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NC_055840.1__YP_010107038.1__KNU98_gp105__00004

Bact-Vir

NC_055840.1__YP_010107038.1__KNU98_gp105__00004

Identity

Accession:
NC_055840 ↗
Kingdom:
phage

Quality

88.7 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 2-56
PDB
Domain cluster: representative
CATH (53)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3qv0A00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.72 55.0 3.84e-01 83.6% 40.2%
4g7nA01 3.30.1120.120 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.70 57.0 4.41e-01 89.1% 50.4%
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.69 56.0 5.14e-01 89.1% 77.5%
4pt4B00 4.10.520.10 Few Secondary Structures › Irregular › HU Protein; Chain A › IHF-like DNA-binding proteins 0.69 39.0 3.20e-01 98.2% 32.0%
3mswA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.67 53.0 3.98e-01 87.3% 41.0%
4r8oA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.67 53.0 4.42e-01 87.3% 58.2%
2kd2A01 2.40.128.180 Mainly Beta › Beta Barrel › Lipocalin › 0.67 46.0 4.07e-01 72.7% 47.6%
4fvmA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.66 52.0 3.47e-01 89.1% 40.2%
5mu3B00 3.40.50.12050 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.65 54.0 3.98e-01 100.0% 38.7%
6kghA02 3.30.450.330 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.63 52.0 3.94e-01 100.0% 54.5%
1vkcA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.61 43.0 3.25e-01 74.5% 60.4%
3cxbA02 3.30.390.70 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Salmonella typhimurium protein 0.61 51.0 4.20e-01 96.4% 81.1%
3ooqF01 2.30.40.10 Mainly Beta › Roll › Urease, subunit C; domain 1 › Urease, subunit C, domain 1 0.60 41.0 3.45e-01 72.7% 46.8%
4fmrA02 4.10.520.10 Few Secondary Structures › Irregular › HU Protein; Chain A › IHF-like DNA-binding proteins 0.59 35.0 2.99e-01 98.2% 36.4%
3dsbA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.59 41.0 3.35e-01 72.7% 86.1%
7r97A02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.59 46.0 4.45e-01 94.5% 94.1%
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.58 51.0 3.83e-01 100.0% 83.6%
4dkwA00 3.30.420.280 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.58 45.0 3.21e-01 90.9% 72.2%
4r80A00 3.10.450.630 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.58 40.0 3.68e-01 74.5% 59.2%
1nyeA00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.58 45.0 3.42e-01 89.1% 39.2%
1luiA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.57 48.0 3.94e-01 98.2% 58.3%
1hq0A00 3.60.100.10 Alpha Beta › 4-Layer Sandwich › Cytotoxic necrotizing factor 1 (CNF1) › Cytotoxic necrotizing factor, Rho-activating domain 0.57 40.0 2.51e-01 96.4% 13.9%
2yfsA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.57 46.0 2.77e-01 100.0% 19.4%
5egjA00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.57 50.0 3.54e-01 100.0% 42.5%
2wbnA00 3.30.420.280 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.56 44.0 3.19e-01 90.9% 76.4%
6asoH00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.56 43.0 3.81e-01 90.9% 56.6%
3icjA01 2.30.40.10 Mainly Beta › Roll › Urease, subunit C; domain 1 › Urease, subunit C, domain 1 0.55 42.0 3.75e-01 83.6% 60.8%
1bp1A01 3.15.10.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Bactericidal permeability-increasing protein; domain 1 0.55 43.0 3.12e-01 90.9% 64.4%
3lm3A02 3.30.1120.110 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.55 43.0 3.67e-01 96.4% 74.8%
2e4uA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.55 37.0 2.67e-01 72.7% 22.0%
2vf9A00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.55 43.0 3.28e-01 87.3% 51.1%
2konA00 3.30.160.350 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 45.0 4.09e-01 100.0% 84.1%
2ciuA00 3.10.450.320 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Mitochondrial import inner membrane translocase subunit Tim21 0.54 46.0 3.57e-01 94.5% 52.0%
3fcxB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 43.0 2.91e-01 100.0% 95.3%
