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Conserved domains on  [gi|1477777490|gb|AYA44865|]
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DNA-dependent DNA polymerase, partial [Trachemys herpesvirus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DNA_pol_B super family cl29029
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
1-222 7.33e-86

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.


The actual alignment was detected with superfamily member pfam00136:

Pssm-ID: 395085  Cd Length: 439  Bit Score: 261.01  E-value: 7.33e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTRDAGALVDLDEGRDYVRFEVQGHTFYYVRPHIKQSLLAELLTDWLALRKTIRLRMKTASPEDQ-LLL 79
Cdd:pfam00136  72 IIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFErAIL 151
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  80 DKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIHAKWnerekfladfpemqthvipeePHSLRI 159
Cdd:pfam00136 152 DKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMY---------------------TYNFRV 210
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1477777490 160 IYGDTDSVFVKATGYTIDGLNEHGGAVAQYISQALFPTPIKLECEKTFTRLLMITKKKYIGMI 222
Cdd:pfam00136 211 IYGDTDSVFIEFGGKDVEEAMKIGDELAEHVNQDLFKSPIKLEFEKVYKPLLLISKKKYAGLK 273
 
Name Accession Description Interval E-value
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
1-222 7.33e-86

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: 261.01  E-value: 7.33e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTRDAGALVDLDEGRDYVRFEVQGHTFYYVRPHIKQSLLAELLTDWLALRKTIRLRMKTASPEDQ-LLL 79
Cdd:pfam00136  72 IIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFErAIL 151
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  80 DKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIHAKWnerekfladfpemqthvipeePHSLRI 159
Cdd:pfam00136 152 DKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMY---------------------TYNFRV 210
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1477777490 160 IYGDTDSVFVKATGYTIDGLNEHGGAVAQYISQALFPTPIKLECEKTFTRLLMITKKKYIGMI 222
Cdd:pfam00136 211 IYGDTDSVFIEFGGKDVEEAMKIGDELAEHVNQDLFKSPIKLEFEKVYKPLLLISKKKYAGLK 273
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
1-221 1.13e-52

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: 174.38  E-value: 1.13e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTRDAGALVDLDEgrDYVRfevQGHTFYYVRPHIKQSLLAELLTDWLALRKTIRLRMKTAS-PEDQLLL 79
Cdd:cd05533    32 IMMAHNLCYTTLLNKNTAKKLPPE--DYIK---TPNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEETdPFKKAVL 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  80 DKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIHAKWNEREKFladfpemqthvipeePHSLRI 159
Cdd:cd05533   107 DGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKYTKANGY---------------SHDAKV 171
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1477777490 160 IYGDTDSVFVKATGYTIDGLNEHGGAVAQYISqALFPTPIKLECEKTFTRLLMITKKKYIGM 221
Cdd:cd05533   172 IYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVS-KKFIKPIKLEFEKVYFPYLLINKKRYAGL 232
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
1-221 9.27e-44

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 156.73  E-value: 9.27e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490    1 IIQAHNLCLSTLTRDAgALVDLDEGrdyvrFEVQGHT-FYYVRPHIKQSLLAELLTDWLALRKTIRLRMKTASpeDQLL- 78
Cdd:PTZ00166   569 IMIAHNLCYSTLVPPN-DANNYPED-----TYVTTPTgDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK--DPLLk 640
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   79 --LDKQQLAIKVTCNSVYGFTG-VAMGLLPCLEVASTVTTVGRNMLIATRDYIHAKWNEREKFladfpemqthvipeePH 155
Cdd:PTZ00166   641 kvLNGRQLALKISANSVYGYTGaQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGY---------------KH 705
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1477777490  156 SLRIIYGDTDSVFVKATGYTIDGLNEHGGAVAQYISQaLFPTPIKLECEKTFTRLLMITKKKYIGM 221
Cdd:PTZ00166   706 DATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISK-KFLKPIKLEFEKVYCPYLLMNKKRYAGL 770
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
1-170 2.87e-42

