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HC-Pro

Euk-Vir

Shallot_yellow_stripe_virus

HC-Pro__YP_331415__Shallot_yellow_stripe_virus__62059

Identity

Accession:
YP_331415 ↗
Protein ID:
HC-Pro
Kingdom:
euk

Quality

85.0 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Stelpaviricetes› Patatavirales› Potyviridae› Potyvirus› Shallot_yellow_stripe_virus

TaxID: 62059

Cluster

View cluster (80 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 194-458
PDB
Domain cluster: rep: HC-Pro__YP_851200__Blackberry_virus_Y__323118__D78-324
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00851.25 best Peptidase_C6 283.9 3.50e-84 99.6% 60.0%
D2 medium residues 30-100
PDB
Domain cluster: representative
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u00A02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.65 44.0 3.96e-01 91.5% 51.0%
5f42A02 1.20.1180.10 Mainly Alpha › Up-down Bundle › Udp N-acetylglucosamine O-acyltransferase; Domain 2 › Udp N-acetylglucosamine O-acyltransferase, C-terminal domain 0.65 42.0 4.08e-01 100.0% 58.5%
3t57A02 1.20.1180.10 Mainly Alpha › Up-down Bundle › Udp N-acetylglucosamine O-acyltransferase; Domain 2 › Udp N-acetylglucosamine O-acyltransferase, C-terminal domain 0.61 45.0 4.46e-01 100.0% 76.0%
4nqwB00 1.10.10.1320 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Anti-sigma factor, zinc-finger domain 0.59 35.0 3.54e-01 90.1% 57.5%
3beyD00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.59 36.0 3.27e-01 97.2% 45.7%
2i7aA00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.58 36.0 2.87e-01 70.4% 28.0%
4iw9A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.58 50.0 4.36e-01 100.0% 82.3%
4gmqA00 1.10.8.840 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ribosome-associated complex head domain 0.57 37.0 3.43e-01 80.3% 50.0%
2wh5A00 1.20.80.10 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.56 47.0 4.30e-01 88.7% 73.3%
1e6bA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 44.0 3.88e-01 100.0% 57.7%
3ebbA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.55 42.0 2.88e-01 100.0% 22.3%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.54 43.0 4.14e-01 87.3% 76.2%
3di2A00 1.20.1250.50 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.54 43.0 3.68e-01 87.3% 61.7%
1hbkA00 1.20.80.10 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.53 47.0 4.32e-01 95.8% 77.5%
1w36C06 1.10.10.990 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.51 36.0 3.60e-01 98.6% 72.2%
1zc6A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 42.0 3.42e-01 98.6% 84.0%
2k85A00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.51 36.0 3.76e-01 95.8% 83.1%
4dgsA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 40.0 3.18e-01 94.4% 40.6%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5044998 2006.1.4.25 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_I 0.64 47.0 3.37e-01 100.0% 27.3%
3500235 621.1.1.0 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain 0.59 44.0 4.30e-01 98.6% 73.8%
3941457 1203.1.2.3 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 › YiaAB 0.59 53.0 4.46e-01 100.0% 65.8%
3323493 170.1.1.15 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Retrotran_gag_2 0.58 38.0 3.26e-01 94.4% 40.0%
3879363 621.1.1.2 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Smg8_Smg9 0.58 43.0 4.30e-01 98.6% 78.7%
4029625 197.1.1.3 ↗ alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › ACBP 0.57 47.0 4.10e-01 88.7% 64.8%
5059007 5059.1.1.0 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter 0.57 50.0 4.24e-01 97.2% 67.8%
4998576 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.57 47.0 4.70e-01 95.8% 100.0%
5022605 3352.1.1.8 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › PTPS_related 0.57 45.0 3.06e-01 91.5% 22.7%
4541653 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.57 44.0 4.09e-01 87.3% 89.5%
3861711 633.10.1.41 ↗ alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like › TMD0_ABC 0.56 45.0 3.40e-01 85.9% 37.6%
3229540 197.1.1.0 ↗ alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like 0.56 46.0 4.37e-01 88.7% 78.8%
3350513 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.56 44.0 3.05e-01 87.3% 30.2%
3481110 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.55 48.0 4.40e-01 100.0% 89.5%
4015729 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.55 43.0 3.64e-01 87.3% 83.2%
4351483 192.7.1.3 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Phe_tRNA-synt_N 0.55 46.0 4.10e-01 97.2% 69.5%
3281023 628.1.1.1 ↗ alpha bundles › Fatty acid responsive transcription factor FadR, C-terminal domain › Fatty acid responsive transcription factor FadR, C-terminal domain › Fatty acid responsive transcription factor FadR, C-terminal domain › FCD 0.54 49.0 3.78e-01 100.0% 72.0%
3643885 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.53 37.0 3.74e-01 97.2% 74.3%
3597736 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.53 40.0 3.77e-01 84.5% 67.1%
3452220 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.53 47.0 2.83e-01 100.0% 22.7%
3683976 197.1.1.3 ↗ alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › ACBP 0.53 48.0 3.81e-01 98.6% 70.4%
3619922 197.1.1.3 ↗ alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › ACBP 0.52 42.0 3.74e-01 97.2% 81.7%
4039771 191.1.1.42 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_41 0.52 43.0 3.71e-01 97.2% 60.8%
3785892 4964.1.1.2 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › RNA_pol 0.52 41.0 2.92e-01 91.5% 52.7%
