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Conserved domains on  [gi|1370456880|ref|XP_024303710|]
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DNA polymerase lambda isoform X9 [Homo sapiens]

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 ...
167-492 3.82e-145

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: 418.14  E-value: 3.82e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 167 HITEKLEVLAKAYSVQG-DKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVP 245
Cdd:cd00141     2 EIADILEELADLLELLGgNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVP 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 246 -VLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQAS--LTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGL 322
Cdd:cd00141    82 pGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGakLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVL 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 323 LCVACGSYRRGKATCGDVDVLITHPDGRShRGIFSRLLDSLrqeavpsVGPGFLTDDLvsqeeNGQQQKYLGVCRLPGpG 402
Cdd:cd00141   162 QVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDAL-------VELGFVTEVL-----SKGDTKASGILKLPG-G 227
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 403 RRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALStavvrnthgcKVGPGRVLPTPTEKDVFRLL 482
Cdd:cd00141   228 WKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLF----------DGVDGERLPGETEEEIFEAL 297
                         330
                  ....*....|
gi 1370456880 483 GLPYREPAER 492
Cdd:cd00141   298 GLPYIEPELR 307
BRCT super family cl00038
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
18-37 4.44e-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.


The actual alignment was detected with superfamily member cd17715:

Pssm-ID: 469589  Cd Length: 80  Bit Score: 39.01  E-value: 4.44e-04
                          10        20
                  ....*....|....*....|
gi 1370456880  18 GAQLVKSAWLSLCLQERRLV 37
Cdd:cd17715    61 GAQLVKSGWLSACIQEKRLV 80
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
167-492 3.82e-145

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: 418.14  E-value: 3.82e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 167 HITEKLEVLAKAYSVQG-DKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVP 245
Cdd:cd00141     2 EIADILEELADLLELLGgNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVP 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 246 -VLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQAS--LTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGL 322
Cdd:cd00141    82 pGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGakLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVL 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 323 LCVACGSYRRGKATCGDVDVLITHPDGRShRGIFSRLLDSLrqeavpsVGPGFLTDDLvsqeeNGQQQKYLGVCRLPGpG 402
Cdd:cd00141   162 QVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDAL-------VELGFVTEVL-----SKGDTKASGILKLPG-G 227
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 403 RRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALStavvrnthgcKVGPGRVLPTPTEKDVFRLL 482
Cdd:cd00141   228 WKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLF----------DGVDGERLPGETEEEIFEAL 297
                         330
                  ....*....|
gi 1370456880 483 GLPYREPAER 492
Cdd:cd00141   298 GLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
163-493 1.47e-87

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


Pssm-ID: 214688  Cd Length: 334  Bit Score: 271.93  E-value: 1.47e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880  163 NHNLHITEKLEVLAKAYSVQGDKWRA-LGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHIS 241
Cdd:smart00483   1 NLNRGIIDALEILAENYEVFGENKRKcSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEIL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880  242 --ESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQA--SLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQA 317
Cdd:smart00483  81 ndEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKelKLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRK 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880  318 FNSGLLCVACGSYRRGKATCGDVDVLITHP---DGRSHRGIFSRLLDSLRQE-AVPSvgpgFLTDDLVsqeenGQQQKYL 393
Cdd:smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPhpaKEKELEVLDLLLLESTFEElQLPS----IRVATLD-----HGQKKFM 231
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880  394 GVCRLP------------GPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKG-MSLSEHAlstavvRNTH 460
Cdd:smart00483 232 ILKLSPsredkeksgkpdEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKFkLMLDGHE------LYDK 305
                          330       340       350
                   ....*....|....*....|....*....|...
gi 1370456880  461 GCKVgpgrVLPTPTEKDVFRLLGLPYREPAERD 493
Cdd:smart00483 306 TKEK----FLKVESEEDIFDHLGLPYIEPEERN 334
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
298-414 1.01e-47

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: 160.42  E-value: 1.01e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 298 RMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHR---GIFSRLLDSLRQEavpsvgpG 374
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSESelkGLLDRLVARLKKS-------G 73
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1370456880 375 FLTDDLVSQEengQQQKYLGVCRLPGPGRRHRRLDIIVVP 414
Cdd:pfam14792  74 FLTDDLAVDS---GGSKWMGVCRLPGSERLHRRIDILVVP 110
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
164-489 4.23e-43

