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VP1
Euk-VirNorovirus_GIV
VP1__YP_009700100__Norovirus_GIV__262897
Identity
- Accession:
- YP_009700100 ↗
- Protein ID:
- VP1
- Kingdom:
- euk
Quality
81.7
mean pLDDT
Taxonomy
Orthornavirae›
Pisuviricota›
Pisoniviricetes›
Picornavirales›
Caliciviridae›
Norovirus›
Norovirus_GIV
TaxID: 262897
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 50-215
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 | 201.0 | 2.90e-59 | 100.0% | 55.1% |
| PF00073.27 | Rhv | 53.1 | 4.20e-14 | 79.5% | 57.9% |
D2
high
residues 281-415
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 | 38.1 | 1.80e-09 | 75.6% | 42.6% |
CATH (19)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4qv2A02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.92 | 78.0 | 8.41e-01 | 91.9% | 100.0% |
| 6j0qA02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.89 | 70.0 | 7.80e-01 | 87.4% | 100.0% |
| 3q39B02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.88 | 70.0 | 7.78e-01 | 87.4% | 100.0% |
| 2zl7A02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.86 | 57.0 | 6.88e-01 | 87.4% | 100.0% |
| 5e6tA02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.85 | 58.0 | 6.96e-01 | 87.4% | 100.0% |
| 4rlzA02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.84 | 67.0 | 7.43e-01 | 87.4% | 100.0% |
| 4rdlA02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.81 | 62.0 | 6.98e-01 | 87.4% | 100.0% |
| 3lq6A02 | 2.40.30.120 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses | 0.79 | 65.0 | 7.03e-01 | 87.4% | 100.0% |
| 3op1A02 | 2.40.30.30 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like | 0.76 | 49.0 | 5.36e-01 | 94.1% | 79.3% |
| 1n08A00 | 2.40.30.30 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like | 0.64 | 48.0 | 4.57e-01 | 94.1% | 67.5% |
| 3lnnA02 | 2.40.30.170 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain | 0.64 | 43.0 | 5.03e-01 | 87.4% | 100.0% |
| 2bhgA02 | 2.40.10.10 | Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases | 0.61 | 35.0 | 3.96e-01 | 75.6% | 73.5% |
| 4kktA02 | 2.40.30.170 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain | 0.61 | 43.0 | 4.77e-01 | 87.4% | 93.3% |
| 3zugB02 | 2.40.30.30 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like | 0.60 | 50.0 | 4.93e-01 | 91.9% | 83.8% |
| 4f4oC03 | 2.40.10.10 | Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases | 0.58 | 37.0 | 4.37e-01 | 79.3% | 95.5% |
| 3bnwB00 | 2.40.30.30 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like | 0.58 | 48.0 | 4.55e-01 | 92.6% | 75.2% |
| 6mv4H02 | 2.40.10.10 | Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases | 0.54 | 35.0 | 3.87e-01 | 79.3% | 80.6% |
| 3tk9A02 | 2.40.10.10 | Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases | 0.54 | 35.0 | 3.82e-01 | 79.3% | 81.3% |
| 5jm6A02 | 2.30.250.10 | Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 | 0.50 | 41.0 | 4.05e-01 | 86.7% | 100.0% |
ECOD (42)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 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) | 0.89 | 79.0 | 5.81e-01 | 100.0% | 40.3% |
| 2553941 | 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 | 79.0 | 5.82e-01 | 100.0% | 40.6% |
| 2505880 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.88 | 60.0 | 5.87e-01 | 78.5% | 64.4% |
| 2505848 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.86 | 80.0 | 7.70e-01 | 100.0% | 87.2% |
| 4881922 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.86 | 71.0 | 7.14e-01 | 100.0% | 85.3% |
| 2505866 | 1.2.1.4 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat, Calici_coat_C | 0.84 | 58.0 | 5.61e-01 | 71.1% | 64.2% |
| 2505857 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.82 | 68.0 | 6.85e-01 | 100.0% | 86.0% |
| 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 | 0.82 | 71.0 | 5.39e-01 | 100.0% | 42.0% |
| 2171578 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.81 | 70.0 | 6.97e-01 | 100.0% | 87.6% |
