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SR-VP_0-2_scaffold_141_316084_prodigal-single.1__X__X__00212

Bact-Vir

SR-VP_0-2_scaffold_141_316084_prodigal-single.1__X__X__00212

Identity

Kingdom:
phage

Quality

87.2 mean pLDDT

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 10-99
PDB
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1c48A00 2.40.50.70 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.65 45.0 5.03e-01 100.0% 95.7%
1n71B00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.62 40.0 3.22e-01 100.0% 33.0%
1x6oA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.60 45.0 4.71e-01 100.0% 91.1%
1d1lA00 3.30.240.10 Alpha Beta › 2-Layer Sandwich › CRO Repressor › CRO Repressor 0.59 35.0 4.05e-01 100.0% 86.9%
3mgdB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.58 40.0 3.35e-01 100.0% 42.1%
2q0yA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 37.0 3.24e-01 100.0% 47.8%
1yaxB00 3.30.450.140 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PhoQ sensor domain 0.52 36.0 3.16e-01 100.0% 48.5%
6cc0A02 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 0.52 34.0 3.70e-01 82.2% 85.7%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3283647 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.74 68.0 6.04e-01 100.0% 92.8%
3591196 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.68 60.0 4.78e-01 100.0% 95.1%
3499266 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.63 56.0 5.08e-01 100.0% 90.2%
4958515 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.62 54.0 4.76e-01 100.0% 85.0%
3479031 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.58 52.0 4.70e-01 100.0% 72.8%
4987839 213.1.1.53 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_6 0.57 37.0 3.08e-01 100.0% 37.4%
3973911 2.1.1.346 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF4824 0.57 44.0 4.42e-01 100.0% 84.4%
5038808 2.10.1.1 beta barrels › OB-fold › CheW › CheW › CheW 0.54 39.0 3.50e-01 100.0% 51.9%
3881118 2.6.1.0 beta barrels › OB-fold › Staphylococcal nuclease › Staphylococcal nuclease 0.53 39.0 3.92e-01 100.0% 80.0%
3839187 2.10.1.1 beta barrels › OB-fold › CheW › CheW › CheW 0.50 41.0 3.48e-01 100.0% 50.0%
D2 high residues 108-224
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ffgA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.60 49.0 3.66e-01 90.6% 51.5%
3qeeB00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.58 47.0 3.54e-01 88.9% 53.5%
2lnjA00 3.40.1000.10 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich 0.57 43.0 3.85e-01 90.6% 54.7%
2fs2B00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.56 42.0 3.99e-01 78.6% 94.9%
2x9oA00 3.40.1500.20 Alpha Beta › 3-Layer(aba) Sandwich › oxygen-dependent coproporphyrinogen oxidase › 0.55 49.0 3.93e-01 100.0% 84.1%
3lbeB00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.52 38.0 3.83e-01 78.6% 100.0%
3zpmA00 3.15.10.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Bactericidal permeability-increasing protein; domain 1 0.52 40.0 3.29e-01 81.2% 82.5%
2r76A00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.51 42.0 4.13e-01 93.2% 93.9%
4jhyA00 3.30.530.80 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.50 38.0 3.47e-01 79.5% 78.8%
1y7uA00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.50 42.0 3.82e-01 93.2% 95.7%
6r3wA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.50 42.0 3.83e-01 94.0% 89.4%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3941745 241.15.1.4 a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › DUF932 0.70 60.0 5.55e-01 91.5% 84.8%
4451012 222.1.1.0 a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.65 44.0 3.90e-01 70.1% 81.8%
5030147 881.1.1.0 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.63 44.0 4.10e-01 88.9% 57.2%
3791149 5.1.3.4 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › WD40 0.61 51.0 3.56e-01 88.9% 52.2%
3929694 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.61 54.0 3.54e-01 98.3% 76.5%
3618875 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.61 54.0 5.20e-01 100.0% 94.1%
