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Conserved domains on  [gi|530387845|ref|XP_005273595|]
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DNA polymerase beta isoform X4 [Homo sapiens]

Protein Classification

nucleotidyltransferase domain-containing protein( domain architecture ID 10065437)

nucleotidyltransferase domain-containing protein of family X DNA polymerases which includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT).

EC:  2.7.7.7
Gene Ontology:  GO:0003887|GO:0003677

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 9-219 1.55e-94

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


:

Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 278.31  E-value: 1.55e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845   9 ADLRKNE-DKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFT 87
Cdd:cd00141  110 EDLRKAAgAKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDAT 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845  88 SestkqPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPskndeKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKN 167
Cdd:cd00141  190 S-----RGLLEKVVDALVELGFVTEVLSKGDTKASGILKLP-----GGWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRA 259

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 530387845 168 MRAHALEKGFTINEYTIRPlgvtGVAGEPLPVDSEKDIFDYIQWKYREPKDR 219
Cdd:cd00141  260 LRRLAKEKGLKLNEYGLFD----GVDGERLPGETEEEIFEALGLPYIEPELR 307
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 9-219 1.55e-94

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 278.31  E-value: 1.55e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845   9 ADLRKNE-DKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFT 87
Cdd:cd00141  110 EDLRKAAgAKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDAT 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845  88 SestkqPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPskndeKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKN 167
Cdd:cd00141  190 S-----RGLLEKVVDALVELGFVTEVLSKGDTKASGILKLP-----GGWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRA 259

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 530387845 168 MRAHALEKGFTINEYTIRPlgvtGVAGEPLPVDSEKDIFDYIQWKYREPKDR 219
Cdd:cd00141  260 LRRLAKEKGLKLNEYGLFD----GVDGERLPGETEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 10-220 5.16e-81

DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases


Pssm-ID: 214688  Cd Length: 334  Bit Score: 244.97  E-value: 5.16e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845    10 DLRKN-EDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFT- 87
Cdd:smart00483 115 ELKKNkELKLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRKILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAk 194

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845    88 --SESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYP--------HRRIDIRLIPKDQYYCGVLY 157
Cdd:smart00483 195 ekELEVLDLLLLESTFEELQLPSIRVATLDHGQKKFMILKLSPSREDKEKSGkpdekgwkARRVDIVLCPEDQYPTALLG 274

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530387845   158 FTGSDIFNKNMRAHALEKGfTINEYTIRPLGVTGvaGEPLPVDSEKDIFDYIQWKYREPKDRS 220
Cdd:smart00483 275 WTGSKQFNRDLRRYATSKF-KLMLDGHELYDKTK--EKFLKVESEEDIFDHLGLPYIEPEERN 334
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
 35-147 3.13e-52

DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.


Pssm-ID: 464318  Cd Length: 110  Bit Score: 163.89  E-value: 3.13e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845   35 RIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSEStKQPKLLHQVVEQLQKVHFITDTL 114
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSES-ELKGLLDRLVARLKKSGFLTDDL 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 530387845  115 S--KGETKFMGVCQLPskndEKEYPHRRIDIRLIP 147
Cdd:pfam14792  80 AvdSGGSKWMGVCRLP----GSERLHRRIDILVVP 110
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
22-209 5.73e-26

DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 104.89  E-value: 5.73e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845  22 QRI--GLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLThpsftsesTKQPKllhQ 99
Cdd:COG1796  140 ENIlkGIELLRKRGGRFLLGEALPLAEEILAYLRALPGVERVEVAGSLRRRKETVGDIDILVA--------SDDPE---A 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845 100 VVEQLQKVHFITDTLSKGETKfmgvCQLPSKNDekeyphRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTI 179
Cdd:COG1796  209 VMDAFVKLPEVKEVLAKGDTK----ASVRLKSG------LQVDLRVVPPESFGAALQYFTGSKEHNVALRQLAKERGLKL 278

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 530387845 180 NEYtirplGVTGVAGEPLPVDSEKDIF-----DYI 209
Cdd:COG1796  279 NEY-----GLFDVGGERIAGETEEEVYaalglPYI 308
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
25-221 3.25e-13

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 68.06  E-value: 3.25e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845  25 GLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLthpsftseSTKQPkllHQVVEQL 104
Cdd:PRK08609 142 AVKELGKRPERLPIAQVLPIAQEIEEYLATIDEIIRFSRAGSLRRARETVKDLDFII--------ATDEP---EAVREQL 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845 105 QKVHFITDTLSKGETKFmgvcqlpSKNDEKEYPhRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYti 184
Cdd:PRK08609 211 LQLPNIVEVIAAGDTKV-------SVELEYEYT-ISVDFRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEY-- 280

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 530387845 185 rplGVTGV-AGEPLPVDSEKDIFDYIQWKYREP---KDRSE 221
Cdd:PRK08609 281 ---GVEQAdTGEVKTFESEEAFFAHFGLPFIPPevrEDGSE 318
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 9-219 1.55e-94

