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Conserved domains on  [gi|226423875|ref|NP_059097|]
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DNA-directed DNA/RNA polymerase mu [Mus musculus]

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 ...
 156-494 2.64e-115

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: 341.87  E-value: 2.64e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 156 LSEALETLAEAAGFE-ANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCsERY 234
Cdd:cd00141    3 IADILEELADLLELLgGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRE-DVP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 235 QTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQ-RLTQQQKAGLQYYQDLSTPVRRADAEALQQLIEAAVRQTLPGA 313
Cdd:cd00141   82 PGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGaKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 314 TVTLTGGFRRGKLQGHDVDFLITHPeEGQEVGLLPKVMSCLQSQGLVLYhqyhrshladsahnlrqrsSTMDAFERSFCI 393
Cdd:cd00141  162 QVEIAGSYRRGKETVGDIDILVTHP-DATSRGLLEKVVDALVELGFVTE-------------------VLSKGDTKASGI 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 394 LGLPQpqqaalagalppcpTWKAVRVDLVVTPSSQFPFALLGWTGSQFFERELRRFSrQEKGLWLNSHGLFDPEQKRVFH 473
Cdd:cd00141  222 LKLPG--------------GWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLA-KEKGLKLNEYGLFDGVDGERLP 286

                        330       340
                 ....*....|....*....|.
gi 226423875 474 ATSEEDVFRLLGLKYLPPEQR 494
Cdd:cd00141  287 GETEEEIFEALGLPYIEPELR 307
BRCT super family cl00038
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 27-123 3.07e-45

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: 153.46  E-value: 3.07e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875  27 RFPDVAIYLAEPRMGRSRRAFLTRLARSKGFRVLDAYSSKVTHVVMEGTSAKEAICWQ-KNMDALPTGCPQPALLDISWF 105
Cdd:cd18442    1 RFPGVCIFLVERRMGASRRAFLTGLARSKGFRVLDAYSSEVTHVVSEQNSAEEVVSWLeRQMAAAPPACTPPALLDISWF 80

                         90
                 ....*....|....*...
gi 226423875 106 TESMAAGQPVPEEGRHHL 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 ...
 156-494 2.64e-115

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: 341.87  E-value: 2.64e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 156 LSEALETLAEAAGFE-ANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCsERY 234
Cdd:cd00141    3 IADILEELADLLELLgGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRE-DVP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 235 QTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQ-RLTQQQKAGLQYYQDLSTPVRRADAEALQQLIEAAVRQTLPGA 313
Cdd:cd00141   82 PGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGaKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 314 TVTLTGGFRRGKLQGHDVDFLITHPeEGQEVGLLPKVMSCLQSQGLVLYhqyhrshladsahnlrqrsSTMDAFERSFCI 393
Cdd:cd00141  162 QVEIAGSYRRGKETVGDIDILVTHP-DATSRGLLEKVVDALVELGFVTE-------------------VLSKGDTKASGI 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 394 LGLPQpqqaalagalppcpTWKAVRVDLVVTPSSQFPFALLGWTGSQFFERELRRFSrQEKGLWLNSHGLFDPEQKRVFH 473
Cdd:cd00141  222 LKLPG--------------GWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLA-KEKGLKLNEYGLFDGVDGERLP 286

                        330       340
                 ....*....|....*....|.
gi 226423875 474 ATSEEDVFRLLGLKYLPPEQR 494
Cdd:cd00141  287 GETEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 152-495 2.87e-107