3785170 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.51 35.0 3.90e-01 100.0% 92.7%
4024470 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.50 39.0 3.10e-01 85.9% 94.2%
3869754 109.16.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › TROVE domain-like › TROVE domain-like › TROVE 0.50 41.0 2.64e-01 94.4% 25.6%
4026731 197.1.1.3 ↗ alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › ACBP 0.50 44.0 4.03e-01 97.2% 76.8%
D3 medium residues 133-186
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3f2bA08 1.10.150.870 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.86 58.0 4.23e-01 70.4% 27.7%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.84 65.0 6.08e-01 83.3% 69.2%
2wyhB04 1.20.1270.50 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Glycoside hydrolase family 38, central domain 0.82 65.0 5.23e-01 85.2% 45.5%
4a17U01 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.81 64.0 5.66e-01 85.2% 79.2%
7rkxR01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.79 61.0 3.88e-01 85.2% 17.7%
6f1eA01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.78 52.0 3.76e-01 74.1% 26.6%
4kzsA02 6.10.140.1870 Special › Helix non-globular › Helix Hairpins › 0.76 55.0 5.05e-01 77.8% 61.4%
2qqyA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.76 57.0 4.17e-01 79.6% 87.7%
3bujA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.75 60.0 3.54e-01 96.3% 11.8%
3k3oA02 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 53.0 4.58e-01 75.9% 59.5%
4rm7A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.74 60.0 4.49e-01 90.7% 44.6%
3n5lA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 55.0 5.43e-01 83.3% 78.9%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 59.0 5.45e-01 92.6% 70.4%
4gltA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.72 55.0 4.24e-01 81.5% 82.5%
1ku9A02 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 54.0 5.16e-01 85.2% 70.3%
4fzsA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.69 54.0 3.66e-01 87.0% 23.0%
4dciA00 6.10.140.1110 Special › Helix non-globular › Helix Hairpins › 0.69 55.0 4.07e-01 90.7% 49.7%
3vprA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.68 53.0 3.95e-01 87.0% 53.8%
2kp8A00 1.20.5.170 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.68 53.0 4.91e-01 87.0% 73.6%
1vt0k00 1.10.3230.20 Mainly Alpha › Orthogonal Bundle › Hypothetical protein yqbg › P22 tail accessory factor (Gp4) 0.68 50.0 3.74e-01 81.5% 31.7%
3lcnB00 1.10.340.40 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain 0.67 45.0 3.74e-01 70.4% 72.2%
2lpeA01 6.10.140.1120 Special › Helix non-globular › Helix Hairpins › 0.67 56.0 5.02e-01 96.3% 66.7%
2ctqA01 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.66 47.0 3.93e-01 75.9% 57.4%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.66 52.0 4.61e-01 87.0% 67.9%
2crbA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.65 53.0 4.50e-01 96.3% 75.3%
8gj8A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.63 48.0 3.10e-01 81.5% 35.2%
2iexA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.61 41.0 4.24e-01 74.1% 76.5%
2ouwB00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.59 46.0 3.55e-01 90.7% 44.1%
5cqgA03 1.10.10.2210 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.51 39.0 3.56e-01 88.9% 79.7%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5056849 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.89 72.0 6.54e-01 87.0% 68.6%
2665702 3146.1.1.3 ↗ a+b complex topology › gH main domain › gH main domain › gH main domain › Phage_glycop_gL 0.87 63.0 4.78e-01 92.6% 35.7%
4075864 192.6.1.0 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.82 61.0 6.09e-01 85.2% 78.2%
4883777 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 0.81 64.0 6.09e-01 87.0% 74.2%
4507542 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.78 60.0 5.11e-01 87.0% 51.1%
3368388 4984.1.1.0 ↗ alpha bundles › Duffy-binding-like domain, C-terminal subdomain › Duffy-binding-like domain, C-terminal subdomain › Duffy-binding-like domain, C-terminal subdomain 0.77 66.0 5.16e-01 100.0% 45.2%
4089826 622.1.1.33 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › T3SS_needle_F 0.76 59.0 5.10e-01 87.0% 54.1%
3277002 3252.1.1.0 ↗ alpha arrays › SHQ1 C-terminal domain-like › SHQ1 C-terminal domain › SHQ1 C-terminal domain 0.75 60.0 3.90e-01 88.9% 63.7%
3629808 3291.1.1.130 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › CHDCT2 0.74 58.0 4.88e-01 92.6% 51.1%
3929573 192.8.1.395 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › CHDCT2 0.74 56.0 4.90e-01 87.0% 54.1%
3927348 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.74 61.0 4.30e-01 100.0% 28.6%
4315986 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.73 58.0 4.93e-01 98.1% 53.3%
3810544 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.72 59.0 4.44e-01 98.1% 37.0%
3699813 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.71 60.0 3.65e-01 100.0% 41.8%
3693258 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.70 60.0 4.82e-01 100.0% 70.9%
5057549 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.70 58.0 4.48e-01 92.6% 47.5%
3180119 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.69 57.0 5.09e-01 100.0% 65.9%
3610620 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.69 53.0 4.19e-01 88.9% 40.0%
3231045 101.1.1.117 ↗ alpha arrays › HTH › HTH › Three-helical HTH › CHDCT2 0.67 58.0 4.75e-01 100.0% 61.9%
3609215 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.65 47.0 4.29e-01 100.0% 56.2%
3483986 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.64 52.0 4.49e-01 98.1% 61.1%