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SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00020

Bact-Vir

SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00020

Identity

Kingdom:
phage

Quality

78.5 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 15-72
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4chkB00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.72 44.0 3.72e-01 100.0% 39.6%
2lqjA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.66 58.0 4.98e-01 100.0% 86.2%
2cyyA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.65 56.0 4.81e-01 100.0% 75.8%
5owvD01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.64 44.0 2.97e-01 100.0% 18.9%
6lxgA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.62 51.0 4.82e-01 93.1% 100.0%
5ja1B00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.62 37.0 3.62e-01 100.0% 51.5%
5yppA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.62 54.0 4.72e-01 100.0% 86.7%
2bkfA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.62 40.0 3.64e-01 100.0% 47.0%
2jheA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.61 53.0 4.76e-01 98.3% 87.7%
4melA02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.60 39.0 3.35e-01 100.0% 41.5%
1jx4A04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.59 51.0 4.29e-01 100.0% 57.1%
1wmdA02 2.60.120.380 Mainly Beta › Sandwich › Jelly Rolls › 0.59 47.0 3.84e-01 100.0% 45.3%
1djsA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 44.0 3.73e-01 100.0% 48.0%
2hlcA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.58 41.0 3.49e-01 100.0% 43.3%
6hj2A00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.58 39.0 2.55e-01 70.7% 94.5%
2mvzA00 2.40.100.10 Mainly Beta › Beta Barrel › Cyclophilin › Cyclophilin-like 0.57 49.0 3.70e-01 100.0% 98.6%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.55 48.0 3.93e-01 100.0% 55.0%
2i02A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 43.0 3.26e-01 100.0% 36.4%
1alo006 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.54 39.0 3.17e-01 81.0% 85.7%
7sz2A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.54 46.0 4.03e-01 100.0% 85.9%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.54 46.0 3.82e-01 100.0% 56.8%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 39.0 3.43e-01 100.0% 49.0%
4jzjC02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 43.0 3.58e-01 100.0% 50.0%
3lgdA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.53 43.0 2.59e-01 93.1% 44.2%
3gasB02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 38.0 2.85e-01 77.6% 55.4%
3zgzD04 2.20.28.290 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.53 40.0 3.94e-01 100.0% 77.4%
2pstX00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.53 41.0 4.07e-01 87.9% 82.0%
2ej9A02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.53 38.0 4.12e-01 91.4% 91.8%
2z8lA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.53 44.0 3.58e-01 96.6% 51.3%
2fg9A01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 40.0 2.99e-01 84.5% 71.7%
3in6A02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 43.0 3.47e-01 100.0% 46.2%
3d34B01 2.60.40.2130 Mainly Beta › Sandwich › Immunoglobulin-like › F-spondin domain 0.52 44.0 3.28e-01 100.0% 50.0%
1ukfA00 3.90.70.20 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.52 44.0 3.19e-01 100.0% 38.8%
2fhqA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 41.0 3.22e-01 100.0% 39.3%
3f59D00 2.60.220.30 Mainly Beta › Sandwich › Chondroitinase Ac; Chain A, domain 3 › 0.51 46.0 3.37e-01 100.0% 40.3%
2vm9A01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 39.0 3.03e-01 100.0% 33.8%
4jonC00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.51 43.0 3.52e-01 100.0% 85.6%
4uzgA01 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 43.0 3.26e-01 100.0% 41.7%
4yn3A02 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.51 43.0 3.40e-01 100.0% 97.8%
1y7eA02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.51 42.0 3.49e-01 100.0% 70.3%
1etb200 2.60.40.180 Mainly Beta › Sandwich › Immunoglobulin-like › Transthyretin/hydroxyisourate hydrolase domain 0.50 41.0 3.47e-01 100.0% 96.6%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3686863 245.1.1.1 a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.78 44.0 3.75e-01 100.0% 36.7%
3838043 264.2.1.0 beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.73 66.0 5.44e-01 100.0% 92.0%
3725727 3792.1.1.0 beta sandwiches › 26S proteasome subunit Rpn2 C-terminal domain › 26S proteasome subunit Rpn2 C-terminal domain › 26S proteasome subunit Rpn2 C-terminal domain 0.72 44.0 3.84e-01 100.0% 42.4%
4355655 264.2.1.0 beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.71 65.0 4.96e-01 100.0% 97.6%
3704338 2004.1.1.26 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin 0.70 60.0 4.22e-01 100.0% 41.5%
3904649 12.5.1.2 beta sandwiches › Glycosyl hydrolase domain-like › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related › GPS 0.69 42.0 2.94e-01 100.0% 20.0%
3971355 304.12.1.2 a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 › MgtC_SapB_C 0.68 61.0 5.35e-01 98.3% 95.3%
3211717 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.68 39.0 4.56e-01 96.6% 91.4%
