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NC_073373.1__YP_010751749.1__QDA09_gp04__00004

Bact-Vir

NC_073373.1__YP_010751749.1__QDA09_gp04__00004

Identity

Accession:
NC_073373 ↗
Kingdom:
phage

Quality

81.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Hodgkinviridae› Metamorphoovirus› Microbacterium_phage_Tyrumbra

TaxID: 2596974

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 7-78
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.75 58.0 5.60e-01 83.3% 73.4%
5k3hB04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.73 46.0 3.73e-01 70.8% 35.3%
4m70B00 1.10.246.200 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › WPP domain 0.72 65.0 5.98e-01 97.2% 92.3%
2jrmA00 1.10.10.620 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › ribosome modulation factor like domain 0.72 36.0 3.88e-01 70.8% 56.7%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 42.0 4.25e-01 81.9% 60.6%
4id0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.68 40.0 3.43e-01 76.4% 37.5%
4iloA00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 42.0 2.87e-01 76.4% 19.1%
4qgpB00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.67 45.0 3.90e-01 76.4% 45.8%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.66 41.0 4.57e-01 76.4% 79.3%
1mhyG01 1.20.1280.10 Mainly Alpha › Up-down Bundle › Monooxygenase › Methane monooxygenase, gamma chain, domain 1 0.66 36.0 3.78e-01 81.9% 58.8%
2y1eA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.65 51.0 4.78e-01 84.7% 72.4%
4rfsS00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.63 57.0 4.17e-01 100.0% 70.1%
4okvE00 6.10.140.1890 Special › Helix non-globular › Helix Hairpins › 0.63 45.0 4.73e-01 80.6% 83.1%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.62 41.0 4.27e-01 81.9% 73.1%
1b25A02 1.10.569.10 Mainly Alpha › Orthogonal Bundle › Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2 › Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2 0.62 48.0 3.62e-01 84.7% 43.8%
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.62 40.0 3.87e-01 72.2% 59.3%
3k2jA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.61 43.0 3.69e-01 76.4% 91.7%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.61 46.0 3.77e-01 81.9% 85.1%
3ns4A00 1.10.357.110 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Vacuolar protein sorting-associated protein 53, C-terminus 0.60 42.0 3.03e-01 72.2% 25.4%
1ij5A01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 44.0 4.31e-01 76.4% 75.0%
2q9rA01 1.20.1590.10 Mainly Alpha › Up-down Bundle › YP_001051499.1 fold like › YP_001051499.1 domain like 0.59 47.0 3.55e-01 91.7% 89.2%
7zxkC01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.58 44.0 3.53e-01 81.9% 92.0%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.58 42.0 4.24e-01 76.4% 74.3%
1t72A02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.58 42.0 3.81e-01 76.4% 56.1%
3wctD00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.58 42.0 3.42e-01 77.8% 78.9%
1kxpD04 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.58 47.0 4.61e-01 95.8% 84.4%
1yrtA03 1.10.150.920 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.58 35.0 4.16e-01 77.8% 91.7%
1kqfC00 1.20.950.20 Mainly Alpha › Up-down Bundle › Fumarate Reductase Cytochrome B subunit › Transmembrane di-heme cytochromes, Chain C 0.57 47.0 3.35e-01 90.3% 68.1%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.56 41.0 4.04e-01 76.4% 79.2%
3ic9A02 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.56 45.0 4.60e-01 88.9% 94.3%
2a3qA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.56 49.0 4.21e-01 97.2% 80.5%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.55 48.0 3.78e-01 97.2% 55.9%
3v5uA01 6.10.280.80 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › NCX, peripheral helical region 0.55 40.0 3.97e-01 76.4% 81.6%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.55 36.0 3.63e-01 76.4% 66.2%
3hr0B01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.54 41.0 4.00e-01 80.6% 84.8%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.54 43.0 3.77e-01 87.5% 80.0%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.54 41.0 3.68e-01 81.9% 57.8%
3cazB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.54 43.0 3.07e-01 87.5% 78.6%
4w4kA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.53 39.0 3.71e-01 76.4% 72.0%
4gycA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.53 44.0 3.26e-01 98.6% 96.8%
3ezhA00 1.20.120.960 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase NarX, sensor domain 0.52 46.0 3.97e-01 100.0% 68.4%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.52 40.0 3.94e-01 81.9% 89.3%
3okqA00 1.20.58.1540 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Actin interacting protein 3, C-terminal domain 0.52 35.0 2.97e-01 70.8% 60.0%