2fggA01 3.30.160.240 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Rv1738 0.54 45.0 4.10e-01 100.0% 70.7%
2qkdA03 2.20.25.420 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ZPR1, zinc finger domain 0.53 37.0 3.80e-01 76.4% 90.2%
5o46A00 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 41.0 3.47e-01 94.5% 79.8%
6u5vB07 3.30.1120.100 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.53 41.0 3.21e-01 87.3% 40.3%
3pnrA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.53 42.0 2.91e-01 98.2% 32.9%
3i3lA02 3.30.390.160 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.53 39.0 3.17e-01 87.3% 37.6%
4dm5A00 3.30.1450.10 Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › 0.53 42.0 3.83e-01 100.0% 64.4%
2ch9A01 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 36.0 3.02e-01 74.5% 67.3%
3rwxA01 2.40.128.340 Mainly Beta › Beta Barrel › Lipocalin › 0.53 40.0 3.30e-01 90.9% 79.2%
2opcA00 2.60.40.2510 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 42.0 3.35e-01 89.1% 86.1%
1pv1A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 44.0 2.86e-01 100.0% 94.5%
4q8gA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.52 42.0 2.69e-01 98.2% 78.5%
5mkiH00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.51 41.0 3.81e-01 90.9% 69.0%
5b6iA02 2.40.30.90 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Bacterial fluorinating enzyme like 0.51 42.0 3.53e-01 100.0% 78.5%
1b34B00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.51 38.0 3.51e-01 90.9% 62.2%
2obdA01 3.15.20.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 2 › Bactericidal permeability-increasing protein; domain 2 0.51 40.0 2.68e-01 98.2% 27.2%
1vq8B03 3.30.1430.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L3; Chain: B; domain 2, › 0.51 41.0 3.44e-01 100.0% 82.0%
2iecD00 3.30.1300.20 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 7,8-dihydroneopterin aldolase (MptD) 0.50 42.0 3.41e-01 100.0% 64.1%
1n7vA01 2.105.10.10 Mainly Beta › 3 Propeller › Pseudo beta propeller › Pseudo beta propeller 0.50 41.0 3.01e-01 100.0% 36.7%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3269927 9.4.1.0 ↗ beta barrels › Lipocalins/Streptavidin › D-aminopeptidase, middle and C-terminal domains › D-aminopeptidase, middle and C-terminal domains 0.81 56.0 4.40e-01 72.7% 51.9%
5043802 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.71 54.0 4.32e-01 85.5% 42.6%
4030017 837.1.1.0 ↗ a+b two layers › Ribosomal protein S16 › Ribosomal protein S16 › Ribosomal protein S16 0.68 47.0 4.26e-01 72.7% 60.0%
3390996 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.68 46.0 3.18e-01 72.7% 37.0%
185414 3347.1.1.1 ↗ beta meanders › Uncharacterized protein BF3112 › Uncharacterized protein BF3112 › Uncharacterized protein BF3112 › DUF3836 0.67 53.0 3.99e-01 87.3% 41.3%
3953024 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.65 44.0 3.52e-01 70.9% 34.8%
3411018 3459.1.1.1 ↗ beta sandwiches › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › FAIM1 0.65 46.0 3.69e-01 80.0% 41.0%
4227571 101.17.1.1 ↗ alpha arrays › HTH › IHF-like DNA-binding proteins › IHF-like DNA-binding proteins › Bac_DNA_binding 0.63 36.0 2.96e-01 96.4% 32.0%
4240651 101.17.1.1 ↗ alpha arrays › HTH › IHF-like DNA-binding proteins › IHF-like DNA-binding proteins › Bac_DNA_binding 0.62 36.0 2.95e-01 96.4% 31.0%
3592141 5.1.2.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed 0.62 53.0 3.74e-01 94.5% 44.8%
3677000 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.61 49.0 3.64e-01 89.1% 84.0%
3744704 5.1.4.173 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_WDR75_2nd 0.60 51.0 3.17e-01 100.0% 24.7%
3672898 295.1.1.3 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PurA 0.60 47.0 3.61e-01 85.5% 40.8%
3470818 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.60 43.0 2.87e-01 76.4% 84.8%
3929256 295.1.1.3 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PurA 0.59 51.0 3.83e-01 100.0% 80.0%