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


Pssm-ID: 214688  Cd Length: 334  Bit Score: 322.39  E-value: 2.87e-107
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875   152 HNTLLSEALETLAEA-AGFEANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRC 230
Cdd:smart00483   2 LNRGIIDALEILAENyEVFGENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILN 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875   231 SERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQ-RLTQQQKAGLQYYQDLSTPVRRADAEALQQLIEAAVRQT 309
Cdd:smart00483  82 DEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKElKLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRKI 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875   310 LPGATVTLTGGFRRGKLQGHDVDFLITHPeeGQEVGLLPKVMsCLQSQGLVLYHQYHRShladsahnlrQRSSTMDAFER 389
Cdd:smart00483 162 LPDAIVTLTGSFRRGKETGHDVDFLITSP--HPAKEKELEVL-DLLLLESTFEELQLPS----------IRVATLDHGQK 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875   390 SFCILGLPQPQQAALAGALPPCPTWKAVRVDLVVTPSSQFPFALLGWTGSQFFERELRRFSRQEKGLWLNSHGLFDPEQK 469
Cdd:smart00483 229 KFMILKLSPSREDKEKSGKPDEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKFKLMLDGHELYDKTKE 308

                          330       340
                   ....*....|....*....|....*.
gi 226423875   470 RVFHATSEEDVFRLLGLKYLPPEQRN 495
Cdd:smart00483 309 KFLKVESEEDIFDHLGLPYIEPEERN 334
BRCT_polymerase_mu cd18442
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins; ...
 27-123 3.07e-45

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: 153.46  E-value: 3.07e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875  27 RFPDVAIYLAEPRMGRSRRAFLTRLARSKGFRVLDAYSSKVTHVVMEGTSAKEAICWQ-KNMDALPTGCPQPALLDISWF 105
Cdd:cd18442    1 RFPGVCIFLVERRMGASRRAFLTGLARSKGFRVLDAYSSEVTHVVSEQNSAEEVVSWLeRQMAAAPPACTPPALLDISWF 80

                         90
                 ....*....|....*...
gi 226423875 106 TESMAAGQPVPEEGRHHL 123
Cdd:cd18442   81 TESMGAGQPVPVECRHRL 98
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
152-494 2.89e-28

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 117.99  E-value: 2.89e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 152 HNTLLSEALETLA---EAAGfeANEGRLLSFSRAASVLKSLPCPVASLSQ---LHGLPYFGEHSTRVIQELLEHGTCEEV 225
Cdd:COG1796    2 DNKEIARILEEIAdllELKG--ENPFKIRAYRRAARAIENLPEDIEELVAegdLTEIPGIGKAIAAKIEELLETGRLEEL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 226 KQVRcsERY-QTMKLFTQVFGVGVKTANRWYQE-GLRTLDELRE--QPQRL---------TQQQ-KAGLQYYQDLSTPVR 291
Cdd:COG1796   80 EELR--EEVpPGLLELLRIPGLGPKKVKKLYEElGITSLEELEAaaEEGRIrelpgfgekTEENiLKGIELLRKRGGRFL 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 292 RADAEALQQLIEAAVRQtLPG-ATVTLTGGFRRGKLQGHDVDFLITHpEEGQEVgllpkvmsclqsqglvlyhqyhrshl 370
Cdd:COG1796  158 LGEALPLAEEILAYLRA-LPGvERVEVAGSLRRRKETVGDIDILVAS-DDPEAV-------------------------- 209

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 371 adsahnlrqrsstMDAFersfciLGLPQPQQAALAGalppcPTwKA-------VRVDLVVTPSSQFPFALLGWTGSQFFE 443
Cdd:COG1796  210 -------------MDAF------VKLPEVKEVLAKG-----DT-KAsvrlksgLQVDLRVVPPESFGAALQYFTGSKEHN 264

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 226423875 444 RELRRFSrQEKGLWLNSHGLFDPEQKRVfHATSEEDVFRLLGLKYLPPEQR 494
Cdd:COG1796  265 VALRQLA-KERGLKLNEYGLFDVGGERI-AGETEEEVYAALGLPYIPPELR 313
DNA_pol_B_thumb pfam14791
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
 432-495 7.50e-24