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: 148.83  E-value: 2.87e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490    1 IIQAHNLCLSTLTRDAGALVDLDEGR--DYVRFE-VQGHTFYYVRPHIKQSLLAELLTDWLALRKTIRLRMKTASPED-- 75
Cdd:smart00486 315 IIIAHNLCYSTLVGVGEVVIKGDLIIpeDLLTIKyEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESee 394
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   76 -QLLLDKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIHAKWNERekfladfpemqthvipeep 154
Cdd:smart00486 395 lKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPK------------------- 455
                          170
                   ....*....|....*.
gi 1477777490  155 HSLRIIYGDTDSVFVK 170
Cdd:smart00486 456 PGFKVIYGDTDSIFVT 471
PolB COG0417
DNA polymerase elongation subunit (family B) [Replication, recombination and repair];
1-224 5.92e-39

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


Pssm-ID: 223494 [Multi-domain]  Cd Length: 792  Bit Score: 142.56  E-value: 5.92e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTRDAGALVDLDEGRDYVRFEVQGHtfyyvrphikqsLLAELLTDWLALRKTIRLRMKTASPEDQ-LLL 79
Cdd:COG0417   434 IIIKYNISPDTLVEEDCSDDYSPPGVGHGFCKREKG------------FLPEILEELLDRRDEIKKKMKKEKDPSErKLL 501
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  80 DKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIhakwnerekfladfpemqthvipeEPHSLRI 159
Cdd:COG0417   502 DGRQLALKVLANSFYGYLGYSNSRFYCIECAESVTAFGREILRETKELA------------------------EEMGLRV 557
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1477777490 160 IYGDTDSVFVKATGYTIDGLNEHGGAVAQYISQALfPTPIKLECEKTFTRLLMIT-KKKYIGMIGE 224
Cdd:COG0417   558 IYGDTDSLFVTLPGATYEEAIKIGEELVEEVNERL-PSGIELEVEKVYKRFLLPTaKKRYAGLLED 622
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
1-218 7.69e-21

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: 90.50  E-value: 7.69e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490    1 IIQAHNLCLSTLTRDagalVDLDEGRDYVRfevqghtfyyvrPHIKQSLLAELLTDWLALRKTIRLRMKT-ASPEDQLLL 79
Cdd:TIGR00592  825 IIQEFNICFTTVQQK----VDEDELPELPD------------SELEMGILPRELRKLVERRKEVKKLMKQdLNPDLRLQY 888
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   80 DKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIhakwneREKFladfpemqthvipeephsLRI 159
Cdd:TIGR00592  889 DIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLV------EEMN------------------LEV 944
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1477777490  160 IYGDTDSVFVKATGYTIDGLNEHGGAVAQYISqALFPtPIKLECEKTFTRLLMITKKKY 218
Cdd:TIGR00592  945 IYGDTDSIMINTPGTKYEEVFKIGKEFKSEVN-KLYK-LLELDIDGVFKRLLLLKKKKY 1001
 
Name Accession Description Interval E-value
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
1-222 7.33e-86

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: 261.01  E-value: 7.33e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTRDAGALVDLDEGRDYVRFEVQGHTFYYVRPHIKQSLLAELLTDWLALRKTIRLRMKTASPEDQ-LLL 79
Cdd:pfam00136  72 IIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEETDPFErAIL 151
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  80 DKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIHAKWnerekfladfpemqthvipeePHSLRI 159
Cdd:pfam00136 152 DKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMY---------------------TYNFRV 210
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1477777490 160 IYGDTDSVFVKATGYTIDGLNEHGGAVAQYISQALFPTPIKLECEKTFTRLLMITKKKYIGMI 222
Cdd:pfam00136 211 IYGDTDSVFIEFGGKDVEEAMKIGDELAEHVNQDLFKSPIKLEFEKVYKPLLLISKKKYAGLK 273
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
1-221 1.13e-52

