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AL2

Euk-Vir

Tomato_bright_yellow_mottle_virus

AL2__YP_009506519__Tomato_bright_yellow_mottle_virus__858512

Identity

Accession:
YP_009506519 ↗
Protein ID:
AL2
Kingdom:
euk

Quality

64.3 mean pLDDT

Taxonomy

Shotokuvirae› Cressdnaviricota› Repensiviricetes› Geplafuvirales› Geminiviridae› Begomovirus› Tomato_bright_yellow_mottle_virus

TaxID: 858512

Cluster

Singleton — not in a non-trivial cluster

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 73-147
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01407.22 best Gemini_AL3 82.5 3.00e-23 100.0% 62.2%
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1so7A00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.68 49.0 3.17e-01 81.3% 16.1%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.66 51.0 3.62e-01 85.3% 39.3%
3bf2A00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.65 56.0 4.81e-01 100.0% 67.2%
2kx2A00 3.30.780.30 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › 0.65 54.0 5.03e-01 93.3% 95.8%
2hqlA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.65 49.0 4.57e-01 82.7% 65.9%
3mg1B02 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.65 41.0 3.42e-01 74.7% 38.4%
2n8xA00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.64 56.0 4.35e-01 100.0% 58.4%
5hp6A01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.63 48.0 3.17e-01 92.0% 18.5%
3g16B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.63 41.0 3.29e-01 80.0% 32.9%
2f1eA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.61 54.0 4.69e-01 98.7% 85.3%
1jz7A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 53.0 4.63e-01 98.7% 88.7%
3pg6B00 3.30.390.130 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.60 53.0 4.40e-01 100.0% 58.2%
2c4iA01 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.59 50.0 4.41e-01 97.3% 75.4%
5i97C00 3.10.450.230 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › VirB8 protein 0.59 45.0 3.66e-01 80.0% 50.4%
1st8A01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.59 44.0 2.88e-01 80.0% 18.0%
2hj1A00 3.10.20.280 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RnfH-like 0.59 35.0 3.51e-01 73.3% 55.8%
6w1kA01 3.10.180.50 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 0.58 48.0 3.30e-01 96.0% 72.4%
2lf2A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.57 49.0 3.83e-01 98.7% 94.9%
3er7B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.57 38.0 3.29e-01 80.0% 42.3%
5cxoB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.55 39.0 3.27e-01 80.0% 41.8%
6yfiB01 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.55 47.0 3.94e-01 100.0% 97.8%
3t1oA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 45.0 3.49e-01 98.7% 82.8%
5xb6A01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 44.0 3.27e-01 98.7% 32.6%
3e8tA00 3.15.10.30 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › TULIP domain 0.54 43.0 3.04e-01 84.0% 64.8%
3qcpA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.54 43.0 3.43e-01 92.0% 67.3%
5aj3Q00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 40.0 3.61e-01 81.3% 67.0%
2vgmA01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.53 36.0 3.11e-01 76.0% 43.4%
3iuzA00 3.10.180.50 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 0.53 44.0 3.01e-01 97.3% 91.6%
4h5iB00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 41.0 2.73e-01 86.7% 24.1%
3grdA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 43.0 3.57e-01 100.0% 50.0%
4pqxA02 2.60.40.2370 Mainly Beta › Sandwich › Immunoglobulin-like › NigD-like, C-terminal beta sandwich domain 0.53 44.0 3.70e-01 92.0% 74.2%
7z0sF01 3.30.70.3270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 36.0 2.91e-01 73.3% 62.7%
2veoA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 45.0 2.99e-01 97.3% 24.9%
2fgeA01 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.52 44.0 3.13e-01 98.7% 96.8%
3eniC00 2.50.10.10 Mainly Beta › Clam › Bacteriochlorophyll-a Protein › Bacteriochlorophyll A 0.52 41.0 2.81e-01 94.7% 96.3%
2y7bA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 39.0 3.29e-01 82.7% 52.2%
4owzA00 3.10.130.10 Alpha Beta › Roll › P-30 Protein › Ribonuclease A-like domain 0.52 38.0 3.19e-01 80.0% 71.6%
4mt4A00 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.51 45.0 2.75e-01 97.3% 54.7%
2rckA01 3.15.10.30 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › TULIP domain 0.51 37.0 2.76e-01 80.0% 64.7%
1s5aB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 41.0 3.34e-01 100.0% 46.9%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3503101 243.1.1.49 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF2358 0.69 50.0 3.83e-01 74.7% 45.2%
4205167 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.69 59.0 4.82e-01 97.3% 95.9%
3252596 719.2.1.1 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like › GBBH-like_N 0.67 51.0 4.21e-01 80.0% 85.4%
3761115 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.67 51.0 3.14e-01 80.0% 22.8%
5040130 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.66 55.0 5.17e-01 98.7% 75.6%
3614755 305.1.1.1 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.66 54.0 4.10e-01 89.3% 92.0%
