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Conserved domains on  [gi|491444601|ref|WP_005302389|]
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MULTISPECIES: 3'-5' exonuclease [Acinetobacter]

Protein Classification

3'-5' exonuclease( domain architecture ID 12103322)

3'-5' exonuclease has a fundamental role in reducing polymerase errors and is involved in proofreading activity

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_pol_B_exo2 pfam10108
Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in ...
 46-253 7.44e-95

Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins.


:

Pssm-ID: 462958 [Multi-domain]  Cd Length: 210  Bit Score: 277.96  E-value: 7.44e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601   46 MDFQRLPLHEIVCISGL-WIDESGFRLFSFSREQYSEAEILQKFLSIFDKRHPTLVSWNGSQFDLPVILFRAMYHGLSAP 124
Cdd:pfam10108   1 SDFLPLPLHRIVAISCVkARDDGGFRVWSLGEPEDSEKELIQRFFDGVEKYTPQLVSFNGRGFDLPVLHYRALKHGVSAP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  125 GLFDQGeiDSQKRFNNYQNRYHHRHIDLMDVMAMFNGRNFQKLDDIACILGLPGKRGESGYHVPEYVRNQQWLKLTSYCE 204
Cdd:pfam10108  81 RYWDTG--DGDFKWNNYFNRYHTRHLDLMDLLAGYGGRANAPLDEVAKLLGFPGKMGMDGSKVWELYQAGRLDEIRDYCE 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 491444601  205 GDVLNTWFIYLRWLVLKGQLSVDEHNHWISSSIEYL---QTMPQQSDFLEVW 253
Cdd:pfam10108 159 TDVLNTYLVYLRFQLLRGRLDLEDYAEEIALLRDYLeegEGKEHLLEFLAAW 210
 
Name Accession Description Interval E-value
DNA_pol_B_exo2 pfam10108
Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in ...
 46-253 7.44e-95

Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins.


Pssm-ID: 462958 [Multi-domain]  Cd Length: 210  Bit Score: 277.96  E-value: 7.44e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601   46 MDFQRLPLHEIVCISGL-WIDESGFRLFSFSREQYSEAEILQKFLSIFDKRHPTLVSWNGSQFDLPVILFRAMYHGLSAP 124
Cdd:pfam10108   1 SDFLPLPLHRIVAISCVkARDDGGFRVWSLGEPEDSEKELIQRFFDGVEKYTPQLVSFNGRGFDLPVLHYRALKHGVSAP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  125 GLFDQGeiDSQKRFNNYQNRYHHRHIDLMDVMAMFNGRNFQKLDDIACILGLPGKRGESGYHVPEYVRNQQWLKLTSYCE 204
Cdd:pfam10108  81 RYWDTG--DGDFKWNNYFNRYHTRHLDLMDLLAGYGGRANAPLDEVAKLLGFPGKMGMDGSKVWELYQAGRLDEIRDYCE 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 491444601  205 GDVLNTWFIYLRWLVLKGQLSVDEHNHWISSSIEYL---QTMPQQSDFLEVW 253
Cdd:pfam10108 159 TDVLNTYLVYLRFQLLRGRLDLEDYAEEIALLRDYLeegEGKEHLLEFLAAW 210
DNA_polB_like1_exo cd05782
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ...
 5-216 3.99e-85

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: 99825 [Multi-domain]  Cd Length: 208  Bit Score: 252.93  E-value: 3.99e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601   5 TLVFDIETLTDLKAGAHLYH-LDLPEADVEQALTKLRRQESGMDFQRLPLHEIVCISGLWIDESG--FRLFSFsrEQYSE 81
Cdd:cd05782    1 ILVFDIETVPDVDLGRRLYLlLELDDLEVLEKRFAQRLEKSGSDFLPLPFHKVVSISALYRDDDGgfLKVRTL--DGADE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  82 AEILQKFLSIFDKRHPTLVSWNGSQFDLPVILFRAMYHGLSAPGLFDQGEIDsqkrfNNYQNRYHHRHIDLMDVMAMFNG 161
Cdd:cd05782   79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKD-----WNYRNRYSERHLDLMDLLAFYGA 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 491444601 162 RNFQKLDDIACILGLPGKRGESGYHVPEYVRNQQWLKLTSYCEGDVLNTWFIYLR 216
Cdd:cd05782  154 RARASLDLLAKLLGIPGKMDVDGSQVWELYAEGKLDEIAEYCETDVLNTYLLYLR 208
COG3298 COG3298
Predicted 3'-5' exonuclease related to the exonuclease domain of PolB [Replication, ...
 4-196 9.03e-52

