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SR-VP_0-2_scaffold_141_6063796_prodigal-single.1__X__X__00119

Bact-Vir

SR-VP_0-2_scaffold_141_6063796_prodigal-single.1__X__X__00119

Identity

Kingdom:
phage

Quality

78.6 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 high residues 5-55
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1a0iA01 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.70 50.0 4.37e-01 100.0% 48.2%
2ahoB03 3.30.70.1130 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › EIF_2_alpha 0.68 56.0 4.77e-01 96.1% 98.9%
3u02A01 3.30.70.2200 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 55.0 4.15e-01 100.0% 62.5%
8c46A01 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 54.0 4.37e-01 100.0% 98.2%
3w7bA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.66 55.0 4.74e-01 100.0% 95.5%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.66 51.0 4.80e-01 100.0% 69.7%
2o3iA01 3.40.1610.10 Alpha Beta › 3-Layer(aba) Sandwich › CV3147-like fold › CV3147-like domain 0.66 57.0 3.70e-01 100.0% 23.7%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.65 53.0 3.84e-01 100.0% 29.9%
3nd1A02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.64 51.0 4.04e-01 100.0% 41.8%
5wm1A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.64 52.0 4.28e-01 100.0% 78.9%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.64 53.0 4.51e-01 100.0% 54.3%
1y6kR01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 50.0 4.14e-01 100.0% 46.1%
1s55A00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.63 55.0 3.91e-01 100.0% 35.9%
2v5yA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 43.0 3.58e-01 100.0% 40.0%
2npnA02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.62 49.0 3.98e-01 100.0% 43.1%
1q8kA03 3.30.70.1130 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › EIF_2_alpha 0.62 50.0 4.03e-01 100.0% 77.6%
1l1lA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.61 49.0 2.86e-01 92.2% 42.7%
7o4xA01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 50.0 4.18e-01 100.0% 82.8%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.60 50.0 4.25e-01 100.0% 54.3%
2re9A01 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.60 53.0 3.79e-01 100.0% 34.4%
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.60 48.0 4.19e-01 100.0% 62.0%
2ed8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 43.0 3.77e-01 100.0% 48.8%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.59 49.0 3.97e-01 100.0% 56.8%
1t8hA00 3.60.140.10 Alpha Beta › 4-Layer Sandwich › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases 0.59 48.0 3.12e-01 100.0% 18.8%
2hn1A01 3.30.460.20 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › CorA soluble domain-like 0.58 41.0 3.18e-01 100.0% 28.9%
1t4aA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.58 46.0 4.19e-01 98.0% 100.0%
2i1sA00 3.10.290.30 Alpha Beta › Roll › Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A › MM3350-like 0.58 47.0 3.41e-01 100.0% 57.9%
2mvzA00 2.40.100.10 Mainly Beta › Beta Barrel › Cyclophilin › Cyclophilin-like 0.58 47.0 3.58e-01 100.0% 100.0%
6hmjA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.57 43.0 3.46e-01 82.4% 85.7%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 44.0 3.74e-01 100.0% 48.0%
3snoA01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.57 41.0 3.23e-01 80.4% 74.4%
4n0rA03 2.60.40.3950 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 49.0 3.88e-01 100.0% 49.1%
6izcA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.56 42.0 2.79e-01 84.3% 45.2%
1f02T00 4.10.820.10 Few Secondary Structures › Irregular › Translocated Intimin Receptor; Chain T › Translocated intimin receptor, central domain 0.56 40.0 3.67e-01 76.5% 87.9%
3doaA03 3.40.970.40 Alpha Beta › 3-Layer(aba) Sandwich › Ribonuclease HI; Chain A › fibrinogen binding protein from staphylococcus aureus domain like 0.55 37.0 3.96e-01 98.0% 81.4%
3ihpA03 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.55 47.0 2.89e-01 100.0% 88.4%
2z5bA00 3.30.230.100 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.54 39.0 3.05e-01 80.4% 33.1%
1wpwA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.54 43.0 2.74e-01 100.0% 45.8%
6bn3A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.53 45.0 2.88e-01 96.1% 82.0%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.53 42.0 4.29e-01 100.0% 96.0%
7eehA01 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.53 46.0 2.99e-01 100.0% 28.5%
5z0uA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 42.0 3.33e-01 100.0% 40.3%
1xfjA00 3.60.140.10 Alpha Beta › 4-Layer Sandwich › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases 0.53 41.0 2.79e-01 100.0% 43.4%
2xy1A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 43.0 3.63e-01 100.0% 54.6%
1ghpA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.52 42.0 2.76e-01 96.1% 85.2%
1ltlA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.51 40.0 4.13e-01 100.0% 95.9%
1qfoC00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 42.0 3.37e-01 100.0% 60.5%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.51 39.0 3.67e-01 100.0% 68.4%
2pn5A03 2.60.40.1940 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 42.0 3.41e-01 100.0% 47.6%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4147528 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.74 63.0 5.74e-01 98.0% 100.0%
4448678 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.72 62.0 5.52e-01 100.0% 97.3%
5001656 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.71 59.0 4.14e-01 100.0% 56.1%
4231372 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.69 57.0 5.29e-01 100.0% 100.0%
4934098 304.19.1.1 ↗ a+b two layers › Alpha-beta plaits › eIF-2-alpha, C-terminal domain › eIF-2-alpha, C-terminal domain › EIF_2_alpha 0.67 56.0 4.86e-01 98.0% 100.0%