| 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 | 0.81 | 71.0 | 5.24e-01 | 100.0% | 39.6% |
| 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 | 0.79 | 63.0 | 6.72e-01 | 95.6% | 94.1% |
| 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 | 0.76 | 61.0 | 6.45e-01 | 85.9% | 94.1% |
| 4426297 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.67 | 46.0 | 4.74e-01 | 94.1% | 73.8% |
| 4033620 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.65 | 48.0 | 4.96e-01 | 94.1% | 80.0% |
| 3267872 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.65 | 45.0 | 4.58e-01 | 87.4% | 73.1% |
| 4381510 | 1.1.8.5 ↗ | beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › tRNA_Me_trans_C | 0.65 | 39.0 | 4.61e-01 | 75.6% | 87.1% |
| 4565791 | 1.1.7.87 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25954 | 0.65 | 43.0 | 5.04e-01 | 96.3% | 100.0% |
| 5051220 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.64 | 41.0 | 4.84e-01 | 87.4% | 95.6% |
| 4606765 | 1.1.7.91 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25940 | 0.64 | 44.0 | 4.78e-01 | 87.4% | 85.5% |
| 3389051 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.63 | 47.0 | 4.61e-01 | 94.1% | 70.0% |
| 4400928 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.63 | 45.0 | 4.73e-01 | 94.1% | 80.0% |
| 4017709 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.63 | 49.0 | 4.35e-01 | 93.3% | 57.9% |
| 4062509 | 1.1.7.91 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25940 | 0.63 | 45.0 | 4.98e-01 | 87.4% | 94.3% |
| 4608778 | 1.1.7.107 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25965 | 0.61 | 42.0 | 4.47e-01 | 88.1% | 80.0% |
| 5014058 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.60 | 46.0 | 4.81e-01 | 87.4% | 86.4% |
| 3592708 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.60 | 50.0 | 4.76e-01 | 93.3% | 75.6% |
| 3410364 | 1.1.7.90 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ZNFX1 | 0.59 | 45.0 | 4.86e-01 | 86.7% | 97.3% |
| 3945834 | 1.1.7.79 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Beta-barrel_RND | 0.59 | 42.0 | 4.73e-01 | 87.4% | 99.0% |
| 3703044 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.58 | 50.0 | 4.68e-01 | 91.9% | 75.2% |
| 4026425 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.58 | 47.0 | 4.57e-01 | 92.6% | 77.9% |
| 4936008 | 1.1.7.28 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › HAS-barrel | 0.58 | 40.0 | 4.61e-01 | 85.9% | 98.9% |
| 3702149 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.58 | 47.0 | 4.47e-01 | 86.7% | 80.6% |
| 4927408 | 2.3.1.0 ↗ | beta barrels › OB-fold › TIMP-like › TIMP-like | 0.58 | 37.0 | 3.89e-01 | 94.1% | 71.7% |
| 1716898 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.58 | 49.0 | 4.73e-01 | 93.3% | 80.0% |
| 3615541 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.57 | 47.0 | 4.86e-01 | 87.4% | 96.8% |
| 3174670 | 1.1.7.10 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase | 0.55 | 48.0 | 4.27e-01 | 93.3% | 72.3% |
| 5035178 | 10.2.1.0 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) | 0.54 | 41.0 | 4.40e-01 | 88.9% | 96.4% |
| 4944288 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.54 | 39.0 | 4.29e-01 | 86.7% | 96.2% |
| 3585350 | 11.1.1.2 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 | 0.54 | 36.0 | 3.88e-01 | 96.3% | 82.7% |
| 4452137 | 1.1.7.7 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 | 0.52 | 46.0 | 4.67e-01 | 97.0% | 97.0% |
| 3495933 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.51 | 35.0 | 3.78e-01 | 86.7% | 86.4% |
| 4628851 | 11.1.5.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f | 0.51 | 30.0 | 3.23e-01 | 85.9% | 67.0% |
D3
medium
residues 226-280_416-547
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 | 167.2 | 6.10e-49 | 87.7% | 59.1% |
| PF00915.27 | Calici_coat | 28.9 | 7.70e-07 | 33.2% | 16.1% |