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: 174.38  E-value: 1.13e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTRDAGALVDLDEgrDYVRfevQGHTFYYVRPHIKQSLLAELLTDWLALRKTIRLRMKTAS-PEDQLLL 79
Cdd:cd05533    32 IMMAHNLCYTTLLNKNTAKKLPPE--DYIK---TPNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEETdPFKKAVL 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  80 DKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIHAKWNEREKFladfpemqthvipeePHSLRI 159
Cdd:cd05533   107 DGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKYTKANGY---------------SHDAKV 171
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1477777490 160 IYGDTDSVFVKATGYTIDGLNEHGGAVAQYISqALFPTPIKLECEKTFTRLLMITKKKYIGM 221
Cdd:cd05533   172 IYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVS-KKFIKPIKLEFEKVYFPYLLINKKRYAGL 232
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
1-221 9.27e-44

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 156.73  E-value: 9.27e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490    1 IIQAHNLCLSTLTRDAgALVDLDEGrdyvrFEVQGHT-FYYVRPHIKQSLLAELLTDWLALRKTIRLRMKTASpeDQLL- 78
Cdd:PTZ00166   569 IMIAHNLCYSTLVPPN-DANNYPED-----TYVTTPTgDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK--DPLLk 640
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   79 --LDKQQLAIKVTCNSVYGFTG-VAMGLLPCLEVASTVTTVGRNMLIATRDYIHAKWNEREKFladfpemqthvipeePH 155
Cdd:PTZ00166   641 kvLNGRQLALKISANSVYGYTGaQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGY---------------KH 705
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1477777490  156 SLRIIYGDTDSVFVKATGYTIDGLNEHGGAVAQYISQaLFPTPIKLECEKTFTRLLMITKKKYIGM 221
Cdd:PTZ00166   706 DATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISK-KFLKPIKLEFEKVYCPYLLMNKKRYAGL 770
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
1-170 2.87e-42

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: 148.83  E-value: 2.87e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490    1 IIQAHNLCLSTLTRDAGALVDLDEGR--DYVRFE-VQGHTFYYVRPHIKQSLLAELLTDWLALRKTIRLRMKTASPED-- 75
Cdd:smart00486 315 IIIAHNLCYSTLVGVGEVVIKGDLIIpeDLLTIKyEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESee 394
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   76 -QLLLDKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIHAKWNERekfladfpemqthvipeep 154
Cdd:smart00486 395 lKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPK------------------- 455
                          170
                   ....*....|....*.
gi 1477777490  155 HSLRIIYGDTDSVFVK 170
Cdd:smart00486 456 PGFKVIYGDTDSIFVT 471
PolB COG0417
DNA polymerase elongation subunit (family B) [Replication, recombination and repair];
1-224 5.92e-39

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


Pssm-ID: 223494 [Multi-domain]  Cd Length: 792  Bit Score: 142.56  E-value: 5.92e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTRDAGALVDLDEGRDYVRFEVQGHtfyyvrphikqsLLAELLTDWLALRKTIRLRMKTASPEDQ-LLL 79
Cdd:COG0417   434 IIIKYNISPDTLVEEDCSDDYSPPGVGHGFCKREKG------------FLPEILEELLDRRDEIKKKMKKEKDPSErKLL 501
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  80 DKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIhakwnerekfladfpemqthvipeEPHSLRI 159
Cdd:COG0417   502 DGRQLALKVLANSFYGYLGYSNSRFYCIECAESVTAFGREILRETKELA------------------------EEMGLRV 557
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1477777490 160 IYGDTDSVFVKATGYTIDGLNEHGGAVAQYISQALfPTPIKLECEKTFTRLLMIT-KKKYIGMIGE 224
Cdd:COG0417   558 IYGDTDSLFVTLPGATYEEAIKIGEELVEEVNERL-PSGIELEVEKVYKRFLLPTaKKRYAGLLED 622
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
1-221 4.31e-30

