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SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00628

Bact-Vir

SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00628

Identity

Kingdom:
phage

Quality

71.7 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 3-69
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.79 62.0 5.94e-01 100.0% 73.7%
1vwxS02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.77 60.0 5.75e-01 100.0% 73.7%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.73 55.0 5.52e-01 100.0% 80.6%
1vwxS01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.72 58.0 5.73e-01 100.0% 83.1%
4njcA00 3.10.20.730 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNAP, epsilon subunit-like 0.71 49.0 5.19e-01 100.0% 81.7%
2hfqA00 3.10.510.10 Alpha Beta › Roll › NE1680-like fold › NE1680-like 0.68 53.0 4.94e-01 100.0% 68.2%
1x9tA02 3.90.1620.10 Alpha Beta › Alpha-Beta Complex › adenovirus 2 penton base, domain 2 › adenovirus 2 penton base, domain 2 0.67 57.0 3.85e-01 100.0% 43.2%
2q7nA05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 48.0 4.25e-01 100.0% 55.1%
7kseA02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.63 54.0 4.30e-01 100.0% 92.5%
2ql8A00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.61 43.0 3.42e-01 74.6% 64.3%
2nytD00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.60 47.0 3.43e-01 100.0% 31.3%
1e25A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.60 41.0 2.82e-01 73.1% 18.3%
2hj1A00 3.10.20.280 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RnfH-like 0.60 46.0 4.48e-01 98.5% 74.0%
6usmB01 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.60 48.0 3.85e-01 92.5% 85.7%
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 0.59 51.0 3.84e-01 100.0% 39.0%
1e7uA04 3.30.1010.10 Alpha Beta › 2-Layer Sandwich › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 0.58 42.0 3.26e-01 77.6% 66.5%
1zvfB01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 39.0 3.00e-01 70.1% 32.9%
2iabA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 44.0 3.57e-01 100.0% 40.6%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.57 45.0 4.11e-01 88.1% 94.6%
5kfzA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.56 48.0 4.04e-01 100.0% 54.5%
5jgfA02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.56 48.0 3.85e-01 100.0% 71.7%
4ntqB00 3.30.2450.20 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.56 43.0 3.48e-01 88.1% 90.3%
2pmvA02 2.170.130.30 Mainly Beta › Beta Complex › Ferric Hydroxamate Uptake Protein; Chain A, domain 1 › 0.56 49.0 4.24e-01 100.0% 89.8%
3e0jB00 3.90.1030.20 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain 0.55 35.0 2.87e-01 100.0% 30.1%
3rb5A02 2.60.40.2030 Mainly Beta › Sandwich › Immunoglobulin-like › CalX-beta domain 0.55 38.0 3.17e-01 100.0% 39.2%
2bs2B01 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.55 47.0 4.15e-01 100.0% 81.1%
3h96C00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 45.0 3.67e-01 98.5% 46.4%
1a3qA01 2.60.40.340 Mainly Beta › Sandwich › Immunoglobulin-like › Rel homology domain (RHD), DNA-binding domain 0.55 47.0 3.54e-01 100.0% 76.0%
2g3wA00 3.10.640.10 Alpha Beta › Roll › Restriction endonuclease-like alpha-beta roll fold › Restriction endonuclease-like alpha-beta roll domain 0.55 45.0 3.41e-01 95.5% 89.9%
3upuA03 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.54 42.0 3.49e-01 88.1% 63.4%
4emeC02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.54 45.0 3.74e-01 100.0% 74.8%
5cvmA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.53 45.0 3.01e-01 100.0% 85.4%
2i9uA02 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.53 43.0 2.93e-01 97.0% 97.4%
3nziA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.52 37.0 3.24e-01 100.0% 48.1%
1ciiA02 3.30.305.10 Alpha Beta › 2-Layer Sandwich › Colicin Ia; domain 2 › Colicin Ia; domain 2 0.52 43.0 3.88e-01 100.0% 93.1%
8bs9A01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.52 44.0 2.97e-01 100.0% 90.3%
3f02B02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.52 43.0 3.89e-01 100.0% 93.0%
2wxfA02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 43.0 3.67e-01 98.5% 64.7%
7r0kB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 39.0 2.77e-01 88.1% 56.7%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 39.0 2.96e-01 100.0% 29.9%
1r9fA01 3.30.390.180 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › RNA silencing suppressor P19 0.51 39.0 3.48e-01 89.6% 82.6%
1cqxA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.50 42.0 3.67e-01 100.0% 63.1%
2mraA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.50 38.0 3.38e-01 91.0% 86.3%
2wliA02 2.60.40.1400 Mainly Beta › Sandwich › Immunoglobulin-like › G protein-activated inward rectifier potassium channel 1 0.50 39.0 3.09e-01 91.0% 70.8%
4d8mA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.50 42.0 3.23e-01 100.0% 38.8%
ECOD (62)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5074648 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.83 65.0 6.25e-01 100.0% 74.7%
4969863 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.82 64.0 6.19e-01 100.0% 74.7%
5065436 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.81 63.0 6.48e-01 100.0% 87.5%
4983090 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.81 63.0 5.96e-01 100.0% 70.9%
4937773 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.81 63.0 6.74e-01 100.0% 96.6%
5067865 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.79 62.0 6.15e-01 100.0% 80.0%
4990637 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.79 63.0 5.85e-01 100.0% 68.7%
4939739 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.79 62.0 6.57e-01 100.0% 94.9%
