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Conserved domains on  [gi|564384284|ref|XP_006251275|]
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DNA-directed DNA/RNA polymerase mu isoform X3 [Rattus norvegicus]

Protein Classification

type-X family DNA polymerase( domain architecture ID 10207094)

type-X family DNA polymerase 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 ...
 156-497 2.32e-108

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: 324.53  E-value: 2.32e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 156 LSEALETLAEAAGFEGKE-GRFLTFYRAASMLKSLPYPVTSLSQLHGLPYFGEHSFRVIQELLEHGTCEEVEQIRCsERH 234
Cdd:cd00141    3 IADILEELADLLELLGGNpFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRE-DVP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 235 QTMKLFTHIFGVGVKTASRWYQEGLRTLDELREQPQ-RLTQQQKAvlptGLQYYQDLSTPVSRAEAEALQQLVEAAMREI 313
Cdd:cd00141   82 PGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGaKLEQNILI----GLEYYEDFQQRIPREEALAIAEIIKEALREV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 314 LPGATVTLTGGFRRGKLQGHDVDFLITHPeEGQEVGLLPRVMRCLQSQGLVLYhqyhrshladsahilrqrSTMDAFERS 393
Cdd:cd00141  158 DPVLQVEIAGSYRRGKETVGDIDILVTHP-DATSRGLLEKVVDALVELGFVTE------------------VLSKGDTKA 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 394 FCILRLPQsqqaalegplhpcpTWKAVRVDLVVTPNSQFPFALLGWTGSQFFERELRRFSrQEKGLCLNSHGLFDPERKT 473
Cdd:cd00141  219 SGILKLPG--------------GWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLA-KEKGLKLNEYGLFDGVDGE 283

                        330       340
                 ....*....|....*....|....
gi 564384284 474 FFHATSEEDVFRFLGLKYLPPEQR 497
Cdd:cd00141  284 RLPGETEEEIFEALGLPYIEPELR 307
BRCT super family cl00038
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 27-123 6.64e-46

C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The BRCT (BRCA1 C-terminus) domain is found within many DNA damage repair and cell cycle checkpoint proteins. BRCT domains interact with each other forming homo/hetero BRCT multimers, but are also involved in BRCT-non-BRCT interactions and interactions within DNA strand breaks. BRCT tandem repeats bind to phosphopeptides; it has been shown that the repeats in human BRCA1 bind specifically to pS-X-X-F motifs, mediating the interaction between BRCA1 and the DNA helicase BACH1, or BRCA1 and CtIP, a transcriptional corepressor. It is assumed that BRCT repeats play similar roles in many signaling pathways associated with the response to DNA damage.


The actual alignment was detected with superfamily member cd18442:

Pssm-ID: 469589  Cd Length: 98  Bit Score: 155.39  E-value: 6.64e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284  27 RFPGVAIYLAEPRMGRSRRAFLTRLARSKGFRILDVYSSEVTHVVMEETSAKEAICWQ-KDMNALLPDCPQPALLDISWF 105
Cdd:cd18442    1 RFPGVCIFLVERRMGASRRAFLTGLARSKGFRVLDAYSSEVTHVVSEQNSAEEVVSWLeRQMAAAPPACTPPALLDISWF 80

                         90
                 ....*....|....*...
gi 564384284 106 TESMAAGQPVPEEVRHRL 123
Cdd:cd18442   81 TESMGAGQPVPVECRHRL 98
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 156-497 2.32e-108

