NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2512276071|gb|WIA70243|]
View 

DNA polymerase, partial [Anguillid herpesvirus 1]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PHA03334 super family cl33727
putative DNA polymerase catalytic subunit; Provisional
 10-88 1.97e-45

putative DNA polymerase catalytic subunit; Provisional


The actual alignment was detected with superfamily member PHA03334:

Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 155.01  E-value: 1.97e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2512276071   10 REYGEAENLYTILLHKSVETGWTRFTTYTSSSLRHYLSMRNKYKGDMKTAKSPGLKKYFNQLQNEMKICANSHYGVSDR 88
Cdd:PHA03334   700 RGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNEMKICANSHYGVAPH 778
 
Name Accession Description Interval E-value
PHA03334 PHA03334
putative DNA polymerase catalytic subunit; Provisional
 10-88 1.97e-45

putative DNA polymerase catalytic subunit; Provisional


Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 155.01  E-value: 1.97e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2512276071   10 REYGEAENLYTILLHKSVETGWTRFTTYTSSSLRHYLSMRNKYKGDMKTAKSPGLKKYFNQLQNEMKICANSHYGVSDR 88
Cdd:PHA03334   700 RGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNEMKICANSHYGVAPH 778
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
 42-84 5.21e-06

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: 42.60  E-value: 5.21e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2512276071  42 LRHYLSMRNKYKGDMKTAKSPGLKKYFNQLQNEMKICANSHYG 84
Cdd:pfam00136 125 LKDLLAKRKAIKKLLKEETDPFERAILDKQQLALKITANSVYG 167
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
 42-84 6.22e-06

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: 42.25  E-value: 6.22e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2512276071  42 LRHYLSMRNKYKGDMKTAKSPGLKKYFNQLQNEMKICANSHYG 84
Cdd:cd05533    80 LEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYG 122
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
 37-85 2.67e-05

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: 40.59  E-value: 2.67e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2512276071   37 YTSSSLRHYLSMRNKYKGDMKTAKSP--GLKKYFNQLQNEMKICANSHYGV 85
Cdd:smart00486 366 ILPKLLKKLLDKRKEIKKLMKKEKDEseELKKLLDSRQLALKLTANSVYGY 416
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
38-86 6.20e-04

DNA polymerase B elongation subunit [Replication, recombination and repair];


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 36.73  E-value: 6.20e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2512276071  38 TSSSLRHYLSMRNKYKGDMKTAKS-PGLKKYFNQLQNEMKICANSHYGVS 86
Cdd:COG0417   477 LPSILEELWDERDEAKKKMKKAKPdSEEYRLYDALQQALKILMNSFYGVL 526
 
Name Accession Description Interval E-value
PHA03334 PHA03334
putative DNA polymerase catalytic subunit; Provisional
 10-88 1.97e-45

putative DNA polymerase catalytic subunit; Provisional


Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 155.01  E-value: 1.97e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2512276071   10 REYGEAENLYTILLHKSVETGWTRFTTYTSSSLRHYLSMRNKYKGDMKTAKSPGLKKYFNQLQNEMKICANSHYGVSDR 88
Cdd:PHA03334   700 RGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNEMKICANSHYGVAPH 778
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
 42-84 5.21e-06

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: 42.60  E-value: 5.21e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2512276071  42 LRHYLSMRNKYKGDMKTAKSPGLKKYFNQLQNEMKICANSHYG 84
Cdd:pfam00136 125 LKDLLAKRKAIKKLLKEETDPFERAILDKQQLALKITANSVYG 167
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
 42-84 6.22e-06

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: 42.25  E-value: 6.22e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2512276071  42 LRHYLSMRNKYKGDMKTAKSPGLKKYFNQLQNEMKICANSHYG 84
Cdd:cd05533    80 LEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYG 122
PHA03036 PHA03036
DNA polymerase; Provisional
 42-86 2.01e-05

DNA polymerase; Provisional


Pssm-ID: 222962 [Multi-domain]  Cd Length: 1004  Bit Score: 40.77  E-value: 2.01e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2512276071   42 LRHYLSMRNKYKGDMKTAKSPGLKKYFNQLQNEMKICANSHYGVS 86
Cdd:PHA03036   629 LKTFLEERARYKKLLKEATSSVEKAIYDSMQYTYKIVANSVYGLM 673
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
 37-85 2.67e-05

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: 40.59  E-value: 2.67e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2512276071   37 YTSSSLRHYLSMRNKYKGDMKTAKSP--GLKKYFNQLQNEMKICANSHYGV 85
Cdd:smart00486 366 ILPKLLKKLLDKRKEIKKLMKKEKDEseELKKLLDSRQLALKLTANSVYGY 416
POLBc cd00145
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
 46-85 2.51e-04

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: 37.73  E-value: 2.51e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2512276071  46 LSMRNKYKGDMKTAK-SPGLKKYFNQLQNEMKICANSHYGV 85
Cdd:cd00145    77 LNFRDEAKKRMKAAKlAPEERVLYDNRQQALKVLANSFYGY 117
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
38-86 6.20e-04

DNA polymerase B elongation subunit [Replication, recombination and repair];


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 36.73  E-value: 6.20e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2512276071  38 TSSSLRHYLSMRNKYKGDMKTAKS-PGLKKYFNQLQNEMKICANSHYGVS 86
Cdd:COG0417   477 LPSILEELWDERDEAKKKMKKAKPdSEEYRLYDALQQALKILMNSFYGVL 526
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
 42-84 1.06e-03

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 36.16  E-value: 1.06e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 2512276071   42 LRHYLSMRNKYKGDMKTAKSPGLKKYFNQLQNEMKICANSHYG 84
Cdd:PTZ00166   617 VEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYG 659
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
 42-84 5.02e-03

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: 34.09  E-value: 5.02e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2512276071  42 LRHYLSMRNKYKGDMKTAKSPGLKKYFNQLQNEMKICANSHYG 84
Cdd:cd05532    77 IRKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYG 119
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH