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NC_055840.1__YP_010107099.1__KNU98_gp044__00065

Bact-Vir

NC_055840.1__YP_010107099.1__KNU98_gp044__00065

Identity

Accession:
NC_055840 ↗
Kingdom:
phage

Quality

71.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Oliverunavirus› Agrobacterium_phage_OLIVR1

TaxID: 2723769

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 3-54
PDB
Domain cluster: representative
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3vpyA00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.67 47.0 3.49e-01 76.9% 37.2%
2ab5B01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.64 41.0 3.15e-01 75.0% 26.6%
4wksC02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.64 45.0 4.00e-01 75.0% 81.3%
1se8A02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.63 52.0 4.21e-01 98.1% 49.5%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.62 45.0 3.55e-01 75.0% 65.6%
2k5qA00 2.40.50.480 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Protein of unknown function DUF1093 0.62 41.0 3.29e-01 71.2% 34.3%
6rupA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.61 49.0 4.05e-01 98.1% 51.4%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 43.0 3.03e-01 100.0% 20.6%
5odnC00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.60 48.0 3.95e-01 98.1% 47.1%
3d2lA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.60 40.0 3.83e-01 73.1% 57.1%
7r5mA01 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.60 43.0 2.89e-01 76.9% 22.9%
5ib9A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.60 45.0 2.84e-01 82.7% 38.9%
5w8mA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.58 42.0 2.88e-01 73.1% 59.2%
3voqA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 42.0 3.37e-01 96.2% 37.9%
1xttB00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.56 40.0 2.74e-01 78.8% 74.5%
1kf6A04 4.10.80.40 Few Secondary Structures › Irregular › Rhinovirus 14, subunit 4 › succinate dehydrogenase protein domain 0.56 36.0 3.83e-01 90.4% 97.1%
2a74A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.56 44.0 3.60e-01 92.3% 89.5%
4zg5A00 3.40.1210.10 Alpha Beta › 3-Layer(aba) Sandwich › Stationary-phase Survival Protein Sure Homolog; Chain: A, › Survival protein SurE-like phosphatase/nucleotidase 0.55 42.0 2.73e-01 84.6% 46.6%
3n77A00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.55 41.0 3.07e-01 80.8% 51.1%
2py5A05 4.10.80.20 Few Secondary Structures › Irregular › Rhinovirus 14, subunit 4 › DNA polymerase; domain 5 0.55 33.0 3.85e-01 96.2% 96.7%
1dt9A01 3.30.960.10 Alpha Beta › 2-Layer Sandwich › Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A › eRF1 domain 1 0.55 44.0 3.68e-01 98.1% 76.2%
3vwdA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 38.0 2.69e-01 76.9% 55.6%
3zqmA00 6.10.140.2160 Special › Helix non-globular › Helix Hairpins › 0.54 41.0 3.98e-01 86.5% 83.1%
1ry6A00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.53 43.0 2.72e-01 96.2% 91.2%
1fs7A01 1.10.1130.10 Mainly Alpha › Orthogonal Bundle › Flavocytochrome C3; Chain A, domain 2 › Flavocytochrome C3; Chain A 0.53 46.0 2.86e-01 100.0% 60.3%
2ogkD00 3.30.1440.10 Alpha Beta › 2-Layer Sandwich › 50s Ribosomal Protein L5; Chain: A, › Ribosomal protein L5 0.53 42.0 3.12e-01 90.4% 38.0%
1bd3A00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 41.0 2.72e-01 86.5% 68.8%
2ebfX01 3.10.670.10 Alpha Beta › Roll › Secreted effector protein ssei fold › Secreted effector protein ssei. 0.53 40.0 2.77e-01 90.4% 22.8%
1p1hB01 3.30.2360.10 Alpha Beta › 2-Layer Sandwich › Glyceraldehyde-3-phosphate dehydrogenase-like fold › Glyceraldehyde-3-phosphate dehydrogenase-like domain 0.52 43.0 3.08e-01 100.0% 88.1%
6le1A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.52 36.0 3.40e-01 76.9% 89.7%
