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NC_055840.1__YP_010107062.1__KNU98_gp081__00028

Bact-Vir

NC_055840.1__YP_010107062.1__KNU98_gp081__00028

Identity

Accession:
NC_055840 ↗
Kingdom:
phage

Quality

73.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Oliverunavirus› Agrobacterium_phage_OLIVR1

TaxID: 2723769

Cluster

Singleton — not in a non-trivial cluster

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 3-58
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3fy6A01 3.30.2210.10 Alpha Beta › 2-Layer Sandwich › Integron cassette protein fold › Integron cassette protein superfamily 0.81 59.0 4.70e-01 76.8% 40.2%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.79 67.0 5.15e-01 91.1% 80.3%
1vq8P03 1.10.1200.60 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.79 54.0 5.50e-01 73.2% 72.7%
3h0dB02 1.10.1200.150 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Transcriptional repressor of class III stress genes, C-terminal domain 0.79 59.0 5.13e-01 78.6% 58.0%
1zoyD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.76 51.0 4.14e-01 76.8% 38.2%
4kb2A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.76 63.0 5.02e-01 91.1% 80.7%
2fe1A00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.75 65.0 4.83e-01 92.9% 50.8%
2mpnA00 6.10.140.1340 Special › Helix non-globular › Helix Hairpins › 0.73 55.0 5.22e-01 82.1% 73.5%
1yozA00 1.10.3200.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af0941 › AF0941-like 0.73 60.0 4.77e-01 91.1% 62.8%
5o5jT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.73 58.0 5.06e-01 87.5% 63.5%
1t7lB01 3.20.20.210 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › 0.71 50.0 3.02e-01 75.0% 11.4%
3zdmB00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.68 49.0 5.14e-01 89.3% 84.0%
5c8aA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.67 57.0 5.19e-01 100.0% 79.5%
2ynqB00 1.25.40.680 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Type VII secretion system EssB, C-terminal-like domain 0.66 54.0 3.92e-01 92.9% 33.1%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.66 51.0 4.57e-01 82.1% 87.0%
2efeA01 1.10.246.120 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.66 58.0 5.14e-01 98.2% 91.4%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.66 54.0 4.42e-01 96.4% 85.1%
2nn4A00 1.10.287.760 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YqgQ-like 0.65 55.0 5.34e-01 94.6% 96.8%
4in3B00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.65 56.0 3.20e-01 100.0% 13.1%
2wmmA01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.64 47.0 5.00e-01 92.9% 89.8%
1y88A02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.64 49.0 4.89e-01 83.9% 100.0%
2jaeA03 1.20.1440.240 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.63 51.0 4.18e-01 87.5% 52.5%
4gf0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.63 45.0 3.61e-01 76.8% 40.7%
1vfrA00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.62 50.0 3.41e-01 92.9% 41.5%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.62 45.0 4.06e-01 94.6% 56.4%
4ioeA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.62 47.0 4.13e-01 83.9% 77.0%
4bx8A03 3.90.830.10 Alpha Beta › Alpha-Beta Complex › Syntaxin Binding Protein 1; Chain A, domain 2 › Sec1/Munc18 (SM) protein, domain 3a 0.61 53.0 4.33e-01 98.2% 58.3%
1zbpA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.61 55.0 4.78e-01 100.0% 87.1%
3craA02 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.60 52.0 3.99e-01 96.4% 45.3%
2a8pA00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.60 46.0 3.24e-01 85.7% 25.0%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.60 46.0 3.79e-01 85.7% 53.8%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 48.0 4.26e-01 92.9% 61.7%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.58 48.0 4.79e-01 94.6% 87.9%
2ficB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.58 42.0 2.95e-01 82.1% 22.4%
2da3A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.58 43.0 4.56e-01 92.9% 95.7%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.57 45.0 4.30e-01 87.5% 75.0%
4asvA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.57 40.0 3.63e-01 80.4% 53.2%
1sr2A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.56 43.0 3.52e-01 87.5% 43.1%
2jgdB02 3.40.50.970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains 0.56 49.0 3.06e-01 100.0% 35.7%
3fp3A01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.56 44.0 3.49e-01 92.9% 54.1%
1qd1B02 3.30.70.670 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Formiminotransferase, C-terminal subdomain 0.56 43.0 3.30e-01 89.3% 95.9%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.55 44.0 3.47e-01 89.3% 61.9%
7tj4A01 1.25.40.1040 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.55 42.0 3.40e-01 85.7% 60.8%
2yf4F00 1.10.3420.10 Mainly Alpha › Orthogonal Bundle › putative ntp pyrophosphohydrolase like fold › putative ntp pyrophosphohydrolase like domain 0.54 42.0 3.16e-01 87.5% 32.9%
2go7A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.52 39.0 3.79e-01 87.5% 95.5%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.52 45.0 4.47e-01 100.0% 93.4%
4cpgA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.52 37.0 3.52e-01 82.1% 63.8%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.51 42.0 2.89e-01 98.2% 52.7%
