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DNA_polymerase
Euk-VirNile_crocodilepox_virus
DNA_polymerase__YP_784249__Nile_crocodilepox_virus__1285600
Identity
- Accession:
- YP_784249 ↗
- Protein ID:
- DNA_polymerase
- Kingdom:
- euk
Quality
81.1
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Pokkesviricetes›
Chitovirales›
Poxviridae›
Crocodylidpoxvirus›
Nile_crocodilepox_virus
TaxID: 1285600
Cluster
View cluster (158 members)3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 153-328_435-464
Domain cluster:
rep: DNA_polymerase_catalytic_subunit__YP_401712__Human_gammaherpesvirus_4__10376__D288-457
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF03104.26 best | DNA_pol_B_exo1 | 84.3 | 1.30e-23 | 87.9% | 69.4% |
| PF08408.17 | DNA_pol_B_3 | 45.8 | 9.90e-12 | 36.4% | 25.0% |
D2
high
residues 332-421
Domain cluster:
rep: DNA_polymerase_elongation_subunit_family_B__YP_009162448__Salmon_gill_poxvirus__1680908__D388-474
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF08408.17 best | DNA_pol_B_3 | 67.0 | 2.60e-18 | 95.6% | 66.4% |
D3
high
residues 813-980
Domain cluster:
rep: IMGVR_UViG_3300021255_003095-3300021255-Ga0223825_1010595139__D209-342
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00136.27 best | DNA_pol_B | 85.1 | 6.50e-24 | 93.5% | 33.6% |
D4
medium
residues 2-148
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF08452.17 best | DNAP_B_exo_N | 45.1 | 6.80e-12 | 14.3% | 95.5% |
CATH (16)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3k59A01 | 2.40.50.590 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › DNA polymerase B, N domain, beta-barrel | 0.77 | 43.0 | 5.52e-01 | 100.0% | 94.1% |
| 2pi2D00 | 2.40.50.140 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins | 0.70 | 35.0 | 3.80e-01 | 97.3% | 56.9% |
| 3u4vA00 | 2.40.50.140 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins | 0.68 | 39.0 | 4.36e-01 | 98.0% | 71.6% |
| 3q8dA01 | 2.40.50.140 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins | 0.67 | 35.0 | 4.66e-01 | 98.6% | 94.8% |
| 2gu3A02 | 3.10.450.40 | Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › | 0.65 | 23.0 | 3.46e-01 | 87.8% | 73.0% |
| 6ro0F00 | 2.40.50.110 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › | 0.65 | 39.0 | 4.69e-01 | 98.6% | 89.8% |
| 3iayA01 | 2.40.50.730 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › | 0.63 | 39.0 | 4.77e-01 | 100.0% | 93.9% |
| 4egvA02 | 2.40.50.840 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › | 0.63 | 31.0 | 4.10e-01 | 95.2% | 89.3% |
| 1fguB02 | 2.40.50.140 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins | 0.61 | 39.0 | 4.28e-01 | 100.0% | 76.6% |
| 4bwgD00 | 2.40.50.110 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › | 0.57 | 35.0 | 4.25e-01 | 98.0% | 92.8% |
| 3kf8A00 | 2.40.50.1040 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › | 0.57 | 39.0 | 3.45e-01 | 100.0% | 49.3% |
| 4dkkA02 | 3.30.160.20 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › | 0.56 | 24.0 | 3.28e-01 | 95.9% | 77.0% |
| 7k98B01 | 2.40.50.140 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins | 0.53 | 35.0 | 3.92e-01 | 100.0% | 86.0% |
| 3i6eA01 | 3.30.390.10 | Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain | 0.50 | 32.0 | 3.69e-01 | 94.6% | 89.3% |
| 1xjvA01 | 2.40.50.140 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins | 0.50 | 38.0 | 3.92e-01 | 100.0% | 82.4% |
| 3ro6C01 | 3.30.390.10 | Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain | 0.50 | 33.0 | 3.77e-01 | 95.2% | 91.5% |
ECOD (58)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5036328 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.81 | 46.0 | 6.00e-01 | 100.0% | 97.6% |