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: 94.36  E-value: 7.50e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 226423875  432 ALLGWTGSQFFERELRRFSRQeKGLWLNSHGLFDPEQKRVFHATSEEDVFRLLGLKYLPPEQRN 495
Cdd:pfam14791   1 ALLYFTGSKEFNRDLRLLAKK-KGLKLNEYGLFDLKDGELLEGETEEDIFEALGLPYIPPELRE 63
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 28-109 2.00e-03

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 36.89  E-value: 2.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875   28 FPDVAIYLAepRMGRSRRAFLTRLARSKGFRVLDAYSSKVTHVVMEGTSAKEAIcWQKNmdalptgcpQPALLDISWFTE 107
Cdd:pfam00533   6 FSGKTFVIT--GLDGLERDELKELIEKLGGKVTDSLSKKTTHVIVEARTKKYLK-AKEL---------GIPIVTEEWLLD 73


                  ..
gi 226423875  108 SM 109
Cdd:pfam00533  74 CI 75
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 156-494 2.64e-115

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: 341.87  E-value: 2.64e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 156 LSEALETLAEAAGFE-ANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCsERY 234
Cdd:cd00141    3 IADILEELADLLELLgGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRE-DVP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 235 QTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQ-RLTQQQKAGLQYYQDLSTPVRRADAEALQQLIEAAVRQTLPGA 313
Cdd:cd00141   82 PGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGaKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 314 TVTLTGGFRRGKLQGHDVDFLITHPeEGQEVGLLPKVMSCLQSQGLVLYhqyhrshladsahnlrqrsSTMDAFERSFCI 393
Cdd:cd00141  162 QVEIAGSYRRGKETVGDIDILVTHP-DATSRGLLEKVVDALVELGFVTE-------------------VLSKGDTKASGI 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 394 LGLPQpqqaalagalppcpTWKAVRVDLVVTPSSQFPFALLGWTGSQFFERELRRFSrQEKGLWLNSHGLFDPEQKRVFH 473
Cdd:cd00141  222 LKLPG--------------GWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLA-KEKGLKLNEYGLFDGVDGERLP 286

                        330       340
                 ....*....|....*....|.
gi 226423875 474 ATSEEDVFRLLGLKYLPPEQR 494
Cdd:cd00141  287 GETEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 152-495 2.87e-107

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


Pssm-ID: 214688  Cd Length: 334  Bit Score: 322.39  E-value: 2.87e-107
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875   152 HNTLLSEALETLAEA-AGFEANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRC 230
Cdd:smart00483   2 LNRGIIDALEILAENyEVFGENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILN 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875   231 SERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQ-RLTQQQKAGLQYYQDLSTPVRRADAEALQQLIEAAVRQT 309
Cdd:smart00483  82 DEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKElKLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRKI 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875   310 LPGATVTLTGGFRRGKLQGHDVDFLITHPeeGQEVGLLPKVMsCLQSQGLVLYHQYHRShladsahnlrQRSSTMDAFER 389
Cdd:smart00483 162 LPDAIVTLTGSFRRGKETGHDVDFLITSP--HPAKEKELEVL-DLLLLESTFEELQLPS----------IRVATLDHGQK 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875   390 SFCILGLPQPQQAALAGALPPCPTWKAVRVDLVVTPSSQFPFALLGWTGSQFFERELRRFSRQEKGLWLNSHGLFDPEQK 469
Cdd:smart00483 229 KFMILKLSPSREDKEKSGKPDEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKFKLMLDGHELYDKTKE 308

                          330       340
                   ....*....|....*....|....*.
gi 226423875   470 RVFHATSEEDVFRLLGLKYLPPEQRN 495
Cdd:smart00483 309 KFLKVESEEDIFDHLGLPYIEPEERN 334
BRCT_polymerase_mu cd18442
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins; ...
 27-123 3.07e-45

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: 153.46  E-value: 3.07e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875  27 RFPDVAIYLAEPRMGRSRRAFLTRLARSKGFRVLDAYSSKVTHVVMEGTSAKEAICWQ-KNMDALPTGCPQPALLDISWF 105
Cdd:cd18442    1 RFPGVCIFLVERRMGASRRAFLTGLARSKGFRVLDAYSSEVTHVVSEQNSAEEVVSWLeRQMAAAPPACTPPALLDISWF 80

