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NC_070860.1__YP_010658690.1__PP754_gp003__00003

Bact-Vir

NC_070860.1__YP_010658690.1__PP754_gp003__00003

Identity

Accession:
NC_070860 ↗
Kingdom:
phage

Quality

58.3 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

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

D1 high residues 4-67
PDB
CATH (54)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2nmlA00 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.75 67.0 5.77e-01 100.0% 94.0%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.74 57.0 4.19e-01 82.8% 93.4%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.72 55.0 4.86e-01 82.8% 95.7%
2l6oA01 2.40.10.320 Mainly Beta › Beta Barrel › Thrombin, subunit H › Uncharacterised protein PF13642 yp_926445, N-terminal domain 0.69 53.0 5.17e-01 90.6% 75.0%
3e3xA01 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.68 54.0 4.51e-01 87.5% 93.8%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.67 58.0 5.51e-01 98.4% 89.5%
2i50A00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.67 48.0 3.95e-01 92.2% 41.0%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.66 52.0 4.62e-01 87.5% 71.3%
4bwsF00 3.30.1490.40 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › GYF domain 0.65 53.0 5.29e-01 100.0% 88.1%
1jw9B00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.65 49.0 3.41e-01 85.9% 62.9%
1cfyA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.64 55.0 4.40e-01 100.0% 80.5%
2vugA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.63 48.0 4.66e-01 84.4% 73.6%
5of3A00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.63 48.0 3.13e-01 85.9% 67.7%
1tk7A01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.61 35.0 4.40e-01 98.4% 100.0%
1itpA00 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.61 44.0 4.13e-01 75.0% 96.1%
3pihA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.61 46.0 4.43e-01 84.4% 72.2%
2jllA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 47.0 4.08e-01 84.4% 57.1%
3lqmA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 47.0 4.05e-01 84.4% 54.9%
1y6kR01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 48.0 4.18e-01 90.6% 64.7%
3d4rE01 2.40.128.400 Mainly Beta › Beta Barrel › Lipocalin › 0.60 49.0 4.45e-01 89.1% 92.9%
4bgdA08 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 42.0 3.03e-01 76.6% 44.8%
2dm4A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 45.0 4.01e-01 84.4% 57.4%
2hx0A01 3.30.1330.80 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 0.58 45.0 3.68e-01 89.1% 71.2%
4m0wA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.58 43.0 3.40e-01 81.2% 96.4%
1n26A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 44.0 3.81e-01 84.4% 56.7%
2o6cA00 2.60.40.2480 Mainly Beta › Sandwich › Immunoglobulin-like › Periplasmic metal-binding protein Tp34-type 0.57 44.0 3.39e-01 84.4% 50.6%
3qyfA01 3.40.50.10770 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Hypothetical protein VC1899 like domain (Restriction endonuclease-like) 0.57 40.0 3.03e-01 73.4% 95.8%
5e55B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 44.0 3.92e-01 84.4% 63.4%
1x9mA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 44.0 3.09e-01 100.0% 24.8%
3su0A01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.56 46.0 3.99e-01 96.9% 71.4%
1sq2N00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 42.0 3.59e-01 84.4% 67.9%
2p4zA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.56 39.0 2.61e-01 75.0% 29.5%
3pl0B00 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.55 49.0 3.27e-01 100.0% 69.0%
5h4eA01 2.60.110.10 Mainly Beta › Sandwich › Thaumatin › Thaumatin 0.55 45.0 3.20e-01 98.4% 92.6%
5nr1A01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 51.0 4.21e-01 100.0% 72.6%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.55 38.0 4.13e-01 71.9% 96.0%
6qm7A00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.55 44.0 3.07e-01 93.8% 81.1%
4x83A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 42.0 3.65e-01 84.4% 57.8%
7lxuE01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.54 43.0 3.17e-01 95.3% 88.8%
3wknF00 6.20.50.120 Special › Other non-globular › N-terminal domain of TfIIb › 0.54 29.0 3.24e-01 90.6% 67.4%
2hpuA02 3.30.70.2050 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 42.0 4.22e-01 85.9% 100.0%
5e3iA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.53 40.0 3.59e-01 85.9% 75.8%
1atiB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.53 41.0 3.51e-01 87.5% 76.8%
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.53 36.0 3.30e-01 70.3% 66.3%
2kp5A00 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.53 44.0 4.02e-01 98.4% 89.0%
4frfA00 3.30.470.160 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Inositol polyphosphate kinase 0.52 41.0 2.99e-01 92.2% 97.7%
1adjB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.52 40.0 3.60e-01 87.5% 74.5%
3snyA00 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.52 44.0 4.02e-01 98.4% 95.4%
1npsA00 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.52 44.0 4.04e-01 98.4% 93.2%
