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Conserved domains on  [gi|21729749|ref|NP_035260|]
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DNA polymerase beta [Mus musculus]

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 ...
15-333 1.24e-148

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: 420.45  E-value: 1.24e-148
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  15 ITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQdDTS 94
Cdd:cd00141   3 IADILEELADLLELLGGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRE-DVP 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  95 SSINFLTRVTGIGPSAARKFVDEGIKTLEDLRKNE-DKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEIKKVDSEY 173
Cdd:cd00141  82 PGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAgAKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVL 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749 174 IATVCGSFRRGAESSGDMDVLLTHPNFTSesskqPKLLHRVVEQLQKVHFITDTLSKGETKFMGVCQLPsekdgKEYPHR 253
Cdd:cd00141 162 QVEIAGSYRRGKETVGDIDILVTHPDATS-----RGLLEKVVDALVELGFVTEVLSKGDTKASGILKLP-----GGWKGR 231
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749 254 RIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPlgvtGVAGEPLPVDSEQDIFDYIQWRYREPKDR 333
Cdd:cd00141 232 RVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFD----GVDGERLPGETEEEIFEALGLPYIEPELR 307
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
15-333 1.24e-148

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: 420.45  E-value: 1.24e-148
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  15 ITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQdDTS 94
Cdd:cd00141   3 IADILEELADLLELLGGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRE-DVP 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  95 SSINFLTRVTGIGPSAARKFVDEGIKTLEDLRKNE-DKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEIKKVDSEY 173
Cdd:cd00141  82 PGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAgAKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVL 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749 174 IATVCGSFRRGAESSGDMDVLLTHPNFTSesskqPKLLHRVVEQLQKVHFITDTLSKGETKFMGVCQLPsekdgKEYPHR 253
Cdd:cd00141 162 QVEIAGSYRRGKETVGDIDILVTHPDATS-----RGLLEKVVDALVELGFVTEVLSKGDTKASGILKLP-----GGWKGR 231
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749 254 RIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPlgvtGVAGEPLPVDSEQDIFDYIQWRYREPKDR 333
Cdd:cd00141 232 RVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFD----GVDGERLPGETEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
10-334 1.57e-135

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


Pssm-ID: 214688  Cd Length: 334  Bit Score: 388.26  E-value: 1.57e-135
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749     10 TLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIR 89
Cdd:smart00483   1 NLNRGIIDALEILAENYEVFGENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEIL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749     90 QDDTSSSINFLTRVTGIGPSAARKFVDEGIKTLEDLRKN-EDKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEIKK 168
Cdd:smart00483  81 NDEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNkELKLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRK 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749    169 VDSEYIATVCGSFRRGAESSGDMDVLLTHPNFT---SESSKQPKLLHRVVEQLQKVHFITDTLSKGETKFMGVCQLPSEK 245
Cdd:smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAkekELEVLDLLLLESTFEELQLPSIRVATLDHGQKKFMILKLSPSRE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749    246 D--------GKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGfTINEYTIRPLGVTGvaGEPLPVDSEQ 317
Cdd:smart00483 241 DkeksgkpdEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKF-KLMLDGHELYDKTK--EKFLKVESEE 317
                          330
                   ....*....|....*..
gi 21729749    318 DIFDYIQWRYREPKDRS 334
Cdd:smart00483 318 DIFDHLGLPYIEPEERN 334
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
149-261 2.73e-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: 168.13  E-value: 2.73e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749   149 RIPREEMLQMQDIVLNEIKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPNFTSEsSKQPKLLHRVVEQLQKVHFITDTL 228
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSE-SELKGLLDRLVARLKKSGFLTDDL 79
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 21729749   229 S--KGETKFMGVCQLPsekdGKEYPHRRIDIRLIP 261
Cdd:pfam14792  80 AvdSGGSKWMGVCRLP----GSERLHRRIDILVVP 110
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
37-323 1.36e-46

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 165.75  E-value: 1.36e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  37 NAYRKAASVIAKYPHKIKSGAEAKKL---PGVGTKIAEKIDEFLATGKLRKLEKIRQDdTSSSINFLTRVTGIGPSAARK 113
Cdd:COG1796  28 RAYRRAARAIENLPEDIEELVAEGDLteiPGIGKAIAAKIEELLETGRLEELEELREE-VPPGLLELLRIPGLGPKKVKK 106
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749 114 FVDE-GIKTLEDLRK--NEDKLNH--------HQRI--GLKYFEDFEKRIPREEMLQMQDIVLNEIKKVDSEYIATVCGS 180
Cdd:COG1796 107 LYEElGITSLEELEAaaEEGRIRElpgfgektEENIlkGIELLRKRGGRFLLGEALPLAEEILAYLRALPGVERVEVAGS 186
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749 181 FRRGAESSGDMDVLLThpnftsesSKQPKllhRVVEQLQKVHFITDTLSKGETKfMGVcQLpseKDGkeyphRRIDIRLI 260
Cdd:COG1796 187 LRRRKETVGDIDILVA--------SDDPE---AVMDAFVKLPEVKEVLAKGDTK-ASV-RL---KSG-----LQVDLRVV 245
                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21729749 261 PKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYtirplGVTGVAGEPLPVDSEQDIF-----DYI 323
Cdd:COG1796 246 PPESFGAALQYFTGSKEHNVALRQLAKERGLKLNEY-----GLFDVGGERIAGETEEEVYaalglPYI 308
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
35-335 9.11e-19