                         90
                 ....*....|....*...
gi 226423875 106 TESMAAGQPVPEEGRHHL 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 3.95e-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: 142.15  E-value: 3.95e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875  27 RFPDVAIYLAEPRMGRSRRAFLTRLARSKGFRVLDAYSSKVTHVVMEGTSAKEAICWQKNMDAlpTGCPQPALLDISWFT 106
Cdd:cd17713    1 KFPDVVIFLVERKMGSSRRAFLTELARSKGFRVEDELSDSVTHVVAENNSAEEVLEWLERQKL--QGSSSPELLDISWFT 78


                 ....*....
gi 226423875 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 1.95e-30

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: 113.74  E-value: 1.95e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875  27 RFPDVAIYLAEPRMGRSRRAFLTRLARSKGFRVLDAYSSKVTHVVMEGTSAKEAICW---QKNMDAlptgcPQPALLDIS 103
Cdd:cd18443    1 KFKDLVIFIVERKMGSTRRTFLMELARKKGFRVEDELSDSVTHIVAENNSGAEVLEWlqgQKLRDS-----SRLELLDIS 75

                         90       100
                 ....*....|....*....|
gi 226423875 104 WFTESMAAGQPVPEEGRHHL 123
Cdd:cd18443   76 WFTECMGAGKPVEIEKRHRL 95
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
152-494 2.89e-28

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 117.99  E-value: 2.89e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 152 HNTLLSEALETLA---EAAGfeANEGRLLSFSRAASVLKSLPCPVASLSQ---LHGLPYFGEHSTRVIQELLEHGTCEEV 225
Cdd:COG1796    2 DNKEIARILEEIAdllELKG--ENPFKIRAYRRAARAIENLPEDIEELVAegdLTEIPGIGKAIAAKIEELLETGRLEEL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 226 KQVRcsERY-QTMKLFTQVFGVGVKTANRWYQE-GLRTLDELRE--QPQRL---------TQQQ-KAGLQYYQDLSTPVR 291
Cdd:COG1796   80 EELR--EEVpPGLLELLRIPGLGPKKVKKLYEElGITSLEELEAaaEEGRIrelpgfgekTEENiLKGIELLRKRGGRFL 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 292 RADAEALQQLIEAAVRQtLPG-ATVTLTGGFRRGKLQGHDVDFLITHpEEGQEVgllpkvmsclqsqglvlyhqyhrshl 370
Cdd:COG1796  158 LGEALPLAEEILAYLRA-LPGvERVEVAGSLRRRKETVGDIDILVAS-DDPEAV-------------------------- 209

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875 371 adsahnlrqrsstMDAFersfciLGLPQPQQAALAGalppcPTwKA-------VRVDLVVTPSSQFPFALLGWTGSQFFE 443
Cdd:COG1796  210 -------------MDAF------VKLPEVKEVLAKG-----DT-KAsvrlksgLQVDLRVVPPESFGAALQYFTGSKEHN 264

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 226423875 444 RELRRFSrQEKGLWLNSHGLFDPEQKRVfHATSEEDVFRLLGLKYLPPEQR 494
Cdd:COG1796  265 VALRQLA-KERGLKLNEYGLFDVGGERI-AGETEEEVYAALGLPYIPPELR 313
DNA_pol_B_thumb pfam14791
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
 432-495 7.50e-24

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: 94.36  E-value: 7.50e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 226423875  432 ALLGWTGSQFFERELRRFSRQeKGLWLNSHGLFDPEQKRVFHATSEEDVFRLLGLKYLPPEQRN 495
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 ...
 238-287 3.91e-19