Predicted 3'-5' exonuclease related to the exonuclease domain of PolB [Replication, recombination and repair];


Pssm-ID: 442527  Cd Length: 211  Bit Score: 168.18  E-value: 9.03e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601   4 PTLVFDIETLTDLKAGAHLYHLD--LPEADVEQALTKLRRQESGMDFQRLPLHEIVCISGLWIDESGFRLFSFSREQYSE 81
Cdd:COG3298    3 PVLVFDIETIPDVAGGRRLYGLDagLSDADVAEAAFQLRREETGSDFLPLHLHRIVAISCVLRDGDGFKVWSLGDPDDDE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  82 AEILQKFLSIFDKRHPTLVSWNGSQFDLPVI------------LFRAMYHGLSAPGlFDQGEIDSQKR-FNNYQNRYHHR 148
Cdd:COG3298   83 AELIQRFFDGIEKYTPQLVSWNGGGFDLPVLhydgiakllgfpGKLGMDGSKVWPA-YQDGEIDEIRDyCETDVLNTYLV 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 491444601 149 HIDLMDVMAMFNGRNFQKLDDIACILGLPGKRGESGyhvpEYVRNQQW 196
Cdd:COG3298  162 YLRFQLMRGLLSPREYAAEIELVRETLAAGAGPHWQ----EFLAAWAA 205
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
 6-162 2.23e-05

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: 45.21  E-value: 2.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601     6 LVFDIETLTDlkagahlyhldlpeadveqaltklrrqESGMDFQRLPLHEIVCISgLWIDESG----FRLFSFSREQY-- 79
Cdd:smart00486   6 LSFDIETYTD---------------------------GGNFPDAEIFDDEIIQIS-LVINDGDkkgaNRRILFTLGTCke 57

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601    80 ----------SEAEILQKFLSIFDKRHP-TLVSWNGSQFDLPVILFRAMYHGLSAPGLFdqGEIDSQKRFNNYQNRYHHR 148
Cdd:smart00486  58 idgievyefnNEKELLLAFFEFIKKYDPdIIYGHNISNFDLPYIISRLEKLKIDPLSKI--GRLKIGLRIPNKKPLFGSK 135

                          170
                   ....*....|....
gi 491444601   149 HIDLMDVMAMFNGR 162
Cdd:smart00486 136 SFGLSDIKVYIKGR 149
PRK05761 PRK05761
DNA-directed DNA polymerase I;
80-148 3.58e-04

DNA-directed DNA polymerase I;


Pssm-ID: 235594 [Multi-domain]  Cd Length: 787  Bit Score: 41.60  E-value: 3.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  80 SEAEILQKFLSIFDkRHPTLVSWNGSQFDLPVILFRAMYHGLSAPGL-----FDQGEIDSQKRFNN-------YQNRYHH 147
Cdd:PRK05761 209 SEKELLAELFDIIL-EYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIpiepgRAGIHIDLYKFFQNkavrsyaFYGKYRH 287


                 .
gi 491444601 148 R 148
Cdd:PRK05761 288 R 288
 
Name Accession Description Interval E-value
DNA_pol_B_exo2 pfam10108
Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in ...
 46-253 7.44e-95

Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins.


