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SR-VP_4-6_scaffold_141_3489769_prodigal-single.1__X__X__00255

Bact-Vir

SR-VP_4-6_scaffold_141_3489769_prodigal-single.1__X__X__00255

Identity

Kingdom:
phage

Quality

80.6 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 medium residues 50-124
PDB
Domain cluster: representative
CATH (54)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2qkdA01 2.20.25.420 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ZPR1, zinc finger domain 0.69 36.0 4.34e-01 100.0% 79.2%
3f6gA02 3.30.160.340 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.65 38.0 4.15e-01 100.0% 69.8%
1s2oA02 3.90.1070.10 Alpha Beta › Alpha-Beta Complex › Hypothetical Protein Ta0175; Chain: A, domain 2 › 0.64 46.0 4.76e-01 100.0% 81.7%
4bj8K00 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.63 40.0 3.43e-01 100.0% 40.0%
2l48A00 3.30.70.2030 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 38.0 3.70e-01 74.7% 55.3%
1weyA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.61 43.0 3.87e-01 81.3% 52.9%
5w2fA01 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.61 45.0 4.37e-01 96.0% 69.8%
4qjvB00 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.61 47.0 4.36e-01 98.7% 66.0%
5l16A01 3.30.1330.10 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › PurM-like, N-terminal domain 0.61 51.0 4.40e-01 96.0% 95.9%
2g1dA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.60 51.0 4.74e-01 100.0% 74.5%
2joeA01 3.30.1830.10 Alpha Beta › 2-Layer Sandwich › YehR-like fold › YehR-like 0.60 51.0 4.36e-01 98.7% 57.0%
1zodA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.59 45.0 3.69e-01 100.0% 44.0%
2bkkA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 46.0 4.40e-01 97.3% 72.2%
2r5rA00 3.10.270.10 Alpha Beta › Roll › Urate Oxidase › Urate Oxidase; 0.57 47.0 3.39e-01 94.7% 64.2%
4q5eA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.57 43.0 4.37e-01 97.3% 84.0%
1dcoA00 3.30.1360.20 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Transcriptional coactivator/pterin dehydratase 0.57 41.0 3.81e-01 94.7% 58.6%
2gukA00 3.30.2190.10 Alpha Beta › 2-Layer Sandwich › PG1857-like › PG1857-like 0.57 44.0 3.90e-01 98.7% 56.8%
1pfsA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 33.0 3.33e-01 97.3% 53.8%
5hb5B00 3.30.1610.10 Alpha Beta › 2-Layer Sandwich › c-terminal autoproteolytic domain of nucleoporin nup98 › Peptidase S59, nucleoporin 0.56 48.0 3.97e-01 97.3% 98.6%
1xkpB00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.56 43.0 3.80e-01 97.3% 53.7%
3lssA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 48.0 3.20e-01 98.7% 43.9%
4dduA07 2.60.510.20 Mainly Beta › Sandwich › EV matrix protein fold › 0.56 33.0 2.97e-01 94.7% 39.3%
3e3xA01 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.55 40.0 3.56e-01 78.7% 54.0%
2dgkA02 3.90.1150.160 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.55 44.0 3.95e-01 100.0% 62.6%
3zxoA00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.54 47.0 3.99e-01 100.0% 58.4%
2plgA01 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.54 42.0 3.63e-01 97.3% 50.0%
2qmaA02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.54 40.0 3.45e-01 100.0% 48.0%
4g6tA00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.54 41.0 3.53e-01 96.0% 49.2%
1b7yB05 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.54 46.0 3.52e-01 98.7% 57.1%
1jyoA00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.54 42.0 3.54e-01 93.3% 49.2%
4v1al00 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.54 44.0 3.72e-01 98.7% 52.6%
4r3aA02 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.54 45.0 3.78e-01 98.7% 54.9%
2nlkA02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.54 43.0 3.04e-01 90.7% 27.7%
3h2gA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 38.0 2.67e-01 77.3% 59.9%
2c4iA01 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.53 40.0 3.48e-01 100.0% 51.7%
4nfnA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.53 38.0 4.01e-01 97.3% 87.5%
2zzeA04 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.53 45.0 4.21e-01 100.0% 76.8%
3icyA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.53 31.0 2.66e-01 92.0% 36.4%
1s12A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.53 38.0 3.60e-01 100.0% 62.8%
5aj3E01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.52 39.0 3.83e-01 98.7% 74.1%
6ya6A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 42.0 3.91e-01 98.7% 70.4%
5d9hA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 42.0 4.05e-01 97.3% 77.3%
2x7gA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 41.0 3.94e-01 97.3% 76.1%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.52 38.0 3.34e-01 82.7% 79.2%
2hq9B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 46.0 3.76e-01 100.0% 71.5%
5jzjA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 41.0 3.88e-01 97.3% 72.3%
3racA00 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.51 43.0 2.90e-01 100.0% 86.7%
1s9iB01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 41.0 3.91e-01 97.3% 73.1%
3nqkA02 2.40.128.440 Mainly Beta › Beta Barrel › Lipocalin › Uncharacterised protein PF14274, DUF4361 0.51 43.0 3.49e-01 98.7% 84.4%
2xzsA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 42.0 4.02e-01 98.7% 78.0%
6n3oA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 41.0 3.94e-01 97.3% 77.8%
