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SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00577

Bact-Vir

SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00577

Identity

Kingdom:
phage

Quality

93.9 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 2-57
PDB
Domain cluster: representative
CATH (54)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1burS00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.77 67.0 5.23e-01 100.0% 65.9%
1svdM00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.77 67.0 5.43e-01 100.0% 63.9%
6oziB00 3.30.2170.10 Alpha Beta › 2-Layer Sandwich › archaeoglobus fulgidus dsm 4304 fold › archaeoglobus fulgidus dsm 4304 superfamily 0.70 45.0 2.85e-01 100.0% 15.4%
8os3A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.68 58.0 5.02e-01 100.0% 65.2%
2yuxA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.68 59.0 4.81e-01 100.0% 54.6%
1fyhB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 59.0 4.94e-01 100.0% 62.9%
2r2cB00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 60.0 4.78e-01 100.0% 64.2%
1hkfA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 58.0 4.70e-01 100.0% 70.4%
4jzjC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 48.0 4.52e-01 100.0% 65.7%
1x67A01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.64 56.0 4.26e-01 100.0% 46.6%
4dohB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 53.0 4.48e-01 100.0% 63.8%
8hi1E01 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 55.0 4.79e-01 100.0% 82.8%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.63 54.0 4.69e-01 100.0% 79.3%
2cuhA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 54.0 4.69e-01 100.0% 62.5%
4lizA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.63 55.0 4.17e-01 100.0% 46.4%
2xf1A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.63 52.0 4.19e-01 100.0% 51.6%
2pn1A03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.63 55.0 4.32e-01 100.0% 65.0%
2b5iC01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 54.0 4.57e-01 100.0% 64.6%
1tj6A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 40.0 3.17e-01 100.0% 32.2%
3cxeC01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 52.0 4.45e-01 100.0% 66.3%
4makB00 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 52.0 4.83e-01 100.0% 94.7%
6x4tA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 52.0 4.63e-01 100.0% 75.3%
5ejrA02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.61 43.0 3.79e-01 82.1% 48.8%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.60 50.0 3.71e-01 100.0% 95.2%
4es8B02 2.60.40.3580 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 50.0 4.22e-01 100.0% 62.4%
3lohE05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 50.0 3.95e-01 100.0% 75.6%
1r9fA01 3.30.390.180 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › RNA silencing suppressor P19 0.59 48.0 4.07e-01 100.0% 61.5%
7pikC01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.59 43.0 2.87e-01 100.0% 21.3%
3ndaA02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.58 54.0 4.00e-01 100.0% 56.8%
5aykA07 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.58 38.0 3.10e-01 100.0% 33.0%
3zhaQ02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.58 53.0 3.93e-01 100.0% 55.7%
2d8bA01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.57 48.0 3.69e-01 100.0% 44.3%
4yo1A03 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.56 41.0 3.54e-01 100.0% 47.4%
5of3A00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.56 46.0 2.95e-01 98.2% 68.7%
2l97A01 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.56 41.0 3.53e-01 100.0% 46.5%
2lstA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.56 39.0 3.03e-01 75.0% 90.8%
1yuzA02 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.55 32.0 3.60e-01 80.4% 81.6%
5i47B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.55 49.0 4.11e-01 100.0% 69.5%
3cxgA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 35.0 2.82e-01 98.2% 29.5%
2je8A01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 46.0 3.25e-01 100.0% 63.5%
1c7sA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 39.0 3.78e-01 96.4% 66.7%
4hslA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.53 46.0 3.31e-01 98.2% 54.2%
3qdkB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 43.0 2.85e-01 96.4% 51.5%
2q1mA00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.53 46.0 3.66e-01 100.0% 47.4%
3onhA01 3.10.290.20 Alpha Beta › Roll › Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A › Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 0.53 44.0 3.63e-01 100.0% 49.5%
4pz7A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 36.0 2.70e-01 100.0% 29.2%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.53 38.0 3.98e-01 83.9% 98.0%
3bp6B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 44.0 3.88e-01 100.0% 65.9%
1zvfB01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 46.0 3.30e-01 100.0% 57.3%
1ilyA00 3.30.420.100 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.52 42.0 3.76e-01 100.0% 86.7%
7wrnA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.52 42.0 2.98e-01 94.6% 52.0%
1te0A03 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.52 38.0 3.22e-01 100.0% 45.0%
