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coat_protein

Euk-Vir

Salvia_divinorum_RNA_virus_1

coat_protein__YP_009553028__Salvia_divinorum_RNA_virus_1__2419804

Identity

Accession:
YP_009553028 ↗
Protein ID:
coat_protein
Kingdom:
euk

Quality

71.8 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Tymovirales› Betaflexiviridae› Salvia_divinorum_RNA_virus_1

TaxID: 2419804

Cluster

View cluster (87 members)

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 9-133
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2v0xA01 1.10.287.3160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 65.0 5.87e-01 96.0% 80.4%
6h2dS01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.73 52.0 4.29e-01 74.4% 43.5%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 49.0 5.71e-01 92.8% 96.7%
1orsC00 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.70 42.0 4.12e-01 98.4% 56.1%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.69 54.0 5.12e-01 90.4% 69.7%
1m56C02 1.20.120.80 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle 0.67 51.0 4.31e-01 79.2% 51.5%
6t0bc02 1.20.120.80 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle 0.67 51.0 4.35e-01 79.2% 52.4%
1avoB00 1.20.120.180 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Proteasome activator pa28, C-terminal domain 0.66 46.0 4.46e-01 72.0% 79.3%
3dyjA01 1.20.1420.10 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain 0.64 48.0 4.36e-01 77.6% 98.2%
1bf5A01 1.20.1050.20 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › STAT transcription factor, all-alpha domain 0.64 53.0 4.74e-01 87.2% 82.7%
3uumA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 51.0 5.17e-01 84.8% 92.6%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.62 35.0 4.39e-01 71.2% 93.2%
2a9uA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.62 43.0 4.35e-01 84.0% 70.6%
2lm9A00 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 42.0 4.77e-01 84.0% 91.7%
2uv8A07 6.10.140.1410 Special › Helix non-globular › Helix Hairpins › 0.61 34.0 4.12e-01 86.4% 81.2%
5af7B03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.60 51.0 4.83e-01 92.0% 95.3%
1rx0A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.60 52.0 4.82e-01 94.4% 93.5%
2b0hA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.59 40.0 4.02e-01 76.0% 67.2%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.59 47.0 4.96e-01 85.6% 93.0%
1t98A02 1.20.58.590 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Chromosome partition protein MukF, middle domain 0.58 50.0 4.58e-01 92.8% 100.0%
4it4A02 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.58 40.0 4.65e-01 91.2% 96.7%
1q16C01 1.20.950.20 Mainly Alpha › Up-down Bundle › Fumarate Reductase Cytochrome B subunit › Transmembrane di-heme cytochromes, Chain C 0.58 43.0 3.62e-01 77.6% 54.7%
1r0dA00 1.20.1410.10 Mainly Alpha › Up-down Bundle › I/LWEQ domain › I/LWEQ domain 0.58 51.0 4.49e-01 100.0% 88.1%
8fbnB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.57 49.0 4.03e-01 92.8% 55.9%
5nl6A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 42.0 4.54e-01 81.6% 90.7%
4u72A01 1.20.58.480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 49.0 4.05e-01 97.6% 83.8%
4yvoA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.55 35.0 3.57e-01 95.2% 66.4%
5bqnA02 1.20.1120.10 Mainly Alpha › Up-down Bundle › "Clostridium botulinum neurotoxin B, ""coiled-coil"" domain" › "Clostridium botulinum neurotoxin b, ""coiled-coil"" domain" 0.53 45.0 3.26e-01 92.8% 59.6%
7ae2A01 1.20.120.580 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › bsu32300-like 0.53 38.0 3.69e-01 73.6% 75.2%
2wdqC00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.51 37.0 3.78e-01 97.6% 76.9%
1wn0A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.51 43.0 4.22e-01 88.0% 87.8%
3tp3A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.50 39.0 3.69e-01 80.0% 79.7%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3836944 3615.1.1.54 ↗ alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › DUF3611 0.83 74.0 7.11e-01 94.4% 100.0%
3470751 3755.3.1.297 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › KIF9 0.81 62.0 5.62e-01 79.2% 93.1%
4991905 3684.1.1.0 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.76 56.0 4.18e-01 75.2% 62.5%
3431118 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.75 60.0 6.41e-01 82.4% 93.6%
3717743 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.75 58.0 4.94e-01 81.6% 58.0%
3276289 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.75 65.0 5.29e-01 92.8% 92.4%
4021316 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.73 62.0 4.94e-01 90.4% 57.1%
4079591 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.72 50.0 5.32e-01 71.2% 94.5%
3722750 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.71 66.0 4.82e-01 100.0% 66.3%
4025845 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.71 62.0 5.19e-01 93.6% 94.3%
3253283 192.5.1.14 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1_TOCA 0.71 52.0 5.96e-01 96.8% 98.9%
3817246 192.29.1.27 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › DUF1218 0.69 54.0 4.72e-01 81.6% 65.0%
4024992 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.69 57.0 5.41e-01 86.4% 82.1%
5056307 3718.1.1.0 ↗ alpha bundles › Flagellar protein fliT › Flagellar protein fliT › Flagellar protein fliT 0.69 53.0 5.61e-01 80.0% 100.0%
4128138 604.12.1.4 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › ATG1-like_MIT1 0.68 56.0 5.07e-01 86.4% 70.9%
3876247 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.68 55.0 5.61e-01 83.2% 96.7%
3928383 5001.1.1.44 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srv 0.68 58.0 4.76e-01 92.8% 72.0%