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 86.93  E-value: 9.11e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749   35 KYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLtRVTGIGPSAARKF 114
Cdd:PRK08609  26 KISAFRKAAQALELDERSLSEIDDFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPEGLLPLL-KLPGLGGKKIAKL 104
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  115 VDE-GIKTLEDL----------------RKNEDKLnhhqrigLKYFEDFEK---RIPREEMLQMQDIVLNEIKKVDSEYI 174
Cdd:PRK08609 105 YKElGVVDKESLkeacengkvqalagfgKKTEEKI-------LEAVKELGKrpeRLPIAQVLPIAQEIEEYLATIDEIIR 177
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  175 ATVCGSFRRGAESSGDMDVLL--THPnftsesskqpkllHRVVEQLQKVHFITDTLSKGETKFMGVCQLpsekdgkEYPh 252
Cdd:PRK08609 178 FSRAGSLRRARETVKDLDFIIatDEP-------------EAVREQLLQLPNIVEVIAAGDTKVSVELEY-------EYT- 236
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  253 RRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYtirplGVTGV-AGEPLPVDSEQDIFDYIQWRYREP- 330
Cdd:PRK08609 237 ISVDFRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEY-----GVEQAdTGEVKTFESEEAFFAHFGLPFIPPe 311

                 ....*..
gi 21729749  331 --KDRSE 335
Cdd:PRK08609 312 vrEDGSE 318
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
15-333 1.24e-148

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: 420.45  E-value: 1.24e-148
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  15 ITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQdDTS 94
Cdd:cd00141   3 IADILEELADLLELLGGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRE-DVP 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  95 SSINFLTRVTGIGPSAARKFVDEGIKTLEDLRKNE-DKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEIKKVDSEY 173
Cdd:cd00141  82 PGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAgAKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVL 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749 174 IATVCGSFRRGAESSGDMDVLLTHPNFTSesskqPKLLHRVVEQLQKVHFITDTLSKGETKFMGVCQLPsekdgKEYPHR 253
Cdd:cd00141 162 QVEIAGSYRRGKETVGDIDILVTHPDATS-----RGLLEKVVDALVELGFVTEVLSKGDTKASGILKLP-----GGWKGR 231
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749 254 RIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPlgvtGVAGEPLPVDSEQDIFDYIQWRYREPKDR 333
Cdd:cd00141 232 RVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFD----GVDGERLPGETEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
10-334 1.57e-135

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


Pssm-ID: 214688  Cd Length: 334  Bit Score: 388.26  E-value: 1.57e-135
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749     10 TLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIR 89
Cdd:smart00483   1 NLNRGIIDALEILAENYEVFGENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEIL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749     90 QDDTSSSINFLTRVTGIGPSAARKFVDEGIKTLEDLRKN-EDKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEIKK 168
Cdd:smart00483  81 NDEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNkELKLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRK 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749    169 VDSEYIATVCGSFRRGAESSGDMDVLLTHPNFT---SESSKQPKLLHRVVEQLQKVHFITDTLSKGETKFMGVCQLPSEK 245
Cdd:smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAkekELEVLDLLLLESTFEELQLPSIRVATLDHGQKKFMILKLSPSRE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749    246 D--------GKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGfTINEYTIRPLGVTGvaGEPLPVDSEQ 317
Cdd:smart00483 241 DkeksgkpdEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKF-KLMLDGHELYDKTK--EKFLKVESEE 317
                          330
                   ....*....|....*..
gi 21729749    318 DIFDYIQWRYREPKDRS 334
Cdd:smart00483 318 DIFDHLGLPYIEPEERN 334
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
149-261 2.73e-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: 168.13  E-value: 2.73e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749   149 RIPREEMLQMQDIVLNEIKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPNFTSEsSKQPKLLHRVVEQLQKVHFITDTL 228
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSE-SELKGLLDRLVARLKKSGFLTDDL 79
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 21729749   229 S--KGETKFMGVCQLPsekdGKEYPHRRIDIRLIP 261
Cdd:pfam14792  80 AvdSGGSKWMGVCRLP----GSERLHRRIDILVVP 110
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
37-323 1.36e-46

