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VP1
Euk-VirEubenangee_virus
VP1__YP_009507705__Eubenangee_virus__40056
Identity
- Accession:
- YP_009507705 ↗
- Protein ID:
- VP1
- Kingdom:
- euk
Quality
86.8
mean pLDDT
Cluster
View cluster (29 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 233-383
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009158901__Chobar_Gorge_virus__1679172__D209-255_289-364
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05788.19 best | Orbi_VP1 | 255.4 | 1.30e-75 | 100.0% | 11.7% |
D2
high
residues 659-714
Domain cluster:
rep: VP1_protein__YP_009507680__Corriparta_virus__40053__D646-703
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05788.19 best | Orbi_VP1 | 45.1 | 4.00e-12 | 100.0% | 4.2% |
D3
medium
residues 32-79_882-920
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_008658416__Wallal_virus__40061__D29-71_886-921
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05788.19 best | Orbi_VP1 | 39.0 | 2.80e-10 | 56.3% | 3.6% |
| PF05788.19 | Orbi_VP1 | 50.9 | 6.80e-14 | 48.3% | 3.0% |
D4
medium
residues 80-142_166-201
Domain cluster:
representative
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05788.19 best | Orbi_VP1 | 67.3 | 7.70e-19 | 66.7% | 4.9% |
| PF05788.19 | Orbi_VP1 | 34.2 | 7.50e-09 | 37.4% | 2.8% |
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 7paxA01 | 3.40.1180.10 | Alpha Beta › 3-Layer(aba) Sandwich › Undecaprenyl pyrophosphate synthetase › Decaprenyl diphosphate synthase-like | 0.51 | 38.0 | 2.87e-01 | 80.8% | 95.8% |
D5
medium
residues 143-165_202-232_853-881
Domain cluster:
representative
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05788.19 best | Orbi_VP1 | 38.0 | 5.60e-10 | 47.0% | 2.7% |
| PF05788.19 | Orbi_VP1 | 39.2 | 2.40e-10 | 38.6% | 2.4% |
CATH (13)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4mi2A02 | 1.10.12.10 | Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 | 0.65 | 29.0 | 3.42e-01 | 97.6% | 56.9% |
| 4jfcA02 | 1.10.12.10 | Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 | 0.63 | 28.0 | 3.35e-01 | 97.6% | 58.9% |
| 3f2bA05 | 6.10.50.10 | Special › Helix non-globular › Insulin-like, subunit E › | 0.59 | 29.0 | 3.80e-01 | 98.8% | 83.3% |
| 2go7A02 | 1.10.150.240 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 | 0.55 | 40.0 | 4.31e-01 | 96.4% | 95.5% |
| 2gscC00 | 1.20.1440.60 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence | 0.55 | 46.0 | 4.17e-01 | 90.4% | 88.2% |
| 3gaeA00 | 1.25.10.10 | Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant | 0.52 | 39.0 | 2.77e-01 | 78.3% | 41.5% |
| 2w02B01 | 1.10.150.640 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle | 0.52 | 39.0 | 4.10e-01 | 100.0% | 93.2% |
| 6ff4Y00 | 1.20.1390.10 | Mainly Alpha › Up-down Bundle › PWI domain › PWI domain | 0.52 | 42.0 | 4.04e-01 | 100.0% | 77.9% |
| 1t7lB01 | 3.20.20.210 | Alpha Beta › Alpha-Beta Barrel › TIM Barrel › | 0.52 | 39.0 | 2.54e-01 | 79.5% | 39.2% |
| 7qpgW01 | 1.10.357.150 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › | 0.51 | 38.0 | 3.00e-01 | 80.7% | 58.4% |
| 1gnlA01 | 1.20.1270.20 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.51 | 43.0 | 3.70e-01 | 96.4% | 74.1% |
| 3ousA00 | 1.10.287.70 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.51 | 38.0 | 3.89e-01 | 90.4% | 81.7% |
| 2v6yA00 | 1.20.58.80 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit | 0.50 | 34.0 | 3.60e-01 | 73.5% | 77.3% |
ECOD (5)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4965615 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.64 | 33.0 | 4.12e-01 | 96.4% | 82.0% |
| 3614867 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.59 | 44.0 | 3.13e-01 | 79.5% | 49.2% |
| 3941995 | 131.1.1.13 ↗ | alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD_5 | 0.54 | 45.0 | 3.46e-01 | 92.8% | 51.0% |
| 3605615 | 174.1.1.51 ↗ | few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › SCAMP | 0.51 | 42.0 | 3.31e-01 | 91.6% | 83.9% |
| 4999330 | 604.12.1.135 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Oxidored_q2 | 0.51 | 37.0 | 3.55e-01 | 78.3% | 80.0% |
D6
medium
residues 405-452_477-499_532-575_601-629
Domain cluster:
representative
Pfam (3)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05788.19 best | Orbi_VP1 | 76.2 | 1.60e-21 | 34.7% | 3.8% |
| PF05788.19 | Orbi_VP1 | 76.6 | 1.20e-21 | 31.2% | 3.4% |
| PF05788.19 | Orbi_VP1 | 31.8 | 4.00e-08 | 20.8% | 2.2% |
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4ip8A00 | 1.10.132.110 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Serum amyloid A protein | 0.61 | 31.0 | 3.61e-01 | 100.0% | 66.7% |
| 1kt1A03 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.55 | 26.0 | 2.58e-01 | 99.3% | 41.8% |
| 2icwG02 | 1.10.10.530 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › mam-mhc complex, Chain D, Domain 2 | 0.53 | 28.0 | 3.48e-01 | 96.5% | 82.0% |
| 2kvcA01 | 1.10.150.430 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DUF3349, helical bundle | 0.53 | 25.0 | 3.03e-01 | 97.9% | 68.2% |
| 1bucA01 | 1.10.540.10 | Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain | 0.51 | 30.0 | 3.23e-01 | 95.1% | 65.9% |
