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Conserved domains on  [gi|817477558|ref|NP_001295311|]
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DNA polymerase lambda isoform c [Homo sapiens]

Protein Classification

nucleotidyltransferase domain-containing protein( domain architecture ID 10065437)

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

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

Graphical summary

 Zoom to residue level

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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 ...
22-298 5.96e-127

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: 364.21  E-value: 5.96e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  22 KEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVP-VLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQAS--LTTQQ 98
Cdd:cd00141   45 EEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPpGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGakLEQNI 124
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  99 AIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRShRGIFSRLLDSLRQ 178
Cdd:cd00141  125 LIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDALVE 203
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558 179 EGFLTDDLvsqeeNGQQQKYLGVCRLPGpGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALS 258
Cdd:cd00141  204 LGFVTEVL-----SKGDTKASGILKLPG-GWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLF 277
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 817477558 259 tavvrnthgcKVGPGRVLPTPTEKDVFRLLGLPYREPAER 298
Cdd:cd00141  278 ----------DGVDGERLPGETEEEIFEALGLPYIEPELR 307
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
22-298 5.96e-127

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: 364.21  E-value: 5.96e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  22 KEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVP-VLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQAS--LTTQQ 98
Cdd:cd00141   45 EEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPpGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGakLEQNI 124
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  99 AIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRShRGIFSRLLDSLRQ 178
Cdd:cd00141  125 LIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDALVE 203
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558 179 EGFLTDDLvsqeeNGQQQKYLGVCRLPGpGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALS 258
Cdd:cd00141  204 LGFVTEVL-----SKGDTKASGILKLPG-GWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLF 277
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 817477558 259 tavvrnthgcKVGPGRVLPTPTEKDVFRLLGLPYREPAER 298
Cdd:cd00141  278 ----------DGVDGERLPGETEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
22-299 7.04e-78

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


Pssm-ID: 214688  Cd Length: 334  Bit Score: 240.35  E-value: 7.04e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558    22 KEACSIPGIGKRMAEKIIEILESGHLRKLDHIS--ESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQA--SLTTQ 97
Cdd:smart00483  48 KDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILndEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKelKLTKQ 127
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558    98 QAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRS-------HRGIFS 170
Cdd:smart00483 128 QKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRKILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAKekelevlDLLLLE 207
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558   171 RLLDSLRQEGFLTDDLVSqeengQQQKYLGVCRLP------------GPGRRHRRLDIIVVPYSEFACALLYFTGSAHFN 238
Cdd:smart00483 208 STFEELQLPSIRVATLDH-----GQKKFMILKLSPsredkeksgkpdEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFN 282
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 817477558   239 RSMRALAKTKG-MSLSEHAlstavvRNTHGCKVgpgrVLPTPTEKDVFRLLGLPYREPAERD 299
Cdd:smart00483 283 RDLRRYATSKFkLMLDGHE------LYDKTKEK----FLKVESEEDIFDHLGLPYIEPEERN 334
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
111-220 5.75e-51

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


Pssm-ID: 464318  Cd Length: 110  Bit Score: 163.51  E-value: 5.75e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  111 RMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHR---GIFSRLLDSLRQEGFLTDDLV 187
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSESelkGLLDRLVARLKKSGFLTDDLA 80
                          90       100       110
                  ....*....|....*....|....*....|...
gi 817477558  188 SQEengQQQKYLGVCRLPGPGRRHRRLDIIVVP 220
Cdd:pfam14792  81 VDS---GGSKWMGVCRLPGSERLHRRIDILVVP 110
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
26-295 3.40e-41

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 149.96  E-value: 3.40e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  26 SIPGIGKRMAEKIIEILESGHLRKLDHISESVP--VLELFSnIWGAGTKTAQMWYQQ-GFRSLEDIRSQA------SL-- 94
Cdd:COG1796   55 EIPGIGKAIAAKIEELLETGRLEELEELREEVPpgLLELLR-IPGLGPKKVKKLYEElGITSLEELEAAAeegrirELpg 133
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  95 ---TTQQAI--GLKHYSDFLERMP----REEATEIEQTVQKAAQAFNsgllCVACGSYRRGKATCGDVDVLITHPDGrsh 165
Cdd:COG1796  134 fgeKTEENIlkGIELLRKRGGRFLlgeaLPLAEEILAYLRALPGVER----VEVAGSLRRRKETVGDIDILVASDDP--- 206
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558 166 rgifSRLLDSLRQEGFLTDDLVSQE-------ENGQQqkylgvcrlpgpgrrhrrLDIIVVPYSEFACALLYFTGSAHFN 238
Cdd:COG1796  207 ----EAVMDAFVKLPEVKEVLAKGDtkasvrlKSGLQ------------------VDLRVVPPESFGAALQYFTGSKEHN 264
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 817477558 239 RSMRALAKTKGMSLSEHALSTAVvrnthgckvgpGRVLPTPTEKDVFRLLGLPYREP 295
Cdd:COG1796  265 VALRQLAKERGLKLNEYGLFDVG-----------GERIAGETEEEVYAALGLPYIPP 310
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
26-298 5.88e-11

