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SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00012

Bact-Vir

SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00012

Identity

Kingdom:
phage

Quality

60.1 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 2-70
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.67 51.0 4.63e-01 82.6% 81.1%
3eipA00 3.10.50.20 Alpha Beta › Roll › Chitinase A; domain 3 › Cloacin immunity protein 0.65 50.0 4.73e-01 84.1% 100.0%
8d8lF01 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.64 49.0 4.14e-01 85.5% 88.6%
2lqjA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.63 55.0 5.00e-01 98.6% 92.6%
2jheA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.62 47.0 4.50e-01 81.2% 95.1%
2cuwA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.62 45.0 4.33e-01 79.7% 97.6%
1hq6B00 3.50.20.10 Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Pyruvoyl-Dependent Histidine Decarboxylase, subunit B 0.62 50.0 3.54e-01 91.3% 60.1%
2hzmG01 3.30.310.180 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.60 47.0 4.03e-01 87.0% 96.5%
6x3aA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 48.0 4.26e-01 89.9% 64.4%
2nmlA00 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.60 47.0 4.28e-01 89.9% 85.0%
3ix3A00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.59 44.0 3.46e-01 82.6% 63.2%
1dgsA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.59 49.0 4.45e-01 94.2% 70.5%
2joqA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.58 46.0 4.55e-01 87.0% 100.0%
1b04A02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.58 48.0 4.33e-01 94.2% 67.7%
6p3xB01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.58 49.0 3.76e-01 100.0% 85.3%
2hw4A01 3.50.20.20 Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Janus/Ocnus 0.57 46.0 4.05e-01 92.8% 65.5%
1egjA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 44.0 3.97e-01 89.9% 58.4%
4hd5A01 2.60.40.3760 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 44.0 4.05e-01 89.9% 63.9%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.57 48.0 3.74e-01 100.0% 84.4%
3nziA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.57 48.0 4.28e-01 100.0% 75.5%
3hvnA01 3.90.840.10 Alpha Beta › Alpha-Beta Complex › HIV-1 Reverse Transcriptase; Chain A, domain 3 › Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain 0.57 47.0 3.69e-01 100.0% 65.7%
1d0nA06 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.56 38.0 3.18e-01 71.0% 74.0%
2jsxA01 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.56 44.0 4.40e-01 87.0% 98.6%
6cc0A01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.56 42.0 3.30e-01 84.1% 62.2%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.55 42.0 3.89e-01 87.0% 70.8%
3fgtA01 2.10.70.60 Mainly Beta › Ribbon › Complement Module; domain 1 › Phospholipase B-like, domain 1 0.55 34.0 3.79e-01 89.9% 80.0%
1vwxS02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.55 39.0 3.87e-01 78.3% 76.3%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.54 38.0 3.78e-01 76.8% 75.0%
2btwA00 3.90.70.30 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Phytochelatin synthase, N-terminal domain 0.54 39.0 2.92e-01 79.7% 76.2%
2j3wC00 3.30.450.70 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.54 40.0 3.28e-01 81.2% 52.6%
2arzA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 44.0 3.61e-01 100.0% 83.3%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.53 44.0 4.08e-01 98.6% 90.2%
2mraA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.53 44.0 3.81e-01 98.6% 81.2%
1vq8B03 3.30.1430.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L3; Chain: B; domain 2, › 0.53 44.0 3.91e-01 100.0% 96.4%
2avxA00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.52 42.0 3.27e-01 94.2% 72.5%
2wliA02 2.60.40.1400 Mainly Beta › Sandwich › Immunoglobulin-like › G protein-activated inward rectifier potassium channel 1 0.52 41.0 3.23e-01 89.9% 54.0%
4dunA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.52 42.0 3.55e-01 94.2% 78.0%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.52 40.0 3.54e-01 89.9% 55.6%
7px0A01 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.52 35.0 3.03e-01 71.0% 40.8%
3dsmA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 46.0 2.96e-01 100.0% 99.7%
3vpbB03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.51 40.0 3.53e-01 89.9% 71.4%
5kfzA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.51 42.0 3.63e-01 98.6% 55.3%
2irmA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.51 42.0 2.81e-01 97.1% 86.1%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.51 42.0 3.92e-01 98.6% 88.3%
4ksnA00 6.20.250.80 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.51 37.0 3.83e-01 79.7% 93.8%
7r3eB02 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.51 41.0 3.22e-01 94.2% 71.2%
4wiwA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.50 35.0 3.51e-01 73.9% 100.0%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3285401 3986.2.1.0 a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.73 54.0 5.32e-01 89.9% 73.3%
3734833 304.14.1.0 a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) 0.72 53.0 4.85e-01 78.3% 100.0%
4808079 304.12.1.1 a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 › Ribosomal_S6 0.70 54.0 4.74e-01 84.1% 93.3%
5034651 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.70 53.0 4.75e-01 81.2% 80.0%
3469819 304.12.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 0.70 52.0 4.39e-01 81.2% 81.7%
5034146 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.69 53.0 4.94e-01 82.6% 90.6%
4929485 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.69 53.0 5.00e-01 84.1% 92.9%
4979323 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.66 50.0 4.63e-01 82.6% 95.6%
