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putative_capsid_protein
Euk-VirRudbeckia_flower_distortion_virus
putative_capsid_protein__YP_002519386__Rudbeckia_flower_distortion_virus__587370
Identity
- Accession:
- YP_002519386 ↗
- Protein ID:
- putative_capsid_protein
- Kingdom:
- euk
Quality
66.8
mean pLDDT
Taxonomy
Pararnavirae›
Artverviricota›
Revtraviricetes›
Ortervirales›
Caulimoviridae›
Ruflodivirus›
Rudbeckia_flower_distortion_virus
TaxID: 587370
Cluster
Singleton — not in a non-trivial cluster
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 180-266
Domain cluster:
rep: hypothetical_protein__NP_043932__Strawberry_vein_banding_virus__47903__D115-200
CATH (12)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4ioeA00 | 1.10.287.850 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain | 0.62 | 36.0 | 3.62e-01 | 95.4% | 56.3% |
| 3llmA01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.58 | 39.0 | 2.95e-01 | 70.1% | 90.2% |
| 4ragA02 | 1.10.10.430 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Phosphatase 2C, C-terminal domain suprefamily | 0.58 | 39.0 | 4.27e-01 | 80.5% | 88.2% |
| 1ij5A03 | 1.10.238.10 | Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand | 0.57 | 45.0 | 4.04e-01 | 92.0% | 59.5% |
| 1ac1A00 | 3.40.30.10 | Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin | 0.56 | 43.0 | 3.44e-01 | 100.0% | 38.8% |
| 2lrmA00 | 1.10.890.30 | Mainly Alpha › Orthogonal Bundle › 10k-s Protein, Hypothetical Protein A; Chain A › YmgD protein | 0.55 | 39.0 | 4.00e-01 | 75.9% | 98.8% |
| 4nrvA02 | 1.10.8.50 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › | 0.55 | 48.0 | 4.10e-01 | 100.0% | 66.4% |
| 2x1dA02 | 1.10.10.2120 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › | 0.54 | 35.0 | 3.79e-01 | 92.0% | 78.4% |
| 3ljcA02 | 1.20.58.1480 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.54 | 39.0 | 3.50e-01 | 100.0% | 53.2% |
| 2d9dA00 | 1.20.58.120 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain | 0.53 | 37.0 | 3.71e-01 | 100.0% | 70.8% |
| 2liuA01 | 1.10.1200.10 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like | 0.53 | 44.0 | 4.50e-01 | 94.3% | 95.3% |
| 4ad9A02 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.52 | 37.0 | 3.77e-01 | 75.9% | 92.9% |
ECOD (15)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3886737 | 110.1.1.2 ↗ | alpha arrays › DEATH domain › DEATH domain › DEATH domain › CARD | 0.72 | 53.0 | 5.12e-01 | 97.7% | 68.0% |
| 4223385 | 150.5.1.1 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 | 0.65 | 37.0 | 3.58e-01 | 95.4% | 49.0% |
| 3298457 | 170.1.1.8 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Retrotran_gag_3 | 0.61 | 54.0 | 5.21e-01 | 100.0% | 85.0% |
| 4989798 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.61 | 44.0 | 3.36e-01 | 75.9% | 73.7% |
| 3790812 | 102.2.1.0 ↗ | alpha arrays › HhH/H2TH › H2TH › H2TH | 0.59 | 42.0 | 4.17e-01 | 88.5% | 70.5% |
| 3581248 | 108.1.1.0 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand | 0.56 | 42.0 | 4.25e-01 | 81.6% | 82.4% |
| 3877909 | 603.1.1.0 ↗ | alpha bundles › STAT-like › t-snare proteins › t-snare proteins | 0.56 | 38.0 | 4.06e-01 | 100.0% | 81.3% |
| 224428 | 185.1.2.2 ↗ | alpha superhelices › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin-like › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin/Protein HNS-dependent expression A HdeA › Protein HNS-dependent expression A HdeA › YmgD | 0.55 | 39.0 | 4.00e-01 | 75.9% | 98.8% |
| 4114000 | 132.1.1.1 ↗ | alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding | 0.55 | 43.0 | 4.33e-01 | 89.7% | 87.1% |
| 2986816 | 563.1.1.0 ↗ | alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase | 0.55 | 43.0 | 3.50e-01 | 95.4% | 43.4% |
| 3601098 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.53 | 40.0 | 3.90e-01 | 80.5% | 95.8% |
| 4545815 | 108.1.1.4 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand | 0.53 | 41.0 | 4.14e-01 | 90.8% | 87.1% |
| 3531386 | 108.1.1.26 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5 | 0.52 | 39.0 | 3.53e-01 | 88.5% | 55.4% |
| 3315602 | 592.2.1.0 ↗ | alpha arrays › PWI domain-like › YugE-like › YugE-like | 0.51 | 38.0 | 3.66e-01 | 79.3% | 70.0% |
| 5002473 | 107.1.1.9 ↗ | alpha arrays › Cytochrome c-like › Cytochrome c › Cytochrome c › Cytochrome_CBB3 | 0.50 | 37.0 | 3.27e-01 | 81.6% | 53.6% |
D2
high
residues 274-389
Domain cluster:
rep: coat_protein_movement_protein__YP_004347414__Sweet_potato_collusive_virus__930168__D560-659