2xzmZ00 3.30.1230.20 Alpha Beta › 2-Layer Sandwich › Hypothetical Cytosolic Protein; Chain: A; › Ribosomal protein S21 0.51 34.0 2.91e-01 78.8% 37.1%
3plsA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 32.0 2.66e-01 71.2% 29.8%
3ua0A00 6.20.280.10 Special › Other non-globular › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.51 36.0 3.27e-01 75.0% 50.6%
3e07A00 2.10.90.10 Mainly Beta › Ribbon › Cystine Knot Cytokines, subunit B › Cystine-knot cytokines 0.50 34.0 3.05e-01 75.0% 58.9%
3nqzA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.50 35.0 3.04e-01 73.1% 46.4%
1pu1A00 3.30.300.100 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › MTH677-like 0.50 31.0 2.74e-01 71.2% 35.2%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3786528 109.4.1.87 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec6 0.79 55.0 3.00e-01 82.7% 4.6%
3249830 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.76 54.0 4.03e-01 75.0% 32.0%
3947849 3609.1.1.4 ↗ alpha arrays › DNA repair protein RAD4 beta-hairpin domain › DNA repair protein RAD4 beta-hairpin domain › DNA repair protein RAD4 beta-hairpin domain › ArdcN 0.75 55.0 4.66e-01 80.8% 80.9%
3486348 101.17.1.0 ↗ alpha arrays › HTH › IHF-like DNA-binding proteins › IHF-like DNA-binding proteins 0.74 52.0 4.88e-01 75.0% 61.5%
4160831 109.4.1.1255 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N, Cnd1 0.74 47.0 2.62e-01 73.1% 4.9%
3238872 11.1.1.9 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_N 0.73 50.0 3.34e-01 71.2% 42.2%
3175102 2008.1.1.79 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Pet127 0.72 53.0 3.15e-01 78.8% 69.5%
3739386 109.4.1.3152 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT, TPR_16, TPR_19, HAT_Syf1_CNRKL1_C, HAT_Syf1_CNRKL1_N, HAT_PRP39_N 0.70 48.0 2.65e-01 71.2% 6.9%
3261509 109.4.1.890 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_CNRKL1_C 0.70 48.0 2.69e-01 73.1% 6.9%
3633076 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.70 49.0 3.92e-01 75.0% 44.8%
3587268 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.69 50.0 3.87e-01 78.8% 93.3%
3832498 4967.1.1.6 ↗ alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › Intron_maturas2 0.69 52.0 3.45e-01 82.7% 75.8%
3902637 385.1.1.5 ↗ few secondary structure elements › Cystine-knot cytokines › Cystine-knot cytokines › Cystine-knot cytokines › PDGF 0.69 47.0 4.00e-01 71.2% 61.2%
3516513 109.2.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid 0.69 44.0 2.43e-01 78.8% 4.4%
3815772 109.4.1.1580 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT, HAT_Syf1_CNRKL1_C, HAT_Syf1_CNRKL1_N, HAT_PRP39_N, HAT_PRP39_C 0.68 47.0 2.68e-01 84.6% 5.9%
3649881 67.1.1.1 ↗ beta sandwiches › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › DnaJ_C 0.68 58.0 4.94e-01 96.2% 85.9%
3497398 395.1.1.0 ↗ few secondary structure elements › Midkine-related › Midkine-related › Midkine-related 0.68 47.0 4.76e-01 78.8% 76.0%
4160692 171.1.1.1 ↗ alpha arrays › RNase III catalytic domain-like › RNase III catalytic domain-like › RNase III catalytic domain-like › Ribonuclease_3 0.67 51.0 3.35e-01 82.7% 78.2%
3436318 230.5.1.0 ↗ a+b two layers › T-fold › Band 7/SPFH domain › Band 7/SPFH domain 0.67 49.0 4.05e-01 78.8% 44.1%
3563069 1086.1.1.5 ↗ beta meanders › C-terminal beta-hairpin in astrotactin-2 › C-terminal beta-hairpin in astrotactin-2 › C-terminal beta-hairpin in astrotactin-2 › EMI 0.65 40.0 4.28e-01 73.1% 71.1%
3894181 101.1.2.115 ↗ alpha arrays › HTH › HTH › winged helix domain › CDC27 0.65 44.0 3.02e-01 71.2% 92.0%
4233683 171.1.1.1 ↗ alpha arrays › RNase III catalytic domain-like › RNase III catalytic domain-like › RNase III catalytic domain-like › Ribonuclease_3 0.65 48.0 3.16e-01 80.8% 51.4%
3737341 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.64 53.0 4.04e-01 96.2% 40.8%
