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VP1
Euk-VirNorovirus_GI
VP1__YP_009700097__Norovirus_GI__122928
Identity
- Accession:
- YP_009700097 ↗
- Protein ID:
- VP1
- Kingdom:
- euk
Quality
80.8
mean pLDDT
Taxonomy
Orthornavirae›
Pisuviricota›
Pisoniviricetes›
Picornavirales›
Caliciviridae›
Norovirus›
Norovirus_GI
TaxID: 122928
Cluster
View cluster (17 members)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 54-221
Domain cluster:
rep: structural_polyprotein__YP_009333175__Bastrovirus-like_virus_VietNam_Bat_17819_21__1906170__D141-305
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00915.27 best | Calici_coat | 235.2 | 1.00e-69 | 100.0% | 55.1% |
| PF00073.27 | Rhv | 34.7 | 1.90e-08 | 67.9% | 49.1% |
D2
medium
residues 235-288_393-529
Domain cluster:
rep: VP1__YP_009679035__Norovirus_GII_Hu_JP_2007_GII.P15_GII.15_Sapporo_HK299__1529918__D230-281_420-543
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF08435.18 best | Calici_coat_C | 234.4 | 1.80e-69 | 95.8% | 63.5% |
| PF00915.27 | Calici_coat | 24.0 | 2.40e-05 | 32.5% | 16.1% |
D3
medium
residues 289-392
Domain cluster:
rep: VP1_capsid_protein__YP_009679041__Norovirus_dog_GVI.1_HKU_Ca026F_2007_HKG__673457__D281-384
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF08435.18 best | Calici_coat_C | 61.2 | 1.50e-16 | 84.6% | 36.5% |
CATH (42)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5e6tA02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.93 | 81.0 | 8.54e-01 | 94.2% | 100.0% |
| 2zl7A02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.92 | 77.0 | 8.27e-01 | 94.2% | 100.0% |
| 4rdlA02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.89 | 81.0 | 8.02e-01 | 94.2% | 100.0% |
| 4rlzA02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.86 | 77.0 | 7.52e-01 | 94.2% | 100.0% |
| 3q39B02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.84 | 74.0 | 7.32e-01 | 94.2% | 100.0% |
| 3lq6A02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.83 | 75.0 | 7.24e-01 | 94.2% | 100.0% |
| 6j0qA02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.83 | 73.0 | 7.24e-01 | 94.2% | 100.0% |
| 4qv2A02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.82 | 76.0 | 7.27e-01 | 100.0% | 100.0% |
| 3op1A02 | 2.40.30.30 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like | 0.67 | 54.0 | 5.32e-01 | 99.0% | 81.1% |
| 6ijfC01 | 3.90.1720.80 | Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › | 0.62 | 38.0 | 4.05e-01 | 100.0% | 68.8% |
| 1mfnA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.61 | 42.0 | 4.44e-01 | 95.2% | 80.6% |
| 3ethA03 | 3.30.1490.20 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain | 0.60 | 35.0 | 4.36e-01 | 91.3% | 98.4% |
| 4ecnA01 | 2.60.40.3540 | Mainly Beta › Sandwich › Immunoglobulin-like › Domain of unknown function DUF4458 | 0.59 | 40.0 | 4.06e-01 | 86.5% | 69.9% |
| 4n0rA03 | 2.60.40.3950 | Mainly Beta › Sandwich › Immunoglobulin-like › | 0.59 | 47.0 | 4.62e-01 | 92.3% | 80.9% |
| 3zugB02 | 2.40.30.30 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like | 0.58 | 51.0 | 4.62e-01 | 98.1% | 81.0% |
| 3wcyA04 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.58 | 38.0 | 4.05e-01 | 93.3% | 80.2% |
| 8b38A01 | 2.60.120.20 | Mainly Beta › Sandwich › Jelly Rolls › | 0.56 | 49.0 | 3.83e-01 | 96.2% | 91.2% |
| 1n08A00 | 2.40.30.30 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like | 0.56 | 50.0 | 4.38e-01 | 99.0% | 66.9% |
| 3l5iA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.56 | 39.0 | 4.11e-01 | 95.2% | 85.2% |
| 2ee2A01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.55 | 38.0 | 4.08e-01 | 93.3% | 85.1% |
| 5utkA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.55 | 37.0 | 3.99e-01 | 90.4% | 84.3% |
| 1wfoA01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.55 | 40.0 | 4.00e-01 | 95.2% | 76.0% |
| 4kktA02 | 2.40.30.170 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain | 0.55 | 47.0 | 4.73e-01 | 94.2% | 93.3% |