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 165.75  E-value: 1.36e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  37 NAYRKAASVIAKYPHKIKSGAEAKKL---PGVGTKIAEKIDEFLATGKLRKLEKIRQDdTSSSINFLTRVTGIGPSAARK 113
Cdd:COG1796  28 RAYRRAARAIENLPEDIEELVAEGDLteiPGIGKAIAAKIEELLETGRLEELEELREE-VPPGLLELLRIPGLGPKKVKK 106
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749 114 FVDE-GIKTLEDLRK--NEDKLNH--------HQRI--GLKYFEDFEKRIPREEMLQMQDIVLNEIKKVDSEYIATVCGS 180
Cdd:COG1796 107 LYEElGITSLEELEAaaEEGRIRElpgfgektEENIlkGIELLRKRGGRFLLGEALPLAEEILAYLRALPGVERVEVAGS 186
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749 181 FRRGAESSGDMDVLLThpnftsesSKQPKllhRVVEQLQKVHFITDTLSKGETKfMGVcQLpseKDGkeyphRRIDIRLI 260
Cdd:COG1796 187 LRRRKETVGDIDILVA--------SDDPE---AVMDAFVKLPEVKEVLAKGDTK-ASV-RL---KSG-----LQVDLRVV 245
                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21729749 261 PKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYtirplGVTGVAGEPLPVDSEQDIF-----DYI 323
Cdd:COG1796 246 PPESFGAALQYFTGSKEHNVALRQLAKERGLKLNEY-----GLFDVGGERIAGETEEEVYaalglPYI 308
DNA_pol_B_thumb pfam14791
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
269-333 9.20e-21

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: 84.34  E-value: 9.20e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21729749   269 VLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLgvtgVAGEPLPVDSEQDIFDYIQWRYREPKDR 333
Cdd:pfam14791   2 LLYFTGSKEFNRDLRLLAKKKGLKLNEYGLFDL----KDGELLEGETEEDIFEALGLPYIPPELR 62
HHH_8 pfam14716
Helix-hairpin-helix domain;
15-78 1.03e-20

Helix-hairpin-helix domain;


Pssm-ID: 434152 [Multi-domain]  Cd Length: 67  Bit Score: 84.09  E-value: 1.03e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21729749    15 ITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLA 78
Cdd:pfam14716   4 IADALEELADLLELKGEDPFRVRAYRRAARALEALPEEITSLEELTKLPGIGKKIAAKIEEILE 67
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
35-335 9.11e-19

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 86.93  E-value: 9.11e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749   35 KYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLtRVTGIGPSAARKF 114
Cdd:PRK08609  26 KISAFRKAAQALELDERSLSEIDDFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPEGLLPLL-KLPGLGGKKIAKL 104
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  115 VDE-GIKTLEDL----------------RKNEDKLnhhqrigLKYFEDFEK---RIPREEMLQMQDIVLNEIKKVDSEYI 174
Cdd:PRK08609 105 YKElGVVDKESLkeacengkvqalagfgKKTEEKI-------LEAVKELGKrpeRLPIAQVLPIAQEIEEYLATIDEIIR 177
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  175 ATVCGSFRRGAESSGDMDVLL--THPnftsesskqpkllHRVVEQLQKVHFITDTLSKGETKFMGVCQLpsekdgkEYPh 252
Cdd:PRK08609 178 FSRAGSLRRARETVKDLDFIIatDEP-------------EAVREQLLQLPNIVEVIAAGDTKVSVELEY-------EYT- 236
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21729749  253 RRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYtirplGVTGV-AGEPLPVDSEQDIFDYIQWRYREP- 330
Cdd:PRK08609 237 ISVDFRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEY-----GVEQAdTGEVKTFESEEAFFAHFGLPFIPPe 311

                 ....*..
gi 21729749  331 --KDRSE 335
Cdd:PRK08609 312 vrEDGSE 318
DNA_pol_lambd_f pfam10391
Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto ...
98-147 3.39e-18

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: 77.11  E-value: 3.39e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 21729749    98 NFLTRVTGIGPSAARKFVDEGIKTLEDLRKNE-DKLNHHQRIGLKYFEDFE 147
Cdd:pfam10391   1 KLFTGIYGVGPTTARKWYAQGYRTLDDLREKKtAKLTRQQQIGLKYYDDFN 51
NT_Pol-beta-like cd05397
Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This ...
156-196 1.56e-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: 44.62  E-value: 1.56e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 21729749 156 LQMQDIVLNEIKKVDSEYIATVCGSFRRGAE-SSGDMDVLLT 196
Cdd:cd05397   1 EELLDIIKERLKKLVPGYEIVVYGSLVRGLLkKSSDIDLACV 42
HHH_5 pfam14520
Helix-hairpin-helix domain;
100-141 1.31e-03

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 36.31  E-value: 1.31e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 21729749   100 LTRVTGIGPSAARKFVDEGIKTLEDL-RKNEDKLNHHQRIGLK 141
Cdd:pfam14520   4 LLSISGIGPKTALALLSAGIGTVEDLaEADVDELAEIPGIGEK 46
 
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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