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capsid_protein

Euk-Vir

Red_clover_powdery_mildew-associated_totivirus_1

capsid_protein__YP_009182173__Red_clover_powdery_mildew-associated_totivirus_1__1714362

Identity

Accession:: YP_009182173 ↗
Protein ID:: capsid_protein
Kingdom:: euk

Quality

67.3 mean pLDDT

Taxonomy

Orthornavirae› Duplornaviricota› Chrymotiviricetes› Ghabrivirales› Orthototiviridae› Totivirus› Red_clover_powdery_mildew-associated_totivirus_1

TaxID: 1714362

Cluster

View cluster (13 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 medium residues 57-70_281-328_341-439

PDB

Domain cluster: rep: putative_coat_protein__YP_009225664__Panax_notoginseng_virus_A__1777016__D291-325_348-435

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF09220.17 best	LA-virus_coat	162.7	1.30e-47	91.9%	35.8%

D2 medium residues 71-114

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF09220.17 best	LA-virus_coat	33.1	2.80e-08	100.0%	10.1%

CATH (28)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1m1cA00	3.90.1840.10	Alpha Beta › Alpha-Beta Complex › Major capsid protein › Major capsid protein	0.80	68.0	3.76e-01	100.0%	6.8%
3kxyT00	6.20.290.10	Special › Other non-globular › Dna Ligase; domain 1 ›	0.72	50.0	4.43e-01	93.2%	49.2%
3m8jA00	1.10.10.2690	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A ›	0.72	48.0	3.86e-01	70.5%	36.7%
8gf5C01	3.30.70.470	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits ›	0.70	57.0	4.05e-01	95.5%	64.8%
2vk9A03	1.10.3730.30	Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold ›	0.66	46.0	3.65e-01	77.3%	36.7%
1pyoB00	3.30.70.1470	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Caspase-like	0.65	48.0	3.84e-01	84.1%	38.8%
3s0aA00	1.10.238.20	Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain	0.65	54.0	4.05e-01	100.0%	37.0%
2be4A03	1.10.238.10	Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand	0.65	51.0	4.26e-01	95.5%	54.5%
1ibcB00	3.30.70.1470	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Caspase-like	0.63	46.0	3.86e-01	84.1%	44.3%
1d2nA02	1.10.8.60	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 ›	0.62	44.0	3.96e-01	95.5%	50.7%
6pw7A01	1.10.238.180	Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 ›	0.62	50.0	4.41e-01	100.0%	76.0%
6xgzE01	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.61	52.0	3.29e-01	100.0%	33.2%
1gcvA00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.61	47.0	3.56e-01	97.7%	78.6%
2r0bA00	3.90.190.10	Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily	0.60	47.0	3.42e-01	97.7%	65.6%
1z8fA01	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.60	50.0	3.67e-01	97.7%	61.2%
3gagA00	3.40.109.10	Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase	0.59	49.0	3.19e-01	95.5%	35.0%
2ve7A02	6.10.250.1950	Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces ›	0.59	43.0	3.25e-01	84.1%	34.4%
2x5fA01	3.40.640.10	Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain)	0.58	42.0	2.55e-01	79.5%	69.7%
4r2fA02	3.40.190.10	Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II	0.57	44.0	2.96e-01	93.2%	75.9%
1owfA00	4.10.520.10	Few Secondary Structures › Irregular › HU Protein; Chain A › IHF-like DNA-binding proteins	0.55	39.0	3.11e-01	81.8%	34.4%
2w2oA00	3.40.50.200	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidase S8/S53 domain	0.55	42.0	2.75e-01	100.0%	98.5%
1i7qA00	3.60.120.10	Alpha Beta › 4-Layer Sandwich › Anthranilate synthase › Anthranilate synthase	0.54	45.0	2.60e-01	100.0%	41.4%
2c5iT00	1.20.58.90	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.53	39.0	3.11e-01	77.3%	41.5%
2co9A00	1.10.30.10	Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain	0.53	37.0	2.98e-01	72.7%	34.3%
3ugjA02	1.10.8.750	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Phosphoribosylformylglycinamidine synthase, linker domain	0.53	38.0	3.57e-01	86.4%	62.9%
3nv9A01	3.40.50.10380	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Malic enzyme, N-terminal domain	0.52	45.0	2.98e-01	100.0%	44.3%
3cq4A02	3.40.640.10	Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain)	0.51	45.0	2.84e-01	100.0%	39.3%
7eu1A02	1.10.132.30	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain	0.51	42.0	3.08e-01	100.0%	82.1%

