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DNA_polymerase

Euk-Vir

Goose_adenovirus_4

DNA_polymerase__YP_006383556__Goose_adenovirus_4__1193422

Identity

Accession:
YP_006383556 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

77.3 mean pLDDT

Taxonomy

Bamfordvirae› Preplasmiviricota› Pharingeaviricetes› Rowavirales› Adenoviridae› Aviadenovirus› Goose_adenovirus_4

TaxID: 1193422

Cluster

View cluster (24 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 69-195
PDB
Domain cluster: rep: DNA_polymerase__YP_009246380__Bat_mastadenovirus_WIV10__1788432__D69-178
D2 medium residues 238-341_390-432
PDB
Domain cluster: rep: hypothetical_protein_CaV1gp07__NP_044189__Canine_mastadenovirus_A__10537__D45-121_189-230
D3 medium residues 635-653_687-794
PDB
Domain cluster: rep: DNA_polymerase__NP_040516__Human_mastadenovirus_C__129951__D703-805
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03175.19 best DNA_pol_B_2 77.1 1.90e-21 85.0% 20.3%
D4 medium residues 795-832_972-993
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03175.19 best DNA_pol_B_2 47.9 1.30e-12 95.0% 8.1%
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3gonA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.84 58.0 4.31e-01 98.3% 32.1%
6he1B01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.83 54.0 5.29e-01 96.7% 62.5%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.83 57.0 6.42e-01 100.0% 93.5%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.82 55.0 5.91e-01 96.7% 80.8%
4ebjA02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.81 56.0 4.24e-01 100.0% 33.1%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.80 59.0 6.57e-01 91.7% 100.0%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.78 57.0 4.87e-01 100.0% 50.0%
3etuA01 1.10.287.3290 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.77 54.0 5.31e-01 100.0% 67.7%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.77 56.0 5.36e-01 100.0% 66.7%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.75 57.0 4.39e-01 100.0% 38.7%
3craB01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.74 55.0 4.82e-01 100.0% 54.7%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.71 55.0 4.42e-01 100.0% 44.2%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.70 57.0 4.99e-01 100.0% 61.2%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.69 57.0 4.48e-01 100.0% 44.6%
5t1dB00 3.10.390.20 Alpha Beta › Roll › SAND domain › Viral glycoprotein L 0.63 42.0 3.62e-01 100.0% 41.4%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.62 46.0 4.63e-01 91.7% 81.4%
3aagA01 3.40.1380.40 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › 0.55 35.0 2.77e-01 86.7% 26.6%
3fedA03 1.20.930.40 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Transferrin receptor-like, dimerisation domain 0.53 44.0 3.38e-01 100.0% 44.5%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3369096 4970.1.1.3 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B_2 0.95 61.0 7.08e-01 96.7% 88.9%
4193 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.89 58.0 6.73e-01 96.7% 93.0%
4682578 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.85 58.0 3.82e-01 100.0% 20.0%
4472442 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.85 55.0 6.62e-01 98.3% 100.0%
3976258 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.83 58.0 6.04e-01 100.0% 78.2%
3967220 632.11.1.13 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › PF27144 0.81 55.0 5.37e-01 100.0% 65.6%
3902516 109.4.1.1448 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1, TPR_7, TPR_10, TPR_12, TPR_MalT 0.81 54.0 3.43e-01 98.3% 15.8%
3174429 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.81 58.0 6.61e-01 100.0% 100.0%
3504819 192.17.1.6 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › CC2D1A-B_DM14 0.80 58.0 5.66e-01 100.0% 70.8%
3513338 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.80 53.0 3.55e-01 100.0% 18.7%
3573745 609.1.1.0 ↗ alpha bundles › Domain of poly(ADP-ribose) polymerase › Domain of poly(ADP-ribose) polymerase › Domain of poly(ADP-ribose) polymerase 0.79 57.0 4.00e-01 100.0% 26.5%
3615115 109.4.1.192 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8 0.79 56.0 3.73e-01 100.0% 20.2%
3774145 192.17.1.6 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › CC2D1A-B_DM14 0.77 56.0 4.24e-01 100.0% 34.1%
4565034 159.1.3.3 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › putative NTP pyrophosphohydrolase Exig_1061 › MazG 0.77 56.0 4.30e-01 100.0% 36.8%
3881336 109.4.1.2896 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1, GoLoco, TPR_7, TPR_8, TPR_12 0.76 58.0 3.71e-01 80.0% 89.8%
3725040 3877.1.1.1 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC › 60KD_IMP 0.75 55.0 3.62e-01 100.0% 20.4%
3707335 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.75 53.0 4.93e-01 100.0% 60.0%
3968795 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 0.74 69.0 4.36e-01 100.0% 31.5%
3943776 159.1.1.1 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 › MazG 0.71 55.0 4.23e-01 100.0% 38.5%
3639102 109.4.1.1129 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_TRAPPC9-Trs120 0.70 57.0 4.36e-01 100.0% 41.6%
5032400 3291.1.1.1 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Snf7 0.69 56.0 4.08e-01 90.0% 80.0%
4995146 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.67 62.0 5.34e-01 100.0% 72.2%
3755359 109.4.1.198 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_12 0.65 55.0 3.78e-01 90.0% 76.8%
4541925 5000.4.1.0 ↗ alpha arrays › Toxins' membrane translocation domains › delta-Endotoxin (insectocide), N-terminal domain › delta-Endotoxin (insectocide), N-terminal domain 0.63 56.0 3.76e-01 100.0% 41.8%
3552824 3877.1.1.1 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC › 60KD_IMP 0.60 56.0 3.66e-01 100.0% 77.3%
3596878 109.40.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › DNA polymerase alpha-binding protein Ctf4 C-terminal domain 0.60 54.0 4.16e-01 100.0% 70.0%
3371182 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.59 54.0 4.43e-01 100.0% 57.1%
D5 medium residues 1120-1209
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6wcsA02 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.53 34.0 2.65e-01 74.4% 28.8%
2np2A00 4.10.520.10 Few Secondary Structures › Irregular › HU Protein; Chain A › IHF-like DNA-binding proteins 0.52 32.0 3.12e-01 90.0% 52.9%
6lpwA02 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.51 33.0 2.58e-01 74.4% 28.3%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3621341 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.53 34.0 3.71e-01 76.7% 78.7%
4855693 323.1.1.5 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.53 30.0 2.64e-01 74.4% 34.7%
3957478 323.1.1.11 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › PapA_C 0.52 32.0 2.73e-01 74.4% 35.6%