3228525 241.15.1.0 a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.61 51.0 5.29e-01 92.3% 96.4%
3995515 5.1.4.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.60 53.0 3.93e-01 97.4% 86.0%
3580087 5.1.4.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.58 50.0 3.33e-01 94.0% 39.8%
3359635 274.1.1.44 a+b two layers › Pili subunits › Pili subunits › Pili subunits › DUF7804 0.58 41.0 4.22e-01 75.2% 76.4%
3628522 5.1.4.489 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Prenyltrans 0.58 51.0 3.08e-01 97.4% 47.3%
3285746 243.1.1.26 a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_4 0.58 40.0 3.65e-01 70.9% 81.9%
3574500 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.58 50.0 3.36e-01 97.4% 79.4%
3322065 5.1.3.118 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.57 47.0 3.52e-01 91.5% 45.8%
4059480 881.1.1.37 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PF27270 0.57 39.0 3.46e-01 89.7% 46.9%
3169840 897.1.1.1 a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 › MAM33 0.57 48.0 4.04e-01 92.3% 65.0%
3999618 5.1.4.5 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40,CAF1C_H4-bd 0.56 42.0 2.96e-01 80.3% 32.1%
5069097 331.9.1.0 a+b two layers › TBP-like › Subdomain of clathrin and coatomer appendage domain › Subdomain of clathrin and coatomer appendage domain 0.56 39.0 3.93e-01 86.3% 70.0%
3832313 5.1.3.67 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_1 0.56 45.0 3.31e-01 88.0% 37.5%
3359195 5.1.3.118 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.56 48.0 3.50e-01 94.9% 47.4%
3468093 243.3.1.19 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › DUF3615 0.55 41.0 4.46e-01 88.9% 95.9%
3605476 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.55 49.0 3.41e-01 99.1% 38.5%
3633634 5.1.4.80 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Utp8_b_propeller 0.54 45.0 3.10e-01 92.3% 30.1%
3204864 5.1.11.3 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed › Utp8_b_propeller 0.54 46.0 3.16e-01 94.9% 34.4%
3408388 4.1.1.326 beta barrels › SH3 › SH3 › SH3 › Chitin_bind_4 0.53 35.0 4.07e-01 75.2% 100.0%
2559741 881.1.1.3 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › FAP 0.52 39.0 3.49e-01 89.7% 54.5%
4642761 331.22.1.2 a+b two layers › TBP-like › Outer membrane protein assembly factor BamC › Outer membrane protein assembly factor BamC › PF29358 0.52 41.0 3.36e-01 82.9% 50.5%
3359496 5.1.3.67 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_1 0.52 43.0 3.32e-01 91.5% 52.8%
3277627 243.1.1.0 a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.51 38.0 3.87e-01 77.8% 91.3%
3400513 77.1.1.4 beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › Chitin_bind_4 0.51 33.0 3.89e-01 73.5% 100.0%
3459442 243.3.1.19 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › DUF3615 0.51 42.0 4.02e-01 89.7% 96.3%
3959748 881.1.1.0 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.51 40.0 4.00e-01 88.9% 82.5%
3881564 220.1.1.32 beta barrels › PH domain-like › PH domain-like › PH domain-like › Sec3-PIP2_bind 0.51 41.0 3.57e-01 86.3% 60.6%
D3 high residues 227-319
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3kfwX03 1.20.58.1460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 32.0 3.58e-01 98.9% 48.7%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.72 41.0 4.89e-01 89.2% 83.9%
3q1pA01 6.10.250.1120 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.71 32.0 4.48e-01 98.9% 97.4%
1u8vB03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.62 54.0 4.20e-01 98.9% 80.3%
2lhrA00 1.20.58.1270 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 34.0 3.66e-01 79.6% 62.8%
2lqgA00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.60 51.0 4.54e-01 95.7% 79.0%
3tjmA02 1.10.1470.20 Mainly Alpha › Orthogonal Bundle › Protein Yjbj; Chain: A; › Fatty acid synthase; domain 2 0.60 41.0 4.23e-01 96.8% 74.4%
2gkmA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.59 46.0 4.18e-01 83.9% 77.2%