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: 324.53  E-value: 2.32e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 156 LSEALETLAEAAGFEGKE-GRFLTFYRAASMLKSLPYPVTSLSQLHGLPYFGEHSFRVIQELLEHGTCEEVEQIRCsERH 234
Cdd:cd00141    3 IADILEELADLLELLGGNpFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRE-DVP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 235 QTMKLFTHIFGVGVKTASRWYQEGLRTLDELREQPQ-RLTQQQKAvlptGLQYYQDLSTPVSRAEAEALQQLVEAAMREI 313
Cdd:cd00141   82 PGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGaKLEQNILI----GLEYYEDFQQRIPREEALAIAEIIKEALREV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 314 LPGATVTLTGGFRRGKLQGHDVDFLITHPeEGQEVGLLPRVMRCLQSQGLVLYhqyhrshladsahilrqrSTMDAFERS 393
Cdd:cd00141  158 DPVLQVEIAGSYRRGKETVGDIDILVTHP-DATSRGLLEKVVDALVELGFVTE------------------VLSKGDTKA 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 394 FCILRLPQsqqaalegplhpcpTWKAVRVDLVVTPNSQFPFALLGWTGSQFFERELRRFSrQEKGLCLNSHGLFDPERKT 473
Cdd:cd00141  219 SGILKLPG--------------GWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLA-KEKGLKLNEYGLFDGVDGE 283

                        330       340
                 ....*....|....*....|....
gi 564384284 474 FFHATSEEDVFRFLGLKYLPPEQR 497
Cdd:cd00141  284 RLPGETEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 152-498 4.40e-108

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


Pssm-ID: 214688  Cd Length: 334  Bit Score: 324.71  E-value: 4.40e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284   152 HNTLLSEALETLAEAAGFEG-KEGRFLTFYRAASMLKSLPYPVTSLSQLHGLPYFGEHSFRVIQELLEHGTCEEVEQIRC 230
Cdd:smart00483   2 LNRGIIDALEILAENYEVFGeNKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILN 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284   231 SERHQTMKLFTHIFGVGVKTASRWYQEGLRTLDELREQPQ-RLTQQQKAvlptGLQYYQDLSTPVSRAEAEALQQLVEAA 309
Cdd:smart00483  82 DEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKElKLTKQQKA----GLKYYEDILKKVSRAEAFAVEYIVKRA 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284   310 MREILPGATVTLTGGFRRGKLQGHDVDFLITHPeeGQEVGLLPRVMrCLQSQGLVLYHQYHRShladsahilRQRSTMDA 389
Cdd:smart00483 158 VRKILPDAIVTLTGSFRRGKETGHDVDFLITSP--HPAKEKELEVL-DLLLLESTFEELQLPS---------IRVATLDH 225

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284   390 FERSFCILRLPQSQQAALEGPLHPCPTWKAVRVDLVVTPNSQFPFALLGWTGSQFFERELRRFSRQEKGLCLNSHGLFDP 469
Cdd:smart00483 226 GQKKFMILKLSPSREDKEKSGKPDEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKFKLMLDGHELYDK 305

                          330       340
                   ....*....|....*....|....*....
gi 564384284   470 ERKTFFHATSEEDVFRFLGLKYLPPEQRN 498
Cdd:smart00483 306 TKEKFLKVESEEDIFDHLGLPYIEPEERN 334
BRCT_polymerase_mu cd18442
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins; ...
 27-123 6.64e-46

BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins; Polymerase Mu (EC 2.7.7.7), also termed Pol mu, or terminal transferase, is a Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). It participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. Polymerase Mu contains a BRCT domain.


Pssm-ID: 349395  Cd Length: 98  Bit Score: 155.39  E-value: 6.64e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284  27 RFPGVAIYLAEPRMGRSRRAFLTRLARSKGFRILDVYSSEVTHVVMEETSAKEAICWQ-KDMNALLPDCPQPALLDISWF 105
Cdd:cd18442    1 RFPGVCIFLVERRMGASRRAFLTGLARSKGFRVLDAYSSEVTHVVSEQNSAEEVVSWLeRQMAAAPPACTPPALLDISWF 80

                         90
                 ....*....|....*...
gi 564384284 106 TESMAAGQPVPEEVRHRL 123
Cdd:cd18442   81 TESMGAGQPVPVECRHRL 98
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
152-497 2.01e-27