3843423 2484.5.1.3 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH_2 0.59 45.0 3.41e-01 83.6% 90.8%
3947929 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.59 50.0 3.49e-01 98.2% 80.4%
3314307 5.1.3.65 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › DUF295 0.58 49.0 3.01e-01 94.5% 24.8%
3712993 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.58 47.0 4.30e-01 90.9% 90.7%
4203354 252.2.1.9 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › PF27551 0.58 50.0 4.24e-01 100.0% 78.9%
3892544 5.1.3.6 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1 0.58 50.0 3.14e-01 100.0% 23.9%
3653968 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.57 50.0 3.03e-01 100.0% 18.9%
3826655 5.1.3.67 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_1 0.57 48.0 3.11e-01 100.0% 29.0%
3484051 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.57 48.0 2.98e-01 100.0% 39.5%
4062195 2004.1.1.159 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.57 48.0 3.25e-01 100.0% 30.4%
4579381 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.56 46.0 3.40e-01 94.5% 86.9%
3805832 7516.1.1.41 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glucan_synthase 0.56 43.0 2.71e-01 90.9% 55.3%
None — 0.56 48.0 3.17e-01 100.0% 32.4%
3466180 206.1.3.14 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › GSH_synth_ATP 0.56 41.0 2.98e-01 80.0% 58.8%
3457141 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.56 43.0 2.72e-01 87.3% 20.0%
3517799 2007.1.2.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.56 37.0 2.61e-01 70.9% 19.0%
3929202 2484.5.1.3 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH_2 0.56 45.0 3.63e-01 89.1% 91.4%
2623870 2484.1.1.44 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pox_A22 0.55 47.0 3.51e-01 98.2% 84.6%
4021815 3541.1.1.0 ↗ beta sandwiches › Atg29-Atg31 › Atg29-Atg31 › Atg29-Atg31 0.55 43.0 3.55e-01 89.1% 71.2%
3704272 2004.1.1.175 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ParA 0.55 48.0 3.01e-01 100.0% 75.2%
3733891 5.1.4.276 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, Beta-prop_WDR75_2nd 0.55 42.0 2.57e-01 89.1% 29.6%
3223450 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.55 44.0 2.77e-01 100.0% 22.6%
3170704 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.55 47.0 2.83e-01 100.0% 18.8%
4936511 304.133.1.1 ↗ a+b two layers › Alpha-beta plaits › 26 kDa periplasmic immunogenic protein › 26 kDa periplasmic immunogenic protein › SIMPL 0.55 36.0 2.99e-01 89.1% 34.5%
5075107 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.54 42.0 3.22e-01 87.3% 86.4%
3788380 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.54 43.0 3.08e-01 98.2% 62.9%
3580844 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.53 38.0 2.17e-01 81.8% 11.3%
5074340 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.53 41.0 3.11e-01 87.3% 87.1%
3297150 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 45.0 3.74e-01 98.2% 79.0%
3487306 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.51 45.0 3.26e-01 98.2% 48.4%
3678781 7516.1.1.41 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glucan_synthase 0.51 39.0 2.27e-01 96.4% 23.7%
3587744 9.9.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Hypothetical protein YwiB › Hypothetical protein YwiB › DUF1934 0.51 37.0 2.92e-01 81.8% 33.6%
4681823 101.17.1.1 ↗ alpha arrays › HTH › IHF-like DNA-binding proteins › IHF-like DNA-binding proteins › Bac_DNA_binding 0.51 28.0 2.36e-01 85.5% 27.0%
5044368 327.17.1.9 ↗ a+b two layers › Alpha-lytic protease prodomain-like › S-adenosylmethionine synthetase › S-adenosylmethionine synthetase › OsmC 0.51 37.0 2.92e-01 85.5% 36.4%
3939681 5001.1.1.41 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srw 0.50 43.0 2.69e-01 100.0% 30.6%
3199683 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 38.0 2.93e-01 89.1% 84.7%
D2 high residues 63-130
PDB
Domain cluster: rep: QC4_scaffold_20_prodigal-single.1__X__X__00085__D111-174