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NC_055841.1__YP_010107231.1__KNU99_gp089__00089

Bact-Vir

NC_055841.1__YP_010107231.1__KNU99_gp089__00089

Identity

Accession:
NC_055841 ↗
Kingdom:
phage

Quality

89.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Heverleevirus› Agrobacterium_phage_OLIVR5

TaxID: 2723773

Cluster

View cluster (4 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 3-86
PDB
Domain cluster: rep: NC_031927.1__YP_009323018.1__BOW86_gp085__00085__D3-79
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01541.31 best GIY-YIG 24.1 5.10e-05 100.0% 92.3%
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.66 59.0 5.76e-01 100.0% 91.3%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.62 37.0 4.05e-01 86.9% 72.7%
3hrzC01 2.20.210.20 Mainly Beta › Single Sheet › ubp-family deubiquitinating enzyme fold › 0.57 33.0 4.00e-01 75.0% 95.9%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.57 36.0 2.94e-01 75.0% 32.3%
6usmB01 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.57 48.0 4.06e-01 96.4% 98.6%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.57 36.0 3.52e-01 73.8% 57.6%
3kalB05 3.30.1490.50 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Glutathione synthase lid domain 0.56 29.0 3.37e-01 85.7% 69.5%
1darA05 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 42.0 4.19e-01 78.6% 85.1%
2iabA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 42.0 3.60e-01 83.3% 62.2%
2b39A10 2.60.120.1540 Mainly Beta › Sandwich › Jelly Rolls › 0.55 32.0 2.86e-01 73.8% 41.4%
1t4aA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.54 39.0 4.02e-01 76.2% 98.7%
2hq9B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 43.0 3.68e-01 88.1% 70.1%
2g9oA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 36.0 3.79e-01 71.4% 97.4%
3m1cA04 2.60.40.3190 Mainly Beta › Sandwich › Immunoglobulin-like › Herpesvirus glycoprotein H, C-terminal domain 0.53 34.0 2.98e-01 72.6% 41.7%
3q8pB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.53 37.0 3.49e-01 75.0% 63.0%
2pjyC00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.53 35.0 3.68e-01 95.2% 74.7%
1w99A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 37.0 2.87e-01 75.0% 37.2%
4rslA02 3.30.9.10 Alpha Beta › 2-Layer Sandwich › D-Amino Acid Oxidase; Chain A, domain 2 › D-Amino Acid Oxidase, subunit A, domain 2 0.51 38.0 2.99e-01 84.5% 59.5%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5080205 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.69 41.0 5.07e-01 73.8% 100.0%
77927 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.66 60.0 5.78e-01 100.0% 89.4%
3505268 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.66 60.0 5.08e-01 98.8% 83.0%
4966853 375.1.1.324 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF1922 0.63 55.0 5.69e-01 98.8% 98.8%
3405824 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.56 42.0 3.83e-01 82.1% 63.3%
4960232 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.54 43.0 3.97e-01 84.5% 96.2%
1875414 244.1.1.4 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › DAO 0.53 44.0 3.42e-01 95.2% 71.2%
4029686 3662.1.1.0 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related 0.52 37.0 3.31e-01 73.8% 100.0%
4028366 212.1.1.0 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like 0.52 35.0 3.72e-01 96.4% 79.7%
5076740 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.52 38.0 3.59e-01 94.0% 62.9%
5031944 304.11.1.5 ↗ a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase › DUF2102 0.51 45.0 4.04e-01 96.4% 73.0%
3698570 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.51 39.0 3.70e-01 81.0% 78.8%
3489893 304.24.1.6 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › SBDS_C 0.51 41.0 4.27e-01 88.1% 97.5%
4345353 322.1.1.2 ↗ a+b two layers › HPr-like › HPr-like › HPr-like › 3H 0.51 35.0 3.11e-01 71.4% 88.3%
3518924 11.1.1.76 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › GMP_PDE_delta 0.50 35.0 2.70e-01 73.8% 37.5%