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DNA_polymerase_catalytic_subunit
Euk-VirColumbid_alphaherpesvirus_1
DNA_polymerase_catalytic_subunit__YP_009352938__Columbid_alphaherpesvirus_1__93386
Identity
- Accession:
- YP_009352938 ↗
- Protein ID:
- DNA_polymerase_catalytic_subunit
- Kingdom:
- euk
Quality
78.1
mean pLDDT
Taxonomy
Heunggongvirae›
Peploviricota›
Herviviricetes›
Herpesvirales›
Orthoherpesviridae›
Mardivirus›
Columbid_alphaherpesvirus_1
TaxID: 93386
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 130-197_319-358
D2
medium
residues 198-231_245-318
D3
medium
residues 370-537
Domain cluster:
rep: DNA_polymerase_catalytic_subunit__YP_401712__Human_gammaherpesvirus_4__10376__D288-457
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF03104.26 best | DNA_pol_B_exo1 | 171.8 | 2.40e-50 | 100.0% | 68.2% |
D4
medium
residues 570-637
Domain cluster:
representative
CATH (3)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4qclA03 | 3.30.420.10 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H | 0.87 | 79.0 | 5.18e-01 | 100.0% | 25.1% |
| 4i3vA01 | 3.40.605.10 | Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 | 0.74 | 44.0 | 2.92e-01 | 97.1% | 15.2% |
| 3r6nA02 | 1.20.58.1060 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.57 | 45.0 | 3.38e-01 | 83.8% | 63.2% |
ECOD (41)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3710418 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.96 | 91.0 | 5.48e-01 | 100.0% | 18.1% |
| 1822623 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.96 | 92.0 | 5.81e-01 | 100.0% | 24.8% |
| None | — | 0.96 | 91.0 | 5.48e-01 | 100.0% | 18.6% | |
| 3368695 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.95 | 90.0 | 5.38e-01 | 100.0% | 17.4% |
| None | — | 0.95 | 89.0 | 5.02e-01 | 100.0% | 10.6% | |
| None | — | 0.95 | 89.0 | 5.02e-01 | 100.0% | 10.7% | |
| 3628202 | 304.48.1.0 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like | 0.95 | 89.0 | 5.00e-01 | 100.0% | 10.2% |
| 3995965 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.94 | 89.0 | 6.26e-01 | 100.0% | 37.3% |
| 3496492 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.92 | 86.0 | 5.44e-01 | 100.0% | 23.8% |
| 3797773 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.91 | 85.0 | 5.39e-01 | 100.0% | 23.4% |
| 5025208 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.91 | 83.0 | 5.53e-01 | 100.0% | 28.7% |
| 3794217 | 2.1.1.0 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein | 0.91 | 85.0 | 4.89e-01 | 100.0% | 13.0% |
| 3705562 | 304.48.1.0 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like | 0.91 | 85.0 | 4.77e-01 | 100.0% | 10.5% |
| 3404726 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.90 | 84.0 | 5.33e-01 | 100.0% | 23.7% |
| 3192875 | 304.114.1.0 ↗ | a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain | 0.89 | 82.0 | 4.81e-01 | 100.0% | 14.3% |
| 4888481 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.89 | 82.0 | 5.33e-01 | 100.0% | 26.3% |
| 3684974 | 304.48.1.0 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like | 0.88 | 81.0 | 4.59e-01 | 100.0% | 10.5% |
| 4805117 | 2484.1.1.161 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.88 | 81.0 | 5.50e-01 | 100.0% | 31.8% |
| 3206356 | 304.114.1.0 ↗ | a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain | 0.88 | 80.0 | 4.85e-01 | 100.0% | 17.2% |
| 3167764 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.87 | 80.0 | 5.07e-01 | 100.0% | 22.3% |
| 3492151 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.87 | 79.0 | 4.96e-01 | 100.0% | 20.6% |
| 4024811 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.87 | 80.0 | 5.16e-01 | 100.0% | 82.1% |
| 4874454 | 2.1.1.25 ↗ | beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 | 0.86 | 78.0 | 5.15e-01 | 100.0% | 25.7% |
| 3214818 | 304.114.1.0 ↗ | a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain | 0.85 | 78.0 | 4.76e-01 | 100.0% | 18.4% |
| 3520437 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.84 | 76.0 | 5.45e-01 | 100.0% | 35.8% |
| 5081878 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.84 | 76.0 | 4.69e-01 | 100.0% | 18.6% |
| 3256261 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.84 | 75.0 | 5.02e-01 | 100.0% | 26.7% |
| 5036329 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.75 | 63.0 | 4.34e-01 | 100.0% | 27.2% |
| 4990754 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.73 | 61.0 | 4.25e-01 | 97.1% | 28.0% |
| 5035328 | 2484.1.1.34 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 | 0.72 | 60.0 | 4.21e-01 | 100.0% | 27.7% |
| 3941043 | 605.1.1.211 ↗ | alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › ATG9 | 0.71 | 47.0 | 2.81e-01 | 92.6% | 9.5% |
| 5073475 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.65 | 49.0 | 3.17e-01 | 80.9% | 43.5% |
| 5025842 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.64 | 49.0 | 3.72e-01 | 80.9% | 81.3% |
| 4931231 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.62 | 46.0 | 3.31e-01 | 80.9% | 67.5% |
| 4549838 | 3567.1.1.152 ↗ | a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › ATG9 | 0.61 | 46.0 | 3.74e-01 | 82.4% | 42.3% |
| 3696570 | 192.15.1.128 ↗ | alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › ATG9 | 0.59 | 45.0 | 3.82e-01 | 83.8% | 50.4% |
| 4005910 | 325.1.7.0 ↗ | a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif | 0.58 | 44.0 | 3.96e-01 | 85.3% | 64.0% |
| 3724315 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.58 | 42.0 | 3.25e-01 | 76.5% | 68.0% |
| 3975777 | 1.1.2.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › double psi | 0.57 | 43.0 | 3.89e-01 | 82.4% | 61.1% |
| 3897097 | 7525.1.1.2 ↗ | a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_2 | 0.52 | 43.0 | 2.66e-01 | 92.6% | 18.0% |
| 3699443 | 3755.3.1.0 ↗ | alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin | 0.52 | 36.0 | 3.08e-01 | 70.6% | 66.1% |
D5
medium
residues 707-727_866-963
Domain cluster:
rep: DNA_polymerase_catalytic_subunit__YP_002608259__Human_herpesvirus_5__10359__D703-718_902-984
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00136.27 best | DNA_pol_B | 93.5 | 1.90e-26 | 82.3% | 19.4% |
D6
medium
residues 728-774_831-865
Domain cluster:
rep: rh87__YP_068180__Macacine_betaherpesvirus_3__47929__D595-644_698-744
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00136.27 best | DNA_pol_B | 41.0 | 1.50e-10 | 59.8% | 10.2% |
| PF00136.27 | DNA_pol_B | 29.9 | 3.70e-07 | 43.9% | 6.8% |
D7
medium
residues 775-830
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 | 66.6 | 2.80e-18 | 100.0% | 12.6% |