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NC_029067.1__YP_009222862.1__VPLG_00013__00013

Bact-Vir

NC_029067.1__YP_009222862.1__VPLG_00013__00013

Identity

Accession:
NC_029067 ↗
Kingdom:
phage

Quality

56.8 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 8-92
PDB
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2pstX00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.72 47.0 5.47e-01 98.8% 93.4%
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.70 60.0 5.84e-01 94.1% 93.5%
4dohE02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 40.0 3.72e-01 76.5% 48.1%
2fhqA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.64 45.0 3.83e-01 72.9% 62.2%
3zoqC00 6.20.250.30 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.62 37.0 4.40e-01 75.3% 94.3%
4eq3A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 41.0 3.80e-01 83.5% 53.7%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.61 37.0 4.16e-01 71.8% 78.8%
3l5iA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 37.0 3.66e-01 81.2% 56.8%
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 36.0 3.76e-01 71.8% 63.7%
3dnhA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.60 44.0 3.68e-01 78.8% 65.6%
5e55B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 38.0 3.71e-01 81.2% 58.1%
4ybnB00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 43.0 3.30e-01 77.6% 79.5%
2hq7B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 41.0 3.54e-01 74.1% 62.0%
4do8A00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.59 36.0 3.88e-01 87.1% 75.8%
4wtxA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 37.0 3.58e-01 77.6% 54.6%
5utkA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 35.0 3.58e-01 81.2% 59.0%
1a21A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 37.0 3.59e-01 74.1% 55.1%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.59 41.0 3.68e-01 71.8% 59.7%
4k22A02 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 0.58 41.0 3.79e-01 72.9% 79.6%
1s4dE02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.58 40.0 3.47e-01 97.6% 43.9%
3r5lA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 44.0 4.00e-01 82.4% 81.9%
3n40P04 2.60.40.2400 Mainly Beta › Sandwich › Immunoglobulin-like › Alphavirus E2 glycoprotein, domain C 0.57 32.0 3.43e-01 70.6% 61.6%
1c77B00 3.10.20.130 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.57 43.0 3.83e-01 82.4% 89.1%
6j0qA02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.57 42.0 3.91e-01 78.8% 87.2%
2qckA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.57 49.0 4.07e-01 96.5% 55.0%
5chtB00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.57 42.0 2.86e-01 77.6% 33.3%
1x5hA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 35.0 3.14e-01 81.2% 40.2%
1bw3A00 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.57 46.0 4.05e-01 88.2% 75.2%
2lgnA00 2.60.40.2850 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 33.0 3.68e-01 74.1% 74.2%
2g5dA01 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.56 40.0 3.15e-01 77.6% 72.1%
4h3wA02 2.60.120.1260 Mainly Beta › Sandwich › Jelly Rolls › 0.56 39.0 3.25e-01 72.9% 42.8%
2eddA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 34.0 3.17e-01 78.8% 45.5%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.54 37.0 3.61e-01 70.6% 64.6%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.54 37.0 3.48e-01 71.8% 60.6%
3ir9A02 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.54 40.0 3.60e-01 80.0% 70.0%
1cfbA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 34.0 3.20e-01 77.6% 50.0%
2l03A00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.53 34.0 3.65e-01 85.9% 75.7%
1dyoA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 41.0 3.39e-01 84.7% 59.6%
2z04B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.51 41.0 3.21e-01 87.1% 87.1%
5cvmA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.51 37.0 2.58e-01 77.6% 32.1%
1jx4A04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.51 35.0 3.43e-01 72.9% 63.3%
4ca1B02 2.60.210.10 Mainly Beta › Sandwich › Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A › Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A 0.51 35.0 3.12e-01 72.9% 52.3%
4ksnA00 6.20.250.80 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.51 34.0 3.87e-01 74.1% 92.3%
5yl6A01 2.60.120.590 Mainly Beta › Sandwich › Jelly Rolls › Alpha-ketoglutarate-dependent dioxygenase AlkB-like 0.50 35.0 2.82e-01 72.9% 73.3%
4aw7A01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.50 31.0 2.83e-01 74.1% 44.1%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4677975 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.75 65.0 5.84e-01 95.3% 74.6%
4344289 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.74 65.0 5.60e-01 96.5% 69.2%
3738959 11.1.1.643 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig-like_POM152 0.69 41.0 3.97e-01 80.0% 52.6%
