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SR-VP_0-2_scaffold_141_4953755_prodigal-single.1__X__X__00032

Bact-Vir

SR-VP_0-2_scaffold_141_4953755_prodigal-single.1__X__X__00032

Identity

Kingdom:
phage

Quality

70.3 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 3-57
PDB
Domain cluster: representative
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3n7zB03 3.30.1050.10 Alpha Beta › 2-Layer Sandwich › Nonspecific Lipid-transfer Protein; Chain A › SCP2 sterol-binding domain 0.68 48.0 4.02e-01 100.0% 43.2%
1o5yA00 3.10.690.10 Alpha Beta › Roll › Bifunctional nuclease domain › Bifunctional nuclease domain 0.64 55.0 4.07e-01 100.0% 37.1%
3oymA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.64 39.0 3.61e-01 85.5% 47.1%
4v0bA00 3.30.720.210 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.62 46.0 4.49e-01 94.5% 73.0%
3do9A01 3.40.1530.30 Alpha Beta › 3-Layer(aba) Sandwich › hypothetical protein tt1805 › Uncharacterised family UPF0302, N-terminal domain 0.62 49.0 3.91e-01 100.0% 41.7%
1nr4C00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.62 45.0 4.28e-01 89.1% 66.7%
1w97L01 3.30.420.380 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.61 53.0 3.89e-01 100.0% 37.0%
1eqtA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.60 44.0 4.20e-01 89.1% 64.2%
4z32A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 49.0 4.18e-01 94.5% 57.3%
1f9qD00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.59 44.0 4.20e-01 87.3% 68.2%
2i00A03 3.30.1050.10 Alpha Beta › 2-Layer Sandwich › Nonspecific Lipid-transfer Protein; Chain A › SCP2 sterol-binding domain 0.59 43.0 3.67e-01 100.0% 46.3%
3kbgA02 2.40.50.740 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Ribosomal protein S4, central domain 0.59 43.0 4.44e-01 80.0% 92.5%
4hcsA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.59 48.0 4.52e-01 92.7% 76.1%
4n9jA02 3.30.1120.130 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.58 44.0 3.70e-01 87.3% 62.6%
1r5pB00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.58 42.0 3.63e-01 100.0% 47.3%
2d9xA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 43.0 3.55e-01 87.3% 42.7%
2el8A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.57 47.0 4.05e-01 96.4% 82.4%
3k8rA01 3.30.2020.40 Alpha Beta › 2-Layer Sandwich › NE0471 N-terminal domain-like › Uncharacterised protein PF10387, DUF2442 0.56 40.0 3.82e-01 78.2% 98.5%
4dq2A03 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.56 40.0 4.25e-01 85.5% 91.5%
2hv2C02 3.30.1050.10 Alpha Beta › 2-Layer Sandwich › Nonspecific Lipid-transfer Protein; Chain A › SCP2 sterol-binding domain 0.56 39.0 3.16e-01 100.0% 35.9%
4m8aA00 3.30.720.210 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.56 41.0 3.98e-01 94.5% 71.6%
2vszB02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 41.0 3.34e-01 85.5% 51.3%
1b1zA02 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.54 46.0 3.54e-01 100.0% 66.2%
5cbeE00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 38.0 3.67e-01 74.5% 65.6%
3d0fA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 38.0 3.51e-01 76.4% 95.9%
7kfuC02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.54 40.0 2.74e-01 85.5% 95.7%
6ckmA00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.53 46.0 3.06e-01 100.0% 32.0%
4g41A00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.53 45.0 3.02e-01 100.0% 81.8%
1ti2B03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 42.0 3.85e-01 100.0% 92.9%
1h2iA01 3.30.390.80 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › DNA repair protein Rad52/59/22 0.52 38.0 2.89e-01 80.0% 54.1%
3e8vA00 2.60.40.1120 Mainly Beta › Sandwich › Immunoglobulin-like › Carboxypeptidase-like, regulatory domain 0.52 42.0 3.84e-01 100.0% 98.8%
1a78A00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.52 40.0 3.12e-01 92.7% 35.8%
6e20A00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.52 42.0 3.21e-01 90.9% 86.4%
