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NC_055840.1__YP_010107047.1__KNU98_gp096__00013

Bact-Vir

NC_055840.1__YP_010107047.1__KNU98_gp096__00013

Identity

Accession:
NC_055840 ↗
Kingdom:
phage

Quality

70.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Oliverunavirus› Agrobacterium_phage_OLIVR1

TaxID: 2723769

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 medium residues 1-34
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1bvsF03 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.82 63.0 5.90e-01 91.2% 68.9%
4p9fA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.76 59.0 4.90e-01 97.1% 47.8%
4hhxA00 1.20.81.30 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › Type II secretion system (T2SS), domain F 0.74 60.0 4.34e-01 97.1% 31.7%
2isyA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.74 59.0 3.94e-01 91.2% 27.5%
3c57B00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.73 62.0 5.58e-01 100.0% 69.4%
4wcgA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.73 56.0 4.78e-01 94.1% 50.8%
2kt0A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.73 57.0 5.22e-01 91.2% 68.1%
1s3jA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.72 60.0 4.92e-01 97.1% 54.7%
1qo0D02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.72 57.0 5.30e-01 94.1% 71.7%
4pt4B00 4.10.520.10 Few Secondary Structures › Irregular › HU Protein; Chain A › IHF-like DNA-binding proteins 0.70 56.0 4.14e-01 94.1% 36.1%
4nb5B01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.70 55.0 4.24e-01 94.1% 42.4%
1rr7A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.70 50.0 4.85e-01 94.1% 71.7%
4ha8A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.69 57.0 4.75e-01 97.1% 84.1%
3jr7A01 3.40.50.10440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Dihydroxyacetone kinase; domain 1 0.69 53.0 3.79e-01 88.2% 25.4%
1kblA04 3.20.20.60 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphoenolpyruvate-binding domains 0.68 56.0 3.24e-01 100.0% 10.2%
1wi9A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 57.0 4.89e-01 97.1% 58.6%
1tfeA02 1.10.286.20 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.68 56.0 5.19e-01 97.1% 73.3%
4i2oA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 58.0 4.42e-01 97.1% 53.8%
2cfxA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.67 56.0 5.06e-01 100.0% 74.0%
2fmyA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.67 57.0 4.35e-01 97.1% 41.5%
6hxlB01 1.10.230.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450-Terp; domain 2 › Cytochrome P450-Terp, domain 2 0.67 52.0 3.66e-01 94.1% 27.3%
2ddmB00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.67 52.0 3.23e-01 100.0% 83.8%
3khyA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.67 55.0 3.47e-01 100.0% 25.4%
2da3A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.66 48.0 4.60e-01 91.2% 72.3%
3iprA00 3.40.50.510 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component 0.66 54.0 3.69e-01 100.0% 79.6%
2k89A00 3.10.20.870 Alpha Beta › Roll › Ubiquitin-like (UB roll) › PFU (PLAA family ubiquitin binding), C-terminal domain 0.65 47.0 3.95e-01 100.0% 48.8%
2ebyA01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.65 53.0 4.21e-01 100.0% 48.1%
3w5mA05 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.62 52.0 3.05e-01 100.0% 29.1%
2ld5A00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.61 46.0 4.03e-01 100.0% 65.7%
3dtyA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 53.0 3.28e-01 100.0% 47.0%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3295850 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.90 74.0 6.46e-01 91.2% 62.0%
4146096 181.1.1.0 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins 0.88 76.0 5.75e-01 100.0% 51.2%
3470303 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.84 68.0 5.20e-01 94.1% 50.0%
3459251 108.1.1.73 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5+EF-hand_7 0.81 61.0 4.81e-01 97.1% 38.7%
5002775 101.1.6.0 ↗ alpha arrays › HTH › HTH › TrpR 0.79 64.0 6.13e-01 94.1% 85.0%
4932940 2006.1.4.2 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN 0.78 63.0 4.54e-01 100.0% 34.5%
3481559 108.1.1.29 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_7 0.77 58.0 5.02e-01 97.1% 51.7%
3259221 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.76 66.0 5.51e-01 100.0% 71.7%
4982570 3604.1.1.1 ↗ a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.76 63.0 5.08e-01 100.0% 88.6%
3480164 108.1.1.96 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_1, EF-hand_6, EF-hand_7 0.75 55.0 4.52e-01 97.1% 41.3%
3335466 108.1.1.28 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_6,EF-hand_7 0.75 55.0 4.29e-01 97.1% 34.4%
3215991 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.75 62.0 5.13e-01 100.0% 66.2%
4970991 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.74 61.0 4.20e-01 97.1% 32.8%
3997742 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.73 62.0 4.91e-01 100.0% 76.0%
3491972 108.1.1.28 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_6,EF-hand_7 0.73 56.0 4.52e-01 97.1% 41.3%
4358938 102.1.1.38 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › RlmN_N 0.73 54.0 4.80e-01 94.1% 55.0%
3274484 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.72 58.0 4.62e-01 94.1% 48.0%
3485420 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.72 62.0 5.21e-01 100.0% 63.3%
3886164 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.71 59.0 5.32e-01 97.1% 74.0%
3495504 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.71 56.0 5.06e-01 94.1% 72.0%
3882807 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.71 58.0 4.59e-01 100.0% 47.5%
4463983 102.1.1.38 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › RlmN_N 0.71 53.0 4.57e-01 94.1% 52.3%
3240028 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.70 59.0 5.14e-01 100.0% 74.5%
5000156 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.69 58.0 5.18e-01 100.0% 86.0%
3955892 101.1.11.2 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix › RHH_1 0.69 57.0 5.02e-01 91.2% 64.0%
3970817 102.1.1.0 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.68 51.0 4.46e-01 94.1% 49.2%
2841761 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.67 55.0 3.33e-01 100.0% 13.6%
3587669 2010.1.1.3 ↗ a/b three-layered sandwiches › EDD domain › EDD domain › EDD domain › EIIA-man 0.67 57.0 3.80e-01 100.0% 37.9%
None — 0.67 58.0 3.32e-01 100.0% 13.4%
5054204 2007.1.5.2 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › ATC-like › CCG 0.65 52.0 3.62e-01 97.1% 27.3%
3620302 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.65 53.0 3.17e-01 100.0% 58.9%
3931118 3075.1.1.1 ↗ a+b two layers › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › PFU 0.65 47.0 4.17e-01 97.1% 60.0%
3419318 101.1.1.10 ↗ alpha arrays › HTH › HTH › Three-helical HTH › ARID 0.62 52.0 3.53e-01 94.1% 33.1%