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HM151342.1__ADK73473.1__RDJLphi1_gp72__00072

Bact-Vir

HM151342.1__ADK73473.1__RDJLphi1_gp72__00072

Identity

Accession:
HM151342 ↗
Kingdom:
phage

Quality

80.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Xiamenvirus› Roseobacter_phage_RDJL_Phi_1

TaxID: 562742

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 60-116
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r0cA02 3.30.9.10 Alpha Beta › 2-Layer Sandwich › D-Amino Acid Oxidase; Chain A, domain 2 › D-Amino Acid Oxidase, subunit A, domain 2 0.64 46.0 3.54e-01 78.9% 71.7%
2mm0A00 2.10.70.110 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.64 54.0 5.27e-01 100.0% 87.5%
8ciwA02 2.40.110.10 Mainly Beta › Beta Barrel › Butyryl-CoA Dehydrogenase, subunit A; domain 2 › Butyryl-CoA Dehydrogenase, subunit A, domain 2 0.61 51.0 3.94e-01 96.5% 53.4%
7b9cA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.59 48.0 2.95e-01 93.0% 18.6%
1ri6A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.59 47.0 2.97e-01 93.0% 24.6%
2x8fA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.59 46.0 2.96e-01 91.2% 33.2%
2ww8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 50.0 4.18e-01 100.0% 93.4%
1amiA04 3.20.19.10 Alpha Beta › Alpha-Beta Barrel › Aconitase; domain 4 › Aconitase, domain 4 0.58 41.0 2.88e-01 78.9% 84.2%
2gu1A01 3.10.450.350 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.58 46.0 4.11e-01 93.0% 76.1%
3f4lA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.57 46.0 3.27e-01 100.0% 74.9%
4dzoA02 3.30.457.60 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › 0.57 41.0 3.78e-01 78.9% 66.2%
2jraA01 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.57 39.0 4.35e-01 89.5% 100.0%
3q48A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 43.0 3.93e-01 87.7% 92.8%
4hcsA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 43.0 4.15e-01 94.7% 73.1%
1szzA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.55 47.0 3.43e-01 100.0% 72.5%
3v0aB03 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.55 39.0 2.76e-01 78.9% 21.5%
4c5wA01 3.30.2020.30 Alpha Beta › 2-Layer Sandwich › NE0471 N-terminal domain-like › 0.55 41.0 3.53e-01 84.2% 90.7%
3aabB00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 40.0 3.44e-01 91.2% 62.3%
3nixB00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 38.0 2.32e-01 78.9% 42.3%
1nr4C00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 41.0 3.89e-01 91.2% 72.7%
1eqtA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 41.0 3.89e-01 91.2% 71.6%
7byjA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 37.0 3.23e-01 78.9% 67.4%
4ydsA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 40.0 2.79e-01 91.2% 97.8%
6l4lA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.50 42.0 3.45e-01 100.0% 91.4%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3982705 101.15.1.2 ↗ alpha arrays › HTH › LysM domain › LysM domain › OapA 0.64 52.0 4.41e-01 89.5% 67.0%
3181119 5.1.4.169 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_RSE1_2nd 0.62 52.0 3.11e-01 94.7% 17.5%
4038568 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.60 40.0 2.83e-01 70.2% 24.2%
3164516 101.15.1.2 ↗ alpha arrays › HTH › LysM domain › LysM domain › OapA 0.60 48.0 4.27e-01 91.2% 69.4%
5028034 4312.1.1.0 ↗ a+b two layers › RelE-like › RelE-like › RelE-like 0.59 43.0 3.78e-01 80.7% 60.0%
3668331 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.58 47.0 3.00e-01 94.7% 23.4%
3670098 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.57 41.0 4.01e-01 80.7% 75.4%
3515664 5.1.4.34 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Nup88 0.57 47.0 2.73e-01 94.7% 74.7%
3647627 2484.1.1.21 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › BcrAD_BadFG 0.55 43.0 3.28e-01 91.2% 49.3%
3989851 11.1.1.1339 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › CFSR 0.54 42.0 3.36e-01 98.2% 71.0%
3968457 101.15.1.2 ↗ alpha arrays › HTH › LysM domain › LysM domain › OapA 0.52 41.0 3.71e-01 91.2% 70.6%