1bcrA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 41.0 2.96e-01 94.7% 55.5%
6kjuB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.50 41.0 3.63e-01 93.3% 94.9%
1b24A01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.50 43.0 4.06e-01 98.7% 80.0%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4955075 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.73 59.0 6.00e-01 98.7% 90.4%
3210232 4955.1.1.0 ↗ a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.66 58.0 4.04e-01 100.0% 91.6%
4943463 304.43.1.0 ↗ a+b two layers › Alpha-beta plaits › Hypothetical protein TT1725 › Hypothetical protein TT1725 0.65 51.0 4.68e-01 89.3% 64.0%
4099004 306.4.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › YggU-like › YggU-like › DUF167 0.64 55.0 4.99e-01 94.7% 84.0%
4890504 330.1.1.21 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5_C 0.64 39.0 3.98e-01 98.7% 63.4%
4478921 304.156.1.1 ↗ a+b two layers › Alpha-beta plaits › DNA translocase FtsK N-terminal domain › DNA translocase FtsK N-terminal domain › FtsK_alpha 0.64 51.0 4.89e-01 98.7% 76.5%
5006953 873.1.1.12 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF27313 0.61 46.0 4.27e-01 100.0% 62.0%
3281355 304.12.1.12 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 › GDH_ACT2 0.61 49.0 4.43e-01 100.0% 64.8%
4946212 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.60 49.0 3.73e-01 100.0% 36.8%
3548897 327.11.2.24 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_12 0.59 51.0 4.44e-01 100.0% 71.7%
3739949 306.6.1.0 ↗ a+b two layers › Glucose permease domain IIB-like › PH0987 N-terminal domain-like › PH0987 N-terminal domain-like 0.58 43.0 4.15e-01 93.3% 69.4%
4068918 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.58 50.0 4.14e-01 100.0% 52.1%
3713527 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.58 47.0 3.21e-01 92.0% 30.0%
3892483 11.1.1.872 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_ENGASE1_C 0.58 50.0 4.35e-01 98.7% 65.0%
4448399 207.11.1.1 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Urease accessory protein ureH › Urease accessory protein ureH › UreD 0.58 51.0 3.47e-01 98.7% 40.4%
3955512 305.1.1.0 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase 0.58 47.0 4.10e-01 100.0% 57.5%
4100027 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.58 49.0 4.07e-01 100.0% 53.3%
4993562 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.57 34.0 3.08e-01 100.0% 41.9%
3407270 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.57 39.0 3.96e-01 82.7% 72.0%
3284552 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.57 48.0 4.20e-01 100.0% 60.8%
3718799 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.56 48.0 3.94e-01 100.0% 52.0%
4010802 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.56 49.0 4.05e-01 100.0% 54.8%
3971474 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.56 49.0 4.05e-01 100.0% 55.7%
5036255 241.1.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone 0.56 42.0 3.77e-01 100.0% 55.7%
3289074 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.55 48.0 4.06e-01 100.0% 56.9%
3914423 2007.2.4.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Phosphoinositide phosphatase › PF27561 0.55 46.0 2.90e-01 97.3% 89.3%
3603042 241.1.1.27 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › PF27355 0.55 49.0 3.70e-01 98.7% 45.7%
4436233 207.11.1.1 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Urease accessory protein ureH › Urease accessory protein ureH › UreD 0.54 45.0 3.15e-01 96.0% 52.4%
3221492 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.54 43.0 2.77e-01 97.3% 16.7%
3219968 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.53 43.0 2.81e-01 97.3% 18.6%
3598105 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.53 45.0 3.97e-01 100.0% 95.0%
3490423 206.1.1.74 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, PK_Tyr_Ser-Thr 0.53 43.0 2.88e-01 97.3% 21.6%
5579 306.8.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › TM1457-like › TM1457-like › Peptidase_Prp 0.53 38.0 3.60e-01 100.0% 62.8%
3163896 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.52 45.0 3.36e-01 100.0% 37.1%
3176674 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.52 42.0 2.75e-01 93.3% 18.2%
4332907 5087.3.1.1 ↗ beta meanders › Lipovitellin-phosvitin complex › Lipovitellin LV-1C › Lipovitellin LV-1C › Vit_open_b-sht 0.52 34.0 2.19e-01 96.0% 13.8%
3867392 304.112.1.0 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain 0.52 39.0 2.63e-01 82.7% 19.8%
139726 241.1.1.3 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › CesT 0.51 40.0 3.41e-01 93.3% 49.6%
3737815 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 44.0 3.02e-01 98.7% 93.2%
3268320 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 42.0 2.87e-01 97.3% 23.3%
3429719 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 45.0 3.17e-01 98.7% 51.3%
3223352 306.3.1.2 ↗ a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › Img2 0.51 43.0 3.56e-01 97.3% 53.1%
3629592 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.51 41.0 3.12e-01 98.7% 35.8%
3531424 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.50 41.0 2.61e-01 97.3% 16.8%
3790940 306.3.1.2 ↗ a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › Img2 0.50 43.0 3.73e-01 97.3% 64.7%