DFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLK 426
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   470 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGYLLSRG 549
Cdd:PTZ00166  427 SYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRG 506
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   550 QQVKVVSQLLRQAMRQGLLMPVVKTEGG---EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAA 626
Cdd:PTZ00166  507 QQIKVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDA 586
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   627 QKlgLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQ 706
Cdd:PTZ00166  587 NN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQ 664
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   707 V-GRLPCLEISQSVTGFGRQMIEKTKQLVETKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHF 785
Cdd:PTZ00166  665 VgGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKF 744
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   786 PSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQD 865
Cdd:PTZ00166  745 LKPIKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKG 823
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   866 VISDLLCNRIDISQLVITKELTRaaADYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVL 945
Cdd:PTZ00166  824 KISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL 901
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   946 EHSLPIDTQYYLEqQLAKPLLRIFEPILGEgraEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLShQGAVC 1025
Cdd:PTZ00166  902 ENNIPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIK-EGALC 976
                         970       980       990      1000      1010      1020      1030
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27806073  1026 KFC-QPRESELYQKEVSHLSALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQERLLRRFG 1099
Cdd:PTZ00166  977 DNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
578-973 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: 821.90  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  578 EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLGltEDQFIKTPTGDEFVKASVRKGLLPQ 657
Cdd:cd05533    1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLP--PEDYIKTPNGDYFVKSSVRKGLLPE 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  658 ILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVETK 737
Cdd:cd05533   79 ILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEK 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  738 YTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRP 817
Cdd:cd05533  159 YTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLW-TNP 237
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  818 DAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADYAGKQ 897
Cdd:cd05533  238 DKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADDYAGKQ 317
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 27806073  898 AHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPIL 973
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 ...
540-972 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: 568.01  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    540 VPLGYLLSRGQQVKVVSQLLRQAMRQGLLMPVVKTEGG--EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 617
Cdd:pfam00136    1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGdeDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    618 TTLLRPGAA---QKLGLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKV 694
Cdd:pfam00136   81 TTLVRSVDEannLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLALKI 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    695 SANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVETKYTvengysTSAKVVYGDTDSVMCRFGVSSVAEAMALG 774
Cdd:pfam00136  161 TANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT------YNFRVIYGDTDSVFIEFGGKDVEEAMKIG 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    775 REAADWVSGH-FPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLID 853
Cdd:pfam00136  235 DELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKY-TAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSD 313
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    854 RDPSGAVAHAQDVI----SDLLCNRIDISQLVITKELTRAAADYAGKQ-AHVELAERMRKRDpGSAPSLGDRVPYVIISA 928
Cdd:pfam00136  314 RGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEVALRMNKRN-GEAPEVGDRIPYVIVKA 392
                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*..
gi 27806073    929 AK---GVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 972
Cdd:pfam00136  393 AKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
119-972 1.50e-179

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


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 544.81  E-value: 1.50e-179
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  119 DSVPILRAFGVTNEGVSVCCHIHGFAPYFYTPAPpgfgpehlselQRELSAAISRDQRGgkeltgpaVLAVELCSRESMF 198
Cdd:COG0417   16 DGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLP-----------DEEKLEELLRDIKE--------ITEVEPVKLKSFF 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  199 GyhghGPSPFLRITLALPRLMAPARRLLEQGIrlaglgtpsFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKyilrpEG 278
Cdd:COG0417   77 G----EPVPVLKIYTRDPRDVRELRDRLKEGG---------IDVYEADIRFHDRYLIDRFLTPGVWYEGEVEE-----DG 138
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  279 KATLCQLEADVLWSDVISHPPegewqriapLRVLSFDIECAGRKGiFPEPERD-PVIQICSlglrwgEPEPFLRLALTLR 357
Cdd:COG0417  139 GKLDYEVKENPRLKPEDYRPK---------LKVLSFDIEVSTPRG-FPDPERDgPIISIGL------AGSDGEKKVLMLG 202
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  358 pcAPILGAKVQSYEREEDLLQAwstFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVPgfPLLGRViGLRSNIRESS 434
Cdd:COG0417  203 --REGVDFEVEYFDDEKALLEA---FFEIIreyDPDIIIGWNVDNFDLPYLQKRAERLGIP--LDLGRD-GSEPSWREHG 274
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  435 FQSRqtgrrdskvVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQngnDQTRRRLAVYCLK 513
Cdd:COG0417  275 GQGF---------ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKLIVDGGEIERLW---DDDKPALAEYNLR 342
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  514 DAFLPLRLLERLMVLVNAMEMARVTGVPLgYLLSRGQQVKVVSQL-LRQAMRQGLLMPVVKTEGGEDYTGATVIEPLKGY 592
Cdd:COG0417  343 DAELTLRIFEKTLLLPFLIELSRITGLPL-DDVGRAGSSAAFENLlLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGL 421
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  593 YDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQklgltEDQFIKTPT-GDEFVKAsvRKGLLPQILENLLSARKRAKA 671
Cdd:COG0417  422 YE-NVLVLDFKSLYPSIIRTFNISPETLVEGGEEP-----CGDEDVAPGfGHRFCRE--PKGILPSILEELWDERDEAKK 493
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  672 ELAK-ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvENGYstsaKV 750
Cdd:COG0417  494 KMKKaKPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAE-----ELGY----KV 564
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  751 VYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLI-SKKRYAGLLfssrPDahDRMDCKGLE 829
Cdd:COG0417  565 IYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPgSKKRYAGLT----ED--GKIDIKGLE 638
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  830 AVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADY-AGKQAHVELAERMRK 908
Cdd:COG0417  639 AVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYeKNVPPHVRAARKLDE 718
                        810       820       830       840       850       860
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 27806073  909 RdpGSAPSLGDRVPYVIISAAKGVaaymksEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 972
Cdd:COG0417  719 R--GRPYQRGDKISYVITKGGGRV------EPVELAKERESEIDYDYYIEKQLKPTADRILEAF 774
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
308-763 4.91e-148

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: 451.60  E-value: 4.91e-148
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073     308 PLRVLSFDIECAGRKGIFPEPE--RDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWSTFIR 385
Cdd:smart00486    2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073     386 IMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRV-IGLRSNIRESSFQSRQTGRRDSKVVsMVGRVQMDMLQVLLR 464
Cdd:smart00486   82 KYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLkIGLRIPNKKPLFGSKSFGLSDIKVY-IKGRLVIDLYRLYKN 160
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073     465 EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGY 544
Cdd:smart00486  161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073     545 LLSRGQQVKVVSQLLRQAMRQGLLMPVVKTEGG----------EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHN 614
Cdd:smart00486  241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073     615 LCYTTLLRPGAAQKLGLT----EDQFIKTPTG--DEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPL--RRQVLD 686
Cdd:smart00486  321 LCYSTLVGVGEVVIKGDLiipeDLLTIKYEKGnkYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESeeLKKLLD 400
                           410       420       430       440       450       460       470
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27806073     687 GRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvENGYST-SAKVVYGDTDSVMCRFG 763
Cdd:smart00486  401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIE-----ENGYPKpGFKVIYGDTDSIFVTKP 473
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
206-970 2.43e-88

