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NIb

Euk-Vir

Hyacinth_mosaic_virus

NIb__YP_009466013__Hyacinth_mosaic_virus__421013

Identity

Accession:: YP_009466013 ↗
Protein ID:: NIb
Kingdom:: euk

Quality

92.1 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Stelpaviricetes› Patatavirales› Potyviridae› Potyvirus› Hyacinth_mosaic_virus

TaxID: 421013

Cluster

View cluster (450 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 medium residues 16-28_63-73_116-133_262-298

PDB

Domain cluster: rep: NIb__YP_009252418__Tobacco_mosqueado_virus__1792583__D13-29_64-80_248-311

D2 medium residues 29-62_410-476

PDB

Domain cluster: rep: NIb_protein__YP_006280739__Tomato_necrotic_stunt_virus__1176153__D28-67_411-488

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00680.26 best	RdRP_1	24.5	1.50e-05	71.3%	12.7%

CATH (11)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2qsbA00	1.20.1440.50	Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like	0.63	47.0	5.04e-01	80.2%	91.8%
3c1yA02	1.20.1260.110	Mainly Alpha › Up-down Bundle › Ferritin › DNA integrity scanning linker region	0.62	43.0	3.82e-01	72.3%	76.4%
1sj8A02	1.20.120.230	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like	0.57	46.0	4.32e-01	87.1%	88.5%
2aboA00	1.10.437.10	Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like	0.56	41.0	3.81e-01	84.2%	59.5%
4q5qB00	1.20.1050.130	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.55	46.0	3.81e-01	92.1%	84.0%
4py6C00	1.20.920.10	Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like	0.55	47.0	4.40e-01	94.1%	99.2%
3mekA04	1.25.40.970	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.53	38.0	4.17e-01	82.2%	96.2%
3h20A04	1.10.1240.50	Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 ›	0.52	36.0	3.77e-01	79.2%	79.8%
2pkeA02	1.10.150.240	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2	0.51	36.0	3.91e-01	84.2%	94.9%
5i1uA00	1.10.600.10	Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase	0.51	44.0	3.22e-01	100.0%	44.3%
1dlwA00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.50	43.0	4.21e-01	99.0%	86.2%

ECOD (10)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
56778	150.3.1.0 ↗	alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine	0.61	50.0	4.70e-01	88.1%	80.2%
4940676	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.58	45.0	4.44e-01	100.0%	76.9%
4582091	3009.2.1.2 ↗	alpha arrays › Insertion subdomain in DsbA-like › STAC domain › STAC domain › PF26309	0.57	41.0	4.46e-01	84.2%	95.0%
4030397	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.57	44.0	3.01e-01	82.2%	30.2%
3700629	633.15.1.1 ↗	alpha bundles › Bromodomain-like › alpha-ketoacid dehydrogenase kinase-N › alpha-ketoacid dehydrogenase kinase-N › BCDHK_Adom3	0.56	48.0	3.90e-01	94.1%	78.4%
3278832	106.1.1.11 ↗	alpha arrays › Globin-like › Globin-like › Globin-like › RsbRD_N	0.55	48.0	4.40e-01	97.0%	82.2%
1878968	103.2.1.2 ↗	alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone	0.55	45.0	4.55e-01	93.1%	92.0%
4285404	206.1.1.1 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase	0.51	45.0	3.48e-01	100.0%	71.2%
5071471	3003.1.1.1 ↗	a+b complex topology › N-terminal subdomain in DNA replication initiator (cdc21/cdc54) › N-terminal subdomain in DNA replication initiator (cdc21/cdc54) › N-terminal subdomain in DNA replication initiator (cdc21/cdc54) › MCM_N	0.51	38.0	3.76e-01	78.2%	84.8%
3516443	5054.1.1.0 ↗	alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels	0.50	42.0	3.53e-01	91.1%	63.5%

D3 medium residues 74-115_196-223_251-261_299-315

PDB

Domain cluster: rep: NIb__YP_010088127__Dendrobium_chlorotic_mosaic_virus__2562807__D81-113_256-322

D4 medium residues 224-250_316-409

PDB

Domain cluster: rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00680.26 best	RdRP_1	42.6	4.90e-11	88.4%	21.1%