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 115.67  E-value: 2.01e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 152 HNTLLSEALETLAEAAGFEGkEGRF--LTFYRAASMLKSLPYPVTSLSQ---LHGLPYFGEHSFRVIQELLEHGTCEEVE 226
Cdd:COG1796    2 DNKEIARILEEIADLLELKG-ENPFkiRAYRRAARAIENLPEDIEELVAegdLTEIPGIGKAIAAKIEELLETGRLEELE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 227 QIRcSERHQTMKLFTHIFGVGVKTASRWYQE-GLRTLDELRE--QPQRL---------TQQqkAVLpTGLQYYQDLSTPV 294
Cdd:COG1796   81 ELR-EEVPPGLLELLRIPGLGPKKVKKLYEElGITSLEELEAaaEEGRIrelpgfgekTEE--NIL-KGIELLRKRGGRF 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 295 SRAEAEALQQLVEAAMREIlPG-ATVTLTGGFRRGKLQGHDVDFLIT--HPEEgqevgllprVMRCLQSQGLVlyhqyhr 371
Cdd:COG1796  157 LLGEALPLAEEILAYLRAL-PGvERVEVAGSLRRRKETVGDIDILVAsdDPEA---------VMDAFVKLPEV------- 219

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 372 shladsAHILRQRSTmdafeRSFCILRlpqsqqaalEGplhpcptwkaVRVDLVVTPNSQFPFALLGWTGSQFFERELRR 451
Cdd:COG1796  220 ------KEVLAKGDT-----KASVRLK---------SG----------LQVDLRVVPPESFGAALQYFTGSKEHNVALRQ 269

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 564384284 452 FSrQEKGLCLNSHGLFDP--ERKTFfhaTSEEDVFRFLGLKYLPPEQR 497
Cdd:COG1796  270 LA-KERGLKLNEYGLFDVggERIAG---ETEEEVYAALGLPYIPPELR 313
DNA_pol_B_thumb pfam14791
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
 435-498 2.26e-23

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: 92.82  E-value: 2.26e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564384284  435 ALLGWTGSQFFERELRRFSRQeKGLCLNSHGLFDPERKTFFHATSEEDVFRFLGLKYLPPEQRN 498
Cdd:pfam14791   1 ALLYFTGSKEFNRDLRLLAKK-KGLKLNEYGLFDLKDGELLEGETEEDIFEALGLPYIPPELRE 63
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 156-497 2.32e-108

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: 324.53  E-value: 2.32e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 156 LSEALETLAEAAGFEGKE-GRFLTFYRAASMLKSLPYPVTSLSQLHGLPYFGEHSFRVIQELLEHGTCEEVEQIRCsERH 234
Cdd:cd00141    3 IADILEELADLLELLGGNpFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRE-DVP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 235 QTMKLFTHIFGVGVKTASRWYQEGLRTLDELREQPQ-RLTQQQKAvlptGLQYYQDLSTPVSRAEAEALQQLVEAAMREI 313
Cdd:cd00141   82 PGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGaKLEQNILI----GLEYYEDFQQRIPREEALAIAEIIKEALREV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 314 LPGATVTLTGGFRRGKLQGHDVDFLITHPeEGQEVGLLPRVMRCLQSQGLVLYhqyhrshladsahilrqrSTMDAFERS 393
Cdd:cd00141  158 DPVLQVEIAGSYRRGKETVGDIDILVTHP-DATSRGLLEKVVDALVELGFVTE------------------VLSKGDTKA 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 394 FCILRLPQsqqaalegplhpcpTWKAVRVDLVVTPNSQFPFALLGWTGSQFFERELRRFSrQEKGLCLNSHGLFDPERKT 473
Cdd:cd00141  219 SGILKLPG--------------GWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLA-KEKGLKLNEYGLFDGVDGE 283

                        330       340
                 ....*....|....*....|....
gi 564384284 474 FFHATSEEDVFRFLGLKYLPPEQR 497
Cdd:cd00141  284 RLPGETEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 152-498 4.40e-108