3856611 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.52 40.0 3.92e-01 91.2% 76.2%
3699568 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.52 41.0 3.88e-01 89.5% 72.9%
3894506 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.52 40.0 3.76e-01 91.2% 68.6%
4813310 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.51 40.0 3.79e-01 91.2% 71.6%
665 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.51 40.0 3.83e-01 94.7% 73.1%
D2 high residues 234-311
PDB
Domain cluster: rep: MT764845.1__QNN99842.1__P67b_00083__00083__D396-459
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4lwsA00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.84 48.0 4.36e-01 100.0% 45.0%
2f8lA01 1.10.150.470 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.72 44.0 4.40e-01 73.1% 59.3%
1x42A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.70 47.0 4.68e-01 70.5% 81.9%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.66 45.0 4.31e-01 70.5% 70.0%
8ctsB01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 42.0 4.04e-01 73.1% 59.8%
2wdqD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.62 42.0 3.84e-01 70.5% 90.5%
3gi7A00 1.20.1270.180 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.62 48.0 4.38e-01 83.3% 97.1%
4kwaB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.61 51.0 3.95e-01 96.2% 80.7%
1mswD04 1.10.287.280 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 41.0 4.16e-01 70.5% 71.8%
1i6zA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.60 49.0 4.04e-01 87.2% 85.2%
2oayA01 3.30.497.10 Alpha Beta › 2-Layer Sandwich › Antithrombin; Chain I, domain 2 › Antithrombin, subunit I, domain 2 0.59 43.0 3.29e-01 76.9% 83.5%
2qffA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.57 39.0 4.07e-01 73.1% 100.0%
2nnwA02 1.10.287.4070 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 48.0 4.16e-01 97.4% 68.5%
7e84A03 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 44.0 3.85e-01 87.2% 55.3%
1sumB01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.56 48.0 4.24e-01 91.0% 100.0%
4ye6A01 1.10.8.1290 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1, domain 1 0.51 35.0 3.23e-01 71.8% 59.6%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1495253 150.5.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.84 48.0 4.36e-01 100.0% 45.0%
3719307 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.73 51.0 3.72e-01 71.8% 32.0%
4985449 5054.1.1.8 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 0.68 50.0 4.85e-01 83.3% 70.6%
4025859 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.66 54.0 5.38e-01 87.2% 100.0%
3261908 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.66 45.0 4.65e-01 75.6% 74.7%
3926770 109.4.1.1288 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_11 0.65 42.0 2.81e-01 70.5% 17.0%
3878853 4044.1.1.13 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › BicD 0.63 54.0 5.31e-01 93.6% 97.6%
4887248 601.7.3.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN 0.61 53.0 3.77e-01 96.2% 41.6%
4221094 611.9.1.6 ↗ alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain › Ran-binding 0.60 48.0 4.05e-01 85.9% 85.4%
3222805 5054.1.1.8 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 0.60 50.0 3.48e-01 92.3% 53.0%
3977082 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.60 50.0 4.28e-01 91.0% 82.4%
5057376 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.58 44.0 4.31e-01 84.6% 74.1%
3692742 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.56 39.0 3.30e-01 74.4% 41.5%
5037396 2003.1.1.22 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › GFO_IDH_MocA 0.53 43.0 3.12e-01 89.7% 99.1%
3581944 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.53 45.0 4.02e-01 97.4% 96.5%
3701004 4133.1.1.0 ↗ alpha arrays › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like 0.52 40.0 3.88e-01 80.8% 91.8%
2169826 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.50 34.0 3.76e-01 73.1% 88.9%