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 62.67  E-value: 5.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  26 SIPGIGKRMAEKIIEILESGHLRKLDHISESVP--VLELFsNIWGAGTKTAQMWYQQ-GFRSLEDIRsQASLT------- 95
Cdd:PRK08609  52 KLKGIGKGTAEVIQEYRETGESSVLQELKKEVPegLLPLL-KLPGLGGKKIAKLYKElGVVDKESLK-EACENgkvqala 129
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  96 -----TQQAI--GLKHYSDFLERMP----REEATEIEQT------VQKAAQAfnsgllcvacGSYRRGKATCGDVDVLI- 157
Cdd:PRK08609 130 gfgkkTEEKIleAVKELGKRPERLPiaqvLPIAQEIEEYlatideIIRFSRA----------GSLRRARETVKDLDFIIa 199
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558 158 -THPDgrshrgifsrlldSLRQEGFLTDDLVSQEENG--------QQQKYLGVcrlpgpgrrhrrlDIIVVPYSEFACAL 228
Cdd:PRK08609 200 tDEPE-------------AVREQLLQLPNIVEVIAAGdtkvsvelEYEYTISV-------------DFRLVEPEAFATTL 253
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558 229 LYFTGSAHFNRSMRALAKTKGMSLSEHALSTAvvrnthgckvGPGRVLPTPTEKDVFRLLGLPYREPAER 298
Cdd:PRK08609 254 HHFTGSKDHNVRMRQLAKERGEKISEYGVEQA----------DTGEVKTFESEEAFFAHFGLPFIPPEVR 313
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
22-298 5.96e-127

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: 364.21  E-value: 5.96e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  22 KEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVP-VLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQAS--LTTQQ 98
Cdd:cd00141   45 EEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPpGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGakLEQNI 124
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  99 AIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRShRGIFSRLLDSLRQ 178
Cdd:cd00141  125 LIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDALVE 203
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558 179 EGFLTDDLvsqeeNGQQQKYLGVCRLPGpGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALS 258
Cdd:cd00141  204 LGFVTEVL-----SKGDTKASGILKLPG-GWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLF 277
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 817477558 259 tavvrnthgcKVGPGRVLPTPTEKDVFRLLGLPYREPAER 298
Cdd:cd00141  278 ----------DGVDGERLPGETEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
22-299 7.04e-78

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


Pssm-ID: 214688  Cd Length: 334  Bit Score: 240.35  E-value: 7.04e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558    22 KEACSIPGIGKRMAEKIIEILESGHLRKLDHIS--ESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQA--SLTTQ 97
Cdd:smart00483  48 KDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILndEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKelKLTKQ 127
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558    98 QAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRS-------HRGIFS 170
Cdd:smart00483 128 QKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRKILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAKekelevlDLLLLE 207
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558   171 RLLDSLRQEGFLTDDLVSqeengQQQKYLGVCRLP------------GPGRRHRRLDIIVVPYSEFACALLYFTGSAHFN 238
Cdd:smart00483 208 STFEELQLPSIRVATLDH-----GQKKFMILKLSPsredkeksgkpdEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFN 282
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 817477558   239 RSMRALAKTKG-MSLSEHAlstavvRNTHGCKVgpgrVLPTPTEKDVFRLLGLPYREPAERD 299
Cdd:smart00483 283 RDLRRYATSKFkLMLDGHE------LYDKTKEK----FLKVESEEDIFDHLGLPYIEPEERN 334
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
111-220 5.75e-51

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


Pssm-ID: 464318  Cd Length: 110  Bit Score: 163.51  E-value: 5.75e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  111 RMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHR---GIFSRLLDSLRQEGFLTDDLV 187
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSESelkGLLDRLVARLKKSGFLTDDLA 80
                          90       100       110
                  ....*....|....*....|....*....|...
gi 817477558  188 SQEengQQQKYLGVCRLPGPGRRHRRLDIIVVP 220
Cdd:pfam14792  81 VDS---GGSKWMGVCRLPGSERLHRRIDILVVP 110
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
26-295 3.40e-41

