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NC_055840.1__YP_010107037.1__KNU98_gp106__00003

Bact-Vir

NC_055840.1__YP_010107037.1__KNU98_gp106__00003

Identity

Accession:
NC_055840 ↗
Kingdom:
phage

Quality

91.8 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 high residues 1-61
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3tl4X02 1.10.10.2420 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.72 60.0 5.72e-01 100.0% 79.2%
1ax4A02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.70 50.0 3.26e-01 75.4% 41.2%
3o2pE00 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 55.0 4.99e-01 100.0% 65.1%
8sl7B01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.68 48.0 3.19e-01 75.4% 44.6%
1ui6A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.67 52.0 3.70e-01 100.0% 27.6%
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.65 44.0 4.07e-01 100.0% 55.1%
2hjmA01 1.20.120.460 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › protein pf1176 like 0.65 47.0 4.20e-01 77.0% 94.2%
3fhnA05 1.10.10.2270 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Dsl1p vesicle tethering complex, Tip20p subunit, domain E 0.65 55.0 5.39e-01 100.0% 89.6%
3s63A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.62 49.0 4.43e-01 100.0% 62.5%
3vw4A01 1.10.340.50 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › 0.61 51.0 4.54e-01 100.0% 64.1%
2dn0A00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.59 44.0 4.17e-01 100.0% 65.8%
3himA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.59 50.0 3.63e-01 100.0% 52.6%
2go7A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.59 45.0 4.47e-01 96.7% 82.1%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.59 36.0 3.24e-01 85.2% 42.4%
4dqlA03 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.58 44.0 3.29e-01 83.6% 89.4%
1ltmA02 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.58 48.0 3.63e-01 100.0% 93.1%
1a5yA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.57 46.0 3.05e-01 100.0% 20.1%
4qdnA00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.57 47.0 3.88e-01 95.1% 72.0%
2qtlA03 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.57 45.0 3.39e-01 88.5% 94.8%
1jr3C02 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.56 41.0 3.40e-01 100.0% 41.0%
3fblA00 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 47.0 4.35e-01 100.0% 73.2%
4xaxB02 1.20.58.1290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › CarD-like, C-terminal domain 0.55 45.0 3.92e-01 93.4% 97.0%
1e1dA02 1.20.1270.20 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.54 34.0 3.06e-01 96.7% 44.0%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.54 37.0 3.47e-01 80.3% 58.1%
3ulqB00 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 0.53 41.0 4.17e-01 96.7% 91.4%
3ezuA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 38.0 2.84e-01 82.0% 69.2%
2of7A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.51 42.0 3.37e-01 100.0% 67.9%
4u04A02 1.10.3290.10 Mainly Alpha › Orthogonal Bundle › Fic-like fold › Fido-like domain 0.51 42.0 2.97e-01 100.0% 43.7%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3576763 101.1.1.332 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Nucleolin_bd 0.80 65.0 6.37e-01 100.0% 83.1%
3837298 101.1.17.0 ↗ alpha arrays › HTH › HTH › FF domain 0.79 64.0 6.53e-01 100.0% 90.0%
3806070 101.1.17.0 ↗ alpha arrays › HTH › HTH › FF domain 0.79 61.0 6.66e-01 90.2% 100.0%
3428573 101.21.1.0 ↗ alpha arrays › HTH › HTH domain in DNA topoisomerase IV alpha subunit › HTH domain in DNA topoisomerase IV alpha subunit 0.77 64.0 6.32e-01 100.0% 86.2%
3416051 101.21.1.2 ↗ alpha arrays › HTH › HTH domain in DNA topoisomerase IV alpha subunit › HTH domain in DNA topoisomerase IV alpha subunit › Nucleolin_bd 0.75 64.0 6.32e-01 100.0% 89.2%
3399908 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.75 45.0 4.22e-01 72.1% 49.3%
3217750 101.21.1.2 ↗ alpha arrays › HTH › HTH domain in DNA topoisomerase IV alpha subunit › HTH domain in DNA topoisomerase IV alpha subunit › Nucleolin_bd 0.74 63.0 6.08e-01 100.0% 82.9%
5025549 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.73 62.0 6.17e-01 100.0% 90.8%