1036625 3122.1.1.1 a+b complex topology › MESD › MESD › MESD › Mesd 0.68 59.0 5.41e-01 100.0% 97.4%
4979735 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.67 59.0 5.09e-01 100.0% 84.4%
3606610 11.1.1.720 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › IG_AIR9 0.67 45.0 3.78e-01 100.0% 41.0%
4929060 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.66 57.0 4.83e-01 100.0% 74.0%
4934810 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.66 59.0 5.30e-01 100.0% 96.2%
3395224 11.1.1.179 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.65 44.0 3.79e-01 100.0% 43.2%
5006179 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.65 57.0 5.10e-01 100.0% 86.7%
3507630 221.1.1.168 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PI3K_rbd, PI3K_p85B 0.65 41.0 2.55e-01 100.0% 12.1%
3998137 304.7.1.4 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › S8_pro-domain 0.64 56.0 5.10e-01 100.0% 91.3%
4947263 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.64 56.0 5.18e-01 100.0% 94.7%
4975915 304.4.1.29 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg_3 0.64 55.0 4.84e-01 100.0% 88.9%
3945401 304.12.1.2 a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 › MgtC_SapB_C 0.64 54.0 4.88e-01 100.0% 96.5%
4929414 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.64 56.0 5.29e-01 100.0% 95.7%
4979323 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.63 55.0 4.80e-01 100.0% 87.8%
4971887 1144.1.1.0 beta sandwiches › Apc (acetophenone carboxylase) beta subunit C-terminal domain › Apc (acetophenone carboxylase) beta subunit C-terminal domain › Apc (acetophenone carboxylase) beta subunit C-terminal domain 0.63 38.0 2.64e-01 100.0% 17.7%
5058314 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 46.0 3.88e-01 100.0% 47.0%
4976641 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.62 53.0 4.94e-01 100.0% 96.0%
5070847 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.62 52.0 4.80e-01 100.0% 90.0%
4985651 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.61 52.0 4.61e-01 100.0% 80.0%
4063927 304.24.1.1 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.60 53.0 3.72e-01 100.0% 39.5%
4394681 862.1.1.4 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › RepB_primase 0.60 52.0 3.58e-01 100.0% 27.8%
3942988 4187.2.1.1 a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 › NAGPA 0.60 42.0 4.10e-01 98.3% 67.7%
5078176 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.60 49.0 4.66e-01 100.0% 96.0%
4547125 375.14.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) 0.59 39.0 4.08e-01 100.0% 78.0%
3552986 11.1.1.275 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › IL3Ra_N 0.59 40.0 3.65e-01 100.0% 50.6%
3600531 4012.3.1.0 a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 0.58 46.0 4.78e-01 100.0% 98.1%
5044658 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.57 49.0 4.37e-01 100.0% 82.4%
4012961 221.17.1.0 a+b two layers › beta-Grasp › C-terminal wheel domain of Cns1 › C-terminal wheel domain of Cns1 0.57 40.0 2.96e-01 100.0% 27.5%
3508689 11.1.1.179 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.57 50.0 4.07e-01 100.0% 57.3%
3996298 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.57 48.0 4.41e-01 100.0% 97.5%
4350613 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.56 47.0 3.97e-01 100.0% 62.9%
3599902 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.55 43.0 3.09e-01 86.2% 70.8%
3621133 5.1.3.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.55 49.0 3.13e-01 100.0% 96.3%
4976844 303.1.1.1 a+b four layers › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › PvlArgDC 0.55 47.0 3.47e-01 100.0% 35.2%
3797677 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.55 48.0 3.08e-01 100.0% 96.3%
3972526 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.55 49.0 4.58e-01 98.3% 91.4%
3187615 221.17.1.1 a+b two layers › beta-Grasp › C-terminal wheel domain of Cns1 › C-terminal wheel domain of Cns1 › Wheel 0.55 38.0 2.82e-01 100.0% 25.9%
3573883 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.55 47.0 3.76e-01 100.0% 48.0%
4937158 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.55 41.0 4.12e-01 100.0% 78.3%
3572785 12.5.1.0 beta sandwiches › Glycosyl hydrolase domain-like › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related 0.54 40.0 3.19e-01 100.0% 36.9%
3273123 3578.1.1.0 beta sandwiches › Third domain in metalloprotease StcE › Third domain in metalloprotease StcE › Third domain in metalloprotease StcE 0.54 48.0 3.74e-01 100.0% 53.2%
3528939 221.1.1.55 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RAWUL 0.54 37.0 2.99e-01 100.0% 35.8%
3228120 11.1.1.408 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF281 0.53 46.0 3.88e-01 100.0% 57.3%
4939058 3457.1.1.3 alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Arc_PepC_II 0.53 41.0 2.79e-01 100.0% 20.0%
5010420 2492.1.1.0 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.52 46.0 3.76e-01 100.0% 100.0%
4555816 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.52 47.0 4.10e-01 100.0% 71.8%
4082091 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.52 45.0 3.66e-01 100.0% 60.0%
5015065 10.1.2.0 beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.51 44.0 3.09e-01 100.0% 47.5%