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


Pssm-ID: 214688  Cd Length: 334  Bit Score: 324.71  E-value: 4.40e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284   152 HNTLLSEALETLAEAAGFEG-KEGRFLTFYRAASMLKSLPYPVTSLSQLHGLPYFGEHSFRVIQELLEHGTCEEVEQIRC 230
Cdd:smart00483   2 LNRGIIDALEILAENYEVFGeNKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILN 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284   231 SERHQTMKLFTHIFGVGVKTASRWYQEGLRTLDELREQPQ-RLTQQQKAvlptGLQYYQDLSTPVSRAEAEALQQLVEAA 309
Cdd:smart00483  82 DEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKElKLTKQQKA----GLKYYEDILKKVSRAEAFAVEYIVKRA 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284   310 MREILPGATVTLTGGFRRGKLQGHDVDFLITHPeeGQEVGLLPRVMrCLQSQGLVLYHQYHRShladsahilRQRSTMDA 389
Cdd:smart00483 158 VRKILPDAIVTLTGSFRRGKETGHDVDFLITSP--HPAKEKELEVL-DLLLLESTFEELQLPS---------IRVATLDH 225

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284   390 FERSFCILRLPQSQQAALEGPLHPCPTWKAVRVDLVVTPNSQFPFALLGWTGSQFFERELRRFSRQEKGLCLNSHGLFDP 469
Cdd:smart00483 226 GQKKFMILKLSPSREDKEKSGKPDEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKFKLMLDGHELYDK 305

                          330       340
                   ....*....|....*....|....*....
gi 564384284   470 ERKTFFHATSEEDVFRFLGLKYLPPEQRN 498
Cdd:smart00483 306 TKEKFLKVESEEDIFDHLGLPYIEPEERN 334
BRCT_polymerase_mu cd18442
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins; ...
 27-123 6.64e-46

BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins; Polymerase Mu (EC 2.7.7.7), also termed Pol mu, or terminal transferase, is a Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). It participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. Polymerase Mu contains a BRCT domain.


Pssm-ID: 349395  Cd Length: 98  Bit Score: 155.39  E-value: 6.64e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284  27 RFPGVAIYLAEPRMGRSRRAFLTRLARSKGFRILDVYSSEVTHVVMEETSAKEAICWQ-KDMNALLPDCPQPALLDISWF 105
Cdd:cd18442    1 RFPGVCIFLVERRMGASRRAFLTGLARSKGFRVLDAYSSEVTHVVSEQNSAEEVVSWLeRQMAAAPPACTPPALLDISWF 80

                         90
                 ....*....|....*...
gi 564384284 106 TESMAAGQPVPEEVRHRL 123
Cdd:cd18442   81 TESMGAGQPVPVECRHRL 98
BRCT_polymerase_mu_like cd17713
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu), DNA ...
 27-115 1.47e-41

BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu), DNA nucleotidylexotransferase and similar proteins; The family includes DNA-directed DNA/RNA polymerase mu (polymerase mu) and DNA nucleotidylexotransferase. Polymerase mu (EC 2.7.7.7), also termed Pol mu, or terminal transferase, is a Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). It participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. DNA nucleotidylexotransferase (EC 2.7.7.31), also termed terminal addition enzyme, or terminal deoxynucleotidyltransferase, or terminal transferase, is a template-independent DNA polymerase which catalyzes the random addition of deoxynucleoside 5'-triphosphate to the 3'-end of a DNA initiator. It is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells. All family members contains a BRCT domain.


Pssm-ID: 349345  Cd Length: 87  Bit Score: 143.30  E-value: 1.47e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284  27 RFPGVAIYLAEPRMGRSRRAFLTRLARSKGFRILDVYSSEVTHVVMEETSAKEAICWQKDMNalLPDCPQPALLDISWFT 106
Cdd:cd17713    1 KFPDVVIFLVERKMGSSRRAFLTELARSKGFRVEDELSDSVTHVVAENNSAEEVLEWLERQK--LQGSSSPELLDISWFT 78


                 ....*....
gi 564384284 107 ESMAAGQPV 115
Cdd:cd17713   79 ESMGAGKPV 87
BRCT_DNTT cd18443
BRCT domain of DNA nucleotidylexotransferase (DNTT) and similar proteins; DNTT (EC 2.7.7.31), ...
 27-123 4.99e-31

BRCT domain of DNA nucleotidylexotransferase (DNTT) and similar proteins; DNTT (EC 2.7.7.31), also termed terminal addition enzyme, or terminal deoxynucleotidyltransferase, or terminal transferase, is a template-independent DNA polymerase which catalyzes the random addition of deoxynucleoside 5'-triphosphate to the 3'-end of a DNA initiator. It is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells. DNA nucleotidylexotransferase contains a BRCT domain.


