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NC_013599.1__YP_003344924.1__Xfas53_gene34__00034

Bact-Vir

NC_013599.1__YP_003344924.1__Xfas53_gene34__00034

Identity

Accession:
NC_013599 ↗
Kingdom:
phage

Quality

83.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Xylella_phage_Xfas53

TaxID: 670252

Cluster

View cluster (166 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 226-333
PDB
Domain cluster: rep: NC_005344.1__NP_958181.1__Sf6p05__00005__D219-349
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2m5sA00 2.40.30.240 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.76 68.0 6.50e-01 95.4% 100.0%
6tdyD01 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.72 48.0 5.58e-01 91.7% 98.7%
2v31A01 2.40.30.180 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Ubiquitin-activating enzyme E1, FCCH domain 0.67 50.0 5.31e-01 96.3% 88.7%
1xe1A00 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.63 49.0 5.26e-01 97.2% 96.7%
2qggA01 2.40.30.60 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › RimM 0.61 47.0 4.97e-01 95.4% 93.5%
2e3vA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 43.0 4.47e-01 96.3% 80.6%
2f1lA01 2.40.30.60 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › RimM 0.59 45.0 4.86e-01 94.4% 96.6%
1cfbA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 42.0 4.39e-01 96.3% 81.8%
3wbiA04 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 53.0 4.84e-01 100.0% 79.3%
2ibgA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 44.0 4.55e-01 95.4% 84.3%
3mcaA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 53.0 5.13e-01 97.2% 93.2%
1e62A01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.58 51.0 4.84e-01 96.3% 100.0%
1ja1A02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.57 49.0 4.70e-01 92.6% 95.1%
4n68A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 41.0 4.24e-01 97.2% 83.8%
1wf5A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 40.0 3.93e-01 97.2% 69.4%
3kw3B01 2.40.37.10 Mainly Beta › Beta Barrel › Lyase, Ornithine Decarboxylase; Chain A, domain 1 › Lyase, Ornithine Decarboxylase; Chain A, domain 1 0.55 47.0 4.27e-01 94.4% 72.8%
4eclA01 2.40.37.10 Mainly Beta › Beta Barrel › Lyase, Ornithine Decarboxylase; Chain A, domain 1 › Lyase, Ornithine Decarboxylase; Chain A, domain 1 0.55 48.0 4.26e-01 95.4% 74.2%
5jtwA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 42.0 4.31e-01 94.4% 88.2%
1x3dA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 38.0 3.77e-01 96.3% 67.8%
1x5xA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 39.0 3.90e-01 96.3% 75.2%
2e8yA04 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 31.0 3.36e-01 98.1% 65.6%
4hljA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 41.0 4.11e-01 96.3% 81.2%
6ea2A04 2.60.40.1840 Mainly Beta › Sandwich › Immunoglobulin-like › Aminopeptidase N, middle-beta domain 0.53 40.0 4.20e-01 95.4% 91.7%
1x5aA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 36.0 3.83e-01 96.3% 83.5%
1x4xA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.74e-01 97.2% 74.5%
4aw7A03 2.60.120.1200 Mainly Beta › Sandwich › Jelly Rolls › 0.52 46.0 4.43e-01 98.1% 97.5%
1egjA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.85e-01 94.4% 81.2%
2zaiB03 2.60.40.3020 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 42.0 4.26e-01 92.6% 88.8%
3k1dA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.52 36.0 3.73e-01 88.9% 76.0%
1y7xA02 2.30.30.550 Mainly Beta › Roll › SH3 type barrels. › Major Vault Protein repeat 0.52 28.0 3.57e-01 83.3% 100.0%
1x6gA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.51 32.0 3.61e-01 93.5% 82.7%
5u8rA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 39.0 3.92e-01 94.4% 83.3%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2048195 3734.1.1.1 ↗ beta barrels › P22 coat protein insertion domain › P22 coat protein insertion domain › P22 coat protein insertion domain › P22_CoatProtein 0.85 81.0 7.57e-01 99.1% 100.0%
4867073 2485.3.1.8 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › P22_CoatProtein 0.85 75.0 7.42e-01 91.7% 100.0%
4849089 2485.3.1.8 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › P22_CoatProtein 0.84 72.0 7.01e-01 88.9% 100.0%
3712506 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.76 52.0 5.85e-01 92.6% 89.4%
2448616 3734.1.1.1 ↗ beta barrels › P22 coat protein insertion domain › P22 coat protein insertion domain › P22 coat protein insertion domain › P22_CoatProtein 0.74 65.0 6.34e-01 93.5% 99.1%
