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NIa

Euk-Vir

Squash_vein_yellowing_virus

NIa__YP_001788999__Squash_vein_yellowing_virus__397544

Identity

Accession:
YP_001788999 ↗
Protein ID:
NIa
Kingdom:
euk

Quality

82.8 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Stelpaviricetes› Patatavirales› Potyviridae› Ipomovirus› Squash_vein_yellowing_virus

TaxID: 397544

Cluster

View cluster (187 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 1-95
PDB
Domain cluster: rep: NIa-VPg-Pro_protein__YP_002956094__Triticum_mosaic_virus__431317__D201-288_375-394
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00863.26 best Peptidase_C4 41.4 1.40e-10 92.6% 27.5%
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1lvmA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.90 72.0 6.89e-01 83.2% 76.4%
2w5eA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.82 55.0 6.54e-01 80.0% 100.0%
5fcrC02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.77 60.0 5.80e-01 82.1% 89.7%
2z9iC01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.77 66.0 6.69e-01 91.6% 97.8%
8e7cA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.77 58.0 6.29e-01 78.9% 100.0%
2r0lA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.77 60.0 5.68e-01 83.2% 88.5%
1p3cA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.74 60.0 5.71e-01 86.3% 88.2%
2zu2A01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.74 63.0 6.31e-01 91.6% 92.9%
1eq9A02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.73 56.0 5.49e-01 82.1% 88.6%
2aiqA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.72 60.0 5.68e-01 89.5% 85.0%
2ynaA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.71 56.0 5.85e-01 84.2% 100.0%
2o8mB01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.71 47.0 5.42e-01 84.2% 97.0%
4b6eB01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.67 50.0 3.90e-01 78.9% 37.1%
1smrA02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.66 54.0 4.59e-01 88.4% 85.8%
3kyfA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.66 51.0 4.80e-01 82.1% 78.9%
2as9A02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.66 59.0 6.00e-01 96.8% 100.0%
1miqA02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.66 53.0 4.58e-01 88.4% 87.5%
5n70A02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.65 53.0 4.48e-01 88.4% 86.3%
1wruA01 2.30.300.10 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Baseplate protein-like domain - beta roll fold 0.63 49.0 4.08e-01 85.3% 90.9%
2a2jA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.62 51.0 4.06e-01 91.6% 85.2%
1uh9A02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.62 54.0 4.66e-01 96.8% 88.6%
1g7sA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.62 43.0 4.19e-01 73.7% 78.7%
5brrE01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.61 45.0 4.03e-01 77.9% 84.3%
2hcjB02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.61 42.0 4.30e-01 72.6% 81.9%
3cddA01 2.30.300.10 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Baseplate protein-like domain - beta roll fold 0.60 47.0 3.84e-01 86.3% 90.2%
1mppA02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.59 49.0 4.15e-01 95.8% 82.9%
1dpjA02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.59 50.0 4.37e-01 96.8% 87.0%
4fxtA01 2.60.40.1120 Mainly Beta › Sandwich › Immunoglobulin-like › Carboxypeptidase-like, regulatory domain 0.58 40.0 4.15e-01 82.1% 79.1%
3d37B01 2.30.300.10 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Baseplate protein-like domain - beta roll fold 0.56 47.0 3.92e-01 94.7% 90.8%
3su0A01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.55 50.0 4.72e-01 98.9% 88.4%
4x8iA02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.55 38.0 3.99e-01 71.6% 85.9%
7l15A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 37.0 3.53e-01 70.5% 99.1%
4pbdA00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 37.0 3.67e-01 72.6% 84.3%
1yjdC00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.50e-01 74.7% 99.2%
6lebA02 2.60.40.1290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 40.0 3.58e-01 84.2% 95.7%
2woyA02 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 40.0 3.45e-01 85.3% 93.7%
1wh0A01 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 36.0 3.50e-01 73.7% 90.1%
2k8qA00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 38.0 3.41e-01 80.0% 67.9%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