Pssm-ID: 462958 [Multi-domain]  Cd Length: 210  Bit Score: 277.96  E-value: 7.44e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601   46 MDFQRLPLHEIVCISGL-WIDESGFRLFSFSREQYSEAEILQKFLSIFDKRHPTLVSWNGSQFDLPVILFRAMYHGLSAP 124
Cdd:pfam10108   1 SDFLPLPLHRIVAISCVkARDDGGFRVWSLGEPEDSEKELIQRFFDGVEKYTPQLVSFNGRGFDLPVLHYRALKHGVSAP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  125 GLFDQGeiDSQKRFNNYQNRYHHRHIDLMDVMAMFNGRNFQKLDDIACILGLPGKRGESGYHVPEYVRNQQWLKLTSYCE 204
Cdd:pfam10108  81 RYWDTG--DGDFKWNNYFNRYHTRHLDLMDLLAGYGGRANAPLDEVAKLLGFPGKMGMDGSKVWELYQAGRLDEIRDYCE 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 491444601  205 GDVLNTWFIYLRWLVLKGQLSVDEHNHWISSSIEYL---QTMPQQSDFLEVW 253
Cdd:pfam10108 159 TDVLNTYLVYLRFQLLRGRLDLEDYAEEIALLRDYLeegEGKEHLLEFLAAW 210
DNA_polB_like1_exo cd05782
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ...
 5-216 3.99e-85

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: 99825 [Multi-domain]  Cd Length: 208  Bit Score: 252.93  E-value: 3.99e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601   5 TLVFDIETLTDLKAGAHLYH-LDLPEADVEQALTKLRRQESGMDFQRLPLHEIVCISGLWIDESG--FRLFSFsrEQYSE 81
Cdd:cd05782    1 ILVFDIETVPDVDLGRRLYLlLELDDLEVLEKRFAQRLEKSGSDFLPLPFHKVVSISALYRDDDGgfLKVRTL--DGADE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  82 AEILQKFLSIFDKRHPTLVSWNGSQFDLPVILFRAMYHGLSAPGLFDQGEIDsqkrfNNYQNRYHHRHIDLMDVMAMFNG 161
Cdd:cd05782   79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKD-----WNYRNRYSERHLDLMDLLAFYGA 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 491444601 162 RNFQKLDDIACILGLPGKRGESGYHVPEYVRNQQWLKLTSYCEGDVLNTWFIYLR 216
Cdd:cd05782  154 RARASLDLLAKLLGIPGKMDVDGSQVWELYAEGKLDEIAEYCETDVLNTYLLYLR 208
COG3298 COG3298
Predicted 3'-5' exonuclease related to the exonuclease domain of PolB [Replication, ...
 4-196 9.03e-52

Predicted 3'-5' exonuclease related to the exonuclease domain of PolB [Replication, recombination and repair];


Pssm-ID: 442527  Cd Length: 211  Bit Score: 168.18  E-value: 9.03e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601   4 PTLVFDIETLTDLKAGAHLYHLD--LPEADVEQALTKLRRQESGMDFQRLPLHEIVCISGLWIDESGFRLFSFSREQYSE 81
Cdd:COG3298    3 PVLVFDIETIPDVAGGRRLYGLDagLSDADVAEAAFQLRREETGSDFLPLHLHRIVAISCVLRDGDGFKVWSLGDPDDDE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  82 AEILQKFLSIFDKRHPTLVSWNGSQFDLPVI------------LFRAMYHGLSAPGlFDQGEIDSQKR-FNNYQNRYHHR 148
Cdd:COG3298   83 AELIQRFFDGIEKYTPQLVSWNGGGFDLPVLhydgiakllgfpGKLGMDGSKVWPA-YQDGEIDEIRDyCETDVLNTYLV 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 491444601 149 HIDLMDVMAMFNGRNFQKLDDIACILGLPGKRGESGyhvpEYVRNQQW 196
Cdd:COG3298  162 YLRFQLMRGLLSPREYAAEIELVRETLAAGAGPHWQ----EFLAAWAA 205
DEDDy_DNA_polB_exo cd05160
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ...
 6-215 2.60e-17

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: 77.78  E-value: 2.60e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601   6 LVFDIETLTDLKAgahlyhldlPEADVEQ--ALTkLRRQESGMDFQRLPLHEIVCISGLWIDesGFRLFSFsreqYSEAE 83
Cdd:cd05160    2 LSFDIETTPPVGG---------PEPDRDPiiCIT-YADSFDGVKVVFLLKTSTVGDDIEFID--GIEVEYF----ADEKE 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  84 ILQKFLSIFDKRHPT-LVSWNGSQFDLPVILFRAMYHGLSAPGLFdQGEIDSQKRfNNYQNRYHHRHIDLMDVMAMFngR 162
Cdd:cd05160   66 LLKRFFDIIREYDPDiLTGYNIDDFDLPYLLKRAEALGIKLTDGI-YRRSGGEKS-SGSTERIAVKGRVVFDLLAAY--K 141