3639274 261.1.1.1 ↗ a+b complex topology › Hect, E3 ligase catalytic domain › Hect, E3 ligase catalytic domain › Hect, E3 ligase catalytic domain › HECT 0.61 52.0 3.04e-01 98.1% 13.3%
3808345 221.7.1.1 ↗ a+b two layers › beta-Grasp › E2-binding domain of E1 › E2-binding domain of E1 › E2_bind 0.61 44.0 3.53e-01 76.9% 61.9%
3477515 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.61 54.0 4.18e-01 100.0% 79.1%
4141464 4099.1.1.22 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › CENP-P 0.61 43.0 3.44e-01 75.0% 46.4%
5043427 3010.1.1.2 ↗ a/b three-layered sandwiches › C-terminal subdomain in Lon-related proteases catalytic domains › C-terminal subdomain in Lon-related proteases catalytic domains › C-terminal subdomain in Lon-related proteases catalytic domains › Lon_C 0.61 50.0 4.03e-01 90.4% 64.6%
4973134 67.1.1.1 ↗ beta sandwiches › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › DnaJ_C 0.61 49.0 4.10e-01 92.3% 77.9%
3174953 69.1.1.2 ↗ beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Hom_end_hint 0.61 50.0 3.38e-01 98.1% 25.3%
3214850 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.59 40.0 2.47e-01 71.2% 12.0%
4399128 7581.1.1.30 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Thiolase_N, ketoacyl-synt, Thiolase_C 0.59 50.0 3.00e-01 94.2% 80.0%
3422000 11.1.5.29 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › Sec23_BS 0.59 39.0 3.19e-01 80.8% 33.3%
4583667 327.16.1.3 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif II in type III secretion system › Ring-building motif II in type III secretion system › Secretin_N 0.59 43.0 3.59e-01 78.8% 46.7%
5010647 1075.1.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain 0.58 51.0 3.33e-01 98.1% 60.4%
4635225 7527.1.1.1 ↗ a/b three-layered sandwiches › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE 0.58 36.0 2.30e-01 71.2% 12.3%
4029824 2484.1.1.20 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_A_exo1 0.57 41.0 2.59e-01 76.9% 15.4%
4996027 304.139.1.2 ↗ a+b two layers › Alpha-beta plaits › Cas7-related › CRISPR-associated protein Cas7/Csa2-related › RAMPs 0.57 38.0 2.45e-01 71.2% 13.8%
4061408 109.4.1.1731 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_CNRKL1_C, HAT_Syf1_CNRKL1_N 0.57 48.0 2.78e-01 94.2% 12.7%
4221575 4099.1.1.52 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › FTA2 0.57 41.0 3.38e-01 80.8% 45.7%
5045478 7527.1.1.1 ↗ a/b three-layered sandwiches › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE 0.57 41.0 2.71e-01 78.8% 50.2%
3356202 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.54 39.0 2.51e-01 82.7% 36.3%
3211918 11.1.1.9 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_N 0.52 41.0 3.06e-01 94.2% 87.5%
3927291 5001.1.1.41 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srw 0.52 38.0 2.33e-01 80.8% 27.6%
3624724 246.2.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.52 34.0 2.29e-01 80.8% 15.1%
3475901 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.52 39.0 3.34e-01 94.2% 48.9%
1893038 11.1.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Cadherin 0.51 37.0 3.54e-01 76.9% 98.3%
4126446 67.1.1.1 ↗ beta sandwiches › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › DnaJ_C 0.51 43.0 3.60e-01 96.2% 73.7%
3606812 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.51 39.0 2.35e-01 88.5% 66.2%
3899230 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.51 38.0 3.19e-01 94.2% 44.0%
4007581 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.51 34.0 3.43e-01 71.2% 90.0%
3939157 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 40.0 2.23e-01 88.5% 11.7%
3958367 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.50 31.0 3.12e-01 75.0% 54.5%
4004108 273.1.1.1 ↗ a+b three layers › PR-1-like › PR-1-like › PR-1-like › CAP 0.50 41.0 2.74e-01 98.1% 54.0%
4923851 224.1.1.2 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.50 36.0 2.67e-01 76.9% 28.2%