| 5055355 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.78 | 45.0 | 5.78e-01 | 98.0% | 94.4% |
| 5012082 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.76 | 47.0 | 5.78e-01 | 100.0% | 95.8% |
| 4213053 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.74 | 38.0 | 4.70e-01 | 97.3% | 77.9% |
| 5005284 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.73 | 47.0 | 5.74e-01 | 100.0% | 98.9% |
| 3969970 | 243.3.1.3 ↗ | a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › PepSY | 0.73 | 25.0 | 3.51e-01 | 87.1% | 61.3% |
| 4449302 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.71 | 39.0 | 4.51e-01 | 98.0% | 73.3% |
| 4997715 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.70 | 65.0 | 6.21e-01 | 100.0% | 97.6% |
| 3788812 | 304.114.1.6 ↗ | a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain › DNA_pol_B_exo1 | 0.70 | 64.0 | 5.41e-01 | 99.3% | 76.2% |
| 5068090 | 4272.1.1.1 ↗ | a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa | 0.69 | 27.0 | 3.27e-01 | 76.9% | 52.0% |
| 4024809 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.69 | 41.0 | 5.08e-01 | 98.0% | 95.6% |
| 3654541 | 2.1.1.223 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF28721 | 0.68 | 42.0 | 4.75e-01 | 100.0% | 80.9% |
| 3626321 | 295.1.1.0 ↗ | a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain | 0.68 | 25.0 | 4.06e-01 | 95.2% | 90.9% |
| 5047563 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.68 | 34.0 | 4.61e-01 | 91.8% | 93.3% |
| 4504110 | 2484.1.1.197 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 | 0.68 | 63.0 | 4.49e-01 | 100.0% | 39.5% |
| 4942684 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.67 | 62.0 | 5.88e-01 | 98.0% | 97.6% |
| 4299557 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.67 | 62.0 | 5.60e-01 | 99.3% | 87.2% |
| 3366703 | 2.1.1.157 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › CDC24_OB2 | 0.67 | 42.0 | 4.41e-01 | 99.3% | 68.9% |
| 5078973 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.67 | 35.0 | 4.64e-01 | 96.6% | 93.8% |
| 3991931 | 2.1.1.130 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF223 | 0.66 | 42.0 | 4.61e-01 | 100.0% | 77.5% |
| 3446499 | 2.1.1.130 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF223 | 0.66 | 43.0 | 4.77e-01 | 100.0% | 80.8% |
| 4500300 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.66 | 61.0 | 4.44e-01 | 99.3% | 41.3% |
| 3374948 | 2.1.1.130 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF223 | 0.66 | 41.0 | 4.91e-01 | 100.0% | 92.0% |
| 3784708 | 2.1.1.44 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Dna2 | 0.66 | 34.0 | 4.38e-01 | 95.2% | 85.9% |
| 3247575 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.65 | 38.0 | 4.23e-01 | 97.3% | 70.8% |
| 5019480 | 304.48.1.3 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B | 0.65 | 60.0 | 3.80e-01 | 100.0% | 25.7% |
| 4999027 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.65 | 34.0 | 4.55e-01 | 91.2% | 97.3% |
| 5000724 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.65 | 38.0 | 4.65e-01 | 97.3% | 90.5% |
| 396 | 2.2.1.8 ↗ | beta barrels › OB-fold › Bacterial enterotoxins › Bacterial enterotoxins › Pertus-S5-tox | 0.64 | 40.0 | 4.74e-01 | 100.0% | 91.8% |
| 4972474 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.64 | 59.0 | 3.80e-01 | 100.0% | 25.0% |
| 3630622 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.64 | 41.0 | 4.50e-01 | 100.0% | 78.3% |
| 3661180 | 2.1.1.223 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF28721 | 0.63 | 40.0 | 4.78e-01 | 100.0% | 94.0% |
| 4976869 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.63 | 46.0 | 5.17e-01 | 100.0% | 94.8% |