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: 309.68  E-value: 2.43e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    206 SPFLRITLALPRLMAPARRLLEQGIrlaglGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKyiLRPEGKATLCQL 285
Cdd:TIGR00592  413 SEYLEVTYELGKEFAPMEALPSDLK-----GQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPD--ELEYPRRSWCKY 485
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    286 EADVLWSDVIShppEGEWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTL--RP--CAP 361
Cdd:TIGR00592  486 EGGYVKPPNVE---KGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVgtRPkdCSF 562
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    362 ILG----------AKVQSYEREEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVigLRSNIR 431
Cdd:TIGR00592  563 PLDlkgefpgkkpSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRL--RRSPKF 640
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    432 ESSFQSRQTGRrdskvvsMVGRVQMDMLQVLlreyKLRSYTLNAVSFHFLG-EQKEDVQHSIITDLQNGNDQTRrrLAVY 510
Cdd:TIGR00592  641 GRRFGERTCGR-------MICDVEISAKELI----RCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLTY--LLEH 707
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    511 CLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGYLLSRGQQVKVVSQLLRQAMRQGLLMP----VVKTEGGED------- 579
Cdd:TIGR00592  708 TWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqiFRKQQKLGDedeeidg 787
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    580 --------YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPgaaqklgLTEDQFIKTPtgdefvKASVR 651
Cdd:TIGR00592  788 ykkgkkaaYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQK-------VDEDELPELP------DSELE 854
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    652 KGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTK 731
Cdd:TIGR00592  855 MGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTR 934
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    732 QLVETKYTvengystsaKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPsPIRLEFEKVYFPYLLISKKRYAGL 811
Cdd:TIGR00592  935 QLVEEMNL---------EVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-LLELDIDGVFKRLLLLKKKKYAAI 1004
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    812 LFS--SRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDL----LCNRIDISQLVITKE 885
Cdd:TIGR00592 1005 KVEgdSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQ 1084
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    886 LTRAAADYAGK--QAHVELAERMRKRDPGSAPSlGDRVPYVIISAAKGVAAYMKS---EDPLFvLEHSLPIDTQYYLEQQ 960
Cdd:TIGR00592 1085 LTRDPKDYPDGasLPHVHVALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAyalEELQR-KHNNLIYDTQYYLEHQ 1162
                          810
                   ....*....|
gi 27806073    961 LAKPLLRIFE 970
Cdd:TIGR00592 1163 IHPVVLRILE 1172
 
Name Accession Description Interval E-value
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
80-1099 0e+00

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 1480.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    80 RPAPPalDPQMEPLIFQQLEIDHYV----APARPLPGAPPPSQDSVPILRAFGVTNEGVSVCCHIHGFAPYFYTPAPPGF 155
Cdd:PTZ00166   31 RPLPP--ISLQKDLVFFQLDADYTEkddkSQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNF 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   156 GPEHLSELQRELSAAISRDQRGGKelTGPAVLAVELCSRESMFGYHGHGPSPFLRITLALPRLMAPARRLLEQGIRL--- 232
Cdd:PTZ00166  109 LPEDSQKLKRELNAQLSEQSQFKK--YQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVcgg 186
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   233 AGLGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYILRPEGKAT-LCQLEADVLWSDVISHPPEGEWQRIAPLRV 311
Cdd:PTZ00166  187 GWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKTsTCQIEVDCSYEDLIPLPPEGEYLTIAPLRI 266
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   312 LSFDIECAGRKGI-FPEPERDPVIQICSLGLRWGEPE-PFLRLALTLRPCAPILGAKVQSYEREEDLLQAWSTFIRIMDP 389
Cdd:PTZ00166  267 LSFDIECIKLKGLgFPEAENDPVIQISSVVTNQGDEEePLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDP 346
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   390 DVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVIGLRSNIRESSFQSRQTGRRDSKVVSMVGRVQMDMLQVLLREYKLR 469
Cdd:PTZ00166  347 DFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLK 426
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   470 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGYLLSRG 549
Cdd:PTZ00166  427 SYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRG 506
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   550 QQVKVVSQLLRQAMRQGLLMPVVKTEGG---EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAA 626
Cdd:PTZ00166  507 QQIKVTSQLLRKCKKLNYVIPTVKYSGGgseEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDA 586
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   627 QKlgLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQ 706
Cdd:PTZ00166  587 NN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYTGAQ 664
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   707 V-GRLPCLEISQSVTGFGRQMIEKTKQLVETKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHF 785
Cdd:PTZ00166  665 VgGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKF 744
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   786 PSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQD 865
Cdd:PTZ00166  745 LKPIKLEFEKVYCPYLLMNKKRYAGLLY-TNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKG 823
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   866 VISDLLCNRIDISQLVITKELTRaaADYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVL 945
Cdd:PTZ00166  824 KISDLLQNRIDISLLVITKSLGK--DDYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVL 901
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   946 EHSLPIDTQYYLEqQLAKPLLRIFEPILGEgraEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLShQGAVC 1025
Cdd:PTZ00166  902 ENNIPIDTQYYLD-QIKNPLLRIFEGVMDN---PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIK-EGALC 976
                         970       980       990      1000      1010      1020      1030
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27806073  1026 KFC-QPRESELYQKEVSHLSALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQERLLRRFG 1099
Cdd:PTZ00166  977 DNCnQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
578-973 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: 821.90  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  578 EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLGltEDQFIKTPTGDEFVKASVRKGLLPQ 657
Cdd:cd05533    1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLP--PEDYIKTPNGDYFVKSSVRKGLLPE 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  658 ILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVETK 737
Cdd:cd05533   79 ILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEK 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  738 YTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRP 817
Cdd:cd05533  159 YTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLW-TNP 237
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  818 DAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADYAGKQ 897
Cdd:cd05533  238 DKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADDYAGKQ 317
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 27806073  898 AHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPIL 973
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 ...
540-972 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: 568.01  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    540 VPLGYLLSRGQQVKVVSQLLRQAMRQGLLMPVVKTEGG--EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCY 617
Cdd:pfam00136    1 IPQSRVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGdeDGYQGATVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLCY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    618 TTLLRPGAA---QKLGLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKV 694
Cdd:pfam00136   81 TTLVRSVDEannLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFERAILDKQQLALKI 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    695 SANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVETKYTvengysTSAKVVYGDTDSVMCRFGVSSVAEAMALG 774
Cdd:pfam00136  161 TANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT------YNFRVIYGDTDSVFIEFGGKDVEEAMKIG 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    775 REAADWVSGH-FPSPIRLEFEKVYFPYLLISKKRYAGLLFsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLID 853
Cdd:pfam00136  235 DELAEHVNQDlFKSPIKLEFEKVYKPLLLISKKKYAGLKY-TAPSNFNKLDMKGVDLVRRDNCPLVKEVIKKVLDLLLSD 313
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    854 RDPSGAVAHAQDVI----SDLLCNRIDISQLVITKELTRAAADYAGKQ-AHVELAERMRKRDpGSAPSLGDRVPYVIISA 928
Cdd:pfam00136  314 RGLPVGLEFVISILndarSDLRNNKVPLEKFVISKELSKPPDNYKSKNlPHVEVALRMNKRN-GEAPEVGDRIPYVIVKA 392
                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*..
gi 27806073    929 AK---GVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 972
Cdd:pfam00136  393 AKglkNLLIYERAEDPEYVLENNLPIDYEYYFSNQLIPPVARLLEPI 439
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
119-972 1.50e-179

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


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 544.81  E-value: 1.50e-179
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  119 DSVPILRAFGVTNEGVSVCCHIHGFAPYFYTPAPpgfgpehlselQRELSAAISRDQRGgkeltgpaVLAVELCSRESMF 198
Cdd:COG0417   16 DGKPVIELWGRTEDGPSVLLDVTGFRPYFYVPLP-----------DEEKLEELLRDIKE--------ITEVEPVKLKSFF 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  199 GyhghGPSPFLRITLALPRLMAPARRLLEQGIrlaglgtpsFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKyilrpEG 278
Cdd:COG0417   77 G----EPVPVLKIYTRDPRDVRELRDRLKEGG---------IDVYEADIRFHDRYLIDRFLTPGVWYEGEVEE-----DG 138
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  279 KATLCQLEADVLWSDVISHPPegewqriapLRVLSFDIECAGRKGiFPEPERD-PVIQICSlglrwgEPEPFLRLALTLR 357
Cdd:COG0417  139 GKLDYEVKENPRLKPEDYRPK---------LKVLSFDIEVSTPRG-FPDPERDgPIISIGL------AGSDGEKKVLMLG 202
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  358 pcAPILGAKVQSYEREEDLLQAwstFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVPgfPLLGRViGLRSNIRESS 434
Cdd:COG0417  203 --REGVDFEVEYFDDEKALLEA---FFEIIreyDPDIIIGWNVDNFDLPYLQKRAERLGIP--LDLGRD-GSEPSWREHG 274
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  435 FQSRqtgrrdskvVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQngnDQTRRRLAVYCLK 513
Cdd:COG0417  275 GQGF---------ASIPGRVVIDLYDALKSaTYKFKSYSLDAVAEELLGEGKLIVDGGEIERLW---DDDKPALAEYNLR 342
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  514 DAFLPLRLLERLMVLVNAMEMARVTGVPLgYLLSRGQQVKVVSQL-LRQAMRQGLLMPVVKTEGGEDYTGATVIEPLKGY 592
Cdd:COG0417  343 DAELTLRIFEKTLLLPFLIELSRITGLPL-DDVGRAGSSAAFENLlLPEAHRRGYLAPNKGEIKGEAYPGGYVLDPKPGL 421
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  593 YDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQklgltEDQFIKTPT-GDEFVKAsvRKGLLPQILENLLSARKRAKA 671
Cdd:COG0417  422 YE-NVLVLDFKSLYPSIIRTFNISPETLVEGGEEP-----CGDEDVAPGfGHRFCRE--PKGILPSILEELWDERDEAKK 493
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  672 ELAK-ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvENGYstsaKV 750
Cdd:COG0417  494 KMKKaKPDSEEYRLYDALQQALKILMNSFYGVLGSEGCRFYDPELAESITARGREIIKQTIEKAE-----ELGY----KV 564
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  751 VYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLI-SKKRYAGLLfssrPDahDRMDCKGLE 829
Cdd:COG0417  565 IYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRFFFPgSKKRYAGLT----ED--GKIDIKGLE 638
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  830 AVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADY-AGKQAHVELAERMRK 908
Cdd:COG0417  639 AVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDDLVIRKRLRKPLSEYeKNVPPHVRAARKLDE 718
                        810       820       830       840       850       860
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 27806073  909 RdpGSAPSLGDRVPYVIISAAKGVaaymksEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 972
Cdd:COG0417  719 R--GRPYQRGDKISYVITKGGGRV------EPVELAKERESEIDYDYYIEKQLKPTADRILEAF 774
DNA_polB_delta_exo cd05777
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ...
303-532 1.48e-148