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: 80.58  E-value: 3.91e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 226423875  238 KLFTQVFGVGVKTANRWYQEGLRTLDELRE-QPQRLTQQQKAGLQYYQDLS 287
Cdd:pfam10391   1 KLFTGIYGVGPTTARKWYAQGYRTLDDLREkKTAKLTRQQQIGLKYYDDFN 51
HHH_8 pfam14716
Helix-hairpin-helix domain;
153-218 5.60e-12

Helix-hairpin-helix domain;


Pssm-ID: 434152 [Multi-domain]  Cd Length: 67  Bit Score: 60.98  E-value: 5.60e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 226423875  153 NTLLSEALETLAEAAGFE-ANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLE 218
Cdd:pfam14716   1 NQEIADALEELADLLELKgEDPFRVRAYRRAARALEALPEEITSLEELTKLPGIGKKIAAKIEEILE 67
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
 292-360 1.04e-11

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: 61.43  E-value: 1.04e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 226423875  292 RADAEALQQLIEAAVRQTLPGATVTLTGGFRRGKLQGHDVDFLITHPE---EGQEVGLLPKVMSCLQSQGLV 360
Cdd:pfam14792   4 REEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDgtsESELKGLLDRLVARLKKSGFL 75
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 302-347 2.71e-05

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: 42.79  E-value: 2.71e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 226423875  302 IEAAVRQTLPGATVTLTGGFRRGK-LQGHDVDFLITHPEEGQEVGLL 347
Cdd:pfam01909   4 LREILKELFPVAEVVLFGSYARGTaLPGSDIDLLVVFPEPVEEERLL 50
BRCT cd00027
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 43-108 3.78e-05

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: 41.58  E-value: 3.78e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 226423875  43 SRRAFLTRLARSKGFRVLDAYSSKVTHVVMEGTSAKEaicwqKNMDALPTGCPqpaLLDISWFTES 108
Cdd:cd00027   11 EEREELKKLIEALGGKVSESLSSKVTHLIAKSPSGEK-----YYLAALAWGIP---IVSPEWLLDC 68
BRCT_Bard1_rpt1 cd17734
first BRCT domain of BRCA1-associated RING domain protein 1 (Bard1) and similar proteins; ...
 42-115 3.87e-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: 39.12  E-value: 3.87e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 226423875  42 RSRRAFLTRLARSKGFRVLDAYSSKVTHVVMEGTSAKEAICWQKNMDALPTGCpqpALLDISWFTESMAAGQPV 115
Cdd:cd17734   10 SEQKKLLEKLAQLLKAKVVTEFSPEVTHVVVPADERGVCPRTMKYLMGILAGK---WIVSFEWVEACLKAKKLV 80
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 28-109 2.00e-03

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 36.89  E-value: 2.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226423875   28 FPDVAIYLAepRMGRSRRAFLTRLARSKGFRVLDAYSSKVTHVVMEGTSAKEAIcWQKNmdalptgcpQPALLDISWFTE 107
Cdd:pfam00533   6 FSGKTFVIT--GLDGLERDELKELIEKLGGKVTDSLSKKTTHVIVEARTKKYLK-AKEL---------GIPIVTEEWLLD 73


                  ..
gi 226423875  108 SM 109
Cdd:pfam00533  74 CI 75
BRCT_PAXIP1_rpt3 cd17711
third BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins; PAXIP1, also ...
 37-73 7.55e-03

third BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins; PAXIP1, also termed PAX transactivation activation domain-interacting protein (PTIP), is involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. It also facilitates ATM-mediated activation of p53 and promotes cellular resistance to ionizing radiation. PAXIP1 contains six BRCT repeats. This family corresponds to the third BRCT domain.


Pssm-ID: 349343  Cd Length: 81  Bit Score: 35.70  E-value: 7.55e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 226423875  37 EPRMGRSRRAFLTRLARSKGFRVLDAYSSKVTHVVME 73
Cdd:cd17711   10 PEQMGDQEIATWKKVIEEHGGEVVDEYSPRVTHVICE 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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