2wfwB02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 40.0 3.83e-01 87.3% 88.1%
1earA01 2.60.260.20 Mainly Beta › Sandwich › HSP40/DNAj peptide-binding domain › Urease metallochaperone UreE, N-terminal domain 0.51 40.0 3.78e-01 94.5% 74.0%
7d8gA01 2.40.380.10 Mainly Beta › Beta Barrel › FomD barrel-like fold › FomD-like 0.51 45.0 3.19e-01 100.0% 57.5%
2wweA01 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.51 40.0 3.29e-01 85.5% 88.5%
3ztvA01 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.51 42.0 2.66e-01 100.0% 25.8%
6jsjA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 40.0 2.69e-01 98.2% 20.2%
2v3uA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.50 41.0 3.11e-01 100.0% 36.1%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3226288 2484.1.1.190 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FBA_2 0.69 62.0 3.94e-01 100.0% 32.8%
4962370 2484.3.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Creatinase/prolidase N-terminal domain › Creatinase/prolidase N-terminal domain › Creatinase_N 0.68 57.0 4.14e-01 96.4% 83.1%
3279562 896.1.1.0 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.68 53.0 4.86e-01 92.7% 65.3%
3262092 3264.1.1.0 ↗ 0.67 51.0 3.65e-01 85.5% 29.4%
4998319 246.2.1.0 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases 0.67 52.0 3.25e-01 98.2% 15.0%
2872794 4263.2.1.1 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain › FtsH_ext 0.66 51.0 4.56e-01 100.0% 59.3%
3955260 3708.1.1.1 ↗ a+b three layers › ESX-1 secretion system protein eccB1 modular domains › ESX-1 secretion system protein eccB1 modular domains › ESX-1 secretion system protein eccB1 modular domains › T7SS_ESX1_EccB 0.65 52.0 4.90e-01 100.0% 71.4%
3949804 3708.1.1.1 ↗ a+b three layers › ESX-1 secretion system protein eccB1 modular domains › ESX-1 secretion system protein eccB1 modular domains › ESX-1 secretion system protein eccB1 modular domains › T7SS_ESX1_EccB 0.65 51.0 4.90e-01 100.0% 75.4%
4302938 292.2.1.0 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain 0.64 43.0 3.70e-01 90.9% 44.7%
4517759 4263.2.1.1 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain › FtsH_ext 0.64 50.0 4.80e-01 94.5% 73.8%
4494129 880.1.1.1 ↗ a+b duplicates or obligate multimers › ADC synthase › ADC synthase › ADC synthase › Chorismate_bind 0.63 53.0 3.12e-01 100.0% 16.5%
3396736 65.1.1.0 ↗ beta sandwiches › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases 0.63 53.0 5.13e-01 100.0% 98.5%
4650292 4.8.1.23 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › RemA-like 0.63 46.0 4.15e-01 81.8% 78.8%
156909 802.1.1.1 ↗ a+b two layers › Hypothetical protein TM0160 › Hypothetical protein TM0160 › Hypothetical protein TM0160 › BFN_dom 0.62 51.0 4.42e-01 98.2% 57.0%
5052071 7528.1.1.0 ↗ a/b three-layered sandwiches › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains 0.62 52.0 3.80e-01 100.0% 45.9%
4352333 3264.1.1.0 ↗ 0.61 48.0 3.53e-01 87.3% 31.0%
3926235 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.61 42.0 3.78e-01 72.7% 58.7%
3931076 214.1.1.0 ↗ a+b two layers › SH2 › SH2 › SH2 0.60 45.0 3.53e-01 81.8% 48.3%
4971681 268.1.1.0 ↗ a+b two layers › Sterol carrier protein-like › Sterol carrier protein, SCP-related › Sterol carrier protein, SCP-related 0.60 44.0 3.44e-01 100.0% 35.2%
4265511 4.8.1.23 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › RemA-like 0.60 44.0 3.81e-01 81.8% 70.0%
1094905 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.59 49.0 4.64e-01 96.4% 75.7%
4977731 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.59 47.0 2.93e-01 98.2% 14.9%
4073849 7572.1.1.1 ↗ a/b three-layered sandwiches › Phosphofructokinase C-terminal domain › Phosphofructokinase C-terminal domain › Phosphofructokinase C-terminal domain › PFK 0.59 51.0 3.74e-01 100.0% 78.0%
4031792 2004.1.1.36 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Dynamin_N 0.59 49.0 3.34e-01 98.2% 26.1%
3398717 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.58 50.0 3.45e-01 100.0% 28.9%