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: 443.17  E-value: 1.48e-148
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  303 WQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWST 382
Cdd:cd05777    1 WSKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  383 FIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVIGLRSNIRESSFQSRQTGRRDSKVVSMVGRVQMDMLQVL 462
Cdd:cd05777   81 FVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVI 160
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  463 LREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAM 532
Cdd:cd05777  161 QRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLVNYI 230
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
308-763 4.91e-148

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: 451.60  E-value: 4.91e-148
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073     308 PLRVLSFDIECAGRKGIFPEPE--RDPVIQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQAWSTFIR 385
Cdd:smart00486    2 PLKILSFDIETYTDGGNFPDAEifDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDGIEVYEFNNEKELLLAFFEFIK 81
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073     386 IMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRV-IGLRSNIRESSFQSRQTGRRDSKVVsMVGRVQMDMLQVLLR 464
Cdd:smart00486   82 KYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLkIGLRIPNKKPLFGSKSFGLSDIKVY-IKGRLVIDLYRLYKN 160
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073     465 EYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGY 544
Cdd:smart00486  161 KLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNGNYEERDELLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLRR 240
                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073     545 LLSRGQQVKVVSQLLRQAMRQGLLMPVVKTEGG----------EDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHN 614
Cdd:smart00486  241 TLYYGSQIRVESLLLREAKKNNYILPSKELYDFkgsepdlkkkVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHN 320
                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073     615 LCYTTLLRPGAAQKLGLT----EDQFIKTPTG--DEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPL--RRQVLD 686
Cdd:smart00486  321 LCYSTLVGVGEVVIKGDLiipeDLLTIKYEKGnkYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESeeLKKLLD 400
                           410       420       430       440       450       460       470
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27806073     687 GRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvENGYST-SAKVVYGDTDSVMCRFG 763
Cdd:smart00486  401 SRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIE-----ENGYPKpGFKVIYGDTDSIFVTKP 473
PRK05762 PRK05762
DNA polymerase II; Reviewed
119-974 9.59e-114

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 371.50  E-value: 9.59e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   119 DSVPILRAFGVTNEGVSVCCHIHGFAPYFYtPAppgfgpEHLSELQRELSAAISRDQR--GGKELTGPAVLAVelcsres 196
Cdd:PRK05762   17 PGGPEVELWLATDEGPRVVLLDPQFRPYFI-PA------EQDERAESLLAGEIGVRLSplALKDFHRRPVLGL------- 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   197 mfgyhghgPSPFLRITLALPRlmaparRLLEQGIRLaglgtpsfapYEANVDFEIRFMVDTDIVGCNWLElpaGKYILR- 275
Cdd:PRK05762   83 --------YCRQHRQLTRLPK------RLREGGVDV----------YEADIRFPERYLMERFITPCVWFS---GEVEQYt 135
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   276 PEGKATLCQLEADVLWsdvishPPegewqriaPLRVLSFDIECAgRKGI-----FPEPERDPVIQIcslglrwGEPEPfl 350
Cdd:PRK05762  136 TDGVLRNARLKPAPDY------RP--------PLKVVSLDIETS-NKGElysigLEGCGQRPVIML-------GPPNG-- 191
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   351 rlaltlrpCAPILGAKVQSyerEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPgfPLLGRViGLRSNI 430
Cdd:PRK05762  192 --------EALDFLEYVAD---EKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIP--LRLGRD-GSELEW 257
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   431 RESSFQSrQTGrrdskVVSMVGRVQMDMLQVLLR-EYKLRSYTLNAVSFHFLGEQKEdvqhsIITDLQNGNDQTRR---- 505
Cdd:PRK05762  258 REHPFRS-GYG-----FASVPGRLVLDGIDALKSaTWVFDSFSLEYVSQRLLGEGKA-----IDDPYDRMDEIDRRfaed 326
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   506 --RLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGyllsR--GQQVKVVSQLLRQAMRQGLLMPVVKTEGGEDYT 581
Cdd:PRK05762  327 kpALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLD----RvgGSVAAFEHLYLPRAHRAGYVAPNLGERPGEASP 402
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   582 GATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPgaaqkLGLTEDQFIKTPTGDEFVKasvRKGLLPQILEN 661
Cdd:PRK05762  403 GGYVMDSKPGLYD-SVLVLDFKSLYPSIIRTFNIDPDGLVEG-----LAQPPEESVAGFLGARFSR---EKHFLPEIVER 473
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   662 LLSARKRAKAELAKEtdplrrqvldgRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvE 741
Cdd:PRK05762  474 LWEGRDEAKREMNKP-----------LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIE-----A 537
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   742 NGYstsaKVVYGDTDSVMCRFGVS-SVAEAMALGREAADWVSGHFPSPIR----------LEFEKVY----FPYLLI--- 803
Cdd:PRK05762  538 QGY----QVIYGDTDSTFVWLGGAhDEEDAAKIGRALVQEINQWWQEHLQqefglesaleLEFEKHYrrffMPTIRGaee 613
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   804 -SKKRYAGLLfsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVahaQDVISDLLCNRIDiSQLVI 882
Cdd:PRK05762  614 gSKKRYAGLI--QEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEPYVDYV---REVIDKLRAGELD-EKLVY 687
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   883 TKELTRAAADYAGKQA-HV----ELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSedplfvlehslPIDTQYYL 957
Cdd:PRK05762  688 RKRLRRPLDEYQRNVPpHVraarLADEMGYKVGRPLQYQNGGKIGYVITVNGPEPLEYRKS-----------PIDYDYYI 756
                         890
                  ....*....|....*..
gi 27806073   958 EQQLaKPLLRIFEPILG 974
Cdd:PRK05762  757 EKQL-QPVADRILPFFG 772
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
129-476 8.80e-105

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: 332.07  E-value: 8.80e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    129 VTNEGVSVCCHIHGFAPYFYTPAPPGFGPEHLSELQRELSAAISRdqrggkeltgpaVLAVELCSRESMFGYHGHgPSPF 208
Cdd:pfam03104    1 KTDEGVSVCVNVFGFKPYFYCLAPDGKELEEVIEEIKELYEGLDK------------IEKIELKLKKSLYGYEED-PVPY 67
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    209 LRITLALPRLMAPARRLLEQGirlaglgtPSFAPYEANVDFEIRFMVDTDIVGCNWLELPagKYILRPEGKATLCQLEAD 288
Cdd:pfam03104   68 LKVSFANPRPLLKIRKYLSPE--------NISDVYEYDVDYLERFLIDNDIVGFGWYKVK--VYPFRAEGRISNCDVEID 137
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    289 VLWSDVISHPPEGEWqriAPLRVLSFDIECAGRKGIFPEPER--DPVIQICSLGLRWGEPEPFLRLALTLRPCAPI---- 362
Cdd:pfam03104  138 CDSPDLISVPFEKEW---PPLRVLSFDIECTSLPGKFPDAENvkDPIIQISCMLDGQGEPEPEPRFLFTLRECDSEdied 214
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    363 ---------LGAKVQSYEREEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRV-IGLRSNIRE 432
Cdd:pfam03104  215 feytpkpiyPGVKVFEFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKELYIVKLSSIGRLnRGGRSKVRE 294
                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....
gi 27806073    433 SSFqsrqtGRRDSKVVSMVGRVQMDMLQVLLREYKLRSYTLNAV 476
Cdd:pfam03104  295 IGF-----GTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
549-972 2.15e-102