3mekA04 1.25.40.970 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.51 40.0 3.50e-01 85.7% 58.7%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3770290 4177.1.1.41 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › EVC2_like 0.84 60.0 3.99e-01 75.0% 22.1%
3416035 104.1.1.0 ↗ alpha duplicates or obligate multimers › TFIIA, alpha-helical domain › TFIIA, alpha-helical domain › TFIIA, alpha-helical domain 0.83 70.0 7.14e-01 91.1% 94.5%
3988447 5043.1.1.0 ↗ extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like 0.83 60.0 6.11e-01 76.8% 78.2%
5066143 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.82 59.0 5.28e-01 75.0% 57.3%
4203622 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.82 70.0 4.76e-01 91.1% 90.3%
3343260 192.15.1.123 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Na_H_Exchanger 0.81 61.0 6.21e-01 89.3% 81.8%
5013989 5069.1.3.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits 0.81 58.0 4.81e-01 76.8% 44.9%
5021741 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.80 67.0 6.15e-01 94.6% 71.4%
3505626 186.2.1.1 ↗ alpha arrays › lambda integrase-N-like › VEFS domain › VEFS domain › VEFS-Box 0.79 64.0 5.30e-01 87.5% 51.6%
3742303 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.78 69.0 4.63e-01 96.4% 90.7%
3842812 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.77 56.0 3.71e-01 76.8% 20.0%
3574221 186.2.1.1 ↗ alpha arrays › lambda integrase-N-like › VEFS domain › VEFS domain › VEFS-Box 0.77 60.0 4.51e-01 85.7% 36.2%
3491875 4146.1.1.0 ↗ alpha bundles › YqgQ-like › YqgQ-like › YqgQ-like 0.77 56.0 5.48e-01 76.8% 71.7%
3412555 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.77 59.0 4.66e-01 82.1% 43.6%
5036455 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.76 55.0 3.44e-01 83.9% 14.8%
4071991 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.76 69.0 4.68e-01 98.2% 91.4%
3374816 192.15.1.3 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Vps23_core 0.76 56.0 3.82e-01 83.9% 23.8%
3268365 192.15.1.3 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Vps23_core 0.75 56.0 3.93e-01 87.5% 26.5%
5055565 192.15.1.224 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › SHOCT 0.74 56.0 4.23e-01 87.5% 34.6%
4220406 375.1.9.14 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase › GvpG 0.74 52.0 4.93e-01 83.9% 61.8%
3957298 604.9.1.1 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p 0.74 60.0 5.14e-01 89.3% 62.2%
4963000 192.15.1.224 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › SHOCT 0.73 56.0 4.98e-01 82.1% 57.5%
3455580 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.72 54.0 3.54e-01 82.1% 18.8%
4452821 101.1.2.604 ↗ alpha arrays › HTH › HTH › winged helix domain › SGIII 0.72 62.0 5.70e-01 98.2% 76.0%
4289855 604.9.1.1 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p 0.72 56.0 5.36e-01 85.7% 81.5%
3791357 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.72 53.0 3.82e-01 89.3% 27.3%
4971500 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.72 54.0 4.16e-01 87.5% 37.5%
3486312 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.71 54.0 4.17e-01 87.5% 37.8%
3189353 548.1.1.1 ↗ alpha duplicates or obligate multimers › GRIP domain › GRIP domain › GRIP domain › GRIP 0.71 47.0 4.95e-01 73.2% 78.0%
3892460 548.1.1.1 ↗ alpha duplicates or obligate multimers › GRIP domain › GRIP domain › GRIP domain › GRIP 0.70 47.0 4.63e-01 75.0% 65.0%
5054079 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.70 53.0 4.72e-01 87.5% 57.5%
4473504 304.136.1.3 ↗ a+b two layers › Alpha-beta plaits › Oligo-peptide binding protein (OPPA) insertion domain › Oligo-peptide binding protein (OPPA) insertion domain › SGIII 0.70 60.0 5.15e-01 98.2% 63.3%
4008053 4168.1.1.7 ↗ alpha duplicates or obligate multimers › HAMP domain › HAMP domain › HAMP domain › PF26769 0.69 51.0 3.64e-01 82.1% 26.7%
4615565 101.1.1.249 ↗ alpha arrays › HTH › HTH › Three-helical HTH › SGIII 0.69 59.0 5.23e-01 98.2% 67.1%
4927448 4995.1.1.1 ↗ alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.69 59.0 5.29e-01 98.2% 80.0%
5065070 192.15.1.3 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Vps23_core 0.69 52.0 5.01e-01 87.5% 70.8%
5045248 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.67 50.0 4.41e-01 87.5% 54.1%
4984709 4995.1.1.1 ↗ alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.66 57.0 5.09e-01 98.2% 95.0%
3837289 509.1.1.0 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain 0.65 42.0 4.05e-01 71.4% 56.9%
5029911 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.64 55.0 5.43e-01 98.2% 93.2%
3799055 188.1.1.1 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Hormone_recep 0.64 56.0 3.54e-01 100.0% 29.5%
3510318 188.1.1.1 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Hormone_recep 0.63 55.0 3.64e-01 100.0% 37.9%
3737108 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.61 47.0 4.50e-01 83.9% 93.8%
4228031 109.4.1.128 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MIF4G_like_2 0.61 48.0 3.12e-01 91.1% 21.2%
4998925 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.58 50.0 4.39e-01 98.2% 96.5%
3654165 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.56 44.0 3.24e-01 92.9% 42.9%