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Vp91

Euk-Vir

Penaeus_monodon_nudivirus

Vp91__YP_009051847__Penaeus_monodon_nudivirus__1529056

Identity

Accession:
YP_009051847 ↗
Protein ID:
Vp91
Kingdom:
euk

Quality

50.0 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Nudiviridae› Gammanudivirus› Penaeus_monodon_nudivirus

TaxID: 1529056

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 31-91
PDB
Domain cluster: rep: vp91__YP_009551773__Esparto_virus__2072209__D30-97
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2it1A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.69 45.0 4.54e-01 70.5% 67.2%
5nslA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.67 49.0 2.96e-01 78.7% 90.2%
3c4bA02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.64 42.0 4.10e-01 73.8% 61.2%
2qlvB02 2.20.25.290 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.63 39.0 4.49e-01 73.8% 100.0%
2lmcB00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.63 42.0 4.26e-01 70.5% 73.8%
1luiA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.62 51.0 4.29e-01 93.4% 80.6%
2qrdB01 2.20.25.290 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.62 37.0 4.35e-01 75.4% 97.3%
4dkkA02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.61 41.0 3.92e-01 73.8% 58.1%
4tkoB01 2.40.30.170 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain 0.61 41.0 3.64e-01 70.5% 89.1%
1wzvA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.60 41.0 3.10e-01 70.5% 58.7%
4k15A00 2.60.40.3860 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 42.0 3.31e-01 75.4% 63.8%
2k31A00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.60 50.0 3.90e-01 100.0% 47.0%
3qkgA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.58 42.0 3.14e-01 77.0% 53.7%
3licA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.58 49.0 3.64e-01 100.0% 38.8%
1s14B00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.57 46.0 3.41e-01 93.4% 37.1%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 39.0 3.74e-01 73.8% 62.0%
2kouA00 3.30.160.380 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Dicer dimerisation domain 0.56 40.0 3.42e-01 78.7% 45.1%
6iw6B01 1.10.1410.10 Mainly Alpha › Orthogonal Bundle › Poly(a)-polymerase, middle domain › 0.56 38.0 2.61e-01 70.5% 42.7%
5yyfA00 2.60.40.1970 Mainly Beta › Sandwich › Immunoglobulin-like › YEATS domain 0.56 43.0 3.40e-01 85.2% 71.7%
2gu1A03 2.70.70.10 Mainly Beta › Distorted Sandwich › Glucose Permease (Domain IIA) › Glucose Permease (Domain IIA) 0.56 39.0 3.12e-01 73.8% 37.9%
2o8bB02 3.30.420.110 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › MutS, connector domain 0.55 40.0 2.91e-01 78.7% 37.6%
2ediA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.55 37.0 2.81e-01 70.5% 58.1%
7qrlA01 2.70.70.10 Mainly Beta › Distorted Sandwich › Glucose Permease (Domain IIA) › Glucose Permease (Domain IIA) 0.55 39.0 3.04e-01 73.8% 37.8%
1sezA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 39.0 2.86e-01 77.0% 64.4%
4iupB01 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.55 37.0 3.76e-01 72.1% 85.5%
1bf5A04 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.54 46.0 3.86e-01 100.0% 85.0%
2hsiB02 2.70.70.10 Mainly Beta › Distorted Sandwich › Glucose Permease (Domain IIA) › Glucose Permease (Domain IIA) 0.54 45.0 3.51e-01 96.7% 67.1%
2r41A00 3.10.450.150 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › enterococcus faecalis protein 0.54 39.0 3.31e-01 77.0% 55.3%
2c4iA01 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.54 40.0 3.26e-01 80.3% 58.5%
6g1yA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 37.0 3.06e-01 77.0% 37.5%
1zubA00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.54 39.0 3.36e-01 80.3% 61.5%
3lbfA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 38.0 2.67e-01 83.6% 22.2%
1aj6A00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.53 41.0 3.02e-01 90.2% 35.6%
1f20A02 1.20.990.10 Mainly Alpha › Up-down Bundle › NADPH-cytochrome p450 Reductase; Chain A, domain 3 › NADPH-cytochrome p450 Reductase; Chain A, domain 3 0.53 37.0 2.77e-01 73.8% 96.2%
2k54A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 38.0 3.09e-01 78.7% 39.8%
4h61A00 3.10.450.580 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Mediator complex, subunit Med6 0.52 36.0 2.77e-01 70.5% 32.1%
2k3aA01 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.51 44.0 3.79e-01 98.4% 92.0%
2rs7A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.50 38.0 3.61e-01 82.0% 71.6%
3cqyB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.50 41.0 3.09e-01 100.0% 51.6%
7r8iA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.50 40.0 2.86e-01 95.1% 31.3%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3510346 209.1.1.0 ↗ a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like 0.69 54.0 4.23e-01 88.5% 40.0%
3974328 2.4.1.11 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_3 0.68 46.0 4.11e-01 70.5% 56.5%
4085451 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.67 45.0 3.71e-01 70.5% 43.6%
3879303 330.1.1.5 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DND1_DSRM 0.66 49.0 4.42e-01 77.0% 62.5%
4988344 223.1.1.23 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_2 0.66 53.0 3.98e-01 93.4% 65.3%
3852952 330.1.1.5 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DND1_DSRM 0.64 47.0 4.28e-01 77.0% 63.7%