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: 329.95  E-value: 2.15e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  549 GQQVKVVSQLLRQAMRQGLLMP-----VVKTEGGEDYTgATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLL-- 621
Cdd:cd05534    1 GSQFRVESMLLRLAKPENYILPspsrqQVAQQRALECL-PLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLgr 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  622 ------------------RPGAAQKLGLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSAR---KRAKAELAKETDPL 680
Cdd:cd05534   80 veelngggkfgflgvklyLPPPPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRimvKKAMKKYKDDKKLQ 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  681 RRqvLDGRQLALKVSANSVYGFTGAQV-GRLPCLEISQSVTGFGRQMIEKTKQLVETkyTVENGystsAKVVYGDTDSVM 759
Cdd:cd05534  160 RI--LDARQLALKLLANVTYGYTAASFsGRMPCVEIADSIVQTGRETLERAIELIES--TPKWG----AKVVYGDTDSLF 231
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  760 CRFGVSSVAEAMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLV 839
Cdd:cd05534  232 VLLPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAV 311
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  840 ANLVTASLRRLLIDRDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADYAGK-QAHVELAERMRKRDPGSAPSLG 918
Cdd:cd05534  312 QKILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGATlPAGAIVALRRMEKDPRAEPQYG 391
                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 27806073  919 DRVPYVIISAAKGVAAYMKSEDP-LFVLEHSLPIDTQYYLEQQLAKPLLRIFEPI 972
Cdd:cd05534  392 ERVPYVVVRGEPGSRLIDLVVSPeEFLADPSLRLDAEYYITKQIIPALDRLFNLV 446
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
206-970 2.43e-88

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: 309.68  E-value: 2.43e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    206 SPFLRITLALPRLMAPARRLLEQGIrlaglGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKyiLRPEGKATLCQL 285
Cdd:TIGR00592  413 SEYLEVTYELGKEFAPMEALPSDLK-----GQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPD--ELEYPRRSWCKY 485
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    286 EADVLWSDVIShppEGEWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTL--RP--CAP 361
Cdd:TIGR00592  486 EGGYVKPPNVE---KGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVgtRPkdCSF 562
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    362 ILG----------AKVQSYEREEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVigLRSNIR 431
Cdd:TIGR00592  563 PLDlkgefpgkkpSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRL--RRSPKF 640
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    432 ESSFQSRQTGRrdskvvsMVGRVQMDMLQVLlreyKLRSYTLNAVSFHFLG-EQKEDVQHSIITDLQNGNDQTRrrLAVY 510
Cdd:TIGR00592  641 GRRFGERTCGR-------MICDVEISAKELI----RCKSYDLSELVQQILKtERKVIPIDNINNMYSESSSLTY--LLEH 707
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    511 CLKDAFLPLRLLERLMVLVNAMEMARVTGVPLGYLLSRGQQVKVVSQLLRQAMRQGLLMP----VVKTEGGED------- 579
Cdd:TIGR00592  708 TWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPdkqiFRKQQKLGDedeeidg 787
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    580 --------YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPgaaqklgLTEDQFIKTPtgdefvKASVR 651
Cdd:TIGR00592  788 ykkgkkaaYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQK-------VDEDELPELP------DSELE 854
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    652 KGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTK 731
Cdd:TIGR00592  855 MGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTR 934
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    732 QLVETKYTvengystsaKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPsPIRLEFEKVYFPYLLISKKRYAGL 811
Cdd:TIGR00592  935 QLVEEMNL---------EVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-LLELDIDGVFKRLLLLKKKKYAAI 1004
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    812 LFS--SRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDL----LCNRIDISQLVITKE 885
Cdd:TIGR00592 1005 KVEgdSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIgknvLNGEVPLEKFVINKQ 1084
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    886 LTRAAADYAGK--QAHVELAERMRKRDPGSAPSlGDRVPYVIISAAKGVAAYMKS---EDPLFvLEHSLPIDTQYYLEQQ 960
Cdd:TIGR00592 1085 LTRDPKDYPDGasLPHVHVALRINARGGRKVKA-GDVVSYVICKDGGNLSARQRAyalEELQR-KHNNLIYDTQYYLEHQ 1162
                          810
                   ....*....|
gi 27806073    961 LAKPLLRIFE 970
Cdd:TIGR00592 1163 IHPVVLRILE 1172
POLBc cd00145
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
578-970 3.63e-87

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: 284.26  E-value: 3.63e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  578 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLgltEDqfiktPTGDEFVKASVRKGLLPQ 657
Cdd:cd00145    1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAP---ED-----YIGVGFRSPKDRKGLLPR 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  658 ILENLLSARKRAKAELAK-ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEt 736
Cdd:cd00145   72 ILEELLNFRDEAKKRMKAaKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVE- 150
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  737 kytvengySTSAKVVYGDTDSVMCRFGVS-SVAEAMALGREAADWVsgHFPSPIRLEFEKVYFPYLLISKKRYAGLLFsS 815
Cdd:cd00145  151 --------EHGARVIYGDTDSIFVSLPKMgTKEDAIKEGREILQEL--ADEHLLELEFEKVYLPFFLGKKKRYAGLDI-W 219
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  816 RPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVIsdllcnridisqlvitkeltraaadyag 895
Cdd:cd00145  220 KGQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERKVEAVKEYIDEL---------------------------- 271
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27806073  896 kqahvelaermrkrdpgsapslgDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 970
Cdd:cd00145  272 -----------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
580-974 7.25e-83

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: 275.23  E-value: 7.25e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  580 YTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLGLTEDQfiktptgdefVKASVRKGLLPQIL 659
Cdd:cd05532    8 YAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPPL----------PPSDQEKGILPRII 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  660 ENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVETKyt 739
Cdd:cd05532   78 RKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKM-- 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  740 venGYStsakVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSpIRLEFEKVYFPYLLISKKRYAGLLFSSRPDA 819
Cdd:cd05532  156 ---NLE----VIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKK-LEIDIDGVFKRLLLLKKKKYAALKVVDDDKG 227
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  820 HDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAV----AHAQDVISDLLCNRIDISQLVITKELTRAAADYAG 895
Cdd:cd05532  228 KLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVenihEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPD 307
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  896 K--QAHVELAERMRKRDPGSAPslGDRVPYVIIS--AAKGVA--AYMKSEdplFVLEHSLPIDTQYYLEQQLAKPLLRIF 969
Cdd:cd05532  308 KksLPHVQVALRMNKRGRKVKA--GDTIPYIICKdgSSKSLAdrAYHPDE---VKKNENLKIDIEYYLSQQILPPISRLC 382

                 ....*
gi 27806073  970 EPILG 974
Cdd:cd05532  383 EPIEG 387
POLBc_B3 cd05536
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ...
578-970 2.41e-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: 256.48  E-value: 2.41e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  578 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAaqklgltEDQFIKTPTGDEFVKAsvRKGLLPQ 657
Cdd:cd05536    2 ESYEGGIVLEPEKGLHE-NIVVLDFSSLYPSIMIKYNISPDTLVREGC-------EDCDVEPQVGHKFRKD--PPGFIPS 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  658 ILENLLSARKRAKAELaKETDP--LRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVE 735
Cdd:cd05536   72 VLEDLLEERRRIKEKM-KKLDPesEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAE 150
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  736 tkytvENGYstsaKVVYGDTDSVmcrFGVSSVAEA-MALGREAADWVSGHFPspIRLEFEKVYFPYLLISKKRYAGLlfs 814
Cdd:cd05536  151 -----EKGF----KVIYGDTDSL---FVKIDGADAvKKKVKKLLKYINEELP--LELEIEKFYKRGFFVTKKRYAGL--- 213
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  815 srpDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADYA 894
Cdd:cd05536  214 ---TEDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYK 290
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 27806073  895 GKQAHVELAERMRKRdpGSAPSLGDRVPYVIIsaaKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFE 970
Cdd:cd05536  291 ATGPHVAAAKKLAKR--GYKVRPGTKIGYVIV---KGSGKISDRAYPYDMVDEKHKYDAEYYIDNQVLPAVLRILE 361
PRK05761 PRK05761
DNA-directed DNA polymerase I;
243-974 3.88e-64