1kxpD02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.51 44.0 4.18e-01 100.0% 85.2%
1u7lA02 1.20.1460.10 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › subunit c (vma5p) of the yeast v-atpase, domain 2 0.51 42.0 3.21e-01 94.4% 70.5%
3s6jE02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.51 35.0 3.62e-01 73.6% 98.6%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.51 44.0 3.82e-01 100.0% 83.1%
5nl6A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 37.0 3.25e-01 77.8% 54.6%
4uavA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.50 40.0 3.78e-01 84.7% 85.9%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3674195 103.9.1.1 ↗ alpha arrays › RuvA-C › RanGAP2 N-terminal domain › RanGAP2 N-terminal domain › WPP 0.77 72.0 6.23e-01 100.0% 86.7%
3487880 5063.1.1.0 ↗ alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK 0.77 58.0 6.07e-01 77.8% 98.5%
3461627 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.76 60.0 6.14e-01 84.7% 90.0%
3591935 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.75 66.0 6.20e-01 100.0% 87.8%
184677 6028.1.1.1 ↗ alpha bundles › Ribosome modulation factor › Ribosome modulation factor › Ribosome modulation factor › RMF 0.72 36.0 3.88e-01 70.8% 56.7%
3628497 4082.1.1.0 ↗ alpha duplicates or obligate multimers › Hairy Orange domain › Hairy Orange domain › Hairy Orange domain 0.71 38.0 4.50e-01 83.3% 76.0%
4207520 6056.1.1.2 ↗ alpha arrays › SP1917-like › SP1917-like › SP1917-like › PrmC_N 0.67 55.0 5.44e-01 90.3% 85.3%
3731914 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.65 51.0 4.05e-01 83.3% 46.4%
3935393 106.1.1.8 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › HisK-N-like 0.65 48.0 3.91e-01 80.6% 68.3%
4259491 131.1.1.4 ↗ alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD,HD_assoc 0.65 58.0 3.60e-01 100.0% 61.7%
3940867 632.22.1.67 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › DUF842 0.65 53.0 4.90e-01 91.7% 94.7%
3709879 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 0.64 52.0 5.15e-01 88.9% 86.7%
3572161 541.1.1.12 ↗ alpha duplicates or obligate multimers › Dimerization-anchoring domain of cAMP-dependent type II PK regulatory subunit › Dimerization-anchoring domain of cAMP-dependent type II PK regulatory subunit › Dimerization-anchoring domain of cAMP-dependent type II PK regulatory subunit › PF30825 0.64 46.0 4.26e-01 81.9% 60.0%
5047411 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.64 57.0 4.16e-01 100.0% 61.5%
4012501 5059.1.1.42 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA, SLC35F, DUF3955 0.63 49.0 3.18e-01 83.3% 96.2%
3909150 5063.1.1.15 ↗ alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › OCIA 0.62 48.0 4.83e-01 87.5% 93.3%
3588816 6056.1.1.2 ↗ alpha arrays › SP1917-like › SP1917-like › SP1917-like › PrmC_N 0.62 49.0 5.01e-01 90.3% 91.4%
3594129 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.60 42.0 2.97e-01 76.4% 24.7%
5004053 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.57 43.0 3.89e-01 80.6% 62.0%
4045132 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.57 42.0 3.60e-01 76.4% 51.8%
4015450 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.56 41.0 4.16e-01 79.2% 81.4%
4029168 4984.1.1.0 ↗ alpha bundles › Duffy-binding-like domain, C-terminal subdomain › Duffy-binding-like domain, C-terminal subdomain › Duffy-binding-like domain, C-terminal subdomain 0.55 40.0 3.31e-01 77.8% 46.2%
4145392 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 0.55 42.0 2.97e-01 81.9% 27.9%
3598168 3755.1.1.0 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related 0.54 42.0 3.16e-01 81.9% 38.8%
3483479 101.8.1.0 ↗ alpha arrays › HTH › An anticodon-binding domain of class I aminoacyl-tRNA synthetases › An anticodon-binding domain of class I aminoacyl-tRNA synthetases 0.54 40.0 3.02e-01 80.6% 35.1%
3595910 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.54 39.0 3.81e-01 77.8% 71.2%
5018556 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.53 46.0 3.96e-01 95.8% 85.2%
3456370 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.53 41.0 3.16e-01 81.9% 41.9%
3924650 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.53 41.0 3.64e-01 81.9% 60.0%
3489761 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.53 47.0 3.33e-01 100.0% 86.7%
3424878 5071.1.1.1 ↗ alpha bundles › cytochrome bc1 complex 11 kDa protein-like › Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) › Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) › UCR_hinge 0.52 39.0 4.03e-01 84.7% 87.0%
3387205 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 0.50 39.0 3.59e-01 81.9% 82.2%
3473158 109.62.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › AFF4 C-terminal homology domain › AFF4 C-terminal homology domain 0.50 39.0 2.67e-01 87.5% 62.6%