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NIb_protein

Euk-Vir

Barley_yellow_mosaic_virus

NIb_protein__NP_734307__Barley_yellow_mosaic_virus__12465

Identity

Accession:: NP_734307 ↗
Protein ID:: NIb_protein
Kingdom:: euk

Quality

91.1 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Stelpaviricetes› Patatavirales› Potyviridae› Bymovirus› Barley_yellow_mosaic_virus

TaxID: 12465

Cluster

View cluster (450 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 427-519

PDB

Domain cluster: rep: NIb__YP_007032445__Cassava_brown_streak_virus__137758__D405-481

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00680.26 best	RdRP_1	31.0	1.60e-07	66.7%	13.6%

CATH (26)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1khvA05	1.20.960.20	Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A ›	0.69	62.0	6.19e-01	100.0%	95.9%
6a7hA01	1.20.140.180	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 ›	0.67	46.0	4.15e-01	72.0%	59.8%
2ckwA04	1.20.960.20	Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A ›	0.66	59.0	5.70e-01	100.0%	87.9%
3purA03	1.20.58.1360	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.66	46.0	4.40e-01	73.1%	94.5%
3c1yA02	1.20.1260.110	Mainly Alpha › Up-down Bundle › Ferritin › DNA integrity scanning linker region	0.65	51.0	4.38e-01	83.9%	87.8%
2odmA00	1.10.287.750	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like	0.65	44.0	4.77e-01	71.0%	93.7%
4epzA00	1.25.40.810	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › UpxZ	0.63	51.0	4.35e-01	89.2%	81.2%
2zcxA00	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.61	45.0	3.50e-01	77.4%	59.5%
4i4cB00	3.40.50.1820	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain	0.61	53.0	3.55e-01	100.0%	74.1%
4dlqA02	1.25.40.610	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.60	48.0	4.83e-01	88.2%	89.5%
4n4gA01	1.20.920.10	Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like	0.59	43.0	4.04e-01	75.3%	64.9%
1eqfA02	1.20.920.10	Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like	0.59	44.0	4.06e-01	81.7%	62.4%
3jq0A00	1.25.40.390	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.59	51.0	3.29e-01	100.0%	86.2%
6tblB01	1.25.10.10	Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant	0.58	44.0	4.21e-01	81.7%	71.2%
1zk8B02	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.58	40.0	3.56e-01	71.0%	93.2%
3behB01	1.20.120.540	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels	0.56	39.0	3.67e-01	72.0%	77.8%
2ddhA04	1.20.140.10	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3	0.54	41.0	3.71e-01	82.8%	90.9%
8befJ01	1.20.120.1200	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ	0.54	39.0	3.26e-01	77.4%	42.9%
3fnbA01	1.20.1440.110	Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › acylaminoacyl peptidase	0.54	43.0	4.06e-01	88.2%	73.7%
1bgcA00	1.20.1250.10	Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; ›	0.53	37.0	3.14e-01	72.0%	57.6%
5lnkJ01	1.20.120.1200	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ	0.53	40.0	3.39e-01	82.8%	46.7%
2yvkA01	1.20.120.420	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1	0.52	41.0	3.49e-01	82.8%	59.5%
3o4zA02	1.25.40.720	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tel2 C-terminal domain	0.51	44.0	3.55e-01	97.8%	81.4%
3o10C00	1.20.120.330	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2	0.51	38.0	3.41e-01	80.6%	77.9%
2dg8D00	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.50	37.0	3.12e-01	79.6%	72.8%
2a2fX02	1.20.58.670	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain D	0.50	39.0	3.62e-01	88.2%	74.4%

