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SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00354

Bact-Vir

SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00354

Identity

Kingdom:
phage

Quality

88.0 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 1-68
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5i47B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.63 37.0 3.39e-01 100.0% 42.1%
4k17B01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 40.0 3.54e-01 100.0% 55.9%
2lstA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 42.0 3.55e-01 100.0% 64.6%
6uioC01 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.50 42.0 3.80e-01 100.0% 94.2%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4461151 4294.1.1.4 ↗ few secondary structure elements › Trm112p-like › Trm112p-like › Trm112p-like › RlmA_N 0.63 41.0 4.65e-01 92.6% 92.0%
3813350 4294.1.1.0 ↗ few secondary structure elements › Trm112p-like › Trm112p-like › Trm112p-like 0.54 39.0 4.20e-01 88.2% 94.5%
4936316 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.52 38.0 4.10e-01 83.8% 100.0%
3452671 314.1.1.19 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Mut7-C 0.51 38.0 4.04e-01 85.3% 100.0%
D2 medium residues 69-138
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3q9oA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.72 59.0 4.13e-01 88.6% 54.2%
2xepB01 3.10.450.280 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.67 43.0 3.65e-01 92.9% 39.5%
3a5vA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.67 46.0 4.06e-01 71.4% 94.9%
1yqfB00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.65 54.0 4.05e-01 100.0% 36.2%
3qv0A00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.64 55.0 4.07e-01 100.0% 36.9%
4k00A00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.64 47.0 3.82e-01 78.6% 98.5%
2w35A00 3.30.2170.10 Alpha Beta › 2-Layer Sandwich › archaeoglobus fulgidus dsm 4304 fold › archaeoglobus fulgidus dsm 4304 superfamily 0.64 51.0 3.60e-01 88.6% 41.7%
2bvbA00 2.60.120.710 Mainly Beta › Sandwich › Jelly Rolls › Toxoplasma gondii micronemal protein 1 TgMIC1 0.62 50.0 4.01e-01 87.1% 70.8%
3mnmA00 2.60.40.1230 Mainly Beta › Sandwich › Immunoglobulin-like › Gamma-adaptin ear (GAE) domain 0.61 53.0 4.47e-01 92.9% 80.4%
4ge1C00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.61 54.0 3.94e-01 98.6% 77.2%
4nspA00 3.30.2170.10 Alpha Beta › 2-Layer Sandwich › archaeoglobus fulgidus dsm 4304 fold › archaeoglobus fulgidus dsm 4304 superfamily 0.61 48.0 3.40e-01 91.4% 26.1%
7snsB01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.60 53.0 4.06e-01 100.0% 90.7%
8aimG01 3.10.450.20 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Bacteriophage PBS2, uracil-glycosylase inhibitor 0.58 45.0 4.33e-01 100.0% 71.6%
1aqbA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.58 52.0 3.89e-01 100.0% 57.1%
3dkzA00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.58 39.0 3.28e-01 70.0% 81.6%
3lbeB00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.58 41.0 3.47e-01 75.7% 84.7%
1qwdB00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 50.0 3.79e-01 98.6% 59.0%
5fq0A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.57 40.0 3.44e-01 72.9% 90.9%
3gm8A05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 47.0 4.04e-01 90.0% 86.4%
7a0hA02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.57 51.0 3.79e-01 100.0% 50.0%
3cqnB00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.56 50.0 3.83e-01 100.0% 57.1%
2l9pA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 49.0 3.76e-01 98.6% 57.3%
5x7qA01 2.60.40.1760 Mainly Beta › Sandwich › Immunoglobulin-like › glycosyl hydrolase (family 31) 0.56 50.0 3.48e-01 100.0% 78.8%
4l8nA03 3.30.160.670 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 47.0 3.71e-01 100.0% 81.7%
4oddA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.55 49.0 3.85e-01 100.0% 61.7%
6gmhC01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.55 30.0 2.44e-01 81.4% 26.6%
2kt4B01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.55 48.0 3.87e-01 100.0% 65.5%
3qszA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.55 48.0 3.60e-01 98.6% 92.7%
1dpgA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.53 38.0 2.47e-01 75.7% 26.9%
2ldkA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.52 45.0 3.44e-01 98.6% 54.1%
4mb7A01 3.20.190.10 Alpha Beta › Alpha-Beta Barrel › N-terminal domain of MutM-like DNA repair proteins › MutM-like, N-terminal 0.52 47.0 3.88e-01 100.0% 66.7%
2jxpA01 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.52 44.0 3.63e-01 100.0% 89.4%
4gyiA02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 43.0 3.89e-01 92.9% 93.9%
4htgA03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.51 45.0 4.39e-01 100.0% 88.6%
2j0wA03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.51 40.0 3.88e-01 85.7% 90.1%
4boeA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.51 43.0 3.41e-01 97.1% 67.5%
2r55A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 46.0 3.26e-01 100.0% 52.4%
3rqbA00 2.40.160.210 Mainly Beta › Beta Barrel › Porin › Acyl-CoA thioesterase, double hotdog domain 0.51 42.0 2.97e-01 100.0% 94.7%
1jyaB00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.50 44.0 3.74e-01 100.0% 89.3%
3kg7B00 3.10.129.110 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Polyketide synthase dehydratase 0.50 42.0 2.91e-01 100.0% 72.3%
3bbjA00 2.40.160.210 Mainly Beta › Beta Barrel › Porin › Acyl-CoA thioesterase, double hotdog domain 0.50 41.0 2.93e-01 100.0% 96.6%