Pssm-ID: 349396  Cd Length: 95  Bit Score: 115.28  E-value: 4.99e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284  27 RFPGVAIYLAEPRMGRSRRAFLTRLARSKGFRILDVYSSEVTHVVMEETSAKEAICWQKDMNalLPDCPQPALLDISWFT 106
Cdd:cd18443    1 KFKDLVIFIVERKMGSTRRTFLMELARKKGFRVEDELSDSVTHIVAENNSGAEVLEWLQGQK--LRDSSRLELLDISWFT 78

                         90
                 ....*....|....*..
gi 564384284 107 ESMAAGQPVPEEVRHRL 123
Cdd:cd18443   79 ECMGAGKPVEIEKRHRL 95
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
152-497 2.01e-27

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 115.67  E-value: 2.01e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 152 HNTLLSEALETLAEAAGFEGkEGRF--LTFYRAASMLKSLPYPVTSLSQ---LHGLPYFGEHSFRVIQELLEHGTCEEVE 226
Cdd:COG1796    2 DNKEIARILEEIADLLELKG-ENPFkiRAYRRAARAIENLPEDIEELVAegdLTEIPGIGKAIAAKIEELLETGRLEELE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 227 QIRcSERHQTMKLFTHIFGVGVKTASRWYQE-GLRTLDELRE--QPQRL---------TQQqkAVLpTGLQYYQDLSTPV 294
Cdd:COG1796   81 ELR-EEVPPGLLELLRIPGLGPKKVKKLYEElGITSLEELEAaaEEGRIrelpgfgekTEE--NIL-KGIELLRKRGGRF 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 295 SRAEAEALQQLVEAAMREIlPG-ATVTLTGGFRRGKLQGHDVDFLIT--HPEEgqevgllprVMRCLQSQGLVlyhqyhr 371
Cdd:COG1796  157 LLGEALPLAEEILAYLRAL-PGvERVEVAGSLRRRKETVGDIDILVAsdDPEA---------VMDAFVKLPEV------- 219

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384284 372 shladsAHILRQRSTmdafeRSFCILRlpqsqqaalEGplhpcptwkaVRVDLVVTPNSQFPFALLGWTGSQFFERELRR 451
Cdd:COG1796  220 ------KEVLAKGDT-----KASVRLK---------SG----------LQVDLRVVPPESFGAALQYFTGSKEHNVALRQ 269

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 564384284 452 FSrQEKGLCLNSHGLFDP--ERKTFfhaTSEEDVFRFLGLKYLPPEQR 497
Cdd:COG1796  270 LA-KERGLKLNEYGLFDVggERIAG---ETEEEVYAALGLPYIPPELR 313
DNA_pol_B_thumb pfam14791
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
 435-498 2.26e-23

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: 92.82  E-value: 2.26e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564384284  435 ALLGWTGSQFFERELRRFSRQeKGLCLNSHGLFDPERKTFFHATSEEDVFRFLGLKYLPPEQRN 498
Cdd:pfam14791   1 ALLYFTGSKEFNRDLRLLAKK-KGLKLNEYGLFDLKDGELLEGETEEDIFEALGLPYIPPELRE 63
DNA_pol_lambd_f pfam10391
Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto ...
 238-291 9.28e-17

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: 74.03  E-value: 9.28e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 564384284  238 KLFTHIFGVGVKTASRWYQEGLRTLDELRE-QPQRLTQQQKAvlptGLQYYQDLS 291
Cdd:pfam10391   1 KLFTGIYGVGPTTARKWYAQGYRTLDDLREkKTAKLTRQQQI----GLKYYDDFN 51
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
 296-364 1.03e-13

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: 67.21  E-value: 1.03e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564384284  296 RAEAEALQQLVEAAMREILPGATVTLTGGFRRGKLQGHDVDFLITHPE---EGQEVGLLPRVMRCLQSQGLV 364
Cdd:pfam14792   4 REEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDgtsESELKGLLDRLVARLKKSGFL 75
HHH_8 pfam14716
Helix-hairpin-helix domain;
153-218 8.75e-12