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 160.74  E-value: 4.23e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 164 HNLHITEKLEVLAKAYSVQG-DKWRALGYAKAINALKSFHKPVTSYQEAC---SIPGIGKRMAEKIIEILESGHLRKLDH 239
Cdd:COG1796     2 DNKEIARILEEIADLLELKGeNPFKIRAYRRAARAIENLPEDIEELVAEGdltEIPGIGKAIAAKIEELLETGRLEELEE 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 240 ISESVP--VLELFSnIWGAGTKTAQMWYQQ-GFRSLEDIRSQA------SL-----TTQQAI--GLKHYSDFLERMP--- 300
Cdd:COG1796    82 LREEVPpgLLELLR-IPGLGPKKVKKLYEElGITSLEELEAAAeegrirELpgfgeKTEENIlkGIELLRKRGGRFLlge 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 301 -REEATEIEQTVQKAAQAFNsgllCVACGSYRRGKATCGDVDVLITHPDGRShrgIFSRLLDSLRQEAVPSVGPGFLTdd 379
Cdd:COG1796   161 aLPLAEEILAYLRALPGVER----VEVAGSLRRRKETVGDIDILVASDDPEA---VMDAFVKLPEVKEVLAKGDTKAS-- 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 380 lvsqeengqqqkylgvCRLpgpgRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALStavvrnt 459
Cdd:COG1796   232 ----------------VRL----KSGLQVDLRVVPPESFGAALQYFTGSKEHNVALRQLAKERGLKLNEYGLF------- 284
                         330       340       350
                  ....*....|....*....|....*....|
gi 1370456880 460 hgcKVGpGRVLPTPTEKDVFRLLGLPYREP 489
Cdd:COG1796   285 ---DVG-GERIAGETEEEVYAALGLPYIPP 310
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
191-492 2.17e-12

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 69.21  E-value: 2.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 191 YAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVP--VLELFsNIWGAGTKTAQMWYQQ- 267
Cdd:PRK08609   30 FRKAAQALELDERSLSEIDDFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPegLLPLL-KLPGLGGKKIAKLYKEl 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 268 GFRSLEDIRsQASLT------------TQQAI--GLKHYSDFLERMP----REEATEIEQT------VQKAAQAfnsgll 323
Cdd:PRK08609  109 GVVDKESLK-EACENgkvqalagfgkkTEEKIleAVKELGKRPERLPiaqvLPIAQEIEEYlatideIIRFSRA------ 181
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 324 cvacGSYRRGKATCGDVDVLI--THPDG-RSHrgifsrLLDSLRQEAVPSVGpgfltDDLVSQEEngQQQKYLGVcrlpg 400
Cdd:PRK08609  182 ----GSLRRARETVKDLDFIIatDEPEAvREQ------LLQLPNIVEVIAAG-----DTKVSVEL--EYEYTISV----- 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 401 pgrrhrrlDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAvvrnthgckvGPGRVLPTPTEKDVFR 480
Cdd:PRK08609  240 --------DFRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEYGVEQA----------DTGEVKTFESEEAFFA 301
                         330
                  ....*....|..
gi 1370456880 481 LLGLPYREPAER 492
Cdd:PRK08609  302 HFGLPFIPPEVR 313
BRCT_polymerase_lambda cd17715
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed ...
18-37 4.44e-04

BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed Pol Lambda, or DNA polymerase beta-2 (Pol beta2), or DNA polymerase kappa, is involved in base excision repair (BER) and is responsible for repair of lesions that give rise to abasic (AP) sites in DNA. It also contributes to DNA double-strand break repair by non-homologous end joining and homologous recombination. DNA polymerase lambda has both template-dependent and template-independent (terminal transferase) DNA polymerase activities, as well as a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity. DNA polymerase lambda contains one BRCT domain.


Pssm-ID: 349347  Cd Length: 80  Bit Score: 39.01  E-value: 4.44e-04
                          10        20
                  ....*....|....*....|
gi 1370456880  18 GAQLVKSAWLSLCLQERRLV 37
Cdd:cd17715    61 GAQLVKSGWLSACIQEKRLV 80
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
167-492 3.82e-145