3579560 2487.1.1.0 a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" 0.68 47.0 3.63e-01 71.8% 97.3%
4995672 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.67 39.0 4.78e-01 74.1% 98.0%
3783477 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.67 44.0 4.06e-01 78.8% 51.8%
3738955 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.67 45.0 4.09e-01 78.8% 52.7%
4128974 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.65 50.0 5.18e-01 85.9% 88.7%
3531766 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.64 38.0 3.70e-01 71.8% 52.6%
3764749 382.1.1.2 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › Toxin_TOLIP 0.63 40.0 4.31e-01 90.6% 77.1%
3879743 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 39.0 4.16e-01 71.8% 72.0%
4086239 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.62 38.0 4.52e-01 71.8% 96.4%
5016546 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.61 43.0 4.52e-01 81.2% 84.0%
5053865 821.1.1.0 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.61 50.0 4.91e-01 90.6% 87.8%
3801207 219.1.1.50 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH_1 0.60 45.0 2.80e-01 77.6% 20.9%
3500825 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.59 48.0 4.77e-01 90.6% 85.6%
3179841 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 40.0 3.64e-01 82.4% 50.0%
3705532 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.58 40.0 3.52e-01 71.8% 53.8%
3272932 219.1.1.50 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH_1 0.57 42.0 2.66e-01 77.6% 20.9%
3608234 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.57 40.0 3.45e-01 71.8% 50.4%
3413058 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.57 44.0 4.38e-01 91.8% 77.8%
5027350 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.57 44.0 3.79e-01 83.5% 65.9%
3621466 219.1.1.3 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.56 42.0 2.71e-01 77.6% 33.1%
3242230 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 41.0 3.09e-01 77.6% 32.6%
4124297 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.56 41.0 2.37e-01 77.6% 14.4%
3950331 1.1.5.15 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › F420H2_quin_red 0.56 38.0 4.28e-01 80.0% 100.0%
5037200 303.1.1.1 a+b four layers › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › PvlArgDC 0.56 47.0 3.97e-01 96.5% 54.5%
5041452 303.1.1.1 a+b four layers › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › PvlArgDC 0.56 47.0 3.95e-01 96.5% 55.6%
3620107 10.32.1.203 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.55 38.0 3.24e-01 71.8% 48.6%
4250793 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.55 38.0 3.24e-01 71.8% 50.0%
5023452 303.1.1.1 a+b four layers › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › PvlArgDC 0.55 46.0 3.93e-01 95.3% 56.6%
3817425 10.32.1.0 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.54 40.0 3.12e-01 78.8% 65.6%
3256023 4026.1.1.0 a+b three layers › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) 0.54 48.0 4.14e-01 100.0% 85.2%
3874464 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.54 45.0 3.02e-01 94.1% 47.9%
4000914 219.1.1.3 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.54 39.0 2.74e-01 77.6% 28.6%
3959474 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.54 37.0 3.22e-01 71.8% 50.0%
4332626 3532.1.1.0 alpha arrays › RNA-binding domain of telomerase › RNA-binding domain of telomerase › RNA-binding domain of telomerase 0.53 45.0 2.74e-01 94.1% 28.4%
4956437 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.53 42.0 3.57e-01 83.5% 77.8%
3621016 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.53 35.0 3.64e-01 90.6% 72.5%
3241391 10.32.1.0 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.53 31.0 3.00e-01 75.3% 48.0%
4946583 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.53 36.0 3.36e-01 72.9% 55.7%
4928513 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.52 36.0 3.43e-01 71.8% 61.2%
3830721 207.1.1.43 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_3 0.52 39.0 2.45e-01 81.2% 15.8%
3502194 221.1.1.6 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.52 36.0 3.57e-01 74.1% 85.3%
3217778 2492.1.1.0 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.52 36.0 3.30e-01 71.8% 58.2%
3999432 11.2.1.52 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2_nem 0.52 36.0 2.94e-01 74.1% 82.9%
3489525 219.1.1.3 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.51 37.0 2.70e-01 75.3% 42.9%
4960572 10.1.2.0 beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.51 35.0 2.83e-01 71.8% 37.0%
4028142 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 39.0 3.56e-01 84.7% 61.7%
3614286 219.1.1.3 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.51 40.0 2.73e-01 87.1% 39.4%
5033505 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 35.0 3.25e-01 71.8% 68.2%
D2 high residues 234-339
PDB