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nucleocapsid_protein

Euk-Vir

Huangpi_Tick_Virus_1

nucleocapsid_protein__YP_009293589__Huangpi_Tick_Virus_1__1608047

Identity

Accession:
YP_009293589 ↗
Protein ID:
nucleocapsid_protein
Kingdom:
euk

Quality

73.8 mean pLDDT

3D Structure

Domains

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

D1 high residues 193-288
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3u3iA02 1.20.58.1110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.81 74.0 7.09e-01 100.0% 88.0%
7xcnM01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.66 50.0 5.37e-01 93.8% 98.7%
4zvaA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.65 54.0 4.71e-01 91.7% 77.9%
2mtqA00 1.20.58.130 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 44.0 4.90e-01 85.4% 94.5%
4i1eA03 1.25.10.30 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › IP3 receptor type 1 binding core, RIH domain 0.60 53.0 4.75e-01 100.0% 93.5%
3pe0A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 49.0 4.83e-01 86.5% 93.1%
1t72A01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.60 49.0 4.59e-01 87.5% 78.6%
1sumB01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.59 48.0 4.64e-01 86.5% 86.9%
3pe0A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 47.0 4.57e-01 86.5% 87.7%
1q6aA00 1.10.1240.30 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain 0.58 49.0 4.80e-01 94.8% 85.0%
1t72A02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.58 47.0 4.68e-01 86.5% 89.8%
3edvB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 46.0 4.15e-01 86.5% 69.9%
4kb2A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.58 46.0 4.43e-01 85.4% 89.9%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.58 45.0 4.32e-01 83.3% 86.5%
6wk3A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.58 48.0 4.24e-01 93.8% 76.6%
2c5iT00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 46.0 4.66e-01 86.5% 92.6%
2a3qA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.57 41.0 3.95e-01 75.0% 74.3%
4l8iB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.57 46.0 4.37e-01 86.5% 90.2%
3i5xA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 49.0 3.67e-01 97.9% 80.8%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.57 45.0 4.21e-01 85.4% 88.9%
3craA02 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.56 44.0 4.05e-01 97.9% 64.1%
3fhnA04 1.20.58.670 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain D 0.55 45.0 4.11e-01 90.6% 84.7%
3bt5A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 44.0 3.83e-01 87.5% 91.4%
2clbA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.54 44.0 3.71e-01 86.5% 85.5%
1s2xA00 1.20.190.30 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › CAG pathogenicity island protein, CagZ 0.54 46.0 3.84e-01 97.9% 89.4%
1cg5B00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.53 44.0 4.03e-01 96.9% 85.8%
1jmwA00 1.20.120.30 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Aspartate receptor, ligand-binding domain 0.53 43.0 3.75e-01 87.5% 63.7%
5nl6A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 43.0 4.14e-01 87.5% 83.3%
3wirA02 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.53 46.0 3.13e-01 100.0% 32.9%
2mabA00 1.10.10.1350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain 0.52 38.0 3.65e-01 79.2% 66.1%
1vw4T01 6.10.330.20 Special › Helix non-globular › Monooxygenase › 0.52 42.0 4.04e-01 90.6% 80.4%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.52 47.0 4.45e-01 100.0% 89.5%
6diiL01 3.90.1300.10 Alpha Beta › Alpha-Beta Complex › Amidase signature (AS) enzymes › Amidase signature (AS) domain 0.52 42.0 2.77e-01 91.7% 31.0%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4890819 3574.1.1.1 alpha complex topology › Nucleocapsid protein › Nucleocapsid protein › Nucleocapsid protein › Nairo_nucleo 0.88 83.0 5.13e-01 100.0% 20.5%
3233929 5050.1.1.0 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.69 51.0 3.79e-01 78.1% 31.7%
3289801 5050.1.1.9 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.68 51.0 3.90e-01 78.1% 35.7%
3970886 5050.1.1.9 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.68 49.0 3.83e-01 78.1% 35.6%
3232181 109.4.1.891 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_HEATR1 0.64 58.0 4.25e-01 100.0% 44.3%
4652720 150.3.1.28 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › GCSF 0.64 45.0 3.69e-01 72.9% 64.0%
4947815 6155.1.1.0 alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.63 54.0 5.36e-01 94.8% 92.0%
4969464 604.5.1.0 alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.62 48.0 4.98e-01 87.5% 87.8%
3489722 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.62 50.0 4.85e-01 86.5% 89.5%
3613756 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.61 52.0 3.56e-01 90.6% 68.4%
3476443 109.3.1.229 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › PF27576 0.61 55.0 4.85e-01 100.0% 74.3%