Helix-hairpin-helix domain;


Pssm-ID: 434152 [Multi-domain]  Cd Length: 67  Bit Score: 60.21  E-value: 8.75e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564384284  153 NTLLSEALETLAEAAGFEGKE-GRFLTFYRAASMLKSLPYPVTSLSQLHGLPYFGEHSFRVIQELLE 218
Cdd:pfam14716   1 NQEIADALEELADLLELKGEDpFRVRAYRRAARALEALPEEITSLEELTKLPGIGKKIAAKIEEILE 67
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 309-351 7.31e-06

Nucleotidyltransferase domain; Members of this family belong to a large family of nucleotidyltransferases. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.


Pssm-ID: 396474  Cd Length: 91  Bit Score: 44.33  E-value: 7.31e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 564384284  309 AMREILPGATVTLTGGFRRGK-LQGHDVDFLITHPEEGQEVGLL 351
Cdd:pfam01909   7 ILKELFPVAEVVLFGSYARGTaLPGSDIDLLVVFPEPVEEERLL 50
BRCT_Bard1_rpt1 cd17734
first BRCT domain of BRCA1-associated RING domain protein 1 (Bard1) and similar proteins; ...
 42-115 3.11e-04

first BRCT domain of BRCA1-associated RING domain protein 1 (Bard1) and similar proteins; Bard1, also termed BARD-1, or RING-type E3 ubiquitin transferase BARD1, is a critical factor in BRCA1-mediated tumor suppression and may also serve as a target for tumorigenic lesions in some human cancers. It associates with BRCA1 (breast cancer-1) to form a heterodimeric BRCA1/BARD1 complex that is responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control. The BRCA1/BARD1 complex catalyzes autoubiquitination of BRCA1 and trans ubiquitination of other protein substrates. Its E3 ligase activity is dramatically reduced in the presence of UBX domain protein 1 (UBXN1). BARD-1 contains an N-terminal C3HC4-type RING-HC finger that binds BRCA1, and a C-terminal region with three ankyrin repeats and tandem BRCT domains that bind CstF-50 (cleavage stimulation factor) to modulate mRNA processing and RNAP II stability in response to DNA damage. The family corresponds to the first BRCT domain.


Pssm-ID: 349366  Cd Length: 80  Bit Score: 39.51  E-value: 3.11e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564384284  42 RSRRAFLTRLARSKGFRILDVYSSEVTHVVMEETSAKEAICWQKDMNALLPDCpqpALLDISWFTESMAAGQPV 115
Cdd:cd17734   10 SEQKKLLEKLAQLLKAKVVTEFSPEVTHVVVPADERGVCPRTMKYLMGILAGK---WIVSFEWVEACLKAKKLV 80
BRCT cd00027
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 43-108 7.84e-04

C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The BRCT (BRCA1 C-terminus) domain is found within many DNA damage repair and cell cycle checkpoint proteins. BRCT domains interact with each other forming homo/hetero BRCT multimers, but are also involved in BRCT-non-BRCT interactions and interactions within DNA strand breaks. BRCT tandem repeats bind to phosphopeptides; it has been shown that the repeats in human BRCA1 bind specifically to pS-X-X-F motifs, mediating the interaction between BRCA1 and the DNA helicase BACH1, or BRCA1 and CtIP, a transcriptional corepressor. It is assumed that BRCT repeats play similar roles in many signaling pathways associated with the response to DNA damage.


Pssm-ID: 349339 [Multi-domain]  Cd Length: 68  Bit Score: 38.11  E-value: 7.84e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564384284  43 SRRAFLTRLARSKGFRILDVYSSEVTHVVMEETSAKEaicwqKDMNALLPDCPqpaLLDISWFTES 108
Cdd:cd00027   11 EEREELKKLIEALGGKVSESLSSKVTHLIAKSPSGEK-----YYLAALAWGIP---IVSPEWLLDC 68
 
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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