3604862 7526.1.1.2 ↗ a/b three-layered sandwiches › Initiation factor IF2/eIF5b, domain 3 › Initiation factor IF2/eIF5b, domain 3 › Initiation factor IF2/eIF5b, domain 3 › EF-G_D2 0.64 48.0 3.66e-01 94.4% 35.0%
5037173 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.64 49.0 5.18e-01 92.6% 91.6%
5001586 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.63 48.0 5.17e-01 92.6% 96.7%
3444354 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.63 51.0 5.31e-01 90.7% 93.0%
3504760 1.1.8.5 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › tRNA_Me_trans_C 0.63 43.0 4.65e-01 85.2% 84.4%
4936008 1.1.7.28 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › HAS-barrel 0.62 50.0 5.29e-01 90.7% 97.9%
4989873 1.1.7.28 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › HAS-barrel 0.61 52.0 5.04e-01 92.6% 98.3%
3271335 1.1.7.34 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › GTP_EFTU_D4 0.61 54.0 4.98e-01 100.0% 77.0%
5056723 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.60 48.0 5.10e-01 92.6% 96.8%
2723599 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.60 52.0 5.04e-01 94.4% 94.3%
3964292 1.1.13.38 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_BR0599 0.60 52.0 5.20e-01 100.0% 92.7%
5023511 1.1.7.28 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › HAS-barrel 0.59 51.0 4.99e-01 92.6% 99.1%
3810482 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.58 50.0 4.63e-01 93.5% 75.6%
1693525 1.2.1.3 ↗ beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Capsid-VNN 0.58 51.0 4.91e-01 97.2% 99.2%
3247934 1.1.7.41 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › UPF1_1B_dom 0.57 47.0 4.95e-01 93.5% 100.0%
4928053 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 49.0 4.77e-01 92.6% 95.0%
4625449 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 44.0 4.79e-01 94.4% 100.0%
4864011 1.1.7.41 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › UPF1_1B_dom 0.57 49.0 4.96e-01 94.4% 95.2%
4929764 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 45.0 4.26e-01 94.4% 87.4%
3898952 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.53 32.0 3.80e-01 70.4% 86.7%
4986214 1.1.4.1 ↗ beta barrels › cradle loop barrel › RIFT-related › Bacterial fluorinating enzyme-C › SAM_HAT_C 0.53 41.0 4.35e-01 90.7% 94.7%
4038585 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.53 40.0 3.79e-01 97.2% 65.9%
4506353 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.53 39.0 3.84e-01 97.2% 73.9%
3401559 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.52 31.0 3.87e-01 91.7% 96.9%
5061798 11.1.1.18 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › LTD 0.52 44.0 4.10e-01 93.5% 75.7%
4412962 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.52 43.0 4.22e-01 97.2% 86.1%
3896234 11.1.1.795 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › FANCAA 0.51 45.0 3.96e-01 99.1% 77.6%
3750163 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.51 31.0 3.80e-01 71.3% 94.3%
3503601 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.51 39.0 3.92e-01 96.3% 82.7%
2625081 11.1.1.339 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › MtrC-MtrF_N 0.51 43.0 3.97e-01 96.3% 85.4%
3538030 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.50 32.0 3.87e-01 74.1% 100.0%
3478357 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 43.0 4.03e-01 96.3% 80.0%
D2 medium residues 108-142_155-165_338-408
PDB
Domain cluster: rep: MW073100.1__QWT28899.1__vBMoxSR1_gp49__00049__D86-130_230-293
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1d5aA01 3.30.342.10 Alpha Beta › 2-Layer Sandwich › DNA Polymerase; Chain A, domain 1 › DNA Polymerase, chain B, domain 1 0.56 26.0 2.43e-01 82.1% 31.1%
2n54B00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 23.0 3.02e-01 76.1% 72.7%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 22.0 2.68e-01 73.5% 56.3%
6m9yA00 3.30.1300.40 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.51 20.0 2.60e-01 70.1% 59.6%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3832419 319.1.1.13 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › PF26144 0.68 27.0 2.91e-01 88.9% 41.0%
3279407 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.57 31.0 3.19e-01 82.1% 56.4%
3726266 3363.1.1.0 ↗ beta sandwiches › avirulence protein AvrPiz-t homologs › avirulence protein AvrPiz-t homologs › avirulence protein AvrPiz-t homologs 0.50 33.0 3.65e-01 92.3% 85.6%