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NC_042001.1__YP_009610153.1__FDI28_gp85__00025

Bact-Vir

NC_042001.1__YP_009610153.1__FDI28_gp85__00025

Identity

Accession:
NC_042001 ↗
Kingdom:
phage

Quality

88.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Amigovirus› Arthrobacter_phage_Molivia

TaxID: 2015839

Cluster

View cluster (116 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 12-62
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3cpfA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.69 48.0 4.45e-01 90.2% 56.9%
3oyyA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.68 50.0 4.61e-01 90.2% 60.6%
1uebA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.68 50.0 4.69e-01 90.2% 63.5%
3prbA02 2.40.10.330 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.67 51.0 5.44e-01 100.0% 95.5%
1wvvB01 2.10.10.20 Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › Carbohydrate-binding module superfamily 5/12 0.63 44.0 4.51e-01 90.2% 79.2%
3p26B02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.63 54.0 4.38e-01 100.0% 56.4%
1iz6A01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.62 46.0 4.21e-01 90.2% 59.4%
7razA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 41.0 3.51e-01 92.2% 43.5%
1goiB03 2.10.10.20 Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › Carbohydrate-binding module superfamily 5/12 0.59 41.0 4.16e-01 92.2% 74.5%
1yueA02 2.10.10.40 Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › 0.59 48.0 4.56e-01 92.2% 85.2%
3va7A07 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.58 49.0 4.43e-01 100.0% 92.1%
3wx7A02 2.10.10.90 Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › 0.57 43.0 3.52e-01 90.2% 44.2%
1ed7A00 2.10.10.20 Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › Carbohydrate-binding module superfamily 5/12 0.55 41.0 4.28e-01 92.2% 93.3%
5tw4A02 2.30.140.20 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Penicillin-binding protein 4, C-terminal domain 0.52 40.0 3.71e-01 88.2% 92.8%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3981632 70.4.1.9 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement_2 0.77 54.0 5.90e-01 100.0% 95.0%
4073200 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.68 50.0 4.65e-01 90.2% 63.1%
4963049 4.1.1.486 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7098 0.63 53.0 4.59e-01 100.0% 61.3%
4996605 70.3.1.12 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like › PF30644 0.60 44.0 3.90e-01 82.4% 82.5%
2389402 64.3.1.0 ↗ beta meanders › WW domain-like › Carbohydrate binding domain › Carbohydrate binding domain 0.58 40.0 4.01e-01 92.2% 70.4%
1322863 64.3.1.1 ↗ beta meanders › WW domain-like › Carbohydrate binding domain › Carbohydrate binding domain › CBM_5_12 0.57 43.0 4.47e-01 90.2% 91.3%
3728868 239.1.1.5 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › tRNA-synt_1c_C 0.56 49.0 3.85e-01 100.0% 80.0%
1694867 64.3.1.1 ↗ beta meanders › WW domain-like › Carbohydrate binding domain › Carbohydrate binding domain › CBM_5_12 0.56 43.0 4.28e-01 90.2% 83.0%
3400618 7102.1.1.2 ↗ a+b three layers › C-terminal segment in 5'->3' exoribonucleases › C-terminal segment in 5'->3' exoribonucleases › C-terminal segment in 5'->3' exoribonucleases › XRN_M 0.54 44.0 3.99e-01 98.0% 97.3%
3818230 376.1.2.16 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1-like_CT 0.52 40.0 3.78e-01 90.2% 69.2%
3502375 391.1.2.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related 0.51 37.0 3.90e-01 92.2% 91.1%
D2 high residues 66-117
PDB
Domain cluster: rep: NC_074638__YP_010772018.1__QIT35-gp28__00028__D11-63
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF09956.16 best Phage_cement_2 28.0 3.20e-06 98.1% 44.7%
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6xgqb01 2.40.300.10 Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D 0.81 72.0 5.91e-01 100.0% 63.4%
1uz5A04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.68 58.0 5.26e-01 100.0% 91.7%
3u28C00 2.40.10.230 Mainly Beta › Beta Barrel › Thrombin, subunit H › Probable tRNA pseudouridine synthase domain 0.63 50.0 4.15e-01 100.0% 48.9%
1yu0A02 2.80.20.10 Mainly Beta › Trefoil › Tail fiber receptor-binding protein › Tail fiber receptor-binding protein 0.61 52.0 3.86e-01 100.0% 71.9%
1g8lA04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.60 49.0 4.51e-01 98.1% 98.6%
5ja1B00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.58 43.0 4.04e-01 80.8% 69.7%
1f39A00 2.10.109.10 Mainly Beta › Ribbon › Umud Fragment, subunit A › Umud Fragment, subunit A 0.57 41.0 3.45e-01 80.8% 90.1%
1f60A03 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.55 46.0 3.76e-01 100.0% 63.0%
3ztdF01 2.60.40.780 Mainly Beta › Sandwich › Immunoglobulin-like › von Hippel-Lindau disease tumour suppressor, beta domain 0.53 39.0 3.30e-01 80.8% 58.9%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3945811 70.4.1.7 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › XM1_gp53_minor_capsid 0.86 77.0 7.35e-01 98.1% 95.0%
3981037 70.4.1.9 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement_2 0.85 77.0 7.59e-01 100.0% 98.2%
5002645 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.81 73.0 6.99e-01 100.0% 96.6%
5033307 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.81 72.0 5.22e-01 100.0% 42.9%
2640772 70.4.1.1 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › HDPD 0.80 71.0 5.70e-01 100.0% 59.0%
5083172 70.4.1.9 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement_2 0.79 66.0 6.56e-01 92.3% 100.0%
4988093 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.76 67.0 5.33e-01 100.0% 66.3%
2559744 70.4.1.2 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr 0.76 67.0 6.41e-01 100.0% 86.4%
5024766 7550.1.1.5 ↗ a/b three-layered sandwiches › Tetrapyrrole methylase N-terminal domain › Tetrapyrrole methylase N-terminal domain › Tetrapyrrole methylase N-terminal domain › DUF7839 0.72 60.0 4.26e-01 94.2% 31.2%
5002644 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.72 61.0 5.52e-01 100.0% 94.7%
5007190 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.71 60.0 6.12e-01 96.2% 98.0%
5075574 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.67 56.0 4.99e-01 100.0% 91.3%
2526359 70.4.1.2 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr 0.64 55.0 5.29e-01 100.0% 95.0%
3907690 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.60 51.0 3.45e-01 100.0% 24.3%
3168968 3008.1.1.0 ↗ a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.59 43.0 3.03e-01 82.7% 40.5%
3401480 389.1.2.0 ↗ few secondary structure elements › EGF-like › EGF-related › Complement control module/SCR domain 0.56 39.0 3.56e-01 78.8% 54.3%
4993709 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 38.0 2.75e-01 71.2% 58.3%
5070918 1.1.7.34 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › GTP_EFTU_D4 0.55 45.0 3.59e-01 100.0% 45.0%
3359444 10.12.1.17 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › 2OG-FeII_Oxy,DIOX_N 0.51 36.0 2.37e-01 76.9% 24.6%
2141919 11.1.5.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › Fimbrial 0.50 35.0 2.65e-01 76.9% 61.4%