| 3514912 | 284.1.3.0 ↗ | a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain | 0.63 | 30.0 | 3.96e-01 | 98.6% | 85.3% |
| 5010618 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.63 | 27.0 | 3.98e-01 | 81.6% | 92.1% |
| 3675935 | 2.1.1.223 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF28721 | 0.62 | 41.0 | 4.25e-01 | 100.0% | 71.9% |
| 3358498 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.62 | 34.0 | 4.07e-01 | 100.0% | 79.0% |
| 3934534 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.62 | 43.0 | 4.43e-01 | 96.6% | 74.3% |
| 4988803 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.62 | 57.0 | 4.08e-01 | 98.6% | 88.1% |
| 3657721 | 2.1.1.223 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF28721 | 0.62 | 40.0 | 4.06e-01 | 100.0% | 64.7% |
| 3444970 | 2.1.1.223 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF28721 | 0.61 | 41.0 | 4.35e-01 | 100.0% | 76.2% |
| 3935835 | 2.1.1.68 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RMI1_C | 0.60 | 43.0 | 4.40e-01 | 96.6% | 75.7% |
| 3621460 | 2.1.1.68 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RMI1_C | 0.60 | 42.0 | 4.30e-01 | 95.9% | 73.1% |
| 4026007 | 330.1.1.0 ↗ | a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like | 0.59 | 25.0 | 3.25e-01 | 95.9% | 67.5% |
| 3650904 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.59 | 38.0 | 4.61e-01 | 98.6% | 100.0% |
| 169352 | 2.2.1.0 ↗ | beta barrels › OB-fold › Bacterial enterotoxins › Bacterial enterotoxins | 0.59 | 37.0 | 4.14e-01 | 98.0% | 79.7% |
| 5081878 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.58 | 49.0 | 3.62e-01 | 99.3% | 36.1% |
| 3679986 | 2.1.1.305 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Rep_fac-A_C, REPA_OB_2 | 0.58 | 40.0 | 3.11e-01 | 100.0% | 34.1% |
| 3654791 | 2.1.1.76 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › REPA_OB_2 | 0.58 | 40.0 | 4.12e-01 | 100.0% | 73.1% |
| 4989633 | 3891.1.1.0 ↗ | a+b two layers › Archaea-specific ribosomal protein L46a › Archaea-specific ribosomal protein L46a › Archaea-specific ribosomal protein L46a | 0.57 | 29.0 | 3.83e-01 | 85.7% | 88.7% |
| 2132960 | 2.2.1.4 ↗ | beta barrels › OB-fold › Bacterial enterotoxins › Bacterial enterotoxins › Pertussis_S2S3 | 0.57 | 37.0 | 4.14e-01 | 98.0% | 83.5% |
| 3585893 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.56 | 42.0 | 4.27e-01 | 95.9% | 78.6% |
| 4087213 | 330.4.1.1 ↗ | a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC | 0.55 | 24.0 | 3.26e-01 | 81.6% | 76.0% |
| 4982659 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.55 | 51.0 | 3.79e-01 | 99.3% | 91.4% |
| 3359808 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.55 | 38.0 | 4.07e-01 | 100.0% | 81.5% |
| 3963716 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.53 | 34.0 | 3.90e-01 | 99.3% | 87.3% |
| 3168835 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.53 | 42.0 | 4.55e-01 | 96.6% | 97.6% |
| 133860 | 218.1.1.1 ↗ | a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N | 0.52 | 33.0 | 3.67e-01 | 94.6% | 81.4% |
D5
medium
residues 465-512_607-657
Domain cluster:
rep: DNA_polymerase__YP_008052566__Phaeocystis_globosa_virus__251749__D724-746_869-928
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00136.27 best | DNA_pol_B | 54.1 | 1.70e-14 | 85.9% | 11.9% |
D6
medium
residues 513-542_677-812
Domain cluster:
rep: NC_004735.1__NP_835679.1__Rm378p092__00092__D1-33_185-289
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00136.27 best | DNA_pol_B | 89.5 | 3.10e-25 | 78.9% | 22.7% |
| PF00136.27 | DNA_pol_B | 28.0 | 1.40e-06 | 19.3% | 6.2% |
D7
medium
residues 543-606_658-676
Domain cluster:
rep: DNA_polymerase__YP_008052566__Phaeocystis_globosa_virus__251749__D724-746_869-928