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NC_055840.1__YP_010107138.1__KNU98_gp005__00104

Bact-Vir

NC_055840.1__YP_010107138.1__KNU98_gp005__00104

Identity

Accession:
NC_055840 ↗
Kingdom:
phage

Quality

77.7 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 34-95
PDB
Domain cluster: representative
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3zgxA02 6.10.140.1720 Special › Helix non-globular › Helix Hairpins › 0.88 80.0 6.96e-01 100.0% 72.5%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.83 71.0 6.20e-01 96.8% 63.0%
4mycA01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.83 74.0 4.60e-01 100.0% 22.0%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.82 72.0 5.42e-01 96.8% 44.1%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.82 70.0 6.72e-01 96.8% 83.1%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.82 72.0 6.08e-01 100.0% 59.2%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.81 70.0 6.31e-01 95.2% 70.6%
4adzA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.81 72.0 6.34e-01 98.4% 72.2%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.81 72.0 6.38e-01 100.0% 82.2%
2qqyA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.81 61.0 4.67e-01 80.6% 38.4%
8fbnB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.81 73.0 4.90e-01 100.0% 41.0%
4p9tA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.81 68.0 5.44e-01 93.5% 49.2%
3na7A00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.80 71.0 4.74e-01 100.0% 26.2%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.80 63.0 5.57e-01 87.1% 59.3%
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.80 61.0 6.02e-01 82.3% 78.8%
2xzmO02 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.79 59.0 5.71e-01 80.6% 71.4%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.79 65.0 6.53e-01 95.2% 91.9%
2ehwA00 6.10.140.1220 Special › Helix non-globular › Helix Hairpins › 0.79 68.0 5.65e-01 100.0% 54.8%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.78 65.0 5.83e-01 91.9% 67.4%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.78 65.0 6.34e-01 93.5% 85.1%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 68.0 5.86e-01 98.4% 64.3%
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.77 66.0 6.63e-01 96.8% 93.7%
3u52D00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.77 64.0 4.00e-01 91.9% 17.7%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.77 68.0 6.23e-01 100.0% 79.0%
2dnxA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.77 67.0 5.26e-01 98.4% 48.5%
2e5yA02 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.76 52.0 5.93e-01 83.9% 100.0%
3m7gA02 1.10.8.1010 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.76 58.0 5.12e-01 87.1% 55.8%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.75 64.0 5.74e-01 96.8% 68.9%
4okvE00 6.10.140.1890 Special › Helix non-globular › Helix Hairpins › 0.75 59.0 5.81e-01 87.1% 80.0%
5b1aC01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.75 62.0 6.09e-01 91.9% 85.3%
6xj1A01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.75 64.0 4.34e-01 100.0% 27.3%
1o5hA00 1.20.120.680 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Formiminotetrahydrofolate cyclodeaminase monomer, up-and-down helical bundle 0.75 66.0 4.60e-01 100.0% 41.0%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.74 60.0 6.06e-01 88.7% 88.7%
1st6A03 1.20.120.810 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vinculin, Vh2 four-helix bundle 0.74 65.0 4.44e-01 100.0% 27.5%
6yz2A01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.74 61.0 4.90e-01 91.9% 52.5%
2mpkA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.74 56.0 5.34e-01 83.9% 86.5%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.73 58.0 5.89e-01 87.1% 91.8%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 59.0 5.56e-01 91.9% 84.2%
1avoB00 1.20.120.180 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Proteasome activator pa28, C-terminal domain 0.72 63.0 4.92e-01 100.0% 47.1%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.72 59.0 5.52e-01 91.9% 82.1%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 54.0 5.54e-01 82.3% 87.9%
1rv2D04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.72 59.0 5.73e-01 95.2% 88.6%
1w9cA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.70 57.0 3.62e-01 91.9% 17.4%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.70 57.0 4.53e-01 88.7% 47.6%
2qr4A01 1.20.140.70 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Oligopeptidase f, N-terminal domain 0.70 61.0 4.61e-01 98.4% 53.8%
2ewfA02 1.20.1270.310 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.69 52.0 4.79e-01 85.5% 63.0%
2pvqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.69 52.0 4.42e-01 82.3% 54.7%
1b04A03 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.68 50.0 5.05e-01 79.0% 80.6%
1br0A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 55.0 4.60e-01 100.0% 83.3%
2ca5A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 53.0 5.33e-01 91.9% 96.8%
3besR03 6.10.140.1480 Special › Helix non-globular › Helix Hairpins › 0.65 46.0 4.81e-01 75.8% 91.1%
