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NC_009543.1__YP_001285718.1__XPphiXo411_gp52__00049

Bact-Vir

NC_009543.1__YP_001285718.1__XPphiXo411_gp52__00049

Identity

Accession:
NC_009543 ↗
Kingdom:
phage

Quality

87.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Xipdecavirus› Xanthomonas_phage_Xop411

TaxID: 2913975

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 2-47
PDB
Domain cluster: representative
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1a7gE00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.72 60.0 5.09e-01 100.0% 95.1%
3mpcA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.70 56.0 4.53e-01 100.0% 44.8%
2bopA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.69 58.0 4.87e-01 100.0% 95.3%
2nydA02 2.20.28.300 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.67 44.0 4.63e-01 100.0% 78.0%
2xzmJ00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.65 52.0 4.20e-01 100.0% 95.2%
2h6uA00 2.60.40.180 Mainly Beta › Sandwich › Immunoglobulin-like › Transthyretin/hydroxyisourate hydrolase domain 0.64 53.0 4.12e-01 100.0% 41.2%
2oa2A01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.63 45.0 3.49e-01 100.0% 31.4%
1o51A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 51.0 4.31e-01 100.0% 93.3%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.62 51.0 4.67e-01 100.0% 69.7%
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.62 48.0 4.82e-01 100.0% 92.0%
5xoyB02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 50.0 3.97e-01 100.0% 97.2%
6tmfM00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.61 50.0 4.02e-01 100.0% 97.1%
6n3dA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.60 49.0 4.14e-01 97.8% 100.0%
5yl1A01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.60 51.0 3.47e-01 100.0% 42.5%
5mmjj00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.59 48.0 3.91e-01 97.8% 99.0%
2m83A00 2.60.40.2440 Mainly Beta › Sandwich › Immunoglobulin-like › Carbohydrate binding type-21 domain 0.59 48.0 3.59e-01 100.0% 41.0%
3kg5A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 48.0 3.85e-01 100.0% 51.5%
2vvfA01 2.60.120.730 Mainly Beta › Sandwich › Jelly Rolls › 0.58 49.0 3.56e-01 100.0% 52.5%
7zxkB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 44.0 3.96e-01 100.0% 59.5%
3fo8D02 2.40.10.380 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.56 47.0 3.88e-01 100.0% 70.3%
1w99A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 44.0 3.06e-01 100.0% 34.6%
1yk9A00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.54 43.0 3.00e-01 100.0% 57.1%
3d3bJ00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.53 43.0 3.69e-01 100.0% 89.7%
3bn6A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 42.0 3.07e-01 100.0% 100.0%
4p04A01 2.60.40.3100 Mainly Beta › Sandwich › Immunoglobulin-like › Arylsulphate sulphotransferase monomer, N-terminal domain 0.52 43.0 3.39e-01 100.0% 46.2%
4ekuA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 44.0 3.34e-01 100.0% 40.2%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3698302 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.71 54.0 5.12e-01 100.0% 69.1%
4964337 3115.5.1.1 ↗ a+b two layers › GP2-like › phenylacetate-CoA oxygenase subunit PaaB › phenylacetate-CoA oxygenase subunit PaaB › PaaB 0.69 57.0 5.51e-01 100.0% 87.3%
3483496 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.66 48.0 4.91e-01 100.0% 82.2%
3269973 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.63 52.0 4.29e-01 100.0% 97.9%
5048876 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.63 46.0 4.30e-01 100.0% 61.5%
3479367 822.1.1.1 ↗ a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF 0.62 49.0 4.51e-01 100.0% 67.2%
3494105 221.1.1.64 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Formin_GBD_N 0.60 49.0 4.19e-01 100.0% 55.0%
3608046 11.1.1.1317 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C, Rgp1 0.60 49.0 3.51e-01 100.0% 63.1%
5038686 10.2.1.0 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.57 47.0 3.67e-01 100.0% 70.4%
3952771 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 47.0 3.71e-01 100.0% 63.8%
3594101 301.1.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like 0.55 43.0 3.16e-01 100.0% 29.0%
4648475 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.54 45.0 4.24e-01 100.0% 93.3%
2530280 284.2.1.0 ↗ a+b two layers › FKBP-like › Chitinase insertion domain › Chitinase insertion domain 0.54 45.0 4.22e-01 100.0% 100.0%
3581044 390.1.1.0 ↗ few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like 0.54 45.0 3.80e-01 100.0% 54.1%
3437270 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.53 38.0 3.51e-01 100.0% 57.1%
4316258 304.56.1.2 ↗ a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like › CRISPR_Cas2 0.53 42.0 3.64e-01 100.0% 81.2%
3620613 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 39.0 4.02e-01 100.0% 91.1%
4547125 375.14.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) 0.52 42.0 4.15e-01 97.8% 84.0%
3551231 221.1.1.87 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › FERM_N_2 0.52 45.0 3.51e-01 100.0% 43.8%
3241250 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.51 38.0 3.08e-01 100.0% 39.0%
3899283 375.1.1.23 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › GCM 0.51 37.0 3.79e-01 91.3% 100.0%
4944077 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 38.0 3.20e-01 100.0% 44.8%