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Conserved domains on  [gi|568979072|ref|XP_006515661|]
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DNA polymerase epsilon subunit 2 isoform X2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Dpoe2NT pfam12213
DNA polymerases epsilon N terminal; This domain is found in eukaryotes, and is approximately ...
 2-74 9.43e-35

DNA polymerases epsilon N terminal; This domain is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam04042. There is a single completely conserved residue F that may be functionally important. This domain is the N terminal domain of DNA polymerase epsilon subunit B. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. This domain has close structural relation to AAA+ protein C terminal domains.


:

Pssm-ID: 463494  Cd Length: 73  Bit Score: 123.73  E-value: 9.43e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568979072    2 APERLRSRTVSAFKLRGLLLRSEATKYLTEALQSVTELELEENLGKIIDAVEKQPLSSNMIERSVVEAAVQEC 74
Cdd:pfam12213   1 EPERLRKRILSAFKLRGLLLRSEAVKYLVEVLLSLDEEEREDWLEKIIEAVEKQPLSSNMIERSVVEAAVQEC 73
DNA_pol_E_B super family cl46471
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 287-404 3.73e-15

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


The actual alignment was detected with superfamily member pfam04042:

Pssm-ID: 461142  Cd Length: 210  Bit Score: 73.88  E-value: 3.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979072  287 FVIVSDVWLDQ-VQVLEKFHVMFSGY-SPAPPTCFILCGNFSSAPY-----GKNQVQALK---DSLKSLADIIceyPSIH 356
Cdd:pfam04042   1 IVFASGLYLDSdNLSLEALRDLLDGYnEDSPPDRLILAGPFLDSKHnliasGAVAGDTLTynfLFLKLLLSIL---EQLL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 568979072  357 QSSRFVFVPGPEDPGFGSILPRPPLAESITQEFRQRVPFsVFTTNPCS 404
Cdd:pfam04042  78 EKTPVILVPGPNDPANSTVLPQPPFPRCLLPRIKKNNSL-IFVTNPCR 124
 
Name Accession Description Interval E-value
Dpoe2NT pfam12213
DNA polymerases epsilon N terminal; This domain is found in eukaryotes, and is approximately ...
 2-74 9.43e-35

DNA polymerases epsilon N terminal; This domain is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam04042. There is a single completely conserved residue F that may be functionally important. This domain is the N terminal domain of DNA polymerase epsilon subunit B. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. This domain has close structural relation to AAA+ protein C terminal domains.


Pssm-ID: 463494  Cd Length: 73  Bit Score: 123.73  E-value: 9.43e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568979072    2 APERLRSRTVSAFKLRGLLLRSEATKYLTEALQSVTELELEENLGKIIDAVEKQPLSSNMIERSVVEAAVQEC 74
Cdd:pfam12213   1 EPERLRKRILSAFKLRGLLLRSEAVKYLVEVLLSLDEEEREDWLEKIIEAVEKQPLSSNMIERSVVEAAVQEC 73
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 287-404 3.73e-15

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


Pssm-ID: 461142  Cd Length: 210  Bit Score: 73.88  E-value: 3.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979072  287 FVIVSDVWLDQ-VQVLEKFHVMFSGY-SPAPPTCFILCGNFSSAPY-----GKNQVQALK---DSLKSLADIIceyPSIH 356
Cdd:pfam04042   1 IVFASGLYLDSdNLSLEALRDLLDGYnEDSPPDRLILAGPFLDSKHnliasGAVAGDTLTynfLFLKLLLSIL---EQLL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 568979072  357 QSSRFVFVPGPEDPGFGSILPRPPLAESITQEFRQRVPFsVFTTNPCS 404
Cdd:pfam04042  78 EKTPVILVPGPNDPANSTVLPQPPFPRCLLPRIKKNNSL-IFVTNPCR 124
PTZ00235 PTZ00235
DNA polymerase epsilon subunit B; Provisional
 282-403 4.08e-06

DNA polymerase epsilon subunit B; Provisional


Pssm-ID: 185521  Cd Length: 291  Bit Score: 48.07  E-value: 4.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979072 282 NKDAMFVIVSDVWLDQVQVLEKFHVMFSGY-SPAP----PTCFILCGNFSSAP--YGKNQVQALKDSLKSLAD-IICEYP 353
Cdd:PTZ00235  25 DKRHNWIIMHDVYLDSPYTFEVLDKMLSLYvNTYPenelPVGFIFMGDFISLKfdYNRNFHKVYIKGFEKLSVmLISKFK 104

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 568979072 354 SIHQSSRFVFVPGPEDP-GFGSILPRPPLAESITQEFRQRVP--FS-----VFTTNPC 403
Cdd:PTZ00235 105 LILEHCYLIFIPGINDPcACKNSIPKMPILPYYIRKFKQNIEsfFSskrniIFATNPC 162
 
Name Accession Description Interval E-value
Dpoe2NT pfam12213
DNA polymerases epsilon N terminal; This domain is found in eukaryotes, and is approximately ...
 2-74 9.43e-35

DNA polymerases epsilon N terminal; This domain is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam04042. There is a single completely conserved residue F that may be functionally important. This domain is the N terminal domain of DNA polymerase epsilon subunit B. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. This domain has close structural relation to AAA+ protein C terminal domains.


Pssm-ID: 463494  Cd Length: 73  Bit Score: 123.73  E-value: 9.43e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568979072    2 APERLRSRTVSAFKLRGLLLRSEATKYLTEALQSVTELELEENLGKIIDAVEKQPLSSNMIERSVVEAAVQEC 74
Cdd:pfam12213   1 EPERLRKRILSAFKLRGLLLRSEAVKYLVEVLLSLDEEEREDWLEKIIEAVEKQPLSSNMIERSVVEAAVQEC 73
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 287-404 3.73e-15

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


Pssm-ID: 461142  Cd Length: 210  Bit Score: 73.88  E-value: 3.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979072  287 FVIVSDVWLDQ-VQVLEKFHVMFSGY-SPAPPTCFILCGNFSSAPY-----GKNQVQALK---DSLKSLADIIceyPSIH 356
Cdd:pfam04042   1 IVFASGLYLDSdNLSLEALRDLLDGYnEDSPPDRLILAGPFLDSKHnliasGAVAGDTLTynfLFLKLLLSIL---EQLL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 568979072  357 QSSRFVFVPGPEDPGFGSILPRPPLAESITQEFRQRVPFsVFTTNPCS 404
Cdd:pfam04042  78 EKTPVILVPGPNDPANSTVLPQPPFPRCLLPRIKKNNSL-IFVTNPCR 124
PTZ00235 PTZ00235
DNA polymerase epsilon subunit B; Provisional
 282-403 4.08e-06

DNA polymerase epsilon subunit B; Provisional


Pssm-ID: 185521  Cd Length: 291  Bit Score: 48.07  E-value: 4.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979072 282 NKDAMFVIVSDVWLDQVQVLEKFHVMFSGY-SPAP----PTCFILCGNFSSAP--YGKNQVQALKDSLKSLAD-IICEYP 353
Cdd:PTZ00235  25 DKRHNWIIMHDVYLDSPYTFEVLDKMLSLYvNTYPenelPVGFIFMGDFISLKfdYNRNFHKVYIKGFEKLSVmLISKFK 104

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 568979072 354 SIHQSSRFVFVPGPEDP-GFGSILPRPPLAESITQEFRQRVP--FS-----VFTTNPC 403
Cdd:PTZ00235 105 LILEHCYLIFIPGINDPcACKNSIPKMPILPYYIRKFKQNIEsfFSskrniIFATNPC 162
 
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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