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: 115.78  E-value: 4.31e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLST---LTRDAGA----------------LVDLDEGRDYVRFEVQGHTFyyVRPHIKQSLLAELLTDWLALR 61
Cdd:cd05534    65 IMIAYNYCYSTclgRVEELNGggkfgflgvklylpppPLDLLLLKDDVTISPNGVMF--VKKSVRKGILPKMLEEILDTR 142
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  62 KTIRLRMK--TASPEDQLLLDKQQLAIKVTCNSVYGFTGVAM-GLLPCLEVASTVTTVGRNMLIATRDYIH--AKWNere 136
Cdd:cd05534   143 IMVKKAMKkyKDDKKLQRILDARQLALKLLANVTYGYTAASFsGRMPCVEIADSIVQTGRETLERAIELIEstPKWG--- 219
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490 137 kfladfpemqthvipeephsLRIIYGDTDSVFVKATGYTIDGLNEHGGAVAQYISqALFPTPIKLECEKTFTRLLMITKK 216
Cdd:cd05534   220 --------------------AKVVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVT-AANPSPIKLKFEKVYHPCVLVTKK 278

                  ....*
gi 1477777490 217 KYIGM 221
Cdd:cd05534   279 RYVGY 283
POLBc cd00145
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
1-222 9.36e-30

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  Cd Length: 323  Bit Score: 112.85  E-value: 9.36e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTRDagalVDLDEgrDYVRFEVqGHTFYYVRPHIKQSLLAELLTDwlalRKTIRLRMKTA--SPEDQLL 78
Cdd:cd00145    31 IIITYNLSPTTLVGN----GEIAA--PEDYIGV-GFRSPKDRKGLLPRILEELLNF----RDEAKKRMKAAklAPEERVL 99
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  79 LDKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIHAkwnerekfladfpemqthvipeepHSLR 158
Cdd:cd00145   100 YDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEE------------------------HGAR 155
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1477777490 159 IIYGDTDSVFVKATGYTIDglnEHGGAVAQYISQALF-PTPIKLECEKTFTRLLMITKKKYIGMI 222
Cdd:cd00145   156 VIYGDTDSIFVSLPKMGTK---EDAIKEGREILQELAdEHLLELEFEKVYLPFFLGKKKRYAGLD 217
POLBc_B3 cd05536
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ...
1-229 5.61e-25

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: 100.48  E-value: 5.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTRDagalvdlDEGRDYVRFEVqGHTFYYVRPHIKQSLLAELLTdwlaLRKTIRLRMKTASPE--DQLL 78
Cdd:cd05536    32 IMIKYNISPDTLVRE-------GCEDCDVEPQV-GHKFRKDPPGFIPSVLEDLLE----ERRRIKEKMKKLDPEseEYKL 99
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  79 LDKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIhakwneREKfladfpemqthvipeephSLR 158
Cdd:cd05536   100 LDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIA------EEK------------------GFK 155
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1477777490 159 IIYGDTDSVFVKATGytIDGLNEHGGAVAQYISQALfptPIKLECEKTFTRLLMITKKKYIGMIGEQKMMM 229
Cdd:cd05536   156 VIYGDTDSLFVKIDG--ADAVKKKVKKLLKYINEEL---PLELEIEKFYKRGFFVTKKRYAGLTEDGKIDV 221
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
1-218 7.69e-21

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: 90.50  E-value: 7.69e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490    1 IIQAHNLCLSTLTRDagalVDLDEGRDYVRfevqghtfyyvrPHIKQSLLAELLTDWLALRKTIRLRMKT-ASPEDQLLL 79
Cdd:TIGR00592  825 IIQEFNICFTTVQQK----VDEDELPELPD------------SELEMGILPRELRKLVERRKEVKKLMKQdLNPDLRLQY 888
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   80 DKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIhakwneREKFladfpemqthvipeephsLRI 159
Cdd:TIGR00592  889 DIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLV------EEMN------------------LEV 944
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1477777490  160 IYGDTDSVFVKATGYTIDGLNEHGGAVAQYISqALFPtPIKLECEKTFTRLLMITKKKY 218
Cdd:TIGR00592  945 IYGDTDSIMINTPGTKYEEVFKIGKEFKSEVN-KLYK-LLELDIDGVFKRLLLLKKKKY 1001
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
1-222 2.53e-18