3261857 101.21.1.2 ↗ alpha arrays › HTH › HTH domain in DNA topoisomerase IV alpha subunit › HTH domain in DNA topoisomerase IV alpha subunit › Nucleolin_bd 0.73 61.0 6.02e-01 100.0% 87.7%
4996283 101.43.1.4 ↗ alpha arrays › HTH › Phage G20C small terminase N-terminal domain › Phage G20C small terminase N-terminal domain › HTH_AsnC-type 0.72 54.0 5.33e-01 90.2% 75.4%
3932714 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.70 56.0 4.98e-01 100.0% 60.0%
4506962 101.1.1.51 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Slx4 0.70 59.0 5.53e-01 95.1% 78.7%
5070731 632.18.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › hypothetical protein PA2901 › hypothetical protein PA2901 0.70 36.0 3.27e-01 91.8% 38.7%
5060249 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.68 36.0 3.58e-01 96.7% 49.2%
5070000 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.67 36.0 3.60e-01 96.7% 50.8%
3603627 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.67 37.0 3.47e-01 93.4% 45.3%
5061319 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.67 38.0 3.01e-01 91.8% 29.6%
4929286 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.66 36.0 3.55e-01 96.7% 50.8%
5070732 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.66 36.0 3.38e-01 91.8% 45.2%
5070001 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.66 36.0 3.49e-01 95.1% 48.6%
3596878 109.40.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › DNA polymerase alpha-binding protein Ctf4 C-terminal domain 0.65 40.0 3.11e-01 100.0% 29.2%
5061375 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.65 36.0 3.49e-01 91.8% 48.6%
3925190 2006.1.1.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.64 54.0 3.69e-01 96.7% 26.1%
3809438 109.40.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › Ctf4_C 0.64 40.0 3.25e-01 100.0% 32.5%
3222274 198.1.1.3 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_1 0.64 50.0 4.32e-01 88.5% 57.0%
3642260 2006.1.1.44 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase, Hydrolase_like 0.61 52.0 3.54e-01 96.7% 25.2%
3804005 2006.1.1.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.61 52.0 3.53e-01 96.7% 25.5%
4504172 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.58 44.0 3.78e-01 100.0% 49.5%
4974859 1075.1.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › ABC2_membrane 0.57 48.0 3.34e-01 100.0% 38.7%
3838730 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.57 46.0 3.53e-01 100.0% 36.0%
3967801 2006.1.3.16 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › DUF1835 0.57 48.0 3.49e-01 96.7% 50.8%
5059275 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.57 32.0 3.23e-01 91.8% 51.7%
3202292 101.38.1.3 ↗ alpha arrays › HTH › DNA-binding domain of the replication initiator protein ColE2-Rep › DNA-binding domain of the replication initiator protein ColE2-Rep › DUF6891 0.57 46.0 4.49e-01 100.0% 81.4%
3325325 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.57 48.0 4.47e-01 100.0% 81.2%
4401833 101.11.1.1 ↗ alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.56 47.0 4.10e-01 100.0% 66.0%
4997858 1075.1.2.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.55 48.0 3.54e-01 100.0% 60.6%
3936293 198.1.1.3 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_1 0.55 44.0 3.91e-01 93.4% 58.9%
4942605 3922.1.1.356 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › AI-2E_transport 0.55 45.0 3.66e-01 100.0% 89.6%
3609170 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.54 41.0 3.28e-01 86.9% 88.6%
5061727 632.23.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical linker domain in nicking endonuclease N.BspD6I › Helical linker domain in nicking endonuclease N.BspD6I 0.53 36.0 3.52e-01 72.1% 66.2%
3499057 304.137.1.0 ↗ a+b two layers › Alpha-beta plaits › NOL1/NOP2/sun N-terminal ferredoxin-like domain › NOL1/NOP2/sun N-terminal ferredoxin-like domain 0.52 40.0 2.87e-01 86.9% 27.2%
3896392 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.51 41.0 4.07e-01 93.4% 92.3%
4937540 1075.1.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain 0.50 41.0 2.84e-01 100.0% 72.8%