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SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00335

Bact-Vir

SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00335

Identity

Kingdom:
phage

Quality

87.4 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 2-78
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h4zB03 3.15.10.50 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › 0.69 61.0 4.61e-01 100.0% 81.2%
1dxkA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.69 57.0 4.05e-01 96.1% 31.2%
1l3aA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.68 60.0 4.73e-01 100.0% 84.9%
1m2xA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.66 50.0 3.60e-01 85.7% 28.3%
2kt4B01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.62 50.0 4.13e-01 88.3% 73.9%
3qkgA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.62 50.0 3.89e-01 88.3% 67.1%
1ko2A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.60 51.0 3.68e-01 97.4% 31.7%
1twfB04 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.60 47.0 3.69e-01 88.3% 95.5%
1a5yA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.59 42.0 2.86e-01 75.3% 29.9%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.59 52.0 4.46e-01 100.0% 77.6%
3htyA00 2.40.128.280 Mainly Beta › Beta Barrel › Lipocalin › 0.58 46.0 4.32e-01 97.4% 70.2%
3vsfC01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.58 51.0 3.32e-01 98.7% 34.5%
6m9yA00 3.30.1300.40 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.57 36.0 4.05e-01 98.7% 86.0%
1i1iP02 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.57 44.0 3.64e-01 85.7% 96.0%
2iayA00 3.30.1820.10 Alpha Beta › 2-Layer Sandwich › Lp2179-like fold › Lp2179-like 0.57 47.0 4.12e-01 100.0% 60.5%
1viuC00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.57 46.0 3.65e-01 92.2% 78.2%
3brnB00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 47.0 3.90e-01 98.7% 49.3%
6mlyB01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.57 52.0 3.53e-01 100.0% 29.4%
4ghbA00 2.40.160.190 Mainly Beta › Beta Barrel › Porin › 0.57 47.0 3.37e-01 96.1% 43.1%
2cm4A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 48.0 3.98e-01 98.7% 51.7%
1bebA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.56 48.0 3.88e-01 98.7% 53.2%
3apuB00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.56 48.0 3.74e-01 96.1% 52.9%
3qc2B00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.56 50.0 3.22e-01 100.0% 35.6%
1t17A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 44.0 3.62e-01 88.3% 77.7%
3nqhA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.55 49.0 3.28e-01 98.7% 34.0%
3f40A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 38.0 3.42e-01 74.0% 82.9%
6i0iA00 3.30.350.10 Alpha Beta › 2-Layer Sandwich › Subtilisin Inhibitor › Subtilisin inhibitor-like 0.54 35.0 3.21e-01 74.0% 47.2%
2vr3B02 2.60.40.1290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 44.0 3.59e-01 92.2% 100.0%
2l3tA02 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.54 45.0 4.11e-01 90.9% 76.0%
1ew3A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.54 46.0 3.73e-01 98.7% 51.6%
3i2nA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 47.0 3.10e-01 100.0% 33.3%
4rt0A00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.53 37.0 3.33e-01 72.7% 77.1%
3tfzB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.53 45.0 3.65e-01 100.0% 80.0%
1cb8A03 2.60.220.10 Mainly Beta › Sandwich › Chondroitinase Ac; Chain A, domain 3 › Polysaccharide lyase family 8-like, C-terminal 0.53 37.0 3.36e-01 74.0% 66.4%
1e5pA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 45.0 3.73e-01 100.0% 52.3%
4u13A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 38.0 3.47e-01 77.9% 98.2%
4gn2A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.52 38.0 2.74e-01 77.9% 61.7%
1yguA02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.52 37.0 2.56e-01 75.3% 29.3%
2oc3A00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.52 37.0 2.54e-01 75.3% 29.7%
6u5vB07 3.30.1120.100 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.52 35.0 3.01e-01 70.1% 48.1%
4hwxA00 3.30.350.10 Alpha Beta › 2-Layer Sandwich › Subtilisin Inhibitor › Subtilisin inhibitor-like 0.51 36.0 3.25e-01 75.3% 93.9%
2hr0B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 43.0 3.84e-01 92.2% 95.4%
4d10F01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.51 39.0 3.05e-01 84.4% 62.6%
4aqcB01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 40.0 3.79e-01 89.6% 84.4%
4ge6A00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.50 43.0 2.99e-01 100.0% 43.2%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4013876 295.1.1.38 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › NPHP3_N 0.65 47.0 4.90e-01 75.3% 94.3%
3625357 2004.1.1.162 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Rad51 0.65 50.0 3.38e-01 100.0% 22.9%