3414136 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.58 49.0 3.56e-01 100.0% 35.2%
4955531 2002.1.1.30 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_18 0.58 45.0 2.87e-01 89.1% 26.8%
5004322 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.58 47.0 4.17e-01 100.0% 96.7%
4517744 4263.2.1.0 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain 0.57 45.0 4.27e-01 96.4% 74.3%
4465313 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.56 46.0 3.19e-01 100.0% 90.0%
3396261 109.1.1.7 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C_3 0.56 47.0 3.35e-01 98.2% 89.2%
3914763 2485.1.1.61 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › DCC1-like 0.55 40.0 3.23e-01 78.2% 72.2%
3520072 7523.1.1.20 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Lig_chan-Glu_bd 0.55 43.0 3.14e-01 100.0% 31.0%
3388989 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.55 45.0 3.38e-01 100.0% 36.4%
3519734 7523.1.1.20 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Lig_chan-Glu_bd 0.54 47.0 3.35e-01 100.0% 32.9%
4107587 55.1.1.1 ↗ beta barrels › Urease metallochperone UreE-N › Urease metallochperone UreE-N › Urease metallochperone UreE-N › UreE_N 0.54 43.0 4.04e-01 98.2% 76.0%
4929271 55.1.1.1 ↗ beta barrels › Urease metallochperone UreE-N › Urease metallochperone UreE-N › Urease metallochperone UreE-N › UreE_N 0.54 42.0 3.91e-01 96.4% 68.8%
3507395 252.1.1.1 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.54 43.0 3.92e-01 96.4% 88.7%
3400184 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.53 45.0 3.32e-01 100.0% 35.9%
4167299 55.1.1.1 ↗ beta barrels › Urease metallochperone UreE-N › Urease metallochperone UreE-N › Urease metallochperone UreE-N › UreE_N 0.53 43.0 4.00e-01 98.2% 74.7%
4302889 55.1.1.1 ↗ beta barrels › Urease metallochperone UreE-N › Urease metallochperone UreE-N › Urease metallochperone UreE-N › UreE_N 0.53 43.0 3.92e-01 100.0% 67.1%
2616801 7523.1.1.20 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Lig_chan-Glu_bd 0.53 44.0 3.46e-01 100.0% 43.3%
3996614 7523.1.1.52 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_3, Lig_chan-Glu_bd 0.53 43.0 2.75e-01 100.0% 17.6%
3605761 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.53 42.0 3.47e-01 92.7% 80.9%
3816810 7523.1.1.52 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_3, Lig_chan-Glu_bd 0.53 46.0 3.01e-01 100.0% 22.9%
4298074 71.1.1.3 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolB 0.53 45.0 3.17e-01 98.2% 66.9%
5026070 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.53 41.0 3.66e-01 94.5% 91.1%
4977389 3374.1.1.1 ↗ a+b complex topology › spore cortex-lytic enzyme catalytic domain › spore cortex-lytic enzyme catalytic domain › spore cortex-lytic enzyme catalytic domain › YceG 0.52 38.0 2.85e-01 76.4% 70.0%
3837131 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.52 44.0 3.62e-01 98.2% 69.5%
3410668 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.52 46.0 3.34e-01 100.0% 36.7%
None — 0.52 41.0 2.45e-01 98.2% 11.4%
3411407 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.52 43.0 3.24e-01 100.0% 36.6%
3416523 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.51 44.0 3.17e-01 100.0% 32.4%
3208748 7514.1.1.0 ↗ a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain 0.51 42.0 3.08e-01 94.5% 65.0%
4420532 55.1.1.0 ↗ beta barrels › Urease metallochperone UreE-N › Urease metallochperone UreE-N › Urease metallochperone UreE-N 0.51 39.0 3.76e-01 92.7% 72.9%
3832176 1.1.11.1 ↗ beta barrels › cradle loop barrel › RIFT-related › Type II restriction endonuclease effector domain › B3 0.51 39.0 3.72e-01 90.9% 91.4%
3395750 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.51 44.0 3.32e-01 100.0% 40.7%
3412223 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.51 43.0 3.18e-01 100.0% 84.5%
3414432 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.50 42.0 3.16e-01 100.0% 86.5%
4968630 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.50 41.0 3.65e-01 100.0% 90.0%