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VP1
Euk-VirTupaia_glis_polyomavirus_1
VP1__YP_009551976__Tupaia_glis_polyomavirus_1__2170402
Identity
- Accession:
- YP_009551976 ↗
- Protein ID:
- VP1
- Kingdom:
- euk
Quality
70.5
mean pLDDT
Taxonomy
Shotokuvirae›
Cossaviricota›
Papovaviricetes›
Sepolyvirales›
Polyomaviridae›
Alphapolyomavirus›
Tupaia_glis_polyomavirus_1
TaxID: 2170402
Cluster
View cluster (117 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
medium
residues 33-54_101-134_245-326
Domain cluster:
representative
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00718.29 best | Polyoma_coat | 146.9 | 9.60e-43 | 60.9% | 28.0% |
| PF00718.29 | Polyoma_coat | 58.2 | 1.00e-15 | 27.5% | 11.8% |
CATH (19)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1sidF00 | 2.60.175.10 | Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus | 0.94 | 81.0 | 5.72e-01 | 88.4% | 78.2% |
| 3s7vC00 | 2.60.175.10 | Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus | 0.89 | 81.0 | 6.26e-01 | 93.5% | 100.0% |
| 4n0rA01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.63 | 32.0 | 3.94e-01 | 80.4% | 77.6% |
| 2g8gA00 | 2.170.30.10 | Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 | 0.57 | 46.0 | 3.14e-01 | 87.7% | 96.6% |
| 5eh1A01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.56 | 35.0 | 3.95e-01 | 84.8% | 81.1% |
| 2vf9A00 | 3.30.380.10 | Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein | 0.54 | 27.0 | 2.76e-01 | 84.1% | 45.0% |
| 1zx5A02 | 2.60.120.10 | Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls | 0.54 | 30.0 | 3.76e-01 | 84.1% | 89.2% |
| 1s55A00 | 2.60.120.40 | Mainly Beta › Sandwich › Jelly Rolls › | 0.53 | 42.0 | 4.09e-01 | 84.8% | 100.0% |
| 2g9gA00 | 2.60.120.1020 | Mainly Beta › Sandwich › Jelly Rolls › PAW domain | 0.53 | 43.0 | 3.87e-01 | 86.2% | 88.4% |
| 1o6uA02 | 2.60.120.680 | Mainly Beta › Sandwich › Jelly Rolls › GOLD domain | 0.53 | 36.0 | 3.99e-01 | 79.7% | 89.6% |
| 1nlqE00 | 2.60.120.340 | Mainly Beta › Sandwich › Jelly Rolls › Nucleoplasmin core domain | 0.53 | 36.0 | 4.25e-01 | 84.1% | 100.0% |
| 5y4mA00 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.52 | 43.0 | 4.19e-01 | 87.0% | 100.0% |
| 3jciA00 | 2.60.120.950 | Mainly Beta › Sandwich › Jelly Rolls › Circovirus capsid protein | 0.52 | 42.0 | 3.82e-01 | 87.7% | 95.8% |
| 1cov100 | 2.60.120.20 | Mainly Beta › Sandwich › Jelly Rolls › | 0.52 | 41.0 | 3.36e-01 | 85.5% | 69.1% |
| 2j1aA00 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.52 | 39.0 | 3.94e-01 | 79.7% | 100.0% |
| 7w3rB01 | 3.90.70.10 | Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases | 0.51 | 43.0 | 3.29e-01 | 91.3% | 88.1% |
| 1w8oA03 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.51 | 40.0 | 3.96e-01 | 82.6% | 100.0% |
| 1k3iA01 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.51 | 40.0 | 3.93e-01 | 84.8% | 95.5% |
| 3qs2A00 | 2.60.40.3290 | Mainly Beta › Sandwich › Immunoglobulin-like › Fimbrial protein EcpA | 0.50 | 40.0 | 3.73e-01 | 85.5% | 100.0% |
ECOD (17)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2666438 | 10.2.1.6 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat | 0.93 | 80.0 | 5.75e-01 | 88.4% | 81.5% |
| 961478 | 10.2.1.6 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat | 0.91 | 72.0 | 5.61e-01 | 80.4% | 100.0% |
| 423236 | 10.2.1.6 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat | 0.86 | 80.0 | 6.14e-01 | 94.9% | 100.0% |
| 2806413 | 10.2.1.4 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Late_protein_L1 | 0.69 | 63.0 | 4.30e-01 | 98.6% | 79.1% |
| 5052641 | 10.1.2.0 ↗ | beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) | 0.62 | 50.0 | 4.32e-01 | 87.0% | 100.0% |
| 3879431 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.55 | 36.0 | 4.06e-01 | 87.7% | 87.6% |
| 3577423 | 11.1.1.588 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Fibulin_C | 0.55 | 33.0 | 3.98e-01 | 81.9% | 92.2% |
| 4954560 | 10.1.2.0 ↗ | beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) | 0.54 | 41.0 | 4.36e-01 | 80.4% | 100.0% |
| 4212858 | 10.1.1.10 ↗ | beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › MAM | 0.54 | 42.0 | 3.87e-01 | 84.1% | 95.1% |
| 4944752 | 10.1.2.0 ↗ | beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) | 0.54 | 41.0 | 4.39e-01 | 81.2% | 97.5% |
| 3397523 | 11.2.1.8 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › PTEN_C2 | 0.53 | 31.0 | 3.15e-01 | 80.4% | 55.6% |
| 1032675 | 10.32.1.21 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › PAW | 0.53 | 43.0 | 3.87e-01 | 86.2% | 88.4% |
| 4954556 | 10.1.2.0 ↗ | beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) | 0.53 | 44.0 | 3.99e-01 | 89.1% | 100.0% |
| 3108819 | 10.2.1.11 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Gemini_coat | 0.53 | 46.0 | 4.02e-01 | 97.1% | 98.1% |
| 3408580 | 10.32.1.0 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like | 0.51 | 42.0 | 4.40e-01 | 86.2% | 95.2% |
| 5057372 | 10.1.2.0 ↗ | beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) | 0.50 | 36.0 | 3.97e-01 | 81.2% | 93.6% |
| 3845477 | 10.32.1.0 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like | 0.50 | 36.0 | 3.70e-01 | 81.2% | 78.5% |
D2
medium
residues 55-100_135-244_327-359
Domain cluster:
rep: VP1__YP_009030020__New_Jersey_polyomavirus-2013__1497391__D86-102_152-364
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00718.29 best | Polyoma_coat | 113.5 | 1.40e-32 | 61.9% | 34.8% |
CATH (2)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1sidF00 | 2.60.175.10 | Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus | 0.84 | 72.0 | 5.63e-01 | 87.3% | 79.4% |
| 3s7vC00 | 2.60.175.10 | Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus | 0.62 | 59.0 | 5.15e-01 | 100.0% | 91.4% |
ECOD (2)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2666438 | 10.2.1.6 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat | 0.84 | 73.0 | 5.82e-01 | 89.4% | 83.8% |
| 961478 | 10.2.1.6 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat | 0.78 | 71.0 | 6.26e-01 | 93.7% | 87.7% |