3hx1B00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.50 44.0 3.85e-01 98.6% 80.2%
1cboA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.50 37.0 2.48e-01 82.9% 94.6%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3173222 4075.1.1.0 ↗ a+b complex topology › RGC domain › RGC domain › RGC domain 0.70 50.0 4.23e-01 75.7% 99.1%
3477607 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.70 60.0 3.40e-01 95.7% 12.4%
3248970 101.1.12.0 ↗ alpha arrays › HTH › HTH › HTH motif inserted in other structures 0.69 62.0 5.32e-01 100.0% 94.5%
3740435 5.1.4.35 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Lactonase 0.67 59.0 3.78e-01 98.6% 26.2%
3505083 5.1.5.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.64 58.0 3.66e-01 100.0% 22.5%
3290321 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.64 57.0 5.08e-01 100.0% 91.0%
5060223 2484.1.1.43 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Endonuclease_5 0.64 52.0 3.71e-01 90.0% 45.8%
3716632 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.63 49.0 3.84e-01 100.0% 40.0%
3875861 5.1.4.146 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.63 55.0 3.34e-01 98.6% 28.1%
5034411 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.63 55.0 3.48e-01 100.0% 24.3%
2885136 5.1.4.32 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Nucleoporin_N 0.62 55.0 3.26e-01 98.6% 21.0%
3508969 5.1.5.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.61 55.0 3.72e-01 100.0% 34.9%
4003315 5.1.5.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40 0.61 54.0 3.43e-01 98.6% 21.1%
3488078 5.1.12.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › PERK and Ire1 luminal domains 0.61 45.0 3.14e-01 80.0% 54.3%
5010092 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.60 43.0 3.67e-01 100.0% 46.1%
3223991 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.60 52.0 3.46e-01 98.6% 26.9%
3782893 210.1.2.8 ↗ a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain › TANGO2 0.60 48.0 3.17e-01 87.1% 76.3%
3693853 210.1.2.8 ↗ a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain › TANGO2 0.60 47.0 3.17e-01 87.1% 78.5%
5079413 5.1.3.272 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › SBBP 0.59 50.0 3.46e-01 97.1% 30.2%
4299499 12.3.1.24 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › YidC_periplas 0.59 52.0 3.61e-01 100.0% 86.7%
3617123 5.1.4.32 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Nucleoporin_N 0.59 51.0 3.15e-01 100.0% 21.9%
4938040 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 46.0 3.66e-01 97.1% 40.0%
3803844 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.59 50.0 3.14e-01 95.7% 22.1%
3001014 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.59 51.0 3.92e-01 97.1% 89.9%
3996785 11.1.1.53 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DOMON 0.58 51.0 3.91e-01 97.1% 83.7%
3928228 2484.1.1.43 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Endonuclease_5 0.58 46.0 3.25e-01 88.6% 42.5%
865437 241.1.1.2 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › Autophagy_act_C 0.58 48.0 3.81e-01 92.9% 71.5%
3614253 5.1.4.16 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CPSF_A 0.58 50.0 3.18e-01 100.0% 24.0%
3343550 243.1.1.53 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › WI12 0.57 51.0 4.02e-01 98.6% 53.8%
3661989 300.1.1.16 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › PLDc, PLDc_2 0.57 40.0 3.17e-01 75.7% 69.5%
119302 3146.1.1.0 ↗ a+b complex topology › gH main domain › gH main domain › gH main domain 0.56 45.0 2.90e-01 87.1% 43.4%
3261416 897.1.1.0 ↗ a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 0.56 52.0 4.06e-01 100.0% 54.3%
3220909 11.10.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like 0.56 48.0 4.04e-01 95.7% 88.3%
4008896 11.1.1.1286 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF27224 0.55 47.0 4.00e-01 100.0% 73.6%
3808882 4051.1.1.1 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F_actin_cap_B 0.55 49.0 3.69e-01 100.0% 56.6%
3779302 7026.1.1.5 ↗ beta meanders › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 › ATG2_CAD 0.55 49.0 3.21e-01 100.0% 39.5%
3947165 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.55 49.0 3.81e-01 100.0% 88.0%
3405306 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.54 45.0 3.79e-01 90.0% 55.7%
3491784 220.1.1.158 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_LRR1 0.54 49.0 4.02e-01 100.0% 70.4%
3734384 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.54 44.0 3.86e-01 88.6% 61.2%
4028900 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.54 47.0 3.56e-01 100.0% 46.3%
3689674 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.53 43.0 3.53e-01 88.6% 49.2%
4466001 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.53 45.0 3.67e-01 95.7% 50.4%
3935550 210.1.2.8 ↗ a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain › TANGO2 0.53 47.0 3.13e-01 97.1% 34.8%
3740252 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.52 44.0 3.84e-01 100.0% 72.2%
3415831 4.25.1.2 ↗ beta barrels › SH3 › Auxin response factor dimerization domain and ancillary domain › Auxin response factor dimerization domain and ancillary domain › BRWD_AD 0.52 40.0 3.46e-01 87.1% 78.3%
1000612 7503.1.1.4 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › LptE 0.52 44.0 3.64e-01 98.6% 95.6%
2420861 3435.1.1.2 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC › CENP-N 0.50 44.0 3.65e-01 100.0% 67.7%