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: 418.14  E-value: 3.82e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 167 HITEKLEVLAKAYSVQG-DKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVP 245
Cdd:cd00141     2 EIADILEELADLLELLGgNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVP 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 246 -VLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQAS--LTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGL 322
Cdd:cd00141    82 pGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGakLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVL 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 323 LCVACGSYRRGKATCGDVDVLITHPDGRShRGIFSRLLDSLrqeavpsVGPGFLTDDLvsqeeNGQQQKYLGVCRLPGpG 402
Cdd:cd00141   162 QVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDAL-------VELGFVTEVL-----SKGDTKASGILKLPG-G 227
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 403 RRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALStavvrnthgcKVGPGRVLPTPTEKDVFRLL 482
Cdd:cd00141   228 WKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLF----------DGVDGERLPGETEEEIFEAL 297
                         330
                  ....*....|
gi 1370456880 483 GLPYREPAER 492
Cdd:cd00141   298 GLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
163-493 1.47e-87

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


Pssm-ID: 214688  Cd Length: 334  Bit Score: 271.93  E-value: 1.47e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880  163 NHNLHITEKLEVLAKAYSVQGDKWRA-LGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHIS 241
Cdd:smart00483   1 NLNRGIIDALEILAENYEVFGENKRKcSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEIL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880  242 --ESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQA--SLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQA 317
Cdd:smart00483  81 ndEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKelKLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRK 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880  318 FNSGLLCVACGSYRRGKATCGDVDVLITHP---DGRSHRGIFSRLLDSLRQE-AVPSvgpgFLTDDLVsqeenGQQQKYL 393
Cdd:smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPhpaKEKELEVLDLLLLESTFEElQLPS----IRVATLD-----HGQKKFM 231
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880  394 GVCRLP------------GPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKG-MSLSEHAlstavvRNTH 460
Cdd:smart00483 232 ILKLSPsredkeksgkpdEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKFkLMLDGHE------LYDK 305
                          330       340       350
                   ....*....|....*....|....*....|...
gi 1370456880  461 GCKVgpgrVLPTPTEKDVFRLLGLPYREPAERD 493
Cdd:smart00483 306 TKEK----FLKVESEEDIFDHLGLPYIEPEERN 334
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
298-414 1.01e-47

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: 160.42  E-value: 1.01e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 298 RMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHR---GIFSRLLDSLRQEavpsvgpG 374
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSESelkGLLDRLVARLKKS-------G 73
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1370456880 375 FLTDDLVSQEengQQQKYLGVCRLPGPGRRHRRLDIIVVP 414
Cdd:pfam14792  74 FLTDDLAVDS---GGSKWMGVCRLPGSERLHRRIDILVVP 110
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
164-489 4.23e-43

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 160.74  E-value: 4.23e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 164 HNLHITEKLEVLAKAYSVQG-DKWRALGYAKAINALKSFHKPVTSYQEAC---SIPGIGKRMAEKIIEILESGHLRKLDH 239
Cdd:COG1796     2 DNKEIARILEEIADLLELKGeNPFKIRAYRRAARAIENLPEDIEELVAEGdltEIPGIGKAIAAKIEELLETGRLEELEE 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 240 ISESVP--VLELFSnIWGAGTKTAQMWYQQ-GFRSLEDIRSQA------SL-----TTQQAI--GLKHYSDFLERMP--- 300
Cdd:COG1796    82 LREEVPpgLLELLR-IPGLGPKKVKKLYEElGITSLEELEAAAeegrirELpgfgeKTEENIlkGIELLRKRGGRFLlge 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 301 -REEATEIEQTVQKAAQAFNsgllCVACGSYRRGKATCGDVDVLITHPDGRShrgIFSRLLDSLRQEAVPSVGPGFLTdd 379
Cdd:COG1796   161 aLPLAEEILAYLRALPGVER----VEVAGSLRRRKETVGDIDILVASDDPEA---VMDAFVKLPEVKEVLAKGDTKAS-- 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 380 lvsqeengqqqkylgvCRLpgpgRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALStavvrnt 459
Cdd:COG1796   232 ----------------VRL----KSGLQVDLRVVPPESFGAALQYFTGSKEHNVALRQLAKERGLKLNEYGLF------- 284
                         330       340       350
                  ....*....|....*....|....*....|
gi 1370456880 460 hgcKVGpGRVLPTPTEKDVFRLLGLPYREP 489
Cdd:COG1796   285 ---DVG-GERIAGETEEEVYAALGLPYIPP 310
DNA_pol_B_thumb pfam14791
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
421-493 2.53e-26