DNA-directed DNA polymerase I;


Pssm-ID: 235594 [Multi-domain]  Cd Length: 787  Bit Score: 233.04  E-value: 3.88e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   243 YEANVDFEIRFMVDTDIVGCNWLELPAGKYILRPE------GKATLCQLEADVLWSDVISHPPegewqriAPLRVLSFDI 316
Cdd:PRK05761  123 WEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEilveeiKKAFKDERKLAEDWLPIFEAPI-------PKIKRIAIDI 195
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   317 ECAGrkgifPEPERDPViqicslglrwgepepflrlaltlrpcapilgakvqsyEREEDLLQAWSTFIRIMDPDVItgYN 396
Cdd:PRK05761  196 EVYT-----PAKGRIPD-------------------------------------DSEKELLAELFDIILEYPPVVT--FN 231
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   397 IQNFDLPYLISRAQTLKVPGFPLLGRVIGLRSNIRESSFQSRqtgrRDSKVVSMVGRvqmdmlqvllreYKLRSYTLNAV 476
Cdd:PRK05761  232 GDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQN----KAVRSYAFYGK------------YRHREARLDAV 295
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   477 SFHFLGEQKEDVQHSIitdlqngNDQTRRRLAVYCLKDAFLPLRL--LERLMVLVNAMEMARVTGVPLGYLlSRGQQVKV 554
Cdd:PRK05761  296 GRALLGISKVELETNI-------SELDLEELAEYNFRDAEITLKLtfFNNELVLKLILLLSRISKLPIEEL-SRATISTW 367
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   555 VSQLL-RQAMRQGLLMP-----------VVK--TEGGEDYTGATVIEPLKG-YYDVpiATLDFSSLYPSIMMAHNLCYTT 619
Cdd:PRK05761  368 ISNLEyWEHRKRGWLIPwkedilrldheVYKkaIIKGKKYRGGLVFQPPPGiFFNV--YVLDFASLYPSIIVKWNLSPET 445
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   620 LLRPGAAQKLGLTEDQFIKTPTGDefvkasvRKGLLPQILENLLSARKRAKAELAKE--TDPLRRQVLDGRQLALKVSAN 697
Cdd:PRK05761  446 VRIPECKCHYDDEVPELGHSVCDD-------RPGLTSVLVGLLRDFRVKIYKKKAKDpnLDEERRAWYDVVQRALKVFLN 518
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   698 SVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvENGYstsaKVVYGDTDSVMCRFGVSSVAEAMalgrea 777
Cdd:PRK05761  519 ASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAE-----ELGL----KVLYGDTDSLFVWGPTKESLEEL------ 583
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   778 ADWVSGHFpsPIRLEFEKVYfPYLLIS--KKRYAGLLFSsrpdahDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRD 855
Cdd:PRK05761  584 IKEIEERT--GIDLEVDKTY-DWVAFSglKKNYFGVLKD------GKVKIKGIVAKKRNTPEFVKELQREVLEVLKSIRS 654
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   856 PSGAV-------AHAQDVISDLLCNRIDISQLVITKELTRAAADYA-GKQAHVELAERMRKRdpGSAPSLGDRVPYVIIS 927
Cdd:PRK05761  655 PEDVEkvkdeieDVLKRYYEKLRAKDYPLDELAIRVRLSKPLDEYTkNTPQHVKAALQLRDY--GVEVSPGDIISYVKVD 732
                         730       740       750       760
                  ....*....|....*....|....*....|....*....|....*..
gi 27806073   928 AAKGVaaymkseDPLFVLEHSlPIDTQYYLEQqlakpLLRIFEPILG 974
Cdd:PRK05761  733 DKRGV-------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 ...
311-523 2.75e-54

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: 187.56  E-value: 2.75e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  311 VLSFDIECAGRKGiFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPCAP-ILGAKVQSYEREEDLLQAWSTFIRIMDP 389
Cdd:cd05160    1 VLSFDIETTPPVG-GPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEfIDGIEVEYFADEKELLKRFFDIIREYDP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  390 DVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVIGlrsNIRESSFQSRqtgrrdskvVSMVGRVQMDMLQVLLREYKLR 469
Cdd:cd05160   80 DILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSG---GEKSSGSTER---------IAVKGRVVFDLLAAYKRDFKLK 147
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 27806073  470 SYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDqtRRRLAVYCLKDAFLPLRLLE 523
Cdd:cd05160  148 SYTLDAVAEELLGEGKEKVDGEIIEDAEWEED--PERLIEYNLKDAELTLQILE 199
POLBc_Pol_II cd05537
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
582-970 1.24e-43

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: 163.21  E-value: 1.24e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  582 GATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKlgltEDQFIKTPTGDEFvkaSVRKGLLPQILEN 661
Cdd:cd05537    5 GGYVMDSKPGLYK-NVLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPD----PEDLIPGFLGARF---SREKHILPDLIAR 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  662 LLSARKRAKaelaKETDPLRRQvldgrqlALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvE 741
Cdd:cd05537   77 LWAARDEAK----REKNAPLSQ-------AIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIE-----Q 140
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  742 NGYstsaKVVYGDTDSVMCRFG-VSSVAEAMALGREAAD----WVSGH------FPSPIRLEFEKVYFPYLLI------- 803
Cdd:cd05537  141 QGY----QVIYGDTDSTFVWLGeELDAAEAQAIGKELASqinqWWAQKlkeefgLESFLEIEFETHYSRFFMPtirgsde 216
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  804 -SKKRYAGLlfsSRPDAHDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSGAVahaQDVISDLLCNRIDiSQLVI 882
Cdd:cd05537  217 gSKKRYAGL---KSTDGGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGFI---KETVEELLAGELD-ELLVY 289
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  883 TKELTRAAADY-AGKQAHVELAermRKRDPgSAPSLGDRVPYVIISaakgvaaYMKSEDPLFVLEH-SLPIDTQYYLEQQ 960
Cdd:cd05537  290 RKRLRRPLSEYtKNVPPHVQAA---RLADQ-INRELGRPRQYQWIE-------YVITVNGPEPLEYrTSPLDYQHYIDKQ 358
                        410
                 ....*....|...
gi 27806073  961 L---AKPLLRIFE 970
Cdd:cd05537  359 LkpiADSILPFLG 371
zf-C4pol pfam14260
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ...
1011-1081 3.78e-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: 113.62  E-value: 3.78e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 27806073   1011 CIGCRTVlshQGAVCKFCQPRESELYQKEVSHLSALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMR 1081
Cdd:pfam14260    1 CLGCGAP---EEPLCKNCRSDPQASYLELLSRLRELERRFNRLWTICQRCQGSLHEEVLCDSRDCPVFYMR 68
POLBc_B2 cd05531
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ...
578-975 1.34e-29