ECOD (26)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3998525	196.1.1.1 ↗	alpha bundles › Regulator of G-protein signaling, RGS › Regulator of G-protein signaling, RGS › Regulator of G-protein signaling, RGS › RGS	0.70	48.0	3.77e-01	71.0%	49.4%
3626760	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.68	48.0	3.62e-01	74.2%	42.1%
3685497	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.67	57.0	4.31e-01	92.5%	67.6%
3628307	109.4.1.2108 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Htt_N-HEAT, Htt_N-HEAT_1, Htt_C-HEAT	0.67	54.0	2.93e-01	88.2%	8.4%
3750000	604.1.1.1 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin	0.67	46.0	4.42e-01	71.0%	91.4%
3935564	109.4.1.1414 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_TTI1_C	0.66	52.0	3.25e-01	84.9%	20.8%
3929749	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.65	51.0	4.10e-01	83.9%	44.0%
4975983	150.1.1.0 ↗	alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin	0.65	48.0	4.10e-01	76.3%	88.3%
3292830	109.52.1.1 ↗	alpha superhelices › Repetitive alpha hairpins › FRIGIDA flowering-time regulator › FRIGIDA flowering-time regulator › Frigida	0.65	47.0	3.40e-01	76.3%	37.0%
3790191	109.4.1.1414 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_TTI1_C	0.64	55.0	3.70e-01	93.5%	45.8%
3584274	109.4.1.1663 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TTI1, TPR_TTI1_C	0.64	55.0	3.66e-01	93.5%	44.5%
3489849	5.1.4.74 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Vps16_N	0.63	56.0	3.59e-01	100.0%	97.1%
3696931	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.63	56.0	4.10e-01	98.9%	96.8%
4095580	604.34.1.1 ↗	alpha bundles › Spectrin repeat-like › Helical bundle domain in arginine decarboxylase › Helical bundle domain in arginine decarboxylase › Arg_decarb_HB	0.62	44.0	4.46e-01	74.2%	85.3%
3408276	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.62	48.0	4.11e-01	84.9%	52.3%
4402843	604.1.1.20 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › AKNA	0.61	42.0	3.91e-01	71.0%	88.7%
3639700	4121.1.1.0 ↗	a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like	0.60	52.0	3.53e-01	95.7%	62.6%
4984330	3651.1.1.0 ↗	alpha bundles › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain	0.58	44.0	4.50e-01	82.8%	88.9%
3601333	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.57	50.0	3.18e-01	100.0%	35.5%
3606115	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.56	49.0	3.49e-01	95.7%	55.4%
3848246	109.12.1.4 ↗	alpha superhelices › Repetitive alpha hairpins › C-terminal domain of Ku80 › C-terminal domain of Ku80 › ZSWIM4-8_C	0.56	45.0	4.23e-01	89.2%	89.6%
3933110	3930.1.1.0 ↗	alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase	0.54	47.0	4.18e-01	96.8%	100.0%
5057633	3651.1.1.0 ↗	alpha bundles › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain	0.54	43.0	4.06e-01	88.2%	80.0%
4343342	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.54	41.0	3.66e-01	84.9%	66.9%
3500273	109.3.1.163 ↗	alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank, Ank_2, Ank_4, Ank_5	0.53	47.0	3.18e-01	98.9%	46.2%
4016106	650.1.1.0 ↗	alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain	0.52	39.0	4.11e-01	81.7%	100.0%

D2 medium residues 1-39_134-193_294-330

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00680.26 best	RdRP_1	37.1	2.30e-09	59.6%	14.9%

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3zrpA02	3.90.1150.10	Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1	0.55	27.0	2.91e-01	84.6%	51.3%

D3 medium residues 40-113_194-244

PDB

Domain cluster: rep: NIb__YP_003725727__Panax_virus_Y__796352__D1-80_166-195

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00680.26 best	RdRP_1	51.6	9.20e-14	44.8%	11.6%
PF00680.26	RdRP_1	24.5	1.50e-05	42.4%	10.4%

D4 medium residues 114-133_245-293_331-423

PDB

Domain cluster: rep: KR816341.1__AKQ06880.1__X__00021__D162-195_238-325

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00680.26 best	RdRP_1	73.8	1.70e-20	58.0%	21.1%
PF00680.26	RdRP_1	52.2	5.90e-14	39.5%	12.0%