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: 101.29  E-value: 2.53e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1370456880 421 ALLYFTGSAHFNRSMRALAKTKGMSLSEHALStavvrnthgcKVGPGRVLPTPTEKDVFRLLGLPYREPAERD 493
Cdd:pfam14791   1 ALLYFTGSKEFNRDLRLLAKKKGLKLNEYGLF----------DLKDGELLEGETEEDIFEALGLPYIPPELRE 63
HHH_8 pfam14716
Helix-hairpin-helix domain;
165-230 9.66e-21

Helix-hairpin-helix domain;


Pssm-ID: 434152 [Multi-domain]  Cd Length: 67  Bit Score: 85.63  E-value: 9.66e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1370456880 165 NLHITEKLEVLAKAYSVQG-DKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILE 230
Cdd:pfam14716   1 NQEIADALEELADLLELKGeDPFRVRAYRRAARALEALPEEITSLEELTKLPGIGKKIAAKIEEILE 67
DNA_pol_lambd_f pfam10391
Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto ...
248-296 1.09e-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: 82.12  E-value: 1.09e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1370456880 248 ELFSNIWGAGTKTAQMWYQQGFRSLEDIR--SQASLTTQQAIGLKHYSDFL 296
Cdd:pfam10391   1 KLFTGIYGVGPTTARKWYAQGYRTLDDLRekKTAKLTRQQQIGLKYYDDFN 51
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
191-492 2.17e-12

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 69.21  E-value: 2.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 191 YAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVP--VLELFsNIWGAGTKTAQMWYQQ- 267
Cdd:PRK08609   30 FRKAAQALELDERSLSEIDDFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPegLLPLL-KLPGLGGKKIAKLYKEl 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 268 GFRSLEDIRsQASLT------------TQQAI--GLKHYSDFLERMP----REEATEIEQT------VQKAAQAfnsgll 323
Cdd:PRK08609  109 GVVDKESLK-EACENgkvqalagfgkkTEEKIleAVKELGKRPERLPiaqvLPIAQEIEEYlatideIIRFSRA------ 181
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 324 cvacGSYRRGKATCGDVDVLI--THPDG-RSHrgifsrLLDSLRQEAVPSVGpgfltDDLVSQEEngQQQKYLGVcrlpg 400
Cdd:PRK08609  182 ----GSLRRARETVKDLDFIIatDEPEAvREQ------LLQLPNIVEVIAAG-----DTKVSVEL--EYEYTISV----- 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 401 pgrrhrrlDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAvvrnthgckvGPGRVLPTPTEKDVFR 480
Cdd:PRK08609  240 --------DFRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEYGVEQA----------DTGEVKTFESEEAFFA 301
                         330
                  ....*....|..
gi 1370456880 481 LLGLPYREPAER 492
Cdd:PRK08609  302 HFGLPFIPPEVR 313
BRCT_polymerase_lambda cd17715
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed ...
18-37 4.44e-04

BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed Pol Lambda, or DNA polymerase beta-2 (Pol beta2), or DNA polymerase kappa, is involved in base excision repair (BER) and is responsible for repair of lesions that give rise to abasic (AP) sites in DNA. It also contributes to DNA double-strand break repair by non-homologous end joining and homologous recombination. DNA polymerase lambda has both template-dependent and template-independent (terminal transferase) DNA polymerase activities, as well as a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity. DNA polymerase lambda contains one BRCT domain.


Pssm-ID: 349347  Cd Length: 80  Bit Score: 39.01  E-value: 4.44e-04
                          10        20
                  ....*....|....*....|
gi 1370456880  18 GAQLVKSAWLSLCLQERRLV 37
Cdd:cd17715    61 GAQLVKSGWLSACIQEKRLV 80
PRK00254 PRK00254
ski2-like helicase; Provisional
179-313 3.12e-03

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 40.19  E-value: 3.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 179 YSVQ-GDKWRALGYAK-AINALKSFHKPVTSYQEacsipgigkrmaekIIEILESGHLRKLDHISES-VPVLELfSNIwg 255
Cdd:PRK00254  591 YNIDpGDLYRILELADwLMYSLIELYKLFEPKQE--------------VLDYLETLHLRVKHGVREElLELMRL-PMI-- 653
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456880 256 aGTKTAQMWYQQGFRSLEDIRSQ--ASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQK 313
Cdd:PRK00254  654 -GRKRARALYNAGFRSIEDIVNAkpSELLKVEGIGAKIVEGIFKHLGVEKEVKIKKKPRK 712
 
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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