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 491444601 163 NFQK-----LDDIACILGLPGKRGESGYHVPEYVRNQQWLKLTSYCEGDVLNTWFIYL 215
Cdd:cd05160  142 RDFKlksytLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQILE 199
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
55-221 1.62e-11

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


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 64.08  E-value: 1.62e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  55 EIVCIsGLWiDESGFR-LFSFSREQ--------YSEAEILQKFLSIFDKRHPT-LVSWNGSQFDLPVILFRAMYHGLSap 124
Cdd:COG0417  183 PIISI-GLA-GSDGEKkVLMLGREGvdfeveyfDDEKALLEAFFEIIREYDPDiIIGWNVDNFDLPYLQKRAERLGIP-- 258

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601 125 glFDQGEIDSQKRFNNYQNRYH----HR-HIDLMDV--MAMFNGRNFqKLDDIACILGLPGKRGESGYHVPEYVRNQQWl 197
Cdd:COG0417  259 --LDLGRDGSEPSWREHGGQGFasipGRvVIDLYDAlkSATYKFKSY-SLDAVAEELLGEGKLIVDGGEIERLWDDDKP- 334

                        170       180
                 ....*....|....*....|....
gi 491444601 198 KLTSYCEGDVLNTWFIYLRWLVLK 221
Cdd:COG0417  335 ALAEYNLRDAELTLRIFEKTLLLP 358
YprB COG3359
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ...
 56-217 2.29e-10

Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];


Pssm-ID: 442587 [Multi-domain]  Cd Length: 198  Bit Score: 58.42  E-value: 2.29e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  56 IVCISGLWIDESGFRLFSF-SREQYSEAEILQKFLSIFDKRhPTLVSWNGSQFDLPVILFRAMYHGLSAPglFDqgeids 134
Cdd:COG3359   34 IFLIGLADGEGDGFVVRQYfGEDPGEEAALLEAFLEWLADY-KLLVTYNGKSFDLPFLKTRFTLHRLPPP--LP------ 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601 135 qkrfnnyqnryHHRHIDLMDV------MAMFNGRnfqkLDDIACILGLPGKRGESGYHVP----EYVRNQQ---WLKLTS 201
Cdd:COG3359  105 -----------EFPHLDLLHParrlwkNRLPSGG----LKTVEELLGIEREDDLPGYEAPrlyrRYLRTGDpeaLETLLE 169

                        170
                 ....*....|....*.
gi 491444601 202 YCEGDVLNTWFIYLRW 217
Cdd:COG3359  170 HNREDVLNLATLLEHL 185
RNase_H_2 pfam13482
RNase_H superfamily;
56-219 4.56e-10

RNase_H superfamily;


Pssm-ID: 433246 [Multi-domain]  Cd Length: 163  Bit Score: 57.22  E-value: 4.56e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601   56 IVCISGLWIDESGFRLFS-FSREQYSEAEILQKFLSIFdKRHPTLVSWNGSQFDLPVIlframyhglsapglfdqgeids 134
Cdd:pfam13482  17 IYLIGVYDVDGDKVRTFVqYLAEGPTEEAAILQLFELL-ADYPLLVTFNGKSFDVPFI---------------------- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  135 QKRFNNYQNRYHHRHIDLMDVMAMFNGRNfqKLDDIACILGLPGKRGE-SGYHVP----EYVR--NQQWL-KLTSYCEGD 206
Cdd:pfam13482  74 KRRFKRYDLDELFRHIDLLHPLRKLGLES--GLKSVERELGIERRDDDlPGSQAVklyfDYLRtgDPALLeTLLAYNEDD 151

                         170
                  ....*....|...
gi 491444601  207 VLNTWFIYlRWLV 219
Cdd:pfam13482 152 VRALATLY-EWLY 163
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
 6-162 2.23e-05

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: 45.21  E-value: 2.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601     6 LVFDIETLTDlkagahlyhldlpeadveqaltklrrqESGMDFQRLPLHEIVCISgLWIDESG----FRLFSFSREQY-- 79
Cdd:smart00486   6 LSFDIETYTD---------------------------GGNFPDAEIFDDEIIQIS-LVINDGDkkgaNRRILFTLGTCke 57