4967222 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.79 62.0 6.51e-01 100.0% 93.3%
5030993 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.78 61.0 5.76e-01 100.0% 70.0%
4013514 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.78 61.0 5.24e-01 100.0% 53.3%
4951473 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.78 61.0 6.31e-01 100.0% 88.9%
4160542 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.78 61.0 6.48e-01 100.0% 96.6%
4943401 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.78 63.0 5.79e-01 100.0% 68.2%
2106285 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.78 61.0 5.14e-01 100.0% 51.9%
4128974 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.77 63.0 5.98e-01 100.0% 75.0%
5012895 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.75 57.0 6.13e-01 100.0% 98.2%
223776 3115.4.1.1 ↗ a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 › DUF1543 0.73 55.0 5.41e-01 100.0% 76.1%
5013194 3115.4.1.0 ↗ a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 0.73 56.0 6.05e-01 97.0% 100.0%
3965010 3115.4.1.1 ↗ a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 › DUF1543 0.73 54.0 4.94e-01 100.0% 60.0%
3941732 3115.6.1.0 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon 0.70 46.0 5.17e-01 100.0% 90.0%
2106284 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.70 56.0 5.67e-01 100.0% 88.1%
3517068 3115.1.1.6 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › DUF4494 0.70 57.0 5.77e-01 100.0% 90.8%
4942818 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.68 57.0 4.49e-01 100.0% 44.3%
5029082 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.64 56.0 4.19e-01 100.0% 57.6%
3568886 2492.1.1.29 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › APOBEC4_like 0.64 49.0 3.49e-01 100.0% 26.5%
3788129 284.1.3.1 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.63 53.0 5.12e-01 97.0% 84.0%
3280008 3115.1.1.2 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › DUF4288 0.63 56.0 5.10e-01 100.0% 81.1%
3562501 3075.1.1.0 ↗ a+b two layers › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA 0.62 53.0 5.08e-01 98.5% 86.3%
3326759 284.1.3.1 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.61 49.0 4.81e-01 100.0% 84.0%
4344712 284.1.3.1 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.61 53.0 4.68e-01 100.0% 72.0%
3940020 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.60 50.0 4.20e-01 98.5% 90.0%
3411558 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 0.60 52.0 4.15e-01 100.0% 51.4%
3725909 284.1.3.1 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.60 51.0 4.63e-01 100.0% 73.4%
3193127 210.2.1.1 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C 0.59 47.0 3.00e-01 92.5% 62.7%
4796845 284.1.3.1 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.59 49.0 4.83e-01 100.0% 88.0%
3827046 284.1.3.1 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.59 50.0 4.64e-01 100.0% 78.9%
3707372 7039.1.1.0 ↗ a+b complex topology › Helical domain of PCIF1/CAPAM › Helical domain of PCIF1/CAPAM › Helical domain of PCIF1/CAPAM 0.59 49.0 3.40e-01 98.5% 91.9%
4978692 1075.1.2.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.59 48.0 3.21e-01 94.0% 97.4%
3179842 11.1.1.644 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_Pom152 0.57 40.0 3.40e-01 100.0% 41.7%
3480623 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.57 47.0 4.56e-01 100.0% 87.3%
5041801 4.15.1.0 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like 0.57 45.0 4.20e-01 100.0% 69.4%
3905094 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 0.57 48.0 3.93e-01 100.0% 50.4%
3941314 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 46.0 3.86e-01 92.5% 75.8%
3449844 10.12.1.3 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_1 0.55 34.0 2.49e-01 100.0% 20.5%
3404995 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.55 47.0 3.03e-01 100.0% 79.2%
3787050 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.55 45.0 4.10e-01 100.0% 67.4%
3582833 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.55 47.0 4.06e-01 100.0% 85.5%
3997639 7563.1.1.0 ↗ a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related 0.55 43.0 2.83e-01 89.6% 28.3%
4332626 3532.1.1.0 ↗ alpha arrays › RNA-binding domain of telomerase › RNA-binding domain of telomerase › RNA-binding domain of telomerase 0.54 45.0 2.69e-01 98.5% 11.1%
3470550 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.54 45.0 3.06e-01 100.0% 82.3%
4181458 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.53 44.0 3.87e-01 100.0% 59.1%
3585116 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.53 37.0 2.63e-01 73.1% 43.0%
3270014 5.1.4.223 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_RIC1_2nd 0.52 38.0 2.40e-01 80.6% 22.1%
5047498 3662.1.1.4 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › PAC_bac 0.52 35.0 3.06e-01 70.1% 73.9%
4927303 525.1.1.1 ↗ a+b two layers › Urease, gamma-subunit › Urease, gamma-subunit › Urease, gamma-subunit › Urease_gamma 0.52 42.0 3.61e-01 97.0% 89.2%
7661 4188.1.1.1 ↗ a+b complex topology › BB1717-like › BB1717-like › BB1717-like › SRAP 0.52 38.0 2.71e-01 83.6% 33.7%
1145963 4012.3.1.1 ↗ a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 › Cas9_PI 0.51 43.0 3.86e-01 98.5% 99.0%
4213219 109.21.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain 0.50 38.0 2.19e-01 83.6% 7.7%
3934164 219.1.1.13 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core 0.50 42.0 2.78e-01 100.0% 44.5%
5079276 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.50 44.0 3.76e-01 100.0% 67.3%
3831882 4004.1.1.5 ↗ beta sandwiches › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like › DAGK_acc 0.50 42.0 3.05e-01 100.0% 89.5%