3177591 633.23.1.9 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 0.67 60.0 4.87e-01 96.8% 91.3%
5043292 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.67 55.0 4.64e-01 85.6% 72.8%
3432339 604.1.1.134 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF28715 0.66 59.0 5.15e-01 93.6% 95.6%
5083475 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.66 56.0 4.39e-01 93.6% 69.8%
4456477 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.66 48.0 4.26e-01 76.0% 97.7%
3734418 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.65 60.0 4.38e-01 100.0% 81.5%
4034363 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.65 47.0 5.04e-01 75.2% 90.9%
3839945 3799.1.1.0 ↗ alpha bundles › SabA N-terminal extracellular adhesion domain › SabA N-terminal extracellular adhesion domain › SabA N-terminal extracellular adhesion domain 0.65 54.0 4.18e-01 89.6% 97.5%
3781234 1065.1.1.0 ↗ alpha bundles › SPX domain › SPX domain › SPX domain 0.65 52.0 4.39e-01 85.6% 67.3%
3788756 620.1.1.7 ↗ alpha bundles › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › Vezatin 0.64 47.0 3.69e-01 76.0% 75.8%
3601072 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.64 58.0 5.57e-01 97.6% 87.9%
5075236 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.64 52.0 5.38e-01 86.4% 88.3%
3712348 5057.1.1.0 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.64 56.0 4.37e-01 92.8% 98.8%
4013484 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.64 59.0 4.98e-01 100.0% 62.0%
3788870 633.23.1.9 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 0.64 51.0 4.40e-01 85.6% 97.0%
3715315 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.64 57.0 4.45e-01 96.8% 80.4%
3615269 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.63 58.0 4.86e-01 100.0% 88.6%
3697260 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.63 58.0 4.77e-01 96.0% 95.6%
3576591 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.63 54.0 5.23e-01 89.6% 97.0%
3789529 604.12.1.4 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › ATG1-like_MIT1 0.62 49.0 4.88e-01 82.4% 95.4%
3820263 7016.1.1.0 ↗ extended segments › Palmitoyltransferase DHHC C-terminal domain › Palmitoyltransferase DHHC C-terminal domain › Palmitoyltransferase DHHC C-terminal domain 0.62 53.0 5.09e-01 92.0% 93.8%
3724992 603.1.1.17 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › SNARE 0.62 54.0 4.19e-01 95.2% 44.5%
3182414 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.62 54.0 4.65e-01 96.0% 75.9%
3620861 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.61 52.0 5.13e-01 92.0% 85.9%
4014443 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.60 53.0 5.20e-01 94.4% 97.0%
3615237 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.60 56.0 3.89e-01 96.8% 55.8%
3577620 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.60 49.0 5.12e-01 86.4% 93.9%
3740106 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.60 47.0 4.90e-01 86.4% 88.7%
4959990 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.60 48.0 4.77e-01 84.0% 82.3%
3517583 4177.1.1.26 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › PKK 0.59 48.0 4.06e-01 85.6% 81.5%
3185833 633.23.1.22 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › MARVEL 0.59 50.0 4.72e-01 92.8% 90.0%
3799 603.6.1.1 ↗ alpha bundles › STAT-like › MukF C-terminal domain-like › MukF C-terminal domain-like › MukF_M 0.58 50.0 4.58e-01 92.8% 100.0%
3220072 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 45.0 4.68e-01 83.2% 87.8%
4613072 101.1.2.721 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR_2, PF27113 0.57 50.0 4.52e-01 92.8% 90.9%
3245542 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.57 44.0 4.52e-01 81.6% 86.7%
4944765 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.57 42.0 2.83e-01 76.8% 41.2%
3190960 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.56 48.0 4.26e-01 96.0% 82.7%
3707729 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 39.0 3.44e-01 72.8% 51.1%
3282876 192.29.1.52 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Anthrone_oxy 0.55 43.0 4.13e-01 82.4% 73.8%
3398025 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.54 40.0 4.37e-01 83.2% 98.0%
4828003 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.53 43.0 4.38e-01 85.6% 100.0%
D2 high residues 179-337
PDB
Domain cluster: rep: coat_protein__YP_009091818__Yam_virus_X__1503864__D37-177
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00286.26 best Flexi_CP 135.4 1.80e-39 86.2% 92.0%
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2n1fA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.55 24.0 3.05e-01 93.7% 66.3%
2wmoA01 1.25.40.410 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › DOCK DHR2 domain, lobe A 0.55 32.0 3.51e-01 88.1% 68.7%
1hbgA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.53 33.0 3.48e-01 93.1% 67.3%
1paqA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.53 40.0 4.00e-01 93.1% 78.3%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2775588 3143.1.1.1 ↗ alpha complex topology › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein-related › Papaya mosaic virus capsid protein › Flexi_CP 0.89 86.0 7.83e-01 100.0% 84.9%
1722663 3143.1.1.1 ↗ alpha complex topology › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein-related › Papaya mosaic virus capsid protein › Flexi_CP 0.88 85.0 7.49e-01 100.0% 84.3%
1818174 3143.1.1.1 ↗ alpha complex topology › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein-related › Papaya mosaic virus capsid protein › Flexi_CP 0.81 77.0 7.02e-01 100.0% 83.8%
3458159 192.29.1.54 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › BPS1 0.56 32.0 2.91e-01 87.4% 40.9%
3669260 192.2.1.35 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Hobbit 0.52 24.0 3.14e-01 78.6% 77.6%