4001627 243.1.1.49 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF2358 0.66 50.0 3.78e-01 80.0% 40.6%
3387903 11.1.1.449 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF2393 0.65 55.0 4.98e-01 90.7% 100.0%
3965322 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.65 54.0 4.96e-01 89.3% 75.8%
4017244 3385.1.1.2 ↗ beta barrels › Allergen Alt a 1 › Allergen Alt a 1 › Allergen Alt a 1 › PF27986 0.65 55.0 4.61e-01 93.3% 79.2%
3582508 330.16.1.2 ↗ a+b two layers › dsRBD-like › ODA16 N-terminal domain › ODA16 N-terminal domain › KAP 0.64 49.0 4.37e-01 81.3% 67.6%
5052639 3435.1.1.0 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC 0.64 48.0 3.34e-01 78.7% 31.3%
3334910 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 43.0 3.68e-01 70.7% 50.4%
3223396 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 43.0 3.73e-01 70.7% 49.6%
3249097 5.1.4.16 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CPSF_A 0.63 45.0 2.89e-01 76.0% 20.5%
3249225 223.2.1.6 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › uDENN 0.63 53.0 4.23e-01 97.3% 47.5%
5076783 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.62 47.0 4.23e-01 92.0% 58.1%
3201142 223.2.1.25 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Avl9 0.62 53.0 4.68e-01 98.7% 71.3%
3839282 11.1.1.449 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF2393 0.62 51.0 4.69e-01 90.7% 100.0%
3221640 243.1.1.49 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF2358 0.61 44.0 3.56e-01 74.7% 51.4%
3380843 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.61 53.0 4.18e-01 98.7% 69.7%
4529976 4263.2.1.0 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain 0.61 44.0 4.20e-01 74.7% 74.1%
5049631 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.60 50.0 4.14e-01 93.3% 50.7%
4864643 5.1.13.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › Propeller domain of DCAF15 › DCAF15_WD40 0.60 52.0 3.91e-01 97.3% 42.4%
3260205 12.3.1.3 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Aldose_epim 0.60 48.0 3.11e-01 85.3% 27.2%
4963509 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 51.0 4.63e-01 93.3% 85.0%
3502357 11.1.1.905 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_ILCR1 0.59 53.0 4.50e-01 98.7% 80.0%
3168414 4099.1.1.46 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › PF30283 0.59 54.0 4.52e-01 100.0% 68.8%
3731945 3385.1.1.0 ↗ beta barrels › Allergen Alt a 1 › Allergen Alt a 1 › Allergen Alt a 1 0.59 46.0 3.77e-01 85.3% 73.2%
5054443 304.109.1.4 ↗ a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e › Ribosomal_S24e 0.58 46.0 4.14e-01 84.0% 93.0%
3998954 223.2.1.37 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › C9orf72-like 0.58 49.0 4.20e-01 100.0% 60.0%
3559721 331.3.1.6 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PRELI 0.57 49.0 3.66e-01 93.3% 74.6%
3415184 5090.1.1.0 ↗ beta complex topology › Viral glycoprotein, central and dimerisation domains-like › Viral glycoprotein, central and dimerisation domains › Viral glycoprotein, central and dimerisation domains 0.57 50.0 3.46e-01 100.0% 74.9%
3614657 5.1.5.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.57 48.0 2.93e-01 94.7% 28.7%
3738837 10.13.1.1 ↗ beta sandwiches › jelly-roll › Calcium ATPase, transduction domain A › Calcium ATPase, transduction domain A › E1-E2_ATPase 0.57 41.0 3.08e-01 77.3% 74.5%
3181589 331.3.1.6 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PRELI 0.56 49.0 3.38e-01 93.3% 74.9%
3942981 2484.1.1.269 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1_4 0.55 48.0 3.12e-01 98.7% 71.6%
3478508 331.3.1.6 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PRELI 0.55 47.0 3.62e-01 93.3% 67.1%
3931232 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 42.0 3.62e-01 82.7% 64.8%
3405436 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 43.0 3.81e-01 96.0% 57.4%
3624550 6043.1.1.4 ↗ a+b two layers › yfeY-like › yfeY-like › yfeY-like › PHAF1 0.55 42.0 3.35e-01 82.7% 42.7%
4353272 2003.1.2.21 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Trp_halogenase 0.54 43.0 2.62e-01 90.7% 67.5%
3270444 331.3.1.6 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PRELI 0.54 47.0 3.55e-01 96.0% 66.7%
3663259 881.1.1.1 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PsbP 0.53 40.0 3.45e-01 100.0% 47.4%
3998371 883.1.1.2 ↗ a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like › LBP_BPI_CETP_C 0.53 39.0 2.92e-01 80.0% 35.5%
3960415 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.53 47.0 4.00e-01 98.7% 70.0%
5044559 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.53 41.0 4.04e-01 85.3% 80.0%
3968999 5085.1.1.1 ↗ a+b duplicates or obligate multimers › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › OEP 0.53 45.0 2.81e-01 97.3% 57.5%
3591439 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.53 43.0 2.81e-01 90.7% 20.9%
4023996 331.3.1.6 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PRELI 0.52 45.0 3.47e-01 98.7% 64.4%
3960045 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.51 45.0 4.27e-01 100.0% 97.8%
4022036 243.1.1.87 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › NTF2_SigF 0.50 44.0 3.30e-01 100.0% 38.8%