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Conserved domains on  [gi|2211111285|gb|UNP34840|]
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DNA-dependent DNA polymerase, partial [Buteo buteo herpesvirus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_pol_B super family cl29029
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
 1-74 2.80e-22

DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.


The actual alignment was detected with superfamily member pfam00136:

Pssm-ID: 395085  Cd Length: 439  Bit Score: 87.67  E-value: 2.80e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2211111285   1 VYGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVHEKWAtpelltsafpdtadyliqgarYEAKIIYGDTDS 74
Cdd:pfam00136 165 VYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT---------------------YNFRVIYGDTDS 217
 
Name Accession Description Interval E-value
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
 1-74 2.80e-22

DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.


Pssm-ID: 395085  Cd Length: 439  Bit Score: 87.67  E-value: 2.80e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2211111285   1 VYGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVHEKWAtpelltsafpdtadyliqgarYEAKIIYGDTDS 74
Cdd:pfam00136 165 VYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT---------------------YNFRVIYGDTDS 217
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
 1-74 1.39e-16

DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.


Pssm-ID: 99916  Cd Length: 393  Bit Score: 71.91  E-value: 1.39e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2211111285   1 VYGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVHEKwatpelltsafpdtadYLIQ-GARYEAKIIYGDTDS 74
Cdd:cd05533   120 VYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEK----------------YTKAnGYSHDAKVIYGDTDS 178
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
 1-74 7.92e-16

DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases


Pssm-ID: 214691 [Multi-domain]  Cd Length: 474  Bit Score: 69.87  E-value: 7.92e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2211111285    1 VYGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVHEKWAtpelltsafpdtadyliqgARYEAKIIYGDTDS 74
Cdd:smart00486 413 VYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGY-------------------PKPGFKVIYGDTDS 467
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
 1-74 3.51e-15

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 68.13  E-value: 3.51e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2211111285    1 VYGFTG-VANGLLPCLYVAATVTTIGRDMLLETRDYVHEKWATPelltsafpdtadyliQGARYEAKIIYGDTDS 74
Cdd:PTZ00166   657 VYGYTGaQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKA---------------NGYKHDATVIYGDTDS 716
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
 1-74 1.11e-06

DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273159 [Multi-domain]  Cd Length: 1172  Bit Score: 43.89  E-value: 1.11e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2211111285    1 VYGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVHEKwatpelltsafpdtadyliqgaryEAKIIYGDTDS 74
Cdd:TIGR00592  902 MYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEM------------------------NLEVIYGDTDS 951
 
Name Accession Description Interval E-value
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
 1-74 2.80e-22

DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.


Pssm-ID: 395085  Cd Length: 439  Bit Score: 87.67  E-value: 2.80e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2211111285   1 VYGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVHEKWAtpelltsafpdtadyliqgarYEAKIIYGDTDS 74
Cdd:pfam00136 165 VYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMYT---------------------YNFRVIYGDTDS 217
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
 1-74 1.39e-16

DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.


Pssm-ID: 99916  Cd Length: 393  Bit Score: 71.91  E-value: 1.39e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2211111285   1 VYGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVHEKwatpelltsafpdtadYLIQ-GARYEAKIIYGDTDS 74
Cdd:cd05533   120 VYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEK----------------YTKAnGYSHDAKVIYGDTDS 178
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
 1-74 7.92e-16

DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases


Pssm-ID: 214691 [Multi-domain]  Cd Length: 474  Bit Score: 69.87  E-value: 7.92e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2211111285    1 VYGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVHEKWAtpelltsafpdtadyliqgARYEAKIIYGDTDS 74
Cdd:smart00486 413 VYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGY-------------------PKPGFKVIYGDTDS 467
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
 1-74 3.51e-15

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 68.13  E-value: 3.51e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2211111285    1 VYGFTG-VANGLLPCLYVAATVTTIGRDMLLETRDYVHEKWATPelltsafpdtadyliQGARYEAKIIYGDTDS 74
Cdd:PTZ00166   657 VYGYTGaQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKA---------------NGYKHDATVIYGDTDS 716
POLBc cd00145
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
 2-74 2.48e-07

DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.


Pssm-ID: 99912 [Multi-domain]  Cd Length: 323  Bit Score: 45.44  E-value: 2.48e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2211111285   2 YGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVHEkwatpelltsafpdtadyliqgarYEAKIIYGDTDS 74
Cdd:cd00145   115 YGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEE------------------------HGARVIYGDTDS 163
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
 1-74 1.11e-06

DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273159 [Multi-domain]  Cd Length: 1172  Bit Score: 43.89  E-value: 1.11e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2211111285    1 VYGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVHEKwatpelltsafpdtadyliqgaryEAKIIYGDTDS 74
Cdd:TIGR00592  902 MYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEM------------------------NLEVIYGDTDS 951
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
 1-74 8.43e-06

DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.


Pssm-ID: 99917  Cd Length: 451  Bit Score: 41.43  E-value: 8.43e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2211111285   1 VYGFTGvAN--GLLPCLYVAATVTTIGRDMLLETRDYVH--EKWatpelltsafpdtadyliqgaryEAKIIYGDTDS 74
Cdd:cd05534   176 TYGYTA-ASfsGRMPCVEIADSIVQTGRETLERAIELIEstPKW-----------------------GAKVVYGDTDS 229
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
 2-74 8.32e-04

DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.


Pssm-ID: 99915  Cd Length: 400  Bit Score: 35.63  E-value: 8.32e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2211111285   2 YGFTGVANGLLPCLYVAATVTTIGRDMLLETRDyvhekwatpelltsafpdtadyLIQGARYEakIIYGDTDS 74
Cdd:cd05532   118 YGCLGFSYSRFYAKPLAALITSKGREILQKTKD----------------------LVEKMNLE--VIYGDTDS 166
PHA03036 PHA03036
DNA polymerase; Provisional
 1-74 3.52e-03

DNA polymerase; Provisional


Pssm-ID: 222962 [Multi-domain]  Cd Length: 1004  Bit Score: 33.84  E-value: 3.52e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2211111285    1 VYGFTGVANGLLPCLYVAATVTTIGRDMLLETRDYVH-EKWATPELLTSAFPD------------TADYLIQG-ARYEAK 66
Cdd:PHA03036   669 VYGLMGFRNSALYSYASAKSCTAIGRNMIKYLNSVLNgSKLINGKLILANCPInpffkddrsidtNYDTNLPVeYNFTFR 748


                   ....*...
gi 2211111285   67 IIYGDTDS 74
Cdd:PHA03036   749 SVYGDTDS 756
 
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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