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: 82.63  E-value: 2.53e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTRDAGALVDLDEGRDYVRFEVQGhtfyyVRPHIKQSLLAelltdwlaLRKTIRLRMKTASPEDQLL-L 79
Cdd:cd05532    37 IIQEYNICFTTVDRADPDDEDDEEPPLPPSDQEKG-----ILPRIIRKLVE--------RRRQVKKLMKSEKDPDKKAqL 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  80 DKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIhakwnerekfladfpemqthvipeEPHSLRI 159
Cdd:cd05532   104 DIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLV------------------------EKMNLEV 159
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1477777490 160 IYGDTDSVFVKaTGytIDGLNEH---GGAVAQYISQALfpTPIKLECEKTFTRLLMITKKKYIGMI 222
Cdd:cd05532   160 IYGDTDSIMIN-TG--TTDYEEAkklGNKIKKEVNKSY--KKLEIDIDGVFKRLLLLKKKKYAALK 220
PHA03036 PHA03036
DNA polymerase; Provisional
46-221 8.75e-16

DNA polymerase; Provisional


Pssm-ID: 222962 [Multi-domain]  Cd Length: 1004  Bit Score: 75.83  E-value: 8.75e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   46 KQSLLAELLTDWLALRKTIRLRMKTASPE-DQLLLDKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIAT 124
Cdd:PHA03036   621 IEGIIPKLLKTFLEERARYKKLLKEATSSvEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKYL 700
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  125 RDYIHAKWNEREKF-LADFPE---------MQTHV---IPEEPH-SLRIIYGDTDSVFV----KATGYTIDGLNEHGGAV 186
Cdd:PHA03036   701 NSVLNGSKLINGKLiLANCPInpffkddrsIDTNYdtnLPVEYNfTFRSVYGDTDSVFLeintKDVDKSIKIAKELERII 780
                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1477777490  187 AQYISQALFptpiKLECEKTFTRLLMITKKKYIGM 221
Cdd:PHA03036   781 NEKVLFDNF----KIEFEAVYKNLIMQSKKKYTTL 811
PRK05762 PRK05762
DNA polymerase II; Reviewed
42-227 1.28e-14

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 72.19  E-value: 1.28e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  42 RPHIKQSLLAELLtdwlALRKTIRLRMKTAspedqllldKQQlAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNML 121
Cdd:PRK05762  463 EKHFLPEIVERLW----EGRDEAKREMNKP---------LSQ-AIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIM 528
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490 122 IATRDYIhakwnerekfladfpemqthvipeEPHSLRIIYGDTDSVFVKATG-YTIDGLNEHGGAVAQYISQALFPTPIK 200
Cdd:PRK05762  529 KQTRELI------------------------EAQGYQVIYGDTDSTFVWLGGaHDEEDAAKIGRALVQEINQWWQEHLQQ 584
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1477777490 201 ---------LECEKTFTRLLMIT--------KKKYIGMI----GEQKM 227
Cdd:PRK05762  585 efglesaleLEFEKHYRRFFMPTirgaeegsKKRYAGLIqegdGDGRI 632
PRK05761 PRK05761
DNA-directed DNA polymerase I;
1-227 3.20e-14

DNA-directed DNA polymerase I;


Pssm-ID: 235594 [Multi-domain]  Cd Length: 787  Bit Score: 71.26  E-value: 3.20e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   1 IIQAHNLCLSTLTrdagalVDLDEGRDYVRFEVQGHTFYYVRPHIkQSLLAELLTDwlaLRKTIRLRM---KTASPEDQL 77
Cdd:PRK05761  435 IIVKWNLSPETVR------IPECKCHYDDEVPELGHSVCDDRPGL-TSVLVGLLRD---FRVKIYKKKakdPNLDEERRA 504
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  78 LLDKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIHAkwnerekfladfpemqthvipeepHSL 157
Cdd:PRK05761  505 WYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAEE------------------------LGL 560
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1477777490 158 RIIYGDTDSVFVkaTGYTIDGLNEhggaVAQYISQAlfpTPIKLECEKTFtRLLMIT--KKKYIGMIGEQKM 227
Cdd:PRK05761  561 KVLYGDTDSLFV--WGPTKESLEE----LIKEIEER---TGIDLEVDKTY-DWVAFSglKKNYFGVLKDGKV 622
POLBc_B1 cd05530
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ...
69-220 1.38e-09

