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NC_028999.1__YP_009217287.1__AVT69_gp206__00205

Bact-Vir

NC_028999.1__YP_009217287.1__AVT69_gp206__00205

Identity

Accession:
NC_028999 ↗
Kingdom:
phage

Quality

78.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Miltoncavirus› Pseudomonas_phage_PhiPA3

TaxID: 998086

Cluster

View cluster (4 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 128-286
PDB
Domain cluster: rep: NC_048792.1__YP_009849274.1__HWC48_gp236__00178__D125-293
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4it4A02 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.66 37.0 4.84e-01 77.4% 97.8%
1b8dA00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.64 46.0 4.63e-01 74.2% 100.0%
1cpcA00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.63 46.0 4.65e-01 76.7% 100.0%
1k90B03 1.20.140.60 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.62 34.0 3.93e-01 82.4% 73.0%
1cg5B00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.61 48.0 5.08e-01 82.4% 100.0%
1st6A04 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.61 35.0 4.01e-01 78.0% 76.1%
3k3uA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.61 46.0 4.89e-01 78.6% 99.3%
4c0nA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.60 49.0 5.04e-01 86.8% 96.0%
1binA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.59 45.0 4.74e-01 79.2% 100.0%
1yo7A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.59 40.0 4.63e-01 83.0% 92.5%
3nqwA00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.59 43.0 4.13e-01 73.6% 79.2%
2fefA01 1.20.1440.70 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › PA2201 N-terminal domain-like 0.58 43.0 4.78e-01 86.2% 96.8%
2fzfA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 37.0 3.84e-01 81.8% 72.7%
3kavA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.55 34.0 4.12e-01 82.4% 96.1%
1ki1B01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.54 40.0 3.74e-01 77.4% 95.0%
2lqgA00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.53 40.0 4.31e-01 83.6% 91.3%
2jx0A00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.52 40.0 4.35e-01 100.0% 96.2%
4etrB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 38.0 4.30e-01 79.2% 96.7%
6dlzA01 1.20.140.150 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.51 42.0 4.01e-01 85.5% 95.6%
1u6zA03 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.51 32.0 3.34e-01 74.8% 65.8%
6t0bc02 1.20.120.80 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle 0.51 42.0 3.91e-01 85.5% 73.3%
3ha4B00 1.20.58.690 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 35.0 3.98e-01 74.2% 92.5%
2ppqA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.51 40.0 3.65e-01 83.6% 94.9%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3260973 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.63 39.0 4.70e-01 80.5% 90.9%
3691841 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.61 44.0 4.09e-01 72.3% 84.6%
3712159 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.59 42.0 4.33e-01 87.4% 75.5%
3966574 633.9.1.1 ↗ alpha bundles › Bromodomain-like › PA2201 N-terminal domain-like › PA2201 N-terminal domain-like › PA2201_N 0.58 43.0 4.79e-01 86.2% 96.8%
3813600 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.57 43.0 4.69e-01 85.5% 91.1%
3954068 633.23.1.7 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › DUF5336 0.56 40.0 4.45e-01 85.5% 92.0%
3977220 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.56 43.0 3.63e-01 79.9% 83.1%
4021431 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.55 43.0 4.58e-01 87.4% 92.1%
3598426 3615.1.1.0 ↗ alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain 0.55 35.0 3.97e-01 84.9% 83.2%
None — 0.55 46.0 3.78e-01 88.7% 80.0%
3559622 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.55 44.0 4.49e-01 87.4% 85.8%
3928215 133.1.1.0 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) 0.55 42.0 3.94e-01 79.2% 96.8%
4057126 109.4.1.1290 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_19 0.54 36.0 2.91e-01 79.9% 33.9%
5001131 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.54 41.0 3.93e-01 89.3% 67.6%
4953520 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.54 45.0 3.70e-01 89.9% 98.6%
3309205 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.53 39.0 4.07e-01 84.9% 82.1%
3814234 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.53 41.0 4.52e-01 85.5% 97.7%
3371270 633.10.1.0 ↗ alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.53 39.0 4.15e-01 85.5% 85.7%
3523225 5059.1.1.4 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › Nuc_sug_transp 0.53 46.0 3.71e-01 95.6% 97.2%
3878144 601.1.2.2 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › I_LWEQ 0.53 39.0 4.27e-01 84.3% 90.4%