3697816 2008.1.1.99 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_12 0.64 49.0 3.64e-01 88.5% 45.7%
4116159 330.1.1.5 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DND1_DSRM 0.64 46.0 4.09e-01 77.0% 57.8%
4575466 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.64 44.0 4.34e-01 72.1% 80.0%
3966247 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.63 44.0 4.35e-01 73.8% 80.0%
4986577 220.1.1.87 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_3 0.62 43.0 3.63e-01 73.8% 43.6%
4338934 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.62 44.0 4.35e-01 75.4% 84.6%
5034876 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.62 45.0 2.67e-01 77.0% 14.3%
3304271 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.61 46.0 4.08e-01 78.7% 89.4%
3404834 292.2.1.0 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain 0.60 44.0 4.04e-01 88.5% 60.0%
5043655 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.58 44.0 3.43e-01 83.6% 50.7%
3191059 705.1.1.0 ↗ beta duplicates or obligate multimers › Cyanovirin-N › Cyanovirin-N › Cyanovirin-N 0.58 42.0 3.47e-01 78.7% 67.5%
3601211 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.57 43.0 2.82e-01 80.3% 57.6%
4961746 304.8.1.122 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › DmsR_N 0.56 41.0 3.42e-01 78.7% 73.9%
5021851 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.56 43.0 2.75e-01 95.1% 15.7%
3576652 2003.1.5.73 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.55 39.0 2.49e-01 73.8% 18.3%
3322492 5.1.4.550 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Kelch_FKB95 0.55 47.0 3.10e-01 100.0% 32.0%
3719938 227.1.1.17 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › DUF7881_N 0.55 40.0 3.17e-01 80.3% 60.0%
5011595 330.10.1.1 ↗ a+b two layers › dsRBD-like › Heterocyclase TruD C-terminal domain › Heterocyclase TruD C-terminal domain › YcaO 0.55 41.0 3.24e-01 80.3% 83.1%
3785641 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 39.0 3.73e-01 75.4% 100.0%
3613921 330.1.1.22 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › PF26536 0.55 39.0 3.16e-01 77.0% 46.4%
3907933 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 37.0 3.25e-01 72.1% 88.0%
4937350 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.54 36.0 3.57e-01 78.7% 64.6%
3620016 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.54 39.0 4.12e-01 77.0% 90.9%
5064370 3518.1.1.1 ↗ a+b two layers › putative RnfG subunit of electron transport complex › putative RnfG subunit of electron transport complex › putative RnfG subunit of electron transport complex › FMN_bind 0.54 37.0 3.14e-01 73.8% 95.4%
3911142 263.1.1.0 ↗ a+b three layers › SRF-like › SRF-like › SRF-like 0.54 45.0 4.02e-01 100.0% 70.5%
3247297 7.1.1.1 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ 0.53 37.0 3.15e-01 75.4% 56.5%
3367984 11.1.1.23 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Expansin_C 0.53 40.0 3.43e-01 83.6% 86.7%
3809302 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.53 39.0 3.52e-01 77.0% 55.3%
3266323 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.53 36.0 3.01e-01 78.7% 35.8%
4609498 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.53 38.0 3.54e-01 78.7% 58.7%
3599554 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.53 37.0 2.95e-01 77.0% 90.7%
3807026 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.52 43.0 3.10e-01 100.0% 43.3%
4336488 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.52 36.0 3.53e-01 75.4% 64.3%
3702918 331.3.1.3 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › START 0.52 42.0 2.89e-01 93.4% 68.0%
3820157 5.1.4.550 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Kelch_FKB95 0.52 42.0 3.18e-01 100.0% 70.3%
4408649 2484.1.1.41 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › AnmK 0.52 42.0 3.02e-01 100.0% 52.9%
5050525 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.51 38.0 2.69e-01 80.3% 36.6%
3948020 283.2.1.1 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › GPW_gp25 0.51 37.0 3.18e-01 80.3% 49.1%
3372482 2004.1.1.88 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › cobW 0.51 41.0 3.00e-01 100.0% 43.2%
3680490 216.1.1.1 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › UQ_con 0.51 39.0 3.04e-01 82.0% 39.3%
3712993 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 36.0 3.49e-01 78.7% 78.7%
3889496 389.1.3.0 ↗ few secondary structure elements › EGF-like › EGF-related › TNF receptor-like 0.51 39.0 3.71e-01 86.9% 94.7%
4336711 2484.1.1.41 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › AnmK 0.51 40.0 2.93e-01 100.0% 60.4%
4181605 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.50 37.0 2.75e-01 95.1% 25.6%
4947810 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.50 38.0 3.20e-01 95.1% 44.2%
4926797 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.50 36.0 2.97e-01 80.3% 64.6%
3878642 2484.1.1.4 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.50 39.0 2.99e-01 96.7% 53.5%
D2 medium residues 133-259
PDB
Domain cluster: rep: Vp91__YP_010087645__Homarus_gammarus_nudivirus__2509616__D142-261
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01607.30 best CBM_14 28.3 2.20e-06 24.4% 54.7%
D3 medium residues 261-344
PDB
D4 medium residues 370-459
PDB
D5 medium residues 460-473_494-568
PDB
D6 medium residues 599-657
PDB