| 3fxhA00 | 1.20.120.600 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Crystal structure from the mobile metagenome of halifax harbour sewage outfall | 0.50 | 33.0 | 3.65e-01 | 99.3% | 82.3% |
ECOD (2)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3272030 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.52 | 45.0 | 3.37e-01 | 97.2% | 51.4% |
| 3267570 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.52 | 42.0 | 3.25e-01 | 88.9% | 57.4% |
D7
medium
residues 453-476_921-989
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05788.19 best | Orbi_VP1 | 96.9 | 9.00e-28 | 77.4% | 5.5% |
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2qg3A00 | 3.30.1960.10 | Alpha Beta › 2-Layer Sandwich › SSo0622-like fold › tRNA wybutosine-synthesizing-like | 0.50 | 36.0 | 2.89e-01 | 75.3% | 80.9% |
D8
medium
residues 500-531_630-654_715-732
Domain cluster:
representative
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05788.19 best | Orbi_VP1 | 50.8 | 7.40e-14 | 44.0% | 2.5% |
| PF05788.19 | Orbi_VP1 | 33.8 | 1.00e-08 | 36.0% | 1.9% |
CATH (7)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1mukA02 | 3.90.1850.10 | Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3 | 0.74 | 67.0 | 4.00e-01 | 100.0% | 35.7% |
| 2r7rA05 | 1.10.357.80 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › | 0.73 | 64.0 | 4.87e-01 | 97.3% | 71.6% |
| 4mi0A00 | 2.170.270.10 | Mainly Beta › Beta Complex › Beta-clip-like › SET domain | 0.61 | 36.0 | 2.61e-01 | 81.3% | 20.2% |
| 2f69A02 | 2.170.270.10 | Mainly Beta › Beta Complex › Beta-clip-like › SET domain | 0.58 | 33.0 | 2.73e-01 | 81.3% | 28.7% |
| 5cflA02 | 3.40.50.12100 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Stimulator of interferon genes protein | 0.53 | 41.0 | 3.43e-01 | 88.0% | 53.7% |
| 4k7cA01 | 3.90.70.10 | Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases | 0.53 | 41.0 | 2.63e-01 | 85.3% | 56.3% |
| 6w1kA01 | 3.10.180.50 | Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › | 0.51 | 40.0 | 2.69e-01 | 85.3% | 33.3% |
ECOD (27)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5368 | 304.48.1.23 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_5 | 0.74 | 67.0 | 4.17e-01 | 100.0% | 46.0% |
| 223786 | 304.48.1.16 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_4 | 0.73 | 65.0 | 4.24e-01 | 100.0% | 48.9% |
| 3983816 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.67 | 60.0 | 4.14e-01 | 100.0% | 67.6% |
| 4152428 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.65 | 58.0 | 3.72e-01 | 100.0% | 48.7% |
| 4497954 | 304.48.1.73 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1, RVT_N | 0.65 | 58.0 | 3.83e-01 | 100.0% | 56.1% |
| 3097450 | 304.48.1.12 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mononeg_RNA_pol | 0.64 | 55.0 | 3.51e-01 | 100.0% | 42.5% |
| 4461237 | 4967.1.1.0 ↗ | alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases | 0.63 | 55.0 | 3.34e-01 | 100.0% | 45.0% |
| 3589612 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.63 | 56.0 | 3.65e-01 | 100.0% | 61.5% |
| 5018583 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.63 | 56.0 | 3.68e-01 | 100.0% | 56.5% |
| 3209439 | 304.48.1.0 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like | 0.61 | 52.0 | 3.50e-01 | 100.0% | 51.9% |
| 3936706 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.60 | 54.0 | 3.73e-01 | 100.0% | 55.7% |
| 3933460 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.60 | 54.0 | 3.69e-01 | 100.0% | 61.5% |
| 4070164 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.60 | 52.0 | 3.38e-01 | 100.0% | 41.4% |
| 3927796 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.59 | 53.0 | 3.64e-01 | 100.0% | 59.2% |
| 5056382 | 232.1.1.0 ↗ | a+b duplicates or obligate multimers › Pentein › Pentein › Pentein | 0.59 | 44.0 | 2.81e-01 | 96.0% | 16.2% |
| 3930235 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.58 | 51.0 | 3.54e-01 | 100.0% | 57.7% |
| 3257066 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.58 | 50.0 | 3.54e-01 | 97.3% | 50.8% |
| 3939017 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.58 | 52.0 | 3.57e-01 | 100.0% | 51.4% |
| 3926633 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.58 | 50.0 | 3.79e-01 | 97.3% | 63.8% |
| 3927691 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.58 | 51.0 | 3.57e-01 | 100.0% | 63.6% |
| 3940234 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.58 | 51.0 | 3.64e-01 | 100.0% | 68.3% |
| 3737895 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.57 | 50.0 | 3.53e-01 | 100.0% | 62.8% |
| 3937813 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.57 | 50.0 | 3.44e-01 | 100.0% | 49.3% |
| 3573721 | 304.48.1.0 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like | 0.56 | 48.0 | 3.82e-01 | 97.3% | 70.6% |
| 3940023 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.54 | 47.0 | 3.37e-01 | 98.7% | 52.4% |
| 3970455 | 246.3.1.1 ↗ | a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like › Exo_endo_phos | 0.51 | 44.0 | 3.07e-01 | 98.7% | 58.1% |
| 4262041 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.51 | 45.0 | 3.14e-01 | 100.0% | 52.9% |