3880919 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.53 42.0 4.39e-01 87.4% 89.9%
3940171 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.52 43.0 4.56e-01 87.4% 96.4%
3746414 109.4.1.311 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ST7 0.52 43.0 3.02e-01 85.5% 45.8%
3826788 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.51 44.0 4.31e-01 89.9% 89.0%
3427750 633.21.1.18 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CASP_dom 0.51 43.0 4.29e-01 87.4% 88.7%
3803172 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.51 44.0 4.44e-01 91.2% 90.6%
3326634 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.51 44.0 4.27e-01 91.2% 88.6%
3841582 633.23.1.22 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › MARVEL 0.51 42.0 4.26e-01 87.4% 89.0%
3597688 171.1.1.0 ↗ alpha arrays › RNase III catalytic domain-like › RNase III catalytic domain-like › RNase III catalytic domain-like 0.51 42.0 3.88e-01 87.4% 92.6%
4801290 601.1.2.4 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Talin_R4 0.51 39.0 4.14e-01 85.5% 90.3%
3675187 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.50 43.0 4.08e-01 89.3% 94.6%
3739123 601.1.2.2 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › I_LWEQ 0.50 41.0 3.76e-01 85.5% 67.3%
3359510 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.50 42.0 4.27e-01 87.4% 92.3%
3764834 601.1.2.2 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › I_LWEQ 0.50 41.0 3.87e-01 85.5% 72.6%
D2 high residues 289-368
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.60 37.0 4.12e-01 90.0% 80.3%
1vw4T01 6.10.330.20 Special › Helix non-globular › Monooxygenase › 0.60 35.0 3.10e-01 91.3% 40.2%
3q2eA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.53 44.0 3.96e-01 100.0% 66.4%
3b0bC02 6.10.130.30 Special › Helix non-globular › GTP Cyclohydrolase I; Chain A, domain 1 › 0.53 27.0 3.29e-01 72.5% 83.7%
1ciiA02 3.30.305.10 Alpha Beta › 2-Layer Sandwich › Colicin Ia; domain 2 › Colicin Ia; domain 2 0.52 37.0 3.46e-01 90.0% 59.4%
3g3tA00 3.20.100.30 Alpha Beta › Alpha-Beta Barrel › mRNA Triphosphatase Cet1; Chain A › VTC, catalytic tunnel domain 0.52 43.0 3.08e-01 96.2% 87.2%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3566658 2006.1.4.33 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › Tim17 0.56 35.0 3.61e-01 83.7% 65.3%
5025014 1075.1.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain 0.55 47.0 3.51e-01 98.8% 79.5%
4129436 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.54 37.0 3.37e-01 87.5% 53.3%
137165 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.53 42.0 3.39e-01 87.5% 69.0%
5013611 1075.1.1.38 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › FLQE3_permease 0.53 45.0 3.37e-01 100.0% 79.0%
3329547 604.6.1.22 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › EMC4 0.53 33.0 3.01e-01 88.7% 45.5%
3658236 604.12.1.69 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › SRP68 0.53 44.0 3.79e-01 100.0% 58.4%
4293733 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.50 34.0 3.19e-01 90.0% 54.3%
D3 medium residues 4-68
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hn2A02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.61 40.0 3.25e-01 100.0% 34.4%
2f1kC02 1.10.3660.10 Mainly Alpha › Orthogonal Bundle › 6-phosphogluconate dehydrogenase C-terminal fold › 6-phosphogluconate dehydrogenase C-terminal like domain 0.60 35.0 2.90e-01 98.5% 33.6%
6z74C02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.58 50.0 3.88e-01 100.0% 86.8%
4i5sA01 1.10.8.500 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › HAMP domain in histidine kinase 0.57 33.0 3.34e-01 87.7% 58.5%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.57 39.0 3.42e-01 70.8% 75.8%
1m6nA05 1.10.1200.230 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.56 48.0 4.44e-01 100.0% 80.0%
6al9B00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.56 40.0 3.60e-01 76.9% 73.6%
1xfiA02 1.20.1700.10 Mainly Alpha › Up-down Bundle › AF1104-like › AF1104-like 0.55 37.0 3.36e-01 100.0% 50.0%
6bekD00 1.10.8.50 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.54 43.0 3.97e-01 90.8% 76.4%
2kmfA01 1.20.58.810 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Photosystem II Pbs27 0.52 44.0 3.86e-01 96.9% 82.4%
6k4yI00 1.10.1810.10 Mainly Alpha › Orthogonal Bundle › Anti-sigma factor AsiA › Anti-Sigma Factor A 0.52 34.0 3.13e-01 95.4% 51.1%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3803076 601.1.1.93 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › DUF1216 0.52 45.0 3.43e-01 100.0% 83.6%
5048087 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.51 44.0 3.80e-01 100.0% 72.4%
3341807 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.50 34.0 2.85e-01 70.8% 67.3%