4316518 304.19.1.1 ↗ a+b two layers › Alpha-beta plaits › eIF-2-alpha, C-terminal domain › eIF-2-alpha, C-terminal domain › EIF_2_alpha 0.67 55.0 4.76e-01 100.0% 100.0%
4966263 304.110.1.1 ↗ a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like › Acylphosphatase 0.66 56.0 4.43e-01 100.0% 67.0%
4004480 2011.1.1.23 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › M20_dimer 0.66 55.0 4.32e-01 100.0% 91.7%
3516671 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.66 53.0 4.30e-01 100.0% 98.3%
4964337 3115.5.1.1 ↗ a+b two layers › GP2-like › phenylacetate-CoA oxygenase subunit PaaB › phenylacetate-CoA oxygenase subunit PaaB › PaaB 0.65 52.0 5.12e-01 100.0% 87.3%
3593420 304.25.1.0 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain 0.65 53.0 4.28e-01 100.0% 98.3%
4561918 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.65 55.0 4.39e-01 100.0% 98.2%
5065393 304.5.1.1 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › P-II 0.64 54.0 4.40e-01 100.0% 73.8%
3404684 10.12.1.84 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › VKGC_lumenal_dom 0.64 55.0 3.69e-01 100.0% 30.5%
3694098 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.63 53.0 4.11e-01 100.0% 41.7%
4017272 221.1.1.188 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › DUF7767 0.62 46.0 3.85e-01 100.0% 44.2%
3200782 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.62 44.0 3.65e-01 100.0% 41.1%
4000362 223.2.1.36 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Intu_longin_3 0.62 45.0 3.70e-01 80.4% 93.3%
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 0.62 45.0 3.12e-01 82.4% 67.3%
3270265 223.2.1.20 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_1 0.61 47.0 3.51e-01 86.3% 38.5%
4927527 304.5.1.1 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › P-II 0.61 49.0 4.05e-01 100.0% 86.4%
3366423 6108.1.1.11 ↗ alpha bundles › Middle and GTPase effector domains in dynamin-related proteins › Middle and GTPase effector domains in dynamin-related proteins › Middle and GTPase effector domains in dynamin-related proteins › Dynamin_N 0.60 51.0 2.86e-01 98.0% 97.2%
2526976 288.1.1.1 ↗ a+b four layers › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › Cu-oxidase_4 0.59 49.0 3.20e-01 100.0% 19.0%
4405873 223.2.1.33 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_3 0.59 42.0 3.33e-01 76.5% 87.8%
3929391 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.58 48.0 3.92e-01 100.0% 80.9%
5017741 221.6.1.1 ↗ a+b two layers › beta-Grasp › MM3350-like › MM3350-like › PRiA4_ORF3 0.58 47.0 3.48e-01 100.0% 67.5%
4944072 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 47.0 3.90e-01 100.0% 49.0%
4220400 288.1.1.1 ↗ a+b four layers › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › Cu-oxidase_4 0.58 48.0 3.20e-01 100.0% 21.7%
4030365 245.1.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.57 42.0 3.36e-01 78.4% 40.0%
3859590 386.1.1.248 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_ZNF592 0.57 42.0 4.24e-01 100.0% 82.0%
3900006 288.1.1.1 ↗ a+b four layers › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › Cu-oxidase_4 0.57 47.0 3.06e-01 100.0% 19.0%
4945301 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.57 44.0 3.37e-01 94.1% 56.0%
3928420 3680.1.1.0 ↗ a+b complex topology › Zinc finger FYVE domain-containing protein 9 C-terminal domain › Zinc finger FYVE domain-containing protein 9 C-terminal domain › Zinc finger FYVE domain-containing protein 9 C-terminal domain 0.57 40.0 2.99e-01 78.4% 29.3%
3216812 382.1.1.20 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › PF29036 0.57 49.0 4.20e-01 100.0% 88.2%
3216210 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.56 42.0 4.26e-01 100.0% 92.0%
5047755 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.56 45.0 3.47e-01 100.0% 50.0%
4189709 288.1.1.1 ↗ a+b four layers › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › Cu-oxidase_4 0.54 43.0 2.95e-01 100.0% 21.7%
4939739 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.54 43.0 4.23e-01 100.0% 84.7%
4599661 2008.1.1.27 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAI1 0.54 41.0 2.44e-01 82.4% 16.4%
3239591 382.1.1.20 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › PF29036 0.54 45.0 3.75e-01 100.0% 86.0%
4098243 7512.1.1.6 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_20 0.54 44.0 2.93e-01 96.1% 51.4%
4160542 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.53 42.0 4.11e-01 100.0% 89.7%
3215294 10.12.1.97 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › CNBH_CNNM2_C 0.53 38.0 2.66e-01 76.5% 60.6%
3743702 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.53 39.0 3.28e-01 86.3% 69.5%
3690210 10.12.1.52 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_8 0.53 43.0 2.71e-01 100.0% 33.4%
4967222 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.52 40.0 3.98e-01 100.0% 86.7%
3935404 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.52 46.0 3.77e-01 98.0% 54.4%
4013514 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.52 41.0 3.49e-01 100.0% 52.4%
3958897 4187.2.1.0 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 0.52 40.0 3.26e-01 100.0% 40.0%
4178430 223.3.1.8 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Beta-lactamase2 0.52 42.0 3.11e-01 96.1% 70.3%
3715442 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 41.0 2.96e-01 98.0% 26.5%
3193216 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.52 37.0 3.09e-01 80.4% 71.8%
2527501 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.52 40.0 3.45e-01 100.0% 52.9%
5067865 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.51 39.0 3.73e-01 100.0% 74.3%
3179826 11.1.1.642 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig-like_Pom152_1 0.50 42.0 3.28e-01 100.0% 48.8%