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NC_070960.1__YP_010669268.1__PQC10_gp006__00006

Bact-Vir

NC_070960.1__YP_010669268.1__PQC10_gp006__00006

Identity

Accession:
NC_070960 ↗
Kingdom:
phage

Quality

74.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Yushanluvirus› Synechococcus_phage_S-H9-2

TaxID: 2783669

Cluster

Singleton — not in a non-trivial cluster

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 medium residues 4-76
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3d4eA01 3.30.1450.10 Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › 0.66 38.0 3.64e-01 100.0% 50.0%
4c89C00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.60 52.0 3.40e-01 98.6% 55.8%
3ga7A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.59 48.0 3.17e-01 89.0% 64.6%
4hrzB00 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.58 41.0 3.51e-01 75.3% 52.0%
3li9A01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.58 40.0 3.38e-01 74.0% 42.7%
3aimA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.58 49.0 3.35e-01 97.3% 62.2%
2nraC02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.58 44.0 4.03e-01 84.9% 95.1%
3wj2B00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.58 49.0 3.29e-01 97.3% 58.3%
3icyA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.57 41.0 3.52e-01 75.3% 53.4%
5l2pA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 49.0 3.27e-01 97.3% 58.5%
5aa5E00 1.10.645.10 Mainly Alpha › Orthogonal Bundle › Cytochrome-c3 Hydrogenase; chain B › Cytochrome-c3 Hydrogenase, chain B 0.57 46.0 2.76e-01 89.0% 58.1%
2kgfA00 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.57 44.0 3.60e-01 84.9% 75.0%
6kmoB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 48.0 3.19e-01 97.3% 55.2%
1qe0A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.57 43.0 2.92e-01 83.6% 52.4%
1fu1A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.56 36.0 3.04e-01 100.0% 39.8%
4wy5A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 47.0 3.13e-01 97.3% 58.1%
1cc1L00 1.10.645.10 Mainly Alpha › Orthogonal Bundle › Cytochrome-c3 Hydrogenase; chain B › Cytochrome-c3 Hydrogenase, chain B 0.56 49.0 2.98e-01 100.0% 75.6%
4omfA00 1.10.645.10 Mainly Alpha › Orthogonal Bundle › Cytochrome-c3 Hydrogenase; chain B › Cytochrome-c3 Hydrogenase, chain B 0.55 48.0 3.09e-01 100.0% 72.2%
4jocA00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.55 44.0 2.89e-01 90.4% 59.3%
3hi0A02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.55 45.0 3.50e-01 94.5% 77.6%
7odhL01 1.10.645.10 Mainly Alpha › Orthogonal Bundle › Cytochrome-c3 Hydrogenase; chain B › Cytochrome-c3 Hydrogenase, chain B 0.55 44.0 2.67e-01 89.0% 54.0%
6uqjA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.55 47.0 3.07e-01 97.3% 63.8%
2hc5A01 3.30.160.170 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › FlaG-like 0.54 41.0 3.83e-01 84.9% 75.5%
3ilvA01 3.60.110.10 Alpha Beta › 4-Layer Sandwich › Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase › Carbon-nitrogen hydrolase 0.53 44.0 3.21e-01 98.6% 46.2%
3udfA01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.53 42.0 2.77e-01 91.8% 63.6%
2arhA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 43.0 3.48e-01 93.2% 58.2%
4k3yC00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.53 43.0 2.82e-01 91.8% 66.8%
1b9vA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.52 45.0 2.89e-01 100.0% 26.9%
2khxA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 32.0 3.21e-01 87.7% 58.2%
1w1hD00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 43.0 3.62e-01 97.3% 64.2%
4gq1A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 44.0 2.93e-01 100.0% 29.1%
2kyyA00 3.30.950.30 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Schlafen, AAA domain 0.52 41.0 3.33e-01 89.0% 88.2%
5yjwA00 3.50.50.100 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › 0.51 43.0 2.71e-01 95.9% 84.8%
5tvfD00 3.60.90.10 Alpha Beta › 4-Layer Sandwich › S-adenosylmethionine decarboxylase › S-adenosylmethionine decarboxylase 0.51 43.0 3.02e-01 98.6% 98.1%