3564106 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.61 49.0 4.77e-01 86.5% 89.5%
4024356 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.60 48.0 4.07e-01 86.5% 81.9%
3841680 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.60 48.0 4.37e-01 86.5% 72.3%
1036846 310.2.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.60 48.0 4.45e-01 85.4% 83.3%
3841673 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.59 48.0 4.76e-01 87.5% 95.0%
3750020 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.59 48.0 4.67e-01 86.5% 90.5%
3749998 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.59 48.0 4.43e-01 86.5% 78.3%
3909893 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.59 48.0 4.20e-01 86.5% 70.7%
3918068 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.59 47.0 4.45e-01 86.5% 83.5%
3583440 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.58 47.0 4.37e-01 87.5% 77.5%
3593068 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 47.0 3.80e-01 92.7% 83.5%
3287859 106.1.1.11 alpha arrays › Globin-like › Globin-like › Globin-like › RsbRD_N 0.57 50.0 4.71e-01 97.9% 85.2%
3768819 109.4.1.43 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SAC3_GANP 0.56 51.0 4.10e-01 100.0% 58.4%
3875883 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.56 45.0 3.09e-01 86.5% 26.7%
3482689 603.2.1.0 alpha bundles › STAT-like › STAT › STAT 0.56 49.0 4.20e-01 100.0% 70.0%
5013099 601.3.1.0 alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.56 47.0 4.21e-01 91.7% 98.5%
4363614 601.25.1.1 alpha bundles › Four-helical up-and-down bundle › TrmE connector domain › TrmE connector domain › MnmE_helical 0.55 43.0 3.61e-01 84.4% 64.8%
3236092 101.11.1.0 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 0.54 38.0 4.12e-01 74.0% 91.3%
3993403 616.1.1.26 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › NPP-6_helical 0.54 47.0 4.06e-01 100.0% 96.2%
3233462 174.1.1.0 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.54 48.0 4.30e-01 95.8% 84.4%
3607465 603.2.1.0 alpha bundles › STAT-like › STAT › STAT 0.53 46.0 3.69e-01 100.0% 74.8%
3386863 192.29.1.104 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › DUF4149 0.53 44.0 3.74e-01 89.6% 85.8%
3762118 633.21.1.23 alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CD20 0.52 47.0 3.92e-01 99.0% 81.8%
3705915 3615.1.1.0 alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain 0.51 47.0 4.34e-01 100.0% 82.5%
3991109 633.21.1.0 alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.51 45.0 4.02e-01 100.0% 80.7%
5047661 633.21.1.0 alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.50 45.0 4.08e-01 100.0% 96.9%
D2 medium residues 16-83
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02477.21 best Nairo_nucleo 30.7 2.10e-07 100.0% 13.1%
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.62 47.0 4.17e-01 82.4% 93.1%
3g80A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.59 45.0 4.47e-01 83.8% 80.8%
4h63H01 1.20.58.1710 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 44.0 4.41e-01 85.3% 88.9%
1x0tA01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.57 41.0 4.29e-01 77.9% 88.5%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.55 44.0 4.33e-01 94.1% 90.9%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 44.0 3.94e-01 94.1% 66.7%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.53 41.0 4.22e-01 88.2% 98.4%
3t98B00 6.10.140.1350 Special › Helix non-globular › Helix Hairpins › 0.52 41.0 3.92e-01 89.7% 75.6%
1bhaA00 1.10.287.170 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 42.0 4.26e-01 94.1% 95.5%
4rg8A04 1.10.287.1240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 40.0 4.13e-01 88.2% 98.4%
1b06A01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.51 39.0 3.96e-01 88.2% 100.0%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3993051 7023.1.1.0 alpha bundles › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein 0.66 46.0 3.95e-01 73.5% 93.6%
4026047 310.2.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.62 43.0 4.06e-01 73.5% 83.5%
3952598 150.7.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PE › PE 0.56 45.0 4.18e-01 94.1% 75.6%
3465927 622.4.1.0 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.54 41.0 3.99e-01 86.8% 78.8%
4612826 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.53 44.0 4.30e-01 98.5% 88.7%
3456370 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.53 42.0 3.36e-01 92.6% 45.2%
3781183 3922.1.1.0 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.52 42.0 3.82e-01 94.1% 64.0%
3594730 192.15.1.0 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.50 40.0 3.85e-01 92.6% 79.8%
D3 medium residues 84-136
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02477.21 best Nairo_nucleo 53.1 3.40e-14 100.0% 11.7%
D4 medium residues 137-186_400-483
PDB
D5 medium residues 297-399
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02477.21 best Nairo_nucleo 98.9 4.40e-28 100.0% 23.0%