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: 121.30  E-value: 1.34e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  578 EDYTGATVIEPLKGYYDvPIATLDFSSLYPSIMMAHNLCYTTLLRPGAAQKLGLTEDQFIKTPtgdefvkasvRKGLLPQ 657
Cdd:cd05531    3 LADRGGLVFQPEPGLYE-NVAQIDFSSMYPSIIVKYNISPETINCRCCECRDHVYLGHRICLK----------RRGFLPE 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  658 ILENLLSARKRAKAELAKETDPlrrqvlDGRQLALKVSANSVYGFTG---AQVGRLPCLEisqSVTGFGRQMIEKTKQLV 734
Cdd:cd05531   72 VLEPLLERRLEYKRLKKEEDPY------AGRQKALKWILVTSFGYLGyknAKFGRIEVHE---AITAYGRKILLRAKEIA 142
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  735 EtkytvENGYstsaKVVYGDTDSVMCRfgVSSVAEAMALGREAadwvsghfPSPIRLEFEKVY-FPYLLISK------KR 807
Cdd:cd05531  143 E-----EMGF----RVLHGIVDSLWIQ--GRGDIEELAREIEE--------RTGIPLKLEGHYdWIVFLPERdglgapNR 203
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  808 YAGLLFSsrpdahDRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPS---GAVAHAQDVIS--DLLCNRIDISQLVI 882
Cdd:cd05531  204 YFGRLSD------GEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEellKLREEALDLFRryLQRLREGDLEDLII 277
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  883 TKELTRAAADYAGKQAHVelAERMRKRdpGSAPSLGDRVPYVIISAAKGVAaymksedplfVLEHSLPIDTQYYLEQqla 962
Cdd:cd05531  278 EKKISKRSSEYKVLASTA--LKALRAK--GVSVVPGMKIEYIVRDGKRPVP----------DLGNDEGYDTKYYREL--- 340
                        410
                 ....*....|...
gi 27806073  963 kpLLRIFEPILGE 975
Cdd:cd05531  341 --LERAAEELLFP 351
POLBc_B1 cd05530
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ...
577-932 3.99e-27

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: 114.76  E-value: 3.99e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  577 GEDYTGATVIEPLKG-YYDVpiATLDFSSLYPSIMMAHNLCYTTLLRPGAaqklgltEDQFIKTPTGDEFVKASvRKGLL 655
Cdd:cd05530   10 GKKYRGAIVLEPPPGiFFNV--VVLDFASLYPSIIKVWNLSYETVNCPHC-------ECKTNEVPEVGHWVCKK-RPGIT 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  656 PQILENLLSAR-----KRAKAelaKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKT 730
Cdd:cd05530   80 SQIIGLLRDLRvkiykKKAKD---KSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITST 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  731 kqlveTKYTVENGYstsaKVVYGDTDSVMCRFGVSSVAEamalgrEAADWVSGHFpsPIRLEFEKVYfPYLLIS--KKRY 808
Cdd:cd05530  157 -----IKKARELGL----KVLYGDTDSLFLWNPPQEQLE------DLVEWVEKEL--GLDLELDKEY-RYVVFSglKKNY 218
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  809 AGLLFSSrpdahdRMDCKGLEAVRRDNCPLVANLVTASLRRLLIDRDPSgAVAHAQDVISDL-------LCNR-IDISQL 880
Cdd:cd05530  219 LGVTKDG------SVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPE-DFEKAREKIRDIvkgvykrLKKKeYTLDQL 291
                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|...
gi 27806073  881 VITKELTRAAADYA-GKQAHVELAERMRKRdpGSAPSLGDRVPYVIISAAKGV 932
Cdd:cd05530  292 AFKVMLSKPPEEYTkNTPQHVKAARQLEKY--GRNVEAGDIISYVKVKGKEGV 342
43 PHA02528
DNA polymerase; Provisional
309-782 1.59e-26

DNA polymerase; Provisional


Pssm-ID: 177369 [Multi-domain]  Cd Length: 881  Bit Score: 117.48  E-value: 1.59e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   309 LRVLSFDIECAGRKGiFPEPERDPViQICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQ----------SYEREEDLLQ 378
Cdd:PHA02528  106 IRIANLDIEVTAEDG-FPDPEEAKY-EIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPqeildkvvymPFDTEREMLL 183
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   379 AWSTFIRIMDPDVITGYNIQNFDLPYLISRaqtlkvpgfplLGRVIGLRSNIRESSF---QSRQT----GRRDSKvVSMV 451
Cdd:PHA02528  184 EYINFWEENTPVIFTGWNVELFDVPYIINR-----------IKNILGEKTAKRLSPWgkvKERTIenmyGREEIA-YDIS 251
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   452 GRVQMDMLQVllreYK------LRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGNDQtrrRLAVYCLKDAFLPLRLLERL 525
Cdd:PHA02528  252 GISILDYLDL----YKkftftnQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQ---KYIEYNIIDVELVDRLDDKR 324
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   526 MVLVNAMEMARVTGVPLGYLLSrgqQVKVVSQLLRQAMR-QGLLMPVVKTEGGEDYTGATVIEPLKGYYDVpIATLDFSS 604
Cdd:PHA02528  325 KLIELVLSMAYYAKINFEDVFS---PIKTWDAIIFNSLKeEKIVIPENKSHKKQKYAGAFVKEPVPGAYRW-VVSFDLTS 400
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   605 LYPSIMMAHNLCYTTLL--RPGA------AQKLGLTEDQFIKTPTGDEFVKAsvRKGLLPQILENLLSARKRAK------ 670
Cdd:PHA02528  401 LYPSIIRQVNISPETIAgtFHVApvheyiNKTAPRPSDEYSCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIYKkkmlaa 478
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   671 ---AELAKET----------------------------DPLRRQVLDGR--------------QLALKVSANSVYGFTGA 705
Cdd:PHA02528  479 ernAELIKTIledlndsvdtpidvdyyfdfsdefkaelKTLTKSSLKALleecekeialcntiQMARKILINSLYGALGN 558
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   706 QVGRLPCLEISQSVTGFG--------RQMIEKTKQLVETKytvengysTSAKVVYGDTDSVMCRFGvsSVAEAMALGR-- 775
Cdd:PHA02528  559 EHFRYYDLRNAEAITLFGqlaiqwieRKMNEYLNKLCKTE--------DEDYVIYGDTDSIYVNLD--PLVEKVGEDKfk 628

                  ....*..
gi 27806073   776 EAADWVS 782
Cdd:PHA02528  629 DTNHWVD 635
PHA03036 PHA03036
DNA polymerase; Provisional
312-837 1.35e-25

DNA polymerase; Provisional


Pssm-ID: 222962 [Multi-domain]  Cd Length: 1004  Bit Score: 114.73  E-value: 1.35e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   312 LSFDIECAGRKGiFPEPERDPV--IQICSLGLRWGEpepfLRLALT---LRPCAPILGAKVQSYEREEDLLQAWSTFIRI 386
Cdd:PHA03036  163 LFLDIECHFDKK-FPSVFINPVshISCCYIDLSGKE----KRFTLInedMLSEDEIEEAVKRGYYEIESLLDMDYSKELI 237
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   387 ----------------MDPDVITGYNIQNFDLPYLISRAQTLKvpgfplLGRVIgLRS-----NIRESSFQSRQTGRRDS 445
Cdd:PHA03036  238 lcseivllriakklleLEFDYVVTFNGHNFDLRYISNRLELLT------GEKII-FRSpdgkeTVHLCIYERNLSSHKGV 310
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   446 KVVSMV--------GRVQMDMLQVLLREYKLRSYTLNAVS---FHFLGEqKEDVQHSIITDLQNGNDQTRRRLAV----- 509
Cdd:PHA03036  311 GGVANTtyhinnnnGTIFFDLYTFIQKTEKLDSYKLDSISknaFNCNAK-VLSENNNEVTFIGDNTTDAKGKASIfsevl 389
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   510 ----YCLKDAFLPLRLLE--------RLMVLVN-------------------------------AMEMAR---------- 536
Cdd:PHA03036  390 stgnYVTINDDDICKILDkdiiensfTVKVICKnnyipgdtytlsfgkddvdlsdmyknynleiALEMARycihdaclck 469
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   537 -----------VTGVPLGYLLSRGQQVKVVS------QLLRQAMRQGLLMPVVKTEGGEDYTGATVIEPLKGYYDVPIAT 599
Cdd:PHA03036  470 ylweyygietkIDAGASTYLLPQSMVFEYRAstlikgPLLKLLLEEKTILVRSETKNKFPYEGGKVFAPKQKMFDNNVLI 549
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   600 LDFSSLYPSIMMAHNLCYTTLL-------RPGAAQKLGLTEDQF-------IK-TPTGDEFV-KASV----RKGLLPQIL 659
Cdd:PHA03036  550 FDYNSLYPNVCIFGNLSPETLVgvvvndnRLEAEINKQELRRKYpypryiyVHcEPRSPDLVsEIAVfdrrIEGIIPKLL 629
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   660 ENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIE----------- 728
Cdd:PHA03036  630 KTFLEERARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKylnsvlngskl 709
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   729 ----------------KTKQLVETKY--TVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGH-FPSPI 789
Cdd:PHA03036  710 ingklilancpinpffKDDRSIDTNYdtNLPVEYNFTFRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINEKvLFDNF 789
                         650       660       670       680       690
                  ....*....|....*....|....*....|....*....|....*....|
gi 27806073   790 RLEFEKVYFPYLLISKKRYAGLLF--SSRPDAHDRMDCKGLEAVRRDNCP 837
Cdd:PHA03036  790 KIEFEAVYKNLIMQSKKKYTTLKYiaSSTDGSVPERVNKGTSETRRDVSK 839
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
308-730 2.46e-24