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601    80 ----------SEAEILQKFLSIFDKRHP-TLVSWNGSQFDLPVILFRAMYHGLSAPGLFdqGEIDSQKRFNNYQNRYHHR 148
Cdd:smart00486  58 idgievyefnNEKELLLAFFEFIKKYDPdIIYGHNISNFDLPYIISRLEKLKIDPLSKI--GRLKIGLRIPNKKPLFGSK 135

                          170
                   ....*....|....
gi 491444601   149 HIDLMDVMAMFNGR 162
Cdd:smart00486 136 SFGLSDIKVYIKGR 149
DNA_polB_Kod1_like_exo cd05780
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ...
 80-156 2.93e-05

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: 43.88  E-value: 2.93e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491444601  80 SEAEILQKFLSIFDKRHP-TLVSWNGSQFDLPVILFRAMYHGLSAPGLFDQGEIDSQKRFNNYQNRYHHR-HIDLMDVM 156
Cdd:cd05780   55 TEKEMIKRFIEIVKEKDPdVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRiHVDLYPVA 133
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
 65-156 8.07e-05

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: 43.17  E-value: 8.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601   65 DESGFRLFSFSreqySEAEILQKFLS-IFDKRHPTLVSWNGSQFDLPVILFRAMY---HGLSAPGLFDQGEIDSQKRFNN 140
Cdd:pfam03104 222 IYPGVKVFEFP----SEKELLRRFFEfIRQYDPDIITGYNGDNFDWPYILNRAKElyiVKLSSIGRLNRGGRSKVREIGF 297

                          90       100
                  ....*....|....*....|..
gi 491444601  141 YQNRYHHR------HIDLMDVM 156
Cdd:pfam03104 298 GTRSYEKVkisgrlHLDLYRVI 319
DNA_polB_B1_exo cd05783
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ...
 80-151 9.54e-05

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: 42.31  E-value: 9.54e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  80 SEAEILQKFLSIFdKRHPTLVSWNGSQFDLPVILFRAMYHGLS---APGLFDQGE--------IDSQKRFNN-------Y 141
Cdd:cd05783   72 SEKELIREAFKII-SEYPIVLTFNGDNFDLPYLYNRALKLGIPkeeIPIYLKRDYatlkhgihIDLYKFFSNraiqvyaF 150

                         90
                 ....*....|
gi 491444601 142 QNRYHHRHID 151
Cdd:cd05783  151 GNKYREYTLD 160
DNA_polB_epsilon_exo cd05779
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase; ...
 80-157 2.88e-04

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: 41.09  E-value: 2.88e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491444601  80 SEAEILQKFLSIFDKRHPTL-VSWNGSQFDLPVILFRAMYHGLSapgLFDqgEIDSQKrfnNYQNRYHHRHIDLMDVMA 157
Cdd:cd05779   72 DEKALLQRFFEHIREVKPHIiVTYNGDFFDWPFVEARAAIHGLS---MEE--EIGFRK---DSEGEYKSRYIIHMDCFR 142
PRK05761 PRK05761
DNA-directed DNA polymerase I;
80-148 3.58e-04

DNA-directed DNA polymerase I;


Pssm-ID: 235594 [Multi-domain]  Cd Length: 787  Bit Score: 41.60  E-value: 3.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491444601  80 SEAEILQKFLSIFDkRHPTLVSWNGSQFDLPVILFRAMYHGLSAPGL-----FDQGEIDSQKRFNN-------YQNRYHH 147
Cdd:PRK05761 209 SEKELLAELFDIIL-EYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIpiepgRAGIHIDLYKFFQNkavrsyaFYGKYRH 287


                 .
gi 491444601 148 R 148
Cdd:PRK05761 288 R 288
PRK05762 PRK05762
DNA polymerase II; Reviewed
 79-121 6.90e-03

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 37.91  E-value: 6.90e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 491444601  79 YSEAEILQKFLSIFDKRHP-TLVSWNGSQFDLPVILFRAMYHGL 121
Cdd:PRK05762 201 ADEKALLEKFNAWFAEHDPdVIIGWNVVQFDLRLLQERAERYGI 244
 
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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