| 1fnfA01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.55 | 39.0 | 4.11e-01 | 95.2% | 84.0% |
| 5e55B02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.54 | 39.0 | 4.09e-01 | 94.2% | 84.9% |
| 2dgyA01 | 2.40.50.140 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins | 0.54 | 29.0 | 3.20e-01 | 90.4% | 64.6% |
| 1x5xA00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.54 | 38.0 | 3.77e-01 | 95.2% | 69.7% |
| 5e53A02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.54 | 39.0 | 4.05e-01 | 94.2% | 84.9% |
| 1owwA00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.53 | 38.0 | 3.98e-01 | 95.2% | 83.9% |
| 2ztnA02 | 2.40.30.190 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › | 0.53 | 47.0 | 4.26e-01 | 100.0% | 92.2% |
| 3b83C00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.52 | 36.0 | 3.66e-01 | 95.2% | 73.7% |
| 3unpA00 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.52 | 40.0 | 3.34e-01 | 83.7% | 77.2% |
| 2erjB02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.52 | 38.0 | 3.86e-01 | 95.2% | 78.8% |
| 3nngA00 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.51 | 39.0 | 3.50e-01 | 82.7% | 86.3% |
| 2cdoA00 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.51 | 40.0 | 3.71e-01 | 85.6% | 89.1% |
| 2orzA01 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.51 | 40.0 | 3.56e-01 | 84.6% | 89.6% |
| 4wz9A01 | 2.60.40.1730 | Mainly Beta › Sandwich › Immunoglobulin-like › tricorn interacting facor f3 domain | 0.51 | 42.0 | 3.34e-01 | 93.3% | 43.5% |
| 4ev0D01 | 2.60.120.10 | Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls | 0.51 | 32.0 | 2.93e-01 | 95.2% | 46.7% |
| 4k4kA01 | 2.60.40.2620 | Mainly Beta › Sandwich › Immunoglobulin-like › Fimbrillin-like | 0.50 | 38.0 | 3.58e-01 | 79.8% | 69.3% |
| 3hwjA00 | 2.60.120.820 | Mainly Beta › Sandwich › Jelly Rolls › PHR domain | 0.50 | 38.0 | 3.41e-01 | 94.2% | 55.7% |
| 4w8jA02 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.50 | 41.0 | 3.64e-01 | 89.4% | 81.4% |
| 1od3A00 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.50 | 40.0 | 3.79e-01 | 88.5% | 88.5% |
ECOD (48)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1695947 | 10.2.1.14 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) | 0.92 | 88.0 | 6.03e-01 | 100.0% | 35.0% |
| 4856093 | 10.2.1.43 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Calici_coat_C | 0.92 | 88.0 | 8.33e-01 | 100.0% | 90.8% |
| 1696469 | 10.2.1.43 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Calici_coat_C | 0.88 | 83.0 | 5.81e-01 | 100.0% | 38.2% |
| 2505857 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.86 | 82.0 | 7.39e-01 | 100.0% | 77.9% |
| 2127918 | 10.2.1.43 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Calici_coat_C | 0.86 | 83.0 | 5.74e-01 | 100.0% | 49.3% |
| 2171578 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.83 | 76.0 | 6.80e-01 | 96.2% | 81.8% |
| 2126884 | 10.2.1.43 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Calici_coat_C | 0.83 | 76.0 | 5.20e-01 | 96.2% | 37.1% |
| 4872941 | 10.2.1.43 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Calici_coat_C | 0.83 | 71.0 | 6.77e-01 | 90.4% | 92.4% |
| 4881921 | 10.2.1.14 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) | 0.82 | 77.0 | 5.36e-01 | 100.0% | 37.0% |
| 4881922 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.81 | 77.0 | 6.92e-01 | 100.0% | 79.4% |
| 3299532 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.66 | 56.0 | 5.56e-01 | 93.3% | 96.4% |
| 3784576 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.62 | 54.0 | 5.38e-01 | 96.2% | 93.3% |
| 3744112 | 1.1.7.7 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 | 0.60 | 54.0 | 5.35e-01 | 100.0% | 100.0% |
| 3598670 | 4081.1.1.0 ↗ | beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related | 0.60 | 41.0 | 3.37e-01 | 91.3% | 37.0% |
| 3387846 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.59 | 50.0 | 4.80e-01 | 98.1% | 80.0% |
| 1031128 | 11.1.4.26 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › DUF4458 | 0.59 | 40.0 | 4.03e-01 | 86.5% | 68.6% |