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: 110.53  E-value: 2.46e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    308 PLRVLSFDIEC--AGRKGIFP--EPERDPVIQI----CSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEREEDLLQA 379
Cdd:TIGR00592  197 ELKLASFDIETyfHDGKDFFPgdENPADEEIMIsttpVIAKQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKR 276
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    380 WSTFIRIMDPDVITGYNIQNFDLPYLISRA----------QTLKVPGFPLLGRviglRSNIRESSFQSRQTGRRDSKVVS 449
Cdd:TIGR00592  277 FWDVIDQEDTDVEITVNGDNFDLVYLADRQvfqfywdayeDPAEKLGVVLLFG----RDVDHVSPCVQVKGINRDLFFLP 352
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    450 MVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITdlQNGNDQTRRRLAVYCLKDAFLPLRLLERLMVLV 529
Cdd:TIGR00592  353 REGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIA--KKYEFEAPDIDAPYSSEYLEVTYELGKEFAPME 430
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    530 NAMEMARVTGVPLGYLLSRGQQVKVVSQL-------LRQAMRQGLLMPVV---KTEGGedYTGATVIEPLKGYYDVPIAT 599
Cdd:TIGR00592  431 ALPSDLKGQTFWHVFGSNTGNLERFLLLRkikgpcwLAVKGPDELEYPRRswcKYEGG--YVKPPNVEKGLDKTPPPLVV 508
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073    600 LDFS--SLYPSIMMAHNLCYT-TLLRPGAAQKLGLTEDQFIKTPTGDEFVKASVR-------KGLLPQILENLLSARKRA 669
Cdd:TIGR00592  509 LDFSmkSLNPSIIRNEIVSIPdTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPldlkgefPGKKPSLVEDLATERALI 588
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 27806073    670 KAELA--KETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSvtgFGRQMIEKT 730
Cdd:TIGR00592  589 KKFMAkvKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPK---FGRRFGERT 648
DNA_polB_Kod1_like_exo cd05780
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ...
309-525 5.18e-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: 5.18e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  309 LRVLSFDIECAGRKGIfPEPERDPVIQI--CSLG----LRW-GEPEPFlrlaltlrpcapilgakVQSYEREEDLLQaws 381
Cdd:cd05780    3 LKILSFDIEVLNHEGE-PNPEKDPIIMIsfADEGgnkvITWkKFDLPF-----------------VEVVKTEKEMIK--- 61
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  382 TFIRIM---DPDVITGYNIQNFDLPYLISRAQTLKVPgFPlLGRviglrsNIRESSFQsRQTGRRDSKVvsmVGRVQMDM 458
Cdd:cd05780   62 RFIEIVkekDPDVIYTYNGDNFDFPYLKKRAEKLGIE-LD-LGR------DGSEIKIQ-RGGFNNASEI---KGRIHVDL 129
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 27806073  459 LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNgNDQTRRRLAVYCLKDAFLPLRLLERL 525
Cdd:cd05780  130 YPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWD-SGENLERLFRYSMEDAKYTYEIGKEF 195
POLBc_Pol_II_B cd05538
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
596-967 4.43e-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: 102.18  E-value: 4.43e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  596 PIATLDFSSLYPSIMMAHNLCyttllrpgaaqklgltedqfiktPTGDEFvkasvrkGLLPQILENLLSARKRAKAELAK 675
Cdd:cd05538   18 PIVHADVASLYPSIMLAYRIC-----------------------PARDSL-------GIFLALLKYLVELRLAAKESARA 67
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  676 ETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGRLPCLEISQSVTGFGRQMIEKTKQLVEtkytvengySTSAKVVYGDT 755
Cdd:cd05538   68 AARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLR---------RRGATPVEVDT 138
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  756 DSV--MCRFGVSSVAEAMALGREaadwVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSsrpdahDRMDCKGLEAVRR 833
Cdd:cd05538  139 DGIyfIPPNGVDTEDEEEELVRE----LSSTLPKGITVEFDGRYRAMFSYKIKNYALLDYD------GKLIVKGSAFRSR 208
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  834 DNCPLVANLVTASLRRLLIDrDPSGAVAHAQDVISDLLCNRIDISQLVITKELTRAAADY-----AGKQAHVELAERMRK 908
Cdd:cd05538  209 GIEPFLREFLREAVRLLLQG-DGAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYlqkvrAGKRNPAAAYEIALA 287
                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 27806073  909 RDPGSAPslGDRVPYVIISAAKGVAAYMK-SEDPLFVLEHSLpIDTQYYLEQ--QLAKPLLR 967
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 ...
309-523 4.18e-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: 96.15  E-value: 4.18e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  309 LRVLSFDIECAGRKGIFPEPERDPVIQIC----------------SLGLRWGEPEPFLRLALTLRPCapiLGAKVQSYER 372
Cdd:cd05778    4 LTILSLEVHVNTRGDLLPDPEFDPISAIFycidddvspfildankVGVIIVDELKSNASNGRIRSGL---SGIPVEVVES 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  373 EEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVPGF-PLLGRVIglrSNiRESSFQSRQTGRRDSK--VVS 449
Cdd:cd05778   81 ELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLlDEISRVP---SD-SNGKFGDRDDEWGYTHtsGIK 156
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27806073  450 MVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIITDLQNGND-QTRRRLAVYCLKDAFLPLRLLE 523
Cdd:cd05778  157 IVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSaSERWRVLEYYLKRVRLNLEILD 231
DNA_polB_II_exo cd05784
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ...
308-523 4.81e-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: 83.39  E-value: 4.81e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  308 PLRVLSFDIECagrkgifpeperDPVIQICSLGLrWGEPEpflRLALTLRPCAPILGAKVQSYEREEDLLQAWSTFIRIM 387
Cdd:cd05784    2 KLKVVSLDIET------------SMDGELYSIGL-YGEGQ---ERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQY 65
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  388 DPDVITGYNIQNFDLPYLISRAQTLKVPgfPLLGRViGLRSNIRESSFQSRQTgrrdskvVSMVGRVQMDMLQvLLRE-- 465
Cdd:cd05784   66 DPDIIIGWNVINFDLRLLQRRAEAHGLP--LRLGRG-GSPLNWRQSGKPGQGF-------LSLPGRVVLDGID-ALKTat 134
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27806073  466 YKLRSYTLNAVSFHFLGEQKedvqhsIITDLQNGNDQTRRR-------LAVYCLKDAFLPLRLLE 523
Cdd:cd05784  135 YHFESFSLENVAQELLGEGK------LIHDVDDRGAEIERLfredklaLARYNLQDCELVWRIFE 193
DNA_polB_B3_exo cd05781
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ...
308-482 5.73e-17

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: 80.06  E-value: 5.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  308 PLRVLSFDIECAGRKGiFPEPERDPVIQIcSLGLRWGEPEPFLrlaltlrpcapilgakvQSYEREEDLLQAWSTFIRIM 387
Cdd:cd05781    2 DLKTLAFDIEVYSKYG-TPNPRRDPIIVI-SLATSNGDVEFIL-----------------AEGLDDRKIIREFVKYVKEY 62
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  388 DPDVITGYNIQNFDLPYLISRAqtlKVPGFPL-LGRVIGlrsnirESSFQSRqTGRrdskvVSMVGRVQMDMLQVLLREY 466
Cdd:cd05781   63 DPDIIVGYNSNAFDWPYLVERA---RVLGVKLdVGRRGG------SEPSTGV-YGH-----YSITGRLNVDLYDFAEEIP 127
                        170
                 ....*....|....*.
gi 27806073  467 KLRSYTLNAVSfHFLG 482
Cdd:cd05781  128 EVKVKTLENVA-EYLG 142
DNA_polB_B1_exo cd05783
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ...
306-521 4.21e-16