5070847 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.65 49.0 4.71e-01 82.6% 97.5%
3789334 302.4.1.0 a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.64 47.0 4.17e-01 79.7% 80.0%
3287357 3115.3.1.0 a+b two layers › GP2-like › P56 › P56 0.62 44.0 4.68e-01 76.8% 98.3%
4964337 3115.5.1.1 a+b two layers › GP2-like › phenylacetate-CoA oxygenase subunit PaaB › phenylacetate-CoA oxygenase subunit PaaB › PaaB 0.62 45.0 4.77e-01 82.6% 98.2%
5013194 3115.4.1.0 a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 0.61 43.0 4.58e-01 73.9% 100.0%
3265857 299.1.1.0 a+b complex topology › YbaK/ProRS associated domain › YbaK/ProRS associated domain › YbaK/ProRS associated domain 0.61 45.0 3.87e-01 85.5% 49.1%
3519371 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 44.0 3.80e-01 89.9% 46.7%
4962335 3115.5.1.1 a+b two layers › GP2-like › phenylacetate-CoA oxygenase subunit PaaB › phenylacetate-CoA oxygenase subunit PaaB › PaaB 0.60 43.0 4.47e-01 85.5% 84.6%
4947071 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.60 52.0 5.04e-01 98.6% 100.0%
3403311 4326.1.1.1 a+b two layers › ERH-like › ERH-like › ERH-like › ER 0.59 47.0 4.23e-01 89.9% 85.0%
2771923 4326.1.1.1 a+b two layers › ERH-like › ERH-like › ERH-like › ER 0.59 47.0 4.29e-01 89.9% 75.8%
4976641 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.59 52.0 5.07e-01 98.6% 100.0%
4951473 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.59 42.0 4.35e-01 76.8% 87.3%
3767551 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 46.0 4.11e-01 89.9% 64.8%
4329174 223.1.1.7 a+b three layers › Profilin-like › sensor domains › sensor domains › Autoind_bind 0.58 43.0 3.34e-01 82.6% 58.2%
4967222 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.58 41.0 4.35e-01 76.8% 91.7%
4971633 4176.1.1.2 a/b three-layered sandwiches › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › S-Me-THD_N 0.58 45.0 3.20e-01 97.1% 26.7%
3609926 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 0.58 44.0 3.71e-01 87.0% 72.3%
4680886 69.1.1.14 beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Hint_2 0.57 50.0 3.81e-01 98.6% 55.2%
3762946 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 45.0 3.96e-01 89.9% 62.7%
3229851 11.10.1.4 beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like › TRAF-mep_MATH 0.57 42.0 3.29e-01 79.7% 49.0%
3484366 284.1.2.1 a+b two layers › FKBP-like › FKBP-like › Conserved carboxy-terminal domain of oxidative-stress-responsive kinase 1-like kinases › OSR1_C 0.57 43.0 3.94e-01 87.0% 70.0%
4973338 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.57 46.0 3.16e-01 95.7% 83.5%
None 0.56 45.0 4.14e-01 91.3% 87.4%
3650990 274.1.1.44 a+b two layers › Pili subunits › Pili subunits › Pili subunits › DUF7804 0.56 46.0 3.89e-01 97.1% 68.5%
3194942 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.56 46.0 3.76e-01 100.0% 66.2%
3577596 304.112.1.0 a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain 0.56 41.0 3.32e-01 79.7% 73.8%
1907312 223.1.1.7 a+b three layers › Profilin-like › sensor domains › sensor domains › Autoind_bind 0.55 45.0 3.44e-01 92.8% 71.5%
5037079 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 44.0 4.52e-01 89.9% 95.4%
4939739 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.55 39.0 4.08e-01 78.3% 98.3%
4928453 206.1.3.21 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.55 45.0 2.95e-01 89.9% 27.1%
3898917 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 43.0 3.51e-01 89.9% 46.4%
5012895 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.55 39.0 4.21e-01 84.1% 100.0%
4160542 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.54 40.0 4.17e-01 84.1% 96.6%
4019479 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.54 45.0 3.03e-01 98.6% 49.1%
4969863 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.54 38.0 3.77e-01 76.8% 76.0%
2106285 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.54 40.0 3.55e-01 82.6% 55.6%
3892842 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.54 38.0 3.92e-01 73.9% 95.4%
3935630 3346.1.1.0 a+b two layers › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 0.54 38.0 2.81e-01 88.4% 25.9%
4013514 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.53 40.0 3.58e-01 84.1% 60.0%
3406669 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.53 36.0 3.21e-01 76.8% 48.0%
3584885 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.53 38.0 4.04e-01 91.3% 91.7%
3483798 11.2.1.72 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › PF29377 0.52 43.0 3.39e-01 100.0% 76.0%
3197773 10.12.1.52 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_8 0.52 43.0 2.92e-01 100.0% 73.4%
3966635 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.52 42.0 3.28e-01 94.2% 69.4%
4412811 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.52 39.0 2.70e-01 85.5% 45.4%
5067865 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.52 38.0 3.84e-01 82.6% 85.7%
4016581 11.1.1.926 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF7136 0.52 41.0 3.23e-01 95.7% 66.1%
5030993 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.52 39.0 3.75e-01 84.1% 78.8%
2831852 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.52 39.0 3.49e-01 84.1% 60.4%
3312666 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.51 36.0 3.65e-01 100.0% 74.3%
3242186 11.2.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.51 42.0 3.63e-01 95.7% 70.8%
5041017 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 41.0 3.77e-01 98.6% 67.8%
3492478 11.10.1.4 beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like › TRAF-mep_MATH 0.51 37.0 2.88e-01 79.7% 45.7%
3712786 3346.1.1.0 a+b two layers › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 0.50 41.0 3.18e-01 97.1% 63.4%