ECOD (19)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
7654	4065.1.1.1 ↗	a+b complex topology › L-A virus major coat protein-related › L-A virus major coat protein-related › L-A virus major coat protein-related › LA-virus_coat	0.80	68.0	3.76e-01	100.0%	6.8%
3246204	386.1.1.0 ↗	few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers	0.71	46.0	4.86e-01	86.4%	75.0%
3621272	708.1.1.16 ↗	beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › RYYR-CCHC	0.69	57.0	4.17e-01	100.0%	91.9%
None	—		0.69	49.0	2.81e-01	84.1%	7.5%
3477278	102.1.1.0 ↗	alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like	0.67	45.0	2.99e-01	75.0%	16.7%
3203608	558.1.1.0 ↗	alpha duplicates or obligate multimers › Lis-homology dimerization domain › Lis-homology dimerization domain › Lis-homology dimerization domain	0.67	56.0	4.48e-01	100.0%	87.4%
3952144	101.1.2.141 ↗	alpha arrays › HTH › HTH › winged helix domain › HTH_24	0.64	41.0	3.67e-01	81.8%	43.1%
3452698	101.1.10.37 ↗	alpha arrays › HTH › HTH › Cyclin-like › PF26138	0.63	49.0	3.91e-01	88.6%	53.7%
3719718	605.6.1.0 ↗	alpha duplicates or obligate multimers › ROP-like › HP1531-like › HP1531-like	0.62	50.0	4.19e-01	93.2%	50.0%
3627838	108.1.1.0 ↗	alpha arrays › EF-hand › EF-hand-related › EF-hand	0.60	50.0	4.28e-01	97.7%	58.7%
3678396	5051.1.1.15 ↗	alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › K_trans	0.60	47.0	2.77e-01	100.0%	81.5%
3469102	102.1.1.0 ↗	alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like	0.60	46.0	3.41e-01	100.0%	31.7%
3370052	101.46.1.1 ↗	alpha arrays › HTH › Parafibromin N-terminal domain › Parafibromin N-terminal domain › CDC73_N	0.59	48.0	3.78e-01	97.7%	53.3%
3244380	109.4.1.326 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RICTOR_M	0.58	51.0	3.06e-01	97.7%	47.7%
3965844	589.1.1.2 ↗	alpha arrays › Triger factor/SurA peptide-binding domain-like › Triger factor/SurA peptide-binding domain-like › Porin chaperone SurA, peptide-binding domain › SurA_N_3	0.55	40.0	2.82e-01	81.8%	25.6%
3238590	2007.2.5.0 ↗	a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase	0.54	36.0	3.04e-01	81.8%	36.5%
1699765	192.7.1.2 ↗	alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N	0.52	37.0	3.40e-01	95.5%	52.4%
3339142	327.5.1.2 ↗	a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C	0.51	39.0	2.96e-01	100.0%	37.9%
3406469	386.1.1.0 ↗	few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers	0.50	41.0	3.82e-01	97.7%	90.0%

D3 medium residues 115-280_329-340

PDB

Domain cluster: rep: capsid_protein__YP_007697650__Xanthophyllomyces_dendrorhous_virus_L1A__1167690__D122-309

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF09220.17 best	LA-virus_coat	180.5	5.40e-53	96.6%	38.4%

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1m1cA00	3.90.1840.10	Alpha Beta › Alpha-Beta Complex › Major capsid protein › Major capsid protein	0.88	85.0	5.51e-01	100.0%	34.3%
2zdiB00	1.10.287.370	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.58	27.0	3.47e-01	97.8%	73.6%

ECOD (3)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
7654	4065.1.1.1 ↗	a+b complex topology › L-A virus major coat protein-related › L-A virus major coat protein-related › L-A virus major coat protein-related › LA-virus_coat	0.88	85.0	5.51e-01	100.0%	34.3%
4821589	4065.1.1.1 ↗	a+b complex topology › L-A virus major coat protein-related › L-A virus major coat protein-related › L-A virus major coat protein-related › LA-virus_coat	0.74	70.0	5.20e-01	100.0%	51.7%
3735533	4065.1.1.0 ↗	a+b complex topology › L-A virus major coat protein-related › L-A virus major coat protein-related › L-A virus major coat protein-related	0.58	52.0	3.88e-01	94.9%	44.5%

D4 medium residues 511-586

PDB