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: 78.13  E-value: 4.21e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  306 IAPLRVLSFDIEC-AGRKGIFPEPERD--PVIQIC---SLGLRwgepepflRLALTLRPCAPIL------GAKVQSYERE 373
Cdd:cd05783    2 IPKLKRIAIDIEVyTPIKGRIPDPKTAeyPVISVAlagSDGLK--------RVLVLKREGVEGLegllpeGAEVEFFDSE 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  374 EDLLQAwstFIRIMD--PDVITgYNIQNFDLPYLISRAQTLkvpGFPLLGRVIGLrsniressfqsrqtgRRDSkvVSMV 451
Cdd:cd05783   74 KELIRE---AFKIISeyPIVLT-FNGDNFDLPYLYNRALKL---GIPKEEIPIYL---------------KRDY--ATLK 129
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27806073  452 GRVQMDM--------LQVLLREYKLRSYTLNAVSFHFLGEQKEDVQHSIitdlqngNDQTRRRLAVYCLKDAFLPLRL 521
Cdd:cd05783  130 HGIHIDLykffsnraIQVYAFGNKYREYTLDAVAKALLGEGKVELEKNI-------SELNLYELAEYNYRDAELTLEL 200
PHA03334 PHA03334
putative DNA polymerase catalytic subunit; Provisional
365-760 6.52e-15

putative DNA polymerase catalytic subunit; Provisional


Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 79.90  E-value: 6.52e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   365 AKVQSYEREEDLLQAWSTFI----RIMDPDVITGYNIQNFDLPYLISRAQTLKVPGFPLLGRVIGLRSNI--------RE 432
Cdd:PHA03334  370 FKQRPHPLTKALMEAWEAFLskdpQLVPAQLLFGSDILNSNYLELLDVIESHKAQFKATCRKAAARKEEIgsymktrdTV 449
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   433 SSFQSRQTGRRDSKVVSMvGRVQMDMLQVLLR---EYKLRSYTLNAVSFHFLGEQK-----------EDVQHSIITDLQN 498
Cdd:PHA03334  450 QDFNDNDKKYLNSTSHGF-GAHIIDLMRVCNTksiKAKCSSRKLDTVARLIISKSKphknppkigkmDDVKYTEMDGMFT 528
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   499 GNDQTRRRLAVYCLKDAFLPLRLLERLMVLVNAMEMARVTgVPLGYL-LSRG--------QQVKVVS-QLLRQAMRQG-- 566
Cdd:PHA03334  529 AGGAALARYLIYNLVDSELLIRIAKNLDPVIEFLNRLRAT-YNIDYVaHGRGvmnfcgfvQSTKSVEvPLLKARLRIGif 607
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   567 ---------LLMP-VVKTEGGEDYT--GATVIEPLKGY-----YDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGAA--- 626
Cdd:PHA03334  608 vatgriaesLCMPeKYARDCRQKIKlkGGYVFAPLTGLtfagpYQGTELTLDFASLYPSNMCDANISPEAIVDPDCTarv 687
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   627 ------------QKLGLTEDQFIKTPTGDEFVKASVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKV 694
Cdd:PHA03334  688 rgwvvfdwkkidRGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNEMKI 767
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 27806073   695 SANSVYGftgaqVGRLPCleiSQSVTGFGRQMIektkQLVETKYTVENGYStsakVVYGDTDSVMC 760
Cdd:PHA03334  768 CANSHYG-----VAPHAC---QHLITTLGRHKI----KLVEEFIKKEPGMT----VNYGDTDSVMF 817
DNA_polB_alpha_exo cd05776
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ...
326-528 3.88e-14

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: 73.03  E-value: 3.88e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  326 PEPERDPVIQICSLGL---RWGEPEPFLRLALTLRPcapilgaKVQSYEREEDLLQAWSTFIRIMDPDVITGYNIQNFDL 402
Cdd:cd05776   39 PTPPPPFQSHTCTLTRplgRSPPPDLFEKNAKKKKT-------KVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDL 111
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  403 PYLISRAQTLKVPGFPLLGRVigLRSNIRE----SSFQSRQTgrrdskvvsMVGRVQMDMlQVLLRE-YKLRSYTLNAVS 477
Cdd:cd05776  112 DVLLSRIQELKVPHWSRIGRL--KRSVWPKkkggGKFGEREL---------TAGRLLCDT-YLSAKElIRCKSYDLTELS 179
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 27806073  478 FHFLGEQKEDVqhsIITDLQNGNDQTRR--RLAVYCLKDAFLPLRLLERLMVL 528
Cdd:cd05776  180 QQVLGIERQDI---DPEEILNMYNDSESllKLLEHTEKDAYLILQLMFKLNIL 229
DNA_polB_like2_exo cd05785
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ...
309-514 3.24e-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: 3.24e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  309 LRVLSFDIECAGRKGIF---PEPERDPVIQIcslGLRwgEPEPFlRLALTLRPCApilgakvqsyerEEDLLQAWSTFIR 385
Cdd:cd05785    9 LRRLQLDIETYSLPGFFfsnPDRGDDRIIIV---ALR--DNRGW-EEVLHAEDAA------------EKELLEELVAIIR 70
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  386 IMDPDVITGYNIQNFDLPYLISRAQTLKVPgfPLLGRvIGLRSNIRESSFQSRQtGRRDSKVVSMVGRVQMDMLQVLLR- 464
Cdd:cd05785   71 ERDPDVIEGHNIFRFDLPYLRRRCRRHGVP--LAIGR-DGSIPRQRPSRFRFAE-RLIDYPRYDIPGRHVIDTYFLVQLf 146
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 27806073  465 ---EYKLRSYTLNAVSFHF--LGEQKEDVQHSIITDLQNGNdqtRRRLAVYCLKD 514
Cdd:cd05785  147 dvsSRDLPSYGLKAVAKHFglASPDRTYIDGRQIAEVWRSD---PARLLAYALDD 198
DNA_polB_epsilon_exo cd05779
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ...
308-439 1.26e-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: 50.34  E-value: 1.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073  308 PLRVLSFDIECAGRKGIFPEPERDPVIQIcSLGLrwgEPEPFLrlaLTLRPcapILGAKVQSYE---------------- 371
Cdd:cd05779    1 DPRVLAFDIETTKLPLKFPDAETDQIMMI-SYMI---DGQGYL---IVNRE---IVSEDIEDFEytpkpeyegpfkvfne 70
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 27806073  372 -REEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLkvpGFPLLgRVIGLRSNiRESSFQSRQ 439
Cdd:cd05779   71 pDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIH---GLSME-EEIGFRKD-SEGEYKSRY 134
43A PHA02524
DNA polymerase subunit A; Provisional
370-670 1.37e-06

DNA polymerase subunit A; Provisional


Pssm-ID: 164925 [Multi-domain]  Cd Length: 498  Bit Score: 52.31  E-value: 1.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   370 YEREEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLkvpgfplLGRviglrsnirESSFQSRQTGRRDSKVVS 449
Cdd:PHA02524  177 FEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNI-------LGE---------KAANQLSPYGKITSKTIT 240
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   450 MV----------GRVQMDMLQVLlREYK---LRSYTLNAVSFHFLGEQKEDVQHSIiTDLQNGNDQtrrRLAVYCLKDAF 516
Cdd:PHA02524  241 NLygekiiykihGIALMDYMDVF-KKFSftpMPDYKLGNVGYREVKADKLDYEGPI-NKFRKADHQ---RYVDYCVRDTD 315
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   517 LPLRLLERLMVLVNAMEMARVTGVPLGYLLSrgqQVKVVSQLLRQAM-RQGLLMPVVKTEGGEDYTGATVIEPLKGYYDV 595
Cdd:PHA02524  316 IILLIDGRRCFIDLILSLSYYAKIRFDDVLG---TIKVWDSIIFNSLvESNVVIPAMKASPKQSFPGAYVKEPVPGGYRY 392
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27806073   596 PIaTLDFSSLYPSIMMAHNLC---YTTLLRP--------GAAQKlglTEDQFIKTPTGDEFVKASVrkGLLPQILENLLS 664
Cdd:PHA02524  393 GL-SFDLTSLYPSILRLLNISpemIAGMFSParledyinKVAPK---PSDQFSCAPNGMMYKKGVV--GVLPNETEKVFL 466

                  ....*.
gi 27806073   665 ARKRAK 670
Cdd:PHA02524  467 QRKSEK 472
 
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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