| 3931783 | 1.1.7.41 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › UPF1_1B_dom | 0.59 | 48.0 | 4.97e-01 | 90.4% | 97.9% |
| 4117582 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.57 | 49.0 | 4.63e-01 | 99.0% | 78.4% |
| 4929404 | 1.1.7.7 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 | 0.56 | 47.0 | 4.76e-01 | 94.2% | 100.0% |
| 3936582 | 4081.1.1.5 ↗ | beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Peptidase_M1_N | 0.56 | 39.0 | 3.18e-01 | 91.3% | 35.0% |
| 4577896 | 10.12.1.0 ↗ | beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix | 0.56 | 35.0 | 3.46e-01 | 96.2% | 58.3% |
| 1548 | 11.1.1.2 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 | 0.55 | 39.0 | 3.85e-01 | 95.2% | 67.5% |
| 4311256 | 10.32.1.18 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Endotoxin_C | 0.54 | 44.0 | 3.84e-01 | 89.4% | 90.3% |
| 3398799 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.53 | 39.0 | 3.96e-01 | 95.2% | 78.1% |
| 4071322 | 10.32.1.18 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Endotoxin_C | 0.53 | 43.0 | 3.76e-01 | 89.4% | 86.9% |
| 3761841 | 11.1.1.2 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 | 0.52 | 38.0 | 3.67e-01 | 95.2% | 66.7% |
| 3687401 | 10.32.1.0 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like | 0.52 | 42.0 | 3.54e-01 | 88.5% | 89.2% |
| 3927514 | 284.1.1.1 ↗ | a+b two layers › FKBP-like › FKBP-like › FKBP-like › FKBP_C | 0.52 | 38.0 | 3.59e-01 | 76.9% | 89.2% |
| 3507893 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.52 | 42.0 | 3.91e-01 | 100.0% | 68.1% |
| 3439345 | 11.1.4.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like | 0.52 | 38.0 | 3.67e-01 | 86.5% | 66.7% |
| 3785517 | 10.41.1.1 ↗ | beta sandwiches › jelly-roll › Protein Hikeshi jelly-roll domain › Protein Hikeshi jelly-roll domain › Hikeshi-like_N | 0.52 | 40.0 | 3.96e-01 | 97.1% | 76.5% |
| 3869986 | 10.32.1.2 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › F5_F8_type_C | 0.52 | 41.0 | 3.48e-01 | 84.6% | 82.9% |
| 3696482 | 4.1.1.0 ↗ | beta barrels › SH3 › SH3 › SH3 | 0.52 | 34.0 | 3.64e-01 | 78.8% | 77.5% |
| 4026702 | 10.32.1.28 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Sad1_UNC | 0.52 | 41.0 | 3.60e-01 | 87.5% | 84.2% |
| 3239514 | 10.2.1.100 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › DUF7154 | 0.52 | 38.0 | 4.07e-01 | 94.2% | 90.0% |
| 3240764 | 10.32.1.203 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin | 0.52 | 44.0 | 4.09e-01 | 95.2% | 97.0% |
| 3580218 | 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 | 3.42e-01 | 95.2% | 48.6% |
| 5051141 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.51 | 38.0 | 3.75e-01 | 94.2% | 72.2% |
| 3213513 | 10.32.1.218 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DUF7154 | 0.51 | 38.0 | 3.73e-01 | 94.2% | 70.4% |
| 3893205 | 10.32.1.172 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DDR1-2_DS-like | 0.51 | 39.0 | 3.26e-01 | 82.7% | 90.3% |
| 3508722 | 10.32.1.0 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like | 0.51 | 38.0 | 3.64e-01 | 94.2% | 68.3% |
| 4366770 | 10.32.1.12 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › CBM_6 | 0.51 | 41.0 | 3.81e-01 | 89.4% | 87.7% |
| 1557262 | 10.32.1.2 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › F5_F8_type_C | 0.51 | 37.0 | 3.55e-01 | 89.4% | 64.5% |
| 5046219 | 10.1.2.0 ↗ | beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) | 0.51 | 41.0 | 4.04e-01 | 96.2% | 81.8% |
| 5062851 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.51 | 37.0 | 3.84e-01 | 94.2% | 85.3% |
| 4976414 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.50 | 36.0 | 3.71e-01 | 93.3% | 82.1% |
| 3794768 | 10.32.1.28 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Sad1_UNC | 0.50 | 40.0 | 3.43e-01 | 87.5% | 76.6% |
| 3398883 | 10.32.1.28 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Sad1_UNC | 0.50 | 38.0 | 3.29e-01 | 82.7% | 84.0% |