3rbtD01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 47.0 3.72e-01 100.0% 61.6%
2c60A01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 41.0 3.91e-01 95.3% 73.4%
2hy5B00 3.40.1260.10 Alpha Beta › 3-Layer(aba) Sandwich › Hypothetical Protein Ychn; Chain: A, › DsrEFH-like 0.51 36.0 2.97e-01 78.1% 50.0%
4fleA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 42.0 3.12e-01 98.4% 62.6%
4nnaA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.50 41.0 2.66e-01 93.8% 90.2%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3704667 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.74 60.0 3.71e-01 85.9% 47.2%
3672250 207.1.1.116 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_FBXL15 0.70 55.0 3.86e-01 96.9% 28.4%
3586250 822.1.1.1 a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF 0.70 56.0 5.80e-01 100.0% 95.0%
4665451 2003.1.9.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.68 53.0 3.60e-01 85.9% 61.6%
4984496 304.139.1.2 a+b two layers › Alpha-beta plaits › Cas7-related › CRISPR-associated protein Cas7/Csa2-related › RAMPs 0.67 53.0 3.78e-01 90.6% 95.3%
3501103 822.1.1.1 a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF 0.67 55.0 5.62e-01 100.0% 93.7%
3268419 224.1.1.1 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.67 56.0 4.68e-01 95.3% 83.5%
5049245 2003.1.9.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.66 51.0 3.47e-01 85.9% 60.0%
3839883 2003.1.9.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.66 51.0 3.48e-01 85.9% 59.6%
4448678 4.1.1.307 beta barrels › SH3 › SH3 › SH3 › PF26132 0.66 46.0 4.40e-01 73.4% 98.7%
3661726 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.66 46.0 3.98e-01 73.4% 82.0%
3479367 822.1.1.1 a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF 0.66 55.0 5.59e-01 100.0% 95.3%
3235447 821.1.1.8 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › ANKLE2_3rd 0.66 49.0 4.35e-01 79.7% 98.9%
3782773 822.1.1.1 a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF 0.65 49.0 5.15e-01 87.5% 94.5%
3282305 4187.1.1.0 a+b two layers › NosL/MerB-like › NosL/MerB-like › NosL/MerB-like 0.64 48.0 4.76e-01 85.9% 77.1%
3959440 4.1.1.180 beta barrels › SH3 › SH3 › SH3 › DUF3107 0.64 43.0 4.34e-01 70.3% 100.0%
5059796 4326.1.1.0 a+b two layers › ERH-like › ERH-like › ERH-like 0.64 56.0 5.51e-01 100.0% 91.3%
3800233 386.1.1.1 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2 0.64 49.0 5.13e-01 96.9% 100.0%
4946875 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.64 49.0 3.30e-01 85.9% 76.2%
5001390 2003.1.9.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins 0.63 48.0 3.45e-01 85.9% 60.5%
3969006 3115.6.1.2 a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.63 41.0 4.60e-01 70.3% 95.6%
3612075 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.62 49.0 3.49e-01 87.5% 34.3%
4946939 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.62 50.0 3.58e-01 90.6% 90.0%
5045395 821.1.1.0 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.62 47.0 4.00e-01 82.8% 96.3%
5075402 210.1.3.3 a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_4 0.62 48.0 3.18e-01 85.9% 23.5%
3675525 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.62 44.0 4.37e-01 85.9% 72.1%
4343263 3019.1.1.1 beta sandwiches › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › Flagellin_IN 0.62 50.0 4.00e-01 90.6% 81.5%
4952123 3986.2.1.0 a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.61 46.0 4.78e-01 84.4% 96.7%
5046788 377.1.1.0 few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.61 54.0 4.42e-01 100.0% 61.7%
5036533 3435.1.1.0 a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC 0.59 44.0 3.06e-01 81.2% 24.9%
3926235 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.58 48.0 4.56e-01 100.0% 77.5%
3550161 11.1.4.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.57 47.0 3.87e-01 100.0% 94.2%
3724489 3949.1.1.1 alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › IPPT 0.56 42.0 2.74e-01 84.4% 86.8%
142425 11.1.1.58 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Beta-APP,V-set 0.56 43.0 3.52e-01 84.4% 69.8%
3816922 4081.1.1.0 beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related 0.56 47.0 3.06e-01 92.2% 33.6%
3596561 376.1.1.0 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.56 41.0 4.03e-01 89.1% 74.3%
5019455 331.1.1.0 a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.55 40.0 2.92e-01 79.7% 29.2%
2081281 2485.1.1.39 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › GST_N_2 0.55 51.0 4.49e-01 100.0% 86.5%
3853799 386.1.1.290 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › Zf-C2H2_ZNF451_C 0.54 38.0 3.64e-01 78.1% 64.0%
3476809 206.1.2.3 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › SAICAR synthase › IPK 0.53 45.0 3.01e-01 98.4% 47.4%
5053437 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.53 43.0 3.15e-01 96.9% 60.0%
3974708 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.52 33.0 2.72e-01 73.4% 32.0%
3879988 4081.1.1.2 beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.50 42.0 3.05e-01 100.0% 92.1%
3599395 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.50 38.0 2.48e-01 89.1% 98.0%
D2 medium residues 71-166
PDB