3bh1A02 1.20.1570.10 Mainly Alpha › Up-down Bundle › dip2346 fold › dip2346 domain like 0.53 47.0 3.91e-01 95.2% 78.2%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3864054 192.10.1.0 ↗ alpha bundles › Long alpha-hairpin › DnaK suppressor protein DksA, alpha-hairpin domain › DnaK suppressor protein DksA, alpha-hairpin domain 0.88 80.0 6.28e-01 100.0% 50.4%
3613914 3922.1.1.0 ↗ 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 0.87 77.0 7.20e-01 96.8% 80.0%
4129936 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.86 72.0 6.13e-01 90.3% 58.9%
3229095 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.85 76.0 6.46e-01 100.0% 62.0%
3469701 3755.1.1.0 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related 0.85 76.0 5.07e-01 100.0% 34.6%
3657123 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.84 76.0 6.55e-01 100.0% 65.3%
4497069 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.84 75.0 6.24e-01 100.0% 59.0%
3530780 310.2.1.2 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › MIX23 0.83 73.0 5.73e-01 100.0% 90.0%
5006188 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.83 66.0 6.74e-01 85.5% 96.7%
3462297 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.82 70.0 6.62e-01 100.0% 78.7%
3231463 632.8.1.2 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › Alpha-2-MRAP_C 0.82 68.0 5.90e-01 91.9% 60.0%
3797118 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.82 72.0 5.87e-01 100.0% 88.7%
3400862 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.82 72.0 5.22e-01 100.0% 37.1%
3416168 4177.1.1.4 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › IMD 0.82 73.0 4.91e-01 100.0% 30.0%
4031046 192.7.1.1 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › FemAB 0.81 65.0 6.62e-01 88.7% 91.7%
3491182 109.1.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C 0.81 64.0 4.83e-01 87.1% 36.9%
3330916 3846.1.1.0 ↗ alpha bundles › IcmR › IcmR › IcmR 0.81 62.0 6.51e-01 83.9% 94.5%
3470995 109.4.1.470 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › INTS2 0.80 63.0 3.80e-01 87.1% 13.1%
5048976 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.80 70.0 5.34e-01 100.0% 50.3%
3650120 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.80 70.0 4.53e-01 100.0% 23.2%
2388286 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.80 64.0 6.12e-01 93.5% 76.4%
4674 192.7.1.1 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › FemAB 0.80 67.0 6.60e-01 98.4% 89.2%
3513582 192.8.1.36 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › M_domain 0.79 70.0 5.80e-01 100.0% 57.3%
4410658 4246.1.1.2 ↗ a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 0.78 61.0 3.64e-01 85.5% 12.5%
3621681 604.1.1.139 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › DUF7799 0.78 65.0 5.71e-01 96.8% 62.1%
3973453 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.78 69.0 6.37e-01 100.0% 77.5%
3377936 3922.1.1.173 ↗ 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 › DUF3493 0.77 67.0 6.03e-01 96.8% 71.8%
3783036 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.77 66.0 4.43e-01 100.0% 35.7%
3611163 2004.1.1.480 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_21, AAA_29 0.77 68.0 4.06e-01 100.0% 39.8%
3720488 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.77 67.0 5.32e-01 100.0% 47.7%
3704 601.1.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Vinculin 0.77 62.0 5.98e-01 93.5% 77.8%
5082774 4323.1.1.0 ↗ alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C 0.76 67.0 5.06e-01 100.0% 42.0%
3960783 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.76 67.0 6.23e-01 100.0% 77.5%
5049144 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.76 64.0 4.32e-01 96.8% 24.6%
3650651 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.75 64.0 4.10e-01 100.0% 19.7%
3163939 192.6.1.0 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.75 54.0 5.73e-01 80.6% 96.0%
4028334 2004.1.1.505 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11, AAA_30 0.74 65.0 4.15e-01 100.0% 21.3%
3459313 616.1.1.1 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Ribosomal_S15 0.74 58.0 5.15e-01 85.5% 58.9%
5007978 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.73 65.0 5.05e-01 100.0% 45.9%
2081586 616.1.1.1 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Ribosomal_S15 0.72 56.0 5.62e-01 85.5% 87.1%
3600869 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.72 63.0 5.13e-01 98.4% 53.9%
2555592 5069.1.1.3 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cyt_bd_oxida_I 0.72 60.0 5.52e-01 98.4% 74.1%
3189035 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.72 58.0 5.46e-01 98.4% 74.7%
4994040 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.71 61.0 5.31e-01 100.0% 97.0%
2492497 601.33.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain › CHAD 0.69 58.0 4.50e-01 100.0% 40.9%
3665862 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.65 54.0 4.50e-01 98.4% 66.7%
D2 medium residues 280-389
PDB
Domain cluster: rep: OR050627.1__WIC41450.1__MA9V1_186__00186__D132-217