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nucleocapsid_protein

Euk-Vir

Citrus_concave_gum-associated_virus

nucleocapsid_protein__YP_009407931__Citrus_concave_gum-associated_virus__2024604

Identity

Accession:: YP_009407931 ↗
Protein ID:: nucleocapsid_protein
Kingdom:: euk

Quality

72.7 mean pLDDT

Taxonomy

Orthornavirae› Negarnaviricota› Bunyaviricetes› Hareavirales› Phenuiviridae› Coguvirus› Citrus_concave_gum-associated_virus

TaxID: 2024604

Cluster

View cluster (83 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 high residues 113-207

PDB

Domain cluster: rep: putative_nucleoprotein__YP_009330282__Hubei_diptera_virus_5__1922886__D214-314

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF05733.17 best	Tenui_N	48.9	8.80e-13	99.0%	38.4%

CATH (19)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4qicC01	1.20.140.160	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › PhyR, sigma-like (SL) domain	0.63	39.0	3.54e-01	88.4%	46.4%
3fbzA01	1.20.58.800	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.61	45.0	4.44e-01	78.9%	92.2%
1hekA00	1.10.150.90	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Immunodeficiency lentiviruses, gag gene matrix protein p17	0.61	45.0	4.30e-01	80.0%	95.7%
1x4oA00	1.10.10.790	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Surp module	0.59	40.0	4.32e-01	92.6%	84.6%
2ds2D01	1.10.110.10	Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins	0.58	31.0	3.73e-01	95.8%	82.5%
3kjxD01	1.10.260.40	Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains	0.58	33.0	3.91e-01	72.6%	86.9%
4mlmA00	1.10.3210.10	Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432	0.57	45.0	3.63e-01	85.3%	76.6%
3ejbH02	1.10.630.10	Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450	0.57	49.0	3.66e-01	98.9%	77.1%
2mx8A01	1.10.274.70	Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, N-terminal domain	0.55	40.0	3.79e-01	75.8%	80.5%
4s3mB02	1.10.1040.10	Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2	0.55	38.0	3.67e-01	71.6%	95.3%
1k87A02	1.10.2060.10	Mainly Alpha › Orthogonal Bundle › PutA proline dehydrogenase (PRODH), domain 2 › PutA proline dehydrogenase (PRODH), domain 2	0.54	46.0	4.41e-01	92.6%	99.1%
3k1hA00	3.30.1120.180	Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › Flagellar FLiS export co-chaperone, HP1076	0.54	42.0	4.01e-01	84.2%	93.9%
1vnsA01	1.20.144.10	Mainly Alpha › Up-down Bundle › Vanadium-containing Chloroperoxidase; domain 1 › Phosphatidic acid phosphatase type 2/haloperoxidase	0.54	42.0	3.44e-01	83.2%	76.6%
3grlA00	1.25.10.10	Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant	0.53	38.0	2.36e-01	74.7%	30.3%
3iqtA01	1.20.120.160	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain	0.53	44.0	4.24e-01	94.7%	96.5%
5li7A00	1.10.630.10	Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450	0.52	46.0	3.13e-01	100.0%	61.7%
3qxlA00	1.10.840.10	Mainly Alpha › Orthogonal Bundle › Son of Sevenless (SoS) protein; Chain S, domain 2 › Ras guanine-nucleotide exchange factors catalytic domain	0.52	39.0	2.98e-01	82.1%	80.8%
4hteA01	1.20.58.1730	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.51	39.0	3.45e-01	83.2%	76.9%
2x2vA00	1.20.20.10	Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C	0.50	27.0	3.19e-01	96.8%	73.5%

ECOD (12)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1007268	3143.1.2.1 ↗	alpha complex topology › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein › Tenui_N	0.89	77.0	5.49e-01	100.0%	34.7%
1030601	3143.1.2.1 ↗	alpha complex topology › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein › Tenui_N	0.89	79.0	5.60e-01	100.0%	35.5%
3820015	3143.1.2.1 ↗	alpha complex topology › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein › Tenui_N	0.87	82.0	5.82e-01	100.0%	37.6%
4348670	152.1.2.1 ↗	alpha arrays › RPB6/omega subunit-like › RPB6/omega subunit-like › RNA polymerase omega subunit › RNA_pol_Rpb6	0.63	35.0	3.54e-01	89.5%	52.5%
5076914	563.2.1.0 ↗	alpha bundles › ATPD N-terminal domain-like › Cas Cmr5-like › Cas Cmr5-like	0.60	54.0	4.97e-01	98.9%	95.8%
2502908	7065.1.1.1 ↗	alpha arrays › Cytoplasmic metal binding domain of VIT1 › Cytoplasmic metal binding domain of VIT1 › Cytoplasmic metal binding domain of VIT1 › VIT1	0.60	32.0	3.62e-01	72.6%	67.6%
3632120	592.1.1.0 ↗	alpha arrays › PWI domain-like › PWI domain › PWI domain	0.58	41.0	4.38e-01	91.6%	86.3%
3537874	320.4.1.5 ↗	a+b two layers › R3H domain-like › PUB domain › PUB domain › Gasdermin_C	0.57	48.0	3.78e-01	95.8%	90.7%
3282047	101.1.3.4 ↗	alpha arrays › HTH › HTH › tetra-helical, LuxR-like › HTH_30	0.57	49.0	4.82e-01	94.7%	91.0%
4116135	4009.1.1.11 ↗	alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › NA37	0.53	47.0	4.44e-01	100.0%	81.7%
4946961	102.3.1.1 ↗	alpha arrays › HhH/H2TH › eIF2alpha middle domain › eIF2alpha middle domain › EIF_2_alpha	0.53	42.0	4.31e-01	87.4%	90.0%
4969561	5065.1.1.1 ↗	alpha bundles › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › ABC-3	0.52	42.0	3.02e-01	87.4%	71.4%

D2 high residues 210-349

PDB

Domain cluster: representative

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1ks9A02	1.10.1040.10	Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2	0.51	42.0	4.40e-01	92.1%	99.2%
1l8qA03	1.10.1750.10	Mainly Alpha › Orthogonal Bundle › Chromosomal Replication Initiator Protein Dnaa; Chain: A; › DnaA protein, C-terminal DNA-binding domain	0.51	32.0	3.56e-01	95.0%	80.4%

ECOD (7)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3820015	3143.1.2.1 ↗	alpha complex topology › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein-related › Rift Valley fever virus nucleocapsid protein › Tenui_N	0.78	74.0	5.84e-01	100.0%	53.5%
150412	150.3.1.25 ↗	alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › IL34	0.59	35.0	3.32e-01	92.1%	47.4%
3932126	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.54	38.0	3.00e-01	70.7%	78.7%
3691319	601.1.1.0 ↗	alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin	0.52	34.0	3.71e-01	91.4%	78.0%
3592297	5059.1.1.0 ↗	alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter	0.52	46.0	3.63e-01	100.0%	95.9%
5019571	5059.1.1.1 ↗	alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA	0.50	37.0	3.01e-01	76.4%	79.0%
5000809	601.1.1.0 ↗	alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin	0.50	38.0	4.10e-01	80.0%	95.7%