4o9dA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 44.0 2.70e-01 98.2% 22.8%
4fchA02 2.60.40.3610 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 40.0 3.48e-01 100.0% 82.7%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4277361 302.2.1.1 ↗ a+b two layers › Reverse ferredoxin › RuBisCO, small subunit › RuBisCO, small subunit › RuBisCO_small 0.76 66.0 4.97e-01 100.0% 60.8%
4659490 302.2.1.1 ↗ a+b two layers › Reverse ferredoxin › RuBisCO, small subunit › RuBisCO, small subunit › RuBisCO_small 0.76 67.0 5.29e-01 100.0% 60.0%
4952123 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.75 66.0 6.53e-01 98.2% 96.7%
3337910 302.2.1.1 ↗ a+b two layers › Reverse ferredoxin › RuBisCO, small subunit › RuBisCO, small subunit › RuBisCO_small 0.74 64.0 5.31e-01 100.0% 80.0%
4378815 302.2.1.1 ↗ a+b two layers › Reverse ferredoxin › RuBisCO, small subunit › RuBisCO, small subunit › RuBisCO_small 0.73 63.0 5.35e-01 100.0% 70.5%
3596840 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.71 55.0 5.11e-01 100.0% 67.1%
4998035 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.70 43.0 4.55e-01 100.0% 70.0%
3752093 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.70 61.0 4.93e-01 100.0% 54.5%
5034720 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.68 59.0 4.99e-01 100.0% 69.5%
3629740 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.68 60.0 4.89e-01 100.0% 68.6%
4939189 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.67 59.0 4.89e-01 100.0% 62.0%
3789849 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.67 59.0 5.81e-01 100.0% 93.3%
3494869 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.67 58.0 5.02e-01 100.0% 64.4%
3887025 11.1.1.117 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › EpoR_lig-bind 0.66 58.0 4.85e-01 100.0% 62.0%
4975837 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 57.0 4.95e-01 100.0% 65.6%
3698302 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.66 43.0 4.42e-01 82.1% 69.1%
5081037 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 58.0 4.80e-01 100.0% 60.0%
4969913 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 57.0 5.24e-01 100.0% 77.3%
3639662 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 59.0 5.23e-01 100.0% 83.7%
3406956 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.64 56.0 4.25e-01 100.0% 45.9%
5022113 4252.1.1.0 ↗ beta barrels › AttH-like › AttH-like › AttH-like 0.64 42.0 3.06e-01 100.0% 26.2%
3535035 11.1.1.232 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › SKICH 0.64 55.0 4.53e-01 100.0% 65.7%
3901601 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.64 55.0 4.68e-01 100.0% 58.9%
3452042 708.1.1.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.63 43.0 4.40e-01 100.0% 72.7%
1318473 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.63 55.0 4.21e-01 100.0% 47.8%
4961190 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.63 54.0 4.62e-01 100.0% 58.9%
3979936 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 55.0 4.42e-01 100.0% 61.8%
5048876 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.62 53.0 5.11e-01 100.0% 93.8%
5041080 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 52.0 4.34e-01 100.0% 65.7%
4960338 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 51.0 4.23e-01 100.0% 96.4%
3251163 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.61 47.0 3.99e-01 100.0% 52.2%
3172253 2004.1.1.212 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Microtub_bd 0.60 51.0 3.12e-01 100.0% 15.3%
1148130 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 50.0 4.18e-01 100.0% 59.0%
4968887 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 50.0 4.36e-01 100.0% 63.3%
3598159 224.1.1.0 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.58 49.0 3.85e-01 100.0% 46.5%
5052830 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 47.0 3.84e-01 100.0% 65.9%
3232211 11.2.1.58 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › PF26186 0.56 48.0 3.31e-01 100.0% 43.3%
5049756 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 46.0 3.99e-01 100.0% 57.9%
4651135 245.1.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.56 47.0 4.05e-01 100.0% 60.0%
3581411 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 48.0 3.72e-01 100.0% 56.2%
3229807 822.1.1.0 ↗ a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain 0.55 47.0 4.25e-01 100.0% 70.0%
3637401 4081.1.1.8 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT_2 0.55 46.0 3.17e-01 98.2% 25.0%
3321727 7.1.1.0 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain 0.54 44.0 4.14e-01 98.2% 75.7%
None — 0.53 47.0 3.27e-01 98.2% 51.1%
None — 0.53 47.0 3.31e-01 100.0% 52.3%
5078886 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.53 43.0 3.60e-01 96.4% 49.1%
5057039 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.53 46.0 4.13e-01 98.2% 96.2%
5037340 10.1.2.182 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) › Glyco_hydro_2_N 0.51 41.0 3.14e-01 100.0% 64.8%
3920450 2484.1.1.145 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1_7 0.51 41.0 2.63e-01 100.0% 20.2%
3710327 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 44.0 3.41e-01 100.0% 45.2%
3166282 7.1.1.1 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ 0.51 36.0 3.29e-01 100.0% 52.9%