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: 56.98  E-value: 1.38e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  69 KTASPEDQLLLDKQQLAIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDyiHAKwnerekfladfpEMqth 148
Cdd:cd05530   101 KSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIK--KAR------------EL--- 163
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1477777490 149 vipeephSLRIIYGDTDSVFVKatGYTIDGLNEhggaVAQYISQALfptPIKLECEKTFtRLLMIT--KKKYIG 220
Cdd:cd05530   164 -------GLKVLYGDTDSLFLW--NPPQEQLED----LVEWVEKEL---GLDLELDKEY-RYVVFSglKKNYLG 220
POLBc_Pol_II cd05537
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
85-227 1.99e-09

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: 56.51  E-value: 1.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  85 AIKVTCNSVYGFTGVAMGLLPCLEVASTVTTVGRNMLIATRDYIhakwnerekfladfpEMQTHvipeephslRIIYGDT 164
Cdd:cd05537    95 AIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWI---------------EQQGY---------QVIYGDT 150
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490 165 DSVFVK-ATGYTIDGLNEHGGAVAQYISQALFPTPIK---------LECEKTFTRLLMIT--------KKKYIGMI---G 223
Cdd:cd05537   151 DSTFVWlGEELDAAEAQAIGKELASQINQWWAQKLKEefglesfleIEFETHYSRFFMPTirgsdegsKKRYAGLKstdG 230

                  ....
gi 1477777490 224 EQKM 227
Cdd:cd05537   231 GDEL 234
PHA03334 PHA03334
putative DNA polymerase catalytic subunit; Provisional
54-167 8.18e-04

putative DNA polymerase catalytic subunit; Provisional


Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 40.22  E-value: 8.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490   54 LTDWLALRKTIRLRMKTAS-PEDQLLLDKQQLAIKVTCNSVYGftgVAMGLLPCLevastVTTVGRNMLIATRDYIhakw 132
Cdd:PHA03334   732 LNHYLSMRTEYKGAMKQAKdPKLKSYHNQLQNEMKICANSHYG---VAPHACQHL-----ITTLGRHKIKLVEEFI---- 799
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1477777490  133 nerekfladfpemqthvipEEPHSLRIIYGDTDSV 167
Cdd:PHA03334   800 -------------------KKEPGMTVNYGDTDSV 815
POLBc_B2 cd05531
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ...
46-227 7.05e-03

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: 36.94  E-value: 7.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490  46 KQSLLAELLTDWLALRKTIRLRMKTASPEDQLlldkqQLAIK---VTCnsvYGFTGVAMGLLPCLEVASTVTTVGRNMLI 122
Cdd:cd05531    65 RRGFLPEVLEPLLERRLEYKRLKKEEDPYAGR-----QKALKwilVTS---FGYLGYKNAKFGRIEVHEAITAYGRKILL 136
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477777490 123 ATRDyihakwnerekfladfpemqthvIPEEpHSLRIIYGDTDSVFVKAtgytidglNEHGGAVAQYISQalfPTPIKLE 202
Cdd:cd05531   137 RAKE-----------------------IAEE-MGFRVLHGIVDSLWIQG--------RGDIEELAREIEE---RTGIPLK 181
                         170       180       190
                  ....*....|....*....|....*....|..
gi 1477777490 203 CEKTFTRLL-MITK------KKYIGMIGEQKM 227
Cdd:cd05531   182 LEGHYDWIVfLPERdglgapNRYFGRLSDGEM 213
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.19
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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