4uobA02 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.59 42.0 3.86e-01 95.7% 56.3%
1u89A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.58 51.0 4.51e-01 97.8% 69.1%
1vnsA01 1.20.144.10 Mainly Alpha › Up-down Bundle › Vanadium-containing Chloroperoxidase; domain 1 › Phosphatidic acid phosphatase type 2/haloperoxidase 0.57 50.0 4.05e-01 96.8% 76.0%
3e3vA03 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 0.56 30.0 3.53e-01 75.3% 80.4%
4etrB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 43.0 3.92e-01 82.8% 93.4%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.55 43.0 4.57e-01 95.7% 97.5%
2n3eA01 1.10.274.70 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, N-terminal domain 0.55 49.0 4.57e-01 98.9% 87.8%
2x48A00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.54 31.0 3.74e-01 93.5% 94.4%
2n00A00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.54 44.0 4.44e-01 98.9% 90.5%
3nkhA00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.53 39.0 3.06e-01 79.6% 72.9%
4od4A02 1.20.120.1780 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › UbiA prenyltransferase 0.53 39.0 3.59e-01 77.4% 72.3%
6vvoE02 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.53 35.0 3.44e-01 83.9% 62.6%
2bnlC00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.53 42.0 3.77e-01 88.2% 86.6%
5yjwA00 3.50.50.100 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › 0.53 44.0 2.85e-01 92.5% 84.8%
1f20A02 1.20.990.10 Mainly Alpha › Up-down Bundle › NADPH-cytochrome p450 Reductase; Chain A, domain 3 › NADPH-cytochrome p450 Reductase; Chain A, domain 3 0.52 37.0 3.16e-01 98.9% 44.0%
3ztaA00 1.10.490.130 Mainly Alpha › Orthogonal Bundle › Globin-like › 0.52 39.0 3.52e-01 83.9% 79.1%
4ksaA02 1.20.140.90 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain 0.51 37.0 3.30e-01 76.3% 95.6%
2rbdA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.51 45.0 3.88e-01 98.9% 62.0%
2q37A00 1.10.3330.10 Mainly Alpha › Orthogonal Bundle › UraD-like › Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase 0.51 36.0 3.21e-01 74.2% 86.6%
2zgyA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 39.0 3.48e-01 84.9% 88.6%
2kj8A00 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.50 38.0 3.58e-01 82.8% 85.6%
4l3tA03 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.50 44.0 3.34e-01 97.8% 72.6%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3518809 5.1.4.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.62 52.0 3.77e-01 98.9% 31.9%
4016106 650.1.1.0 alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.61 34.0 3.61e-01 93.5% 61.3%
3778682 150.1.1.24 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Prominin 0.61 53.0 4.61e-01 95.7% 67.1%
5026526 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.59 53.0 5.19e-01 98.9% 92.0%
5057581 102.1.1.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.58 43.0 4.72e-01 100.0% 98.7%
3573862 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 40.0 3.15e-01 96.8% 32.9%
3491942 309.1.1.5 a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16_C,M16C_assoc 0.56 51.0 3.60e-01 100.0% 67.8%
3611035 1189.1.1.3 alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › GARP 0.55 41.0 3.13e-01 78.5% 75.0%
3904838 110.1.1.4 alpha arrays › DEATH domain › DEATH domain › DEATH domain › PYRIN 0.54 47.0 4.83e-01 98.9% 100.0%
4180013 1128.1.1.8 alpha bundles › LYR protein › LYR protein › LYR protein › PF29574 0.54 36.0 3.66e-01 97.8% 68.9%
4956725 4041.1.1.1 a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.53 40.0 3.26e-01 80.6% 68.1%
3417164 3687.1.1.1 alpha bundles › NADPH-cytochrome p450 reductase helical insertion domain › NADPH-cytochrome p450 reductase helical insertion domain › NADPH-cytochrome p450 reductase helical insertion domain › FAD_binding_1 0.53 37.0 3.38e-01 100.0% 53.1%
3197759 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.52 39.0 3.36e-01 80.6% 94.2%
3602308 4095.1.1.1 alpha bundles › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › DNA_ligase_A_N 0.50 29.0 2.76e-01 74.2% 44.5%