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF22909.2 best | Caulimovir_coat_dom | 31.2 | 3.30e-07 | 94.0% | 92.0% |
CATH (16)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4dvyP01 | 1.10.357.130 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › | 0.67 | 46.0 | 3.88e-01 | 71.6% | 83.2% |
| 3u9jA00 | 1.20.120.520 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › nmb1532 protein domain like | 0.61 | 45.0 | 4.06e-01 | 75.9% | 91.1% |
| 3gwlA00 | 1.20.120.310 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain | 0.58 | 43.0 | 4.46e-01 | 81.9% | 84.0% |
| 1csnA02 | 1.10.510.10 | Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 | 0.58 | 41.0 | 3.44e-01 | 74.1% | 85.8% |
| 6x6nA01 | 1.20.120.260 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Virulence factor YopE uncharacterised domain | 0.55 | 43.0 | 4.38e-01 | 94.8% | 86.3% |
| 2fupA00 | 1.20.58.300 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › FlgN-like | 0.53 | 37.0 | 3.64e-01 | 71.6% | 97.6% |
| 4k0dA00 | 1.20.120.1730 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › | 0.53 | 46.0 | 4.29e-01 | 94.8% | 76.2% |
| 3l8rA00 | 1.20.58.80 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit | 0.53 | 41.0 | 4.38e-01 | 82.8% | 100.0% |
| 2vzbB00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.53 | 43.0 | 3.80e-01 | 87.9% | 93.4% |
| 2rsvA00 | 1.10.510.10 | Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 | 0.53 | 44.0 | 3.03e-01 | 90.5% | 63.5% |
| 3vprA02 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.52 | 41.0 | 3.90e-01 | 86.2% | 100.0% |
| 4lqkA00 | 1.10.437.20 | Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › dsDNA poxvirus | 0.52 | 39.0 | 3.73e-01 | 94.8% | 67.4% |
| 2b7mA00 | 1.20.1280.170 | Mainly Alpha › Up-down Bundle › Monooxygenase › Exocyst complex component Exo70 | 0.52 | 45.0 | 3.00e-01 | 98.3% | 45.6% |
| 2odvA01 | 1.20.58.60 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.52 | 44.0 | 4.50e-01 | 90.5% | 100.0% |
| 1vcsA00 | 1.20.58.400 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins | 0.51 | 38.0 | 4.02e-01 | 76.7% | 90.2% |
| 2xqyA02 | 1.20.58.1340 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.51 | 37.0 | 3.51e-01 | 76.7% | 72.7% |
ECOD (18)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3342226 | 170.1.1.16 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Caulimovir_coat_dom | 0.88 | 72.0 | 7.28e-01 | 84.5% | 87.0% |
| 3336919 | 170.1.1.16 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Caulimovir_coat_dom | 0.85 | 71.0 | 7.05e-01 | 87.1% | 88.3% |
| 3933535 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.74 | 59.0 | 6.27e-01 | 84.5% | 99.0% |
| 3462982 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.71 | 53.0 | 5.83e-01 | 95.7% | 95.8% |
| 3519786 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.70 | 49.0 | 5.58e-01 | 83.6% | 100.0% |
| 3504253 | 601.16.1.3 ↗ | alpha bundles › Four-helical up-and-down bundle › FAT domain of focal adhesion kinase › FAT domain of focal adhesion kinase › GIT1_C | 0.58 | 46.0 | 4.56e-01 | 95.7% | 78.4% |
| 3935029 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.55 | 46.0 | 4.48e-01 | 87.9% | 92.8% |
| 3808386 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.55 | 45.0 | 3.64e-01 | 87.1% | 68.2% |
| 4933006 | 4163.1.1.1 ↗ | alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 | 0.55 | 40.0 | 4.12e-01 | 87.9% | 80.0% |
| 5037501 | 4163.1.1.1 ↗ | alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 | 0.53 | 39.0 | 3.99e-01 | 90.5% | 78.3% |
| 3594748 | 632.22.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats | 0.53 | 29.0 | 2.94e-01 | 97.4% | 49.2% |
| 3940167 | 109.38.1.1 ↗ | alpha superhelices › Repetitive alpha hairpins › Telomere length regulation protein TEL2 › Telomere length regulation protein TEL2 › Telomere_reg-2 | 0.53 | 47.0 | 2.90e-01 | 100.0% | 19.0% |
| 3600074 | 603.2.1.0 ↗ | alpha bundles › STAT-like › STAT › STAT | 0.53 | 42.0 | 3.96e-01 | 85.3% | 75.0% |
| 3520972 | 206.1.1.1 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase | 0.52 | 45.0 | 3.18e-01 | 96.6% | 58.2% |
| 3613535 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.52 | 46.0 | 2.87e-01 | 100.0% | 31.6% |
| 3300142 | 601.1.2.0 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) | 0.52 | 39.0 | 3.61e-01 | 80.2% | 76.7% |
| 3167985 | 109.4.1.890 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_CNRKL1_C | 0.51 | 42.0 | 3.97e-01 | 89.7% | 100.0% |
| 4368996 | 109.4.1.2396 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Vac14_Fab1_bd, ARM_ECM29 | 0.50 | 46.0 | 2.78e-01 | 100.0% | 24.4% |