3226909 331.15.1.0 ↗ a+b two layers › TBP-like › Anti-CRISPR protein AcrID1 › Anti-CRISPR protein AcrID1 0.63 45.0 4.60e-01 100.0% 77.3%
3935168 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.63 44.0 3.00e-01 88.3% 20.4%
3506907 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.63 49.0 4.50e-01 93.5% 65.0%
3883246 9.1.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › Lipocalin 0.62 50.0 3.92e-01 88.3% 64.7%
3992783 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.62 46.0 3.23e-01 83.1% 25.0%
5040814 331.2.1.0 ↗ a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain 0.60 53.0 4.68e-01 100.0% 67.8%
3282696 243.1.1.80 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › PF26580 0.59 43.0 3.96e-01 76.6% 98.0%
3245832 145.1.1.30 ↗ alpha arrays › F-box domain › F-box domain › F-box domain › FBA_2 0.59 41.0 2.75e-01 72.7% 20.0%
5025460 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.59 33.0 3.54e-01 85.7% 64.6%
3892482 883.1.1.10 ↗ a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like › SMP_C2CD2L 0.58 49.0 3.74e-01 100.0% 68.1%
5018457 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 39.0 4.15e-01 71.4% 94.3%
1281147 9.23.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Hypothetical protein BT_0869 › Hypothetical protein BT_0869 › Lipocalin_3 0.57 45.0 4.25e-01 97.4% 70.2%
5047048 246.2.1.9 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos_2 0.57 38.0 2.91e-01 70.1% 98.4%
3396847 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.57 46.0 3.88e-01 88.3% 72.7%
None — 0.56 38.0 2.61e-01 71.4% 25.8%
3422058 5.1.3.144 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › b-prop_At3g26010-like 0.56 48.0 3.29e-01 97.4% 27.7%
3426677 252.1.1.1 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.56 44.0 4.12e-01 84.4% 81.9%
4887870 9.1.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › Lipocalin 0.56 49.0 3.85e-01 98.7% 49.1%
3969155 283.2.1.1 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › GPW_gp25 0.56 39.0 3.12e-01 72.7% 44.5%
4958553 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.55 38.0 2.81e-01 72.7% 93.6%
3230977 4099.1.1.48 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Rgr-1_C 0.55 41.0 3.56e-01 83.1% 76.9%
3951937 330.8.1.1 ↗ a+b two layers › dsRBD-like › Rv2632c-like › Rv2632c-like › Rv2632c-like 0.55 38.0 3.62e-01 71.4% 64.0%
3909234 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.55 45.0 3.93e-01 89.6% 79.1%
4632710 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 30.0 3.66e-01 87.0% 88.9%
3193880 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.54 49.0 3.08e-01 100.0% 30.0%
4980867 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 45.0 4.07e-01 93.5% 94.3%
3506561 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 37.0 3.84e-01 72.7% 81.3%
3953220 2484.1.1.216 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF7159 0.53 44.0 3.92e-01 96.1% 77.3%
3235791 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.53 46.0 3.19e-01 100.0% 40.6%
3966494 1.1.5.25 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.53 39.0 3.55e-01 80.5% 84.5%
3242530 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.53 37.0 2.54e-01 75.3% 27.9%
3309307 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.53 48.0 2.76e-01 98.7% 18.7%
3260045 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.53 39.0 3.96e-01 80.5% 86.7%
3791021 5.1.3.135 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1, Kelch_KLHDC2_KLHL20_DRC7, Beta-prop_ATRN-LZTR1 0.52 46.0 3.09e-01 100.0% 24.4%
5032125 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 45.0 3.09e-01 100.0% 28.1%
4081842 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.52 39.0 2.90e-01 83.1% 29.3%
3532417 2007.2.3.21 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase, PTP-SAK 0.52 37.0 2.53e-01 75.3% 29.5%
4004011 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 35.0 3.21e-01 71.4% 53.6%
None — 0.51 36.0 2.47e-01 75.3% 26.4%
3510577 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.51 44.0 3.00e-01 100.0% 41.0%
3938060 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.51 44.0 3.49e-01 100.0% 68.0%
3882821 2007.2.3.21 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase, PTP-SAK 0.51 44.0 3.01e-01 100.0% 44.3%
3316054 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 44.0 2.82e-01 100.0% 30.4%
3860966 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.51 44.0 2.94e-01 100.0% 39.7%
3889825 3570.1.1.1 ↗ a+b two layers › FAM3 superfamily › FAM3 superfamily › FAM3 superfamily › ILEI 0.50 44.0 3.46e-01 100.0% 82.4%
3397960 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.50 35.0 2.46e-01 75.3% 27.7%
4161565 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.50 36.0 3.47e-01 79.2% 84.2%
None — 0.50 43.0 2.98e-01 100.0% 44.7%