2p25A01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.51 30.0 2.56e-01 74.0% 34.5%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3929759 2007.1.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like 0.71 50.0 3.63e-01 75.3% 28.1%
3213425 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.68 49.0 3.52e-01 75.3% 29.5%
5036065 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.68 40.0 3.97e-01 98.6% 56.0%
4946520 244.4.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › Ni-Fe binding domain in nickel-iron hydrogenase large subunit › Ni-Fe binding domain in nickel-iron hydrogenase large subunit 0.63 41.0 3.82e-01 100.0% 53.3%
3741704 719.1.1.2 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › XLF 0.62 37.0 3.04e-01 100.0% 33.1%
None — 0.62 43.0 3.03e-01 71.2% 88.8%
5018537 5090.1.1.0 ↗ beta complex topology › Viral glycoprotein, central and dimerisation domains-like › Viral glycoprotein, central and dimerisation domains › Viral glycoprotein, central and dimerisation domains 0.61 35.0 3.21e-01 100.0% 41.0%
3164763 2004.1.1.99 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Terminase_6N 0.61 45.0 3.13e-01 79.5% 26.8%
3521820 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 0.60 51.0 3.70e-01 100.0% 91.9%
3695479 244.2.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain 0.60 37.0 3.07e-01 89.0% 37.5%
None — 0.60 51.0 3.70e-01 100.0% 95.6%
4953685 244.4.1.2 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › Ni-Fe binding domain in nickel-iron hydrogenase large subunit › Ni-Fe binding domain in nickel-iron hydrogenase large subunit › NiFeSe_Hases 0.59 40.0 3.75e-01 100.0% 56.7%
4974130 210.1.1.0 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits 0.59 50.0 3.54e-01 100.0% 59.6%
4121524 304.125.1.1 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in Api92-like proteins › ferredoxin-like domain in Api92-like proteins › DUF1281_C 0.59 49.0 4.11e-01 100.0% 53.1%
2099381 7579.1.1.36 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_3 0.57 49.0 3.27e-01 97.3% 58.5%
4981973 2004.1.1.146 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase 0.57 46.0 3.32e-01 91.8% 34.8%
1830108 2484.8.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Separase pseudo-protease domain (PPD) › Separase pseudo-protease domain (PPD) › Peptidase_C50 0.56 47.0 3.19e-01 94.5% 78.5%
3179206 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.56 36.0 3.54e-01 90.4% 59.5%
3439448 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.56 46.0 3.25e-01 93.2% 49.2%
4932312 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.56 40.0 3.38e-01 78.1% 50.4%
3242741 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.56 47.0 3.30e-01 100.0% 48.7%
4013556 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.55 45.0 2.80e-01 90.4% 57.3%
3573645 7556.1.1.1 ↗ a/b three-layered sandwiches › Fe-only hydrogenase › Fe-only hydrogenase › Fe-only hydrogenase › Fe_hyd_lg_C 0.55 41.0 2.80e-01 80.8% 65.2%
3619473 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.55 43.0 3.15e-01 84.9% 41.0%
4960081 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.54 37.0 3.44e-01 72.6% 56.0%
3928764 11.1.1.53 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DOMON 0.54 38.0 3.39e-01 74.0% 69.5%
5008207 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 33.0 3.21e-01 100.0% 53.8%
3265510 267.1.1.3 ↗ a+b complex topology › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Cation_ATPase 0.53 40.0 3.08e-01 83.6% 96.8%
3994622 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.52 40.0 3.44e-01 84.9% 66.4%
3279818 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.52 44.0 3.67e-01 100.0% 67.4%
3974671 243.19.1.0 ↗ a+b two layers › Cystatin-like › Phi ETA orf 56-like protein C-terminal domains › Phi ETA orf 56-like protein C-terminal domains 0.51 43.0 4.18e-01 97.3% 96.5%
3600658 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 44.0 2.88e-01 100.0% 29.0%
3172537 301.8.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › 4'-phosphopantetheinyl transferase › 4'-phosphopantetheinyl transferase › ACPS 0.51 35.0 2.79e-01 74.0% 70.2%