257 1.1.5.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Peptidase_C4 0.90 79.0 5.83e-01 92.6% 41.6%
3284072 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.78 68.0 4.98e-01 93.7% 40.2%
134018 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.77 61.0 5.07e-01 92.6% 49.4%
4221728 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.76 65.0 4.79e-01 96.8% 37.4%
3284172 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.76 65.0 4.94e-01 93.7% 42.0%
1099000 1.1.5.19 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Peptidase_C30 0.75 65.0 5.10e-01 92.6% 49.2%
4852372 1.1.5.19 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Peptidase_C30 0.74 64.0 4.99e-01 92.6% 49.2%
3415364 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.73 65.0 4.71e-01 94.7% 47.3%
3909175 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.73 65.0 4.53e-01 95.8% 42.5%
3404225 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.72 60.0 4.63e-01 90.5% 42.9%
3860909 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.71 64.0 4.68e-01 96.8% 43.8%
3545090 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.71 62.0 4.68e-01 94.7% 40.5%
3500586 1.1.5.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin 0.71 62.0 4.47e-01 93.7% 79.6%
3388883 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.70 62.0 4.54e-01 94.7% 80.0%
3552125 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.69 61.0 4.49e-01 96.8% 42.6%
4587424 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.67 60.0 4.55e-01 96.8% 45.5%
3522295 1.1.1.2 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp,A1_Propeptide 0.66 53.0 3.56e-01 88.4% 35.1%
3412933 1.1.1.28 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp, TAXi_C, TAXi_N 0.63 55.0 3.68e-01 96.8% 34.9%
4988102 1.1.13.47 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Dit_like 0.62 46.0 4.44e-01 78.9% 100.0%
2125379 1.1.1.1 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.62 53.0 4.62e-01 96.8% 88.8%
3619310 1.1.1.27 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp, TAXi_N 0.62 53.0 3.59e-01 96.8% 36.5%
1322884 1.1.1.1 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.61 53.0 3.98e-01 96.8% 57.2%
3471292 1.1.1.38 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp, A1_Propeptide, TAXi_C 0.61 53.0 3.58e-01 96.8% 36.8%
3879529 1.1.1.1 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.61 53.0 3.57e-01 96.8% 37.1%
3218850 1.1.1.27 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp, TAXi_N 0.61 53.0 3.51e-01 96.8% 34.1%
3468289 1.1.1.20 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › TAXi_C+TAXi_N 0.60 51.0 3.56e-01 95.8% 46.5%
2723108 1.1.1.27 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp, TAXi_N 0.60 51.0 3.54e-01 96.8% 42.3%
None — 0.59 48.0 3.40e-01 90.5% 73.9%
5037092 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.57 35.0 3.93e-01 76.8% 81.4%
5000763 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 41.0 4.18e-01 74.7% 85.6%
3218584 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 40.0 4.36e-01 75.8% 100.0%
3995220 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 45.0 3.81e-01 87.4% 95.0%
3181118 1.1.1.1 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.56 48.0 3.39e-01 100.0% 64.6%
4678749 306.1.1.0 ↗ a+b two layers › Glucose permease domain IIB-like › Glucose permease domain IIB › Glucose permease domain IIB 0.56 36.0 4.11e-01 78.9% 95.4%
4506558 1.1.1.1 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.55 48.0 3.25e-01 100.0% 68.4%
2475124 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.55 43.0 4.40e-01 86.3% 100.0%
3501491 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.55 45.0 4.10e-01 92.6% 80.0%
184486 1.1.13.26 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › GpP-like_1st 0.54 42.0 4.53e-01 85.3% 100.0%
3846973 11.1.1.3 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ig 0.52 36.0 3.60e-01 73.7% 100.0%
4316618 12.3.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich 0.51 41.0 2.91e-01 91.6% 85.9%
D2 medium residues 96-195
PDB
Domain cluster: rep: ORF1a__YP_009047079__Human_astrovirus_BF34__1518575__D522-618
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00863.26 best Peptidase_C4 44.2 2.00e-11 100.0% 38.1%
PF00548.27 Peptidase_C3 22.4 1.50e-04 67.0% 28.9%