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 278.31  E-value: 1.55e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845   9 ADLRKNE-DKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFT 87
Cdd:cd00141  110 EDLRKAAgAKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDAT 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845  88 SestkqPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPskndeKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKN 167
Cdd:cd00141  190 S-----RGLLEKVVDALVELGFVTEVLSKGDTKASGILKLP-----GGWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRA 259

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 530387845 168 MRAHALEKGFTINEYTIRPlgvtGVAGEPLPVDSEKDIFDYIQWKYREPKDR 219
Cdd:cd00141  260 LRRLAKEKGLKLNEYGLFD----GVDGERLPGETEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 10-220 5.16e-81

DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases


Pssm-ID: 214688  Cd Length: 334  Bit Score: 244.97  E-value: 5.16e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845    10 DLRKN-EDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFT- 87
Cdd:smart00483 115 ELKKNkELKLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRKILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAk 194

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845    88 --SESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYP--------HRRIDIRLIPKDQYYCGVLY 157
Cdd:smart00483 195 ekELEVLDLLLLESTFEELQLPSIRVATLDHGQKKFMILKLSPSREDKEKSGkpdekgwkARRVDIVLCPEDQYPTALLG 274

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530387845   158 FTGSDIFNKNMRAHALEKGfTINEYTIRPLGVTGvaGEPLPVDSEKDIFDYIQWKYREPKDRS 220
Cdd:smart00483 275 WTGSKQFNRDLRRYATSKF-KLMLDGHELYDKTK--EKFLKVESEEDIFDHLGLPYIEPEERN 334
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
 35-147 3.13e-52

DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.


Pssm-ID: 464318  Cd Length: 110  Bit Score: 163.89  E-value: 3.13e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845   35 RIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSEStKQPKLLHQVVEQLQKVHFITDTL 114
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSES-ELKGLLDRLVARLKKSGFLTDDL 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 530387845  115 S--KGETKFMGVCQLPskndEKEYPHRRIDIRLIP 147
Cdd:pfam14792  80 AvdSGGSKWMGVCRLP----GSERLHRRIDILVVP 110
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
22-209 5.73e-26

DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 104.89  E-value: 5.73e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845  22 QRI--GLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLThpsftsesTKQPKllhQ 99
Cdd:COG1796  140 ENIlkGIELLRKRGGRFLLGEALPLAEEILAYLRALPGVERVEVAGSLRRRKETVGDIDILVA--------SDDPE---A 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845 100 VVEQLQKVHFITDTLSKGETKfmgvCQLPSKNDekeyphRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTI 179
Cdd:COG1796  209 VMDAFVKLPEVKEVLAKGDTK----ASVRLKSG------LQVDLRVVPPESFGAALQYFTGSKEHNVALRQLAKERGLKL 278

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 530387845 180 NEYtirplGVTGVAGEPLPVDSEKDIF-----DYI 209
Cdd:COG1796  279 NEY-----GLFDVGGERIAGETEEEVYaalglPYI 308
DNA_pol_B_thumb pfam14791
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
 155-219 1.42e-22

DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain.


Pssm-ID: 464317 [Multi-domain]  Cd Length: 63  Bit Score: 86.66  E-value: 1.42e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530387845  155 VLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLgvtgVAGEPLPVDSEKDIFDYIQWKYREPKDR 219
Cdd:pfam14791   2 LLYFTGSKEFNRDLRLLAKKKGLKLNEYGLFDL----KDGELLEGETEEDIFEALGLPYIPPELR 62
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
25-221 3.25e-13

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 68.06  E-value: 3.25e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845  25 GLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLthpsftseSTKQPkllHQVVEQL 104
Cdd:PRK08609 142 AVKELGKRPERLPIAQVLPIAQEIEEYLATIDEIIRFSRAGSLRRARETVKDLDFII--------ATDEP---EAVREQL 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387845 105 QKVHFITDTLSKGETKFmgvcqlpSKNDEKEYPhRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYti 184
Cdd:PRK08609 211 LQLPNIVEVIAAGDTKV-------SVELEYEYT-ISVDFRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEY-- 280

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 530387845 185 rplGVTGV-AGEPLPVDSEKDIFDYIQWKYREP---KDRSE 221
Cdd:PRK08609 281 ---GVEQAdTGEVKTFESEEAFFAHFGLPFIPPevrEDGSE 318
NT_Pol-beta-like cd05397
Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This ...
 42-82 1.87e-06

Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism for Rel-Spo enzymes.


Pssm-ID: 143387 [Multi-domain]  Cd Length: 49  Bit Score: 43.47  E-value: 1.87e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 530387845  42 LQMQDIVLNEVKKVDSEYIATVCGSFRRGAE-SSGDMDVLLT 82
Cdd:cd05397    1 EELLDIIKERLKKLVPGYEIVVYGSLVRGLLkKSSDIDLACV 42
DNA_pol_lambd_f pfam10391
Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto ...
 10-33 1.71e-04

Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone.


Pssm-ID: 463069 [Multi-domain]  Cd Length: 51  Bit Score: 38.20  E-value: 1.71e-04
                          10        20
                  ....*....|....*....|....*
gi 530387845   10 DLRKNE-DKLNHHQRIGLKYFGDFE 33
Cdd:pfam10391  27 DLREKKtAKLTRQQQIGLKYYDDFN 51
 
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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