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


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 149.96  E-value: 3.40e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  26 SIPGIGKRMAEKIIEILESGHLRKLDHISESVP--VLELFSnIWGAGTKTAQMWYQQ-GFRSLEDIRSQA------SL-- 94
Cdd:COG1796   55 EIPGIGKAIAAKIEELLETGRLEELEELREEVPpgLLELLR-IPGLGPKKVKKLYEElGITSLEELEAAAeegrirELpg 133
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  95 ---TTQQAI--GLKHYSDFLERMP----REEATEIEQTVQKAAQAFNsgllCVACGSYRRGKATCGDVDVLITHPDGrsh 165
Cdd:COG1796  134 fgeKTEENIlkGIELLRKRGGRFLlgeaLPLAEEILAYLRALPGVER----VEVAGSLRRRKETVGDIDILVASDDP--- 206
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558 166 rgifSRLLDSLRQEGFLTDDLVSQE-------ENGQQqkylgvcrlpgpgrrhrrLDIIVVPYSEFACALLYFTGSAHFN 238
Cdd:COG1796  207 ----EAVMDAFVKLPEVKEVLAKGDtkasvrlKSGLQ------------------VDLRVVPPESFGAALQYFTGSKEHN 264
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 817477558 239 RSMRALAKTKGMSLSEHALSTAVvrnthgckvgpGRVLPTPTEKDVFRLLGLPYREP 295
Cdd:COG1796  265 VALRQLAKERGLKLNEYGLFDVG-----------GERIAGETEEEVYAALGLPYIPP 310
DNA_pol_B_thumb pfam14791
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
227-299 3.81e-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: 97.83  E-value: 3.81e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 817477558  227 ALLYFTGSAHFNRSMRALAKTKGMSLSEHALStavvrnthgcKVGPGRVLPTPTEKDVFRLLGLPYREPAERD 299
Cdd:pfam14791   1 ALLYFTGSKEFNRDLRLLAKKKGLKLNEYGLF----------DLKDGELLEGETEEDIFEALGLPYIPPELRE 63
DNA_pol_lambd_f pfam10391
Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto ...
61-109 1.64e-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: 79.80  E-value: 1.64e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 817477558   61 ELFSNIWGAGTKTAQMWYQQGFRSLEDIR--SQASLTTQQAIGLKHYSDFL 109
Cdd:pfam10391   1 KLFTGIYGVGPTTARKWYAQGYRTLDDLRekKTAKLTRQQQIGLKYYDDFN 51
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
26-298 5.88e-11

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 62.67  E-value: 5.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  26 SIPGIGKRMAEKIIEILESGHLRKLDHISESVP--VLELFsNIWGAGTKTAQMWYQQ-GFRSLEDIRsQASLT------- 95
Cdd:PRK08609  52 KLKGIGKGTAEVIQEYRETGESSVLQELKKEVPegLLPLL-KLPGLGGKKIAKLYKElGVVDKESLK-EACENgkvqala 129
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  96 -----TQQAI--GLKHYSDFLERMP----REEATEIEQT------VQKAAQAfnsgllcvacGSYRRGKATCGDVDVLI- 157
Cdd:PRK08609 130 gfgkkTEEKIleAVKELGKRPERLPiaqvLPIAQEIEEYlatideIIRFSRA----------GSLRRARETVKDLDFIIa 199
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558 158 -THPDgrshrgifsrlldSLRQEGFLTDDLVSQEENG--------QQQKYLGVcrlpgpgrrhrrlDIIVVPYSEFACAL 228
Cdd:PRK08609 200 tDEPE-------------AVREQLLQLPNIVEVIAAGdtkvsvelEYEYTISV-------------DFRLVEPEAFATTL 253
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558 229 LYFTGSAHFNRSMRALAKTKGMSLSEHALSTAvvrnthgckvGPGRVLPTPTEKDVFRLLGLPYREPAER 298
Cdd:PRK08609 254 HHFTGSKDHNVRMRQLAKERGEKISEYGVEQA----------DTGEVKTFESEEAFFAHFGLPFIPPEVR 313
HHH_8 pfam14716
Helix-hairpin-helix domain;
22-43 1.56e-05

Helix-hairpin-helix domain;


Pssm-ID: 434152 [Multi-domain]  Cd Length: 67  Bit Score: 42.11  E-value: 1.56e-05
                          10        20
                  ....*....|....*....|..
gi 817477558   22 KEACSIPGIGKRMAEKIIEILE 43
Cdd:pfam14716  46 EELTKLPGIGKKIAAKIEEILE 67
PRK00254 PRK00254
ski2-like helicase; Provisional
36-126 2.34e-03

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 39.42  E-value: 2.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 817477558  36 EKIIEILESGHLRKLDHISES-VPVLELfSNIwgaGTKTAQMWYQQGFRSLEDIRSQ--ASLTTQQAIGLKHYSDFLERM 112
Cdd:PRK00254 623 QEVLDYLETLHLRVKHGVREElLELMRL-PMI---GRKRARALYNAGFRSIEDIVNAkpSELLKVEGIGAKIVEGIFKHL 698
                         90
                 ....*....|....
gi 817477558 113 PREEATEIEQTVQK 126
Cdd:PRK00254 699 GVEKEVKIKKKPRK 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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