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OL676770.1__UIW11071.1__VP5_059__00058

Bact-Vir

OL676770.1__UIW11071.1__VP5_059__00058

Identity

Accession:
OL676770 ↗
Kingdom:
phage

Quality

72.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Zobellviridae› Vibrio_virus_VPMCC5

TaxID: 2900301

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 387-515
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2lfpA01 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.60 49.0 4.89e-01 87.6% 100.0%
2piaA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.60 36.0 4.01e-01 73.6% 74.0%
4kh9B02 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.58 36.0 3.87e-01 78.3% 70.8%
1iarB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 31.0 3.47e-01 72.1% 70.8%
3wdhA01 2.60.40.2320 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 34.0 3.83e-01 74.4% 82.3%
4jx0A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 39.0 3.79e-01 74.4% 77.6%
4pqqA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 39.0 3.74e-01 79.1% 76.3%
2vrsA03 2.60.90.40 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › 0.52 41.0 4.10e-01 83.7% 100.0%
2xqxA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 40.0 3.88e-01 81.4% 83.0%
1jhjA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 39.0 3.63e-01 78.3% 72.0%
6kmoB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 38.0 2.88e-01 78.3% 80.5%
2vdrB02 2.60.40.1510 Mainly Beta › Sandwich › Immunoglobulin-like › ntegrin, alpha v. Chain A, domain 3 0.51 40.0 3.84e-01 84.5% 80.4%
4aw7A01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.50 39.0 4.06e-01 82.9% 94.1%
1rtqA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.50 37.0 2.98e-01 79.8% 79.0%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1070873 11.1.1.299 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF4785_2nd 0.63 36.0 3.93e-01 72.1% 67.9%
5058314 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 34.0 3.86e-01 72.1% 71.0%
4882601 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 0.59 38.0 4.13e-01 75.2% 78.5%
3264437 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 34.0 3.72e-01 72.1% 71.4%
3593442 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.57 40.0 4.37e-01 72.9% 96.2%
4087539 243.3.1.52 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › UPF0182 0.55 32.0 3.58e-01 87.6% 74.7%
3472486 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.54 38.0 3.72e-01 72.9% 74.3%
3933157 11.1.1.1085 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › GBD_IRG7_N 0.53 34.0 3.82e-01 72.1% 83.0%
3637520 221.1.1.52 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Ubiquitin_2 0.53 37.0 4.03e-01 72.1% 96.2%
4990061 12.1.1.118 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Hydantoinase_B 0.53 37.0 4.01e-01 73.6% 100.0%
3727776 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 30.0 3.74e-01 71.3% 96.0%
999431 10.32.1.2 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › F5_F8_type_C 0.52 40.0 3.89e-01 81.4% 84.1%
4099249 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.51 36.0 3.45e-01 72.9% 89.0%
3924188 11.1.1.12 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Filamin 0.51 35.0 3.90e-01 89.1% 91.0%
3727797 7577.1.1.4 ↗ a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Pyridoxal_deC 0.51 45.0 2.96e-01 99.2% 52.5%
D2 high residues 666-735
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ioyX01 2.30.29.150 Mainly Beta › Roll › PH-domain like › 0.55 40.0 3.33e-01 77.1% 91.4%
1cs3A00 3.30.710.10 Alpha Beta › 2-Layer Sandwich › Potassium Channel Kv1.1; Chain A › Potassium Channel Kv1.1; Chain A 0.53 32.0 2.76e-01 72.9% 36.2%
3ga1A00 3.30.710.10 Alpha Beta › 2-Layer Sandwich › Potassium Channel Kv1.1; Chain A › Potassium Channel Kv1.1; Chain A 0.52 32.0 2.79e-01 74.3% 38.9%
4hspA00 2.40.50.870 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Protein of unknown function (DUF3299) 0.50 38.0 3.09e-01 84.3% 92.6%
8fbcA01 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.50 37.0 2.41e-01 82.9% 80.4%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4599978 221.2.1.0 ↗ a+b two layers › beta-Grasp › IF3-N › IF3-N 0.61 50.0 4.87e-01 94.3% 82.5%
5069936 2.1.1.16 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_bind 0.57 49.0 3.60e-01 97.1% 83.2%
None — 0.57 46.0 2.70e-01 90.0% 14.2%
3611207 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 41.0 2.99e-01 77.1% 81.5%
3235624 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.56 46.0 4.54e-01 90.0% 89.3%
4300446 4263.2.1.0 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain 0.56 43.0 4.12e-01 82.9% 88.7%
3536274 220.1.1.55 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SYCP2_SLD 0.55 41.0 3.51e-01 80.0% 85.0%
159340 2.1.1.16 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_bind 0.55 47.0 4.10e-01 95.7% 89.9%
3248470 3468.1.1.0 ↗ a+b two layers › HLTF protein HIRAN domain › HLTF protein HIRAN domain › HLTF protein HIRAN domain 0.55 44.0 3.74e-01 90.0% 88.3%
3674262 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.54 30.0 3.31e-01 71.4% 68.0%
3957839 243.1.1.18 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.53 44.0 3.62e-01 91.4% 87.7%
3236179 708.1.2.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like 0.51 42.0 3.30e-01 95.7% 59.4%
1019410 2.1.1.56 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF3299 0.50 38.0 3.13e-01 85.7% 93.9%
D3 medium residues 145-164_178-283
PDB
D4 medium residues 746-880
PDB
D5 medium residues 881-951
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1q2yA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 41.0 3.33e-01 76.1% 69.3%
1kewA02 3.90.25.10 Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 0.55 35.0 3.39e-01 70.4% 56.0%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3622474 7516.1.1.69 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glyco_transf_92 0.52 38.0 2.49e-01 76.1% 77.3%
D6 medium residues 986-1151
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1c9bA02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.55 28.0 3.31e-01 95.8% 70.8%
2wdqC00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.54 27.0 3.09e-01 77.7% 62.8%
2gfhA02 1.20.120.710 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Haloacid dehalogenase hydrolase-like domain 0.52 27.0 3.53e-01 98.2% 93.0%
3lnnB03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.52 23.0 3.40e-01 72.9% 100.0%
5xs2B02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.50 30.0 3.36e-01 100.0% 73.5%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4249009 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.58 30.0 3.49e-01 74.1% 69.2%
3904130 1203.1.2.1 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 › ASD2 0.56 32.0 3.72e-01 84.3% 77.5%
3361214 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.54 29.0 3.24e-01 75.3% 64.6%
4677861 604.1.1.63 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin_SESTD1 0.54 31.0 2.88e-01 84.3% 43.9%
3919897 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.51 41.0 2.86e-01 83.1% 77.4%
D7 medium residues 1458-1510
PDB