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OM868079.1__UPT53212.1__X__00087

Bact-Vir

OM868079.1__UPT53212.1__X__00087

Identity

Accession:
OM868079 ↗
Kingdom:
phage

Quality

80.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Synechococcus_phage_Yong-M4-211

TaxID: 2928849

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 medium residues 4-36
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1nh8A03 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 58.0 4.75e-01 100.0% 95.5%
4v19I01 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.62 50.0 4.36e-01 100.0% 66.7%
2hvfA00 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.61 49.0 4.44e-01 100.0% 73.1%
3ezjA03 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.60 41.0 3.87e-01 90.9% 90.9%
3uaqB01 2.40.128.250 Mainly Beta › Beta Barrel › Lipocalin › 0.53 40.0 3.03e-01 100.0% 90.9%
3w7tA04 3.30.1390.40 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L30p/L7e 0.53 37.0 3.69e-01 97.0% 96.9%
2e7zA02 3.40.50.740 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.50 39.0 2.39e-01 100.0% 66.8%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3514894 386.1.1.337 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › CCDC174_GRSR 0.72 52.0 5.35e-01 93.9% 86.7%
3274093 6108.1.1.11 ↗ alpha bundles › Middle and GTPase effector domains in dynamin-related proteins › Middle and GTPase effector domains in dynamin-related proteins › Middle and GTPase effector domains in dynamin-related proteins › Dynamin_N 0.68 55.0 3.03e-01 100.0% 6.3%
D2 medium residues 54-90
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1a62A01 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.87 77.0 7.18e-01 100.0% 80.4%
2qbyA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.85 71.0 4.58e-01 97.3% 21.4%
1e7lA02 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.84 70.0 6.31e-01 100.0% 67.3%
2r9iA00 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.81 56.0 4.48e-01 73.0% 42.3%
1kblA05 1.20.80.30 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.80 66.0 5.11e-01 100.0% 70.8%
2ld7A00 6.10.160.20 Special › Helix non-globular › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.79 65.0 4.91e-01 97.3% 38.3%
4nv0A02 1.10.150.340 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain 0.78 54.0 4.14e-01 73.0% 39.0%
5nohA00 1.20.120.1350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pneumovirus matrix protein 2 (M2), zinc-binding domain 0.77 63.0 4.71e-01 100.0% 76.7%
1sw2A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.77 60.0 3.95e-01 91.9% 21.7%
2jdiH02 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 0.75 50.0 4.85e-01 70.3% 69.0%
1a3qA01 2.60.40.340 Mainly Beta › Sandwich › Immunoglobulin-like › Rel homology domain (RHD), DNA-binding domain 0.75 53.0 3.34e-01 75.7% 21.2%
4i43B02 3.30.43.40 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain 0.74 52.0 3.69e-01 75.7% 27.2%
3l0oA01 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.73 57.0 5.34e-01 94.6% 69.4%
2glzA00 3.30.1330.130 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › 0.73 55.0 3.67e-01 83.8% 76.5%
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.72 48.0 4.13e-01 70.3% 50.8%
3obfA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.70 58.0 3.78e-01 97.3% 60.8%
1mdyA00 4.10.280.10 Few Secondary Structures › Irregular › MYOD Basic-Helix-Loop-Helix Domain, subunit B › Helix-loop-helix DNA-binding domain 0.70 54.0 4.61e-01 100.0% 50.0%
7z67A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.70 48.0 2.95e-01 73.0% 12.4%
1e6cA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.69 52.0 3.38e-01 83.8% 21.8%
2o7gA00 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.68 59.0 4.48e-01 100.0% 67.0%
7cgpJ01 1.10.287.810 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Mitochondrial import inner membrane translocase subunit tim13 like domains 0.68 49.0 3.83e-01 78.4% 42.7%
3sllA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.67 48.0 4.17e-01 78.4% 52.5%
4j0eA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.67 50.0 3.12e-01 81.1% 18.3%
3lphC00 6.10.140.630 Special › Helix non-globular › Helix Hairpins › 0.66 46.0 3.91e-01 94.6% 46.6%
3axjB01 1.20.58.190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 0.65 49.0 3.21e-01 81.1% 22.6%
1hjrA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.62 50.0 3.39e-01 100.0% 22.8%
1gkuB03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.61 52.0 3.41e-01 100.0% 82.2%
4c2dA02 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.61 54.0 4.10e-01 100.0% 83.5%
1m3sB00 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.58 45.0 3.04e-01 97.3% 66.7%
2z3xA00 6.10.10.80 Special › Helix non-globular › Helicase, Ruva Protein; domain 3 › Small, acid-soluble spore protein, alpha/beta type-like 0.57 50.0 4.37e-01 100.0% 100.0%
1e2tA01 6.10.140.1930 Special › Helix non-globular › Helix Hairpins › 0.53 44.0 3.58e-01 94.6% 74.6%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3249598 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.94 86.0 6.78e-01 100.0% 52.9%
3172901 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.94 73.0 7.55e-01 83.8% 88.6%
3172891 130.1.1.16 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Ish1 0.93 77.0 6.95e-01 97.3% 68.0%
3208160 130.1.1.16 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Ish1 0.92 83.0 7.47e-01 100.0% 74.0%
4113879 1.1.7.2 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Ribosomal_L3 0.90 80.0 4.67e-01 100.0% 13.7%
3252664 130.1.1.31 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › RNF34L-like_3rd 0.90 80.0 6.96e-01 100.0% 67.3%
4428371 130.1.1.3 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.88 71.0 6.75e-01 91.9% 75.6%
4260463 130.1.1.3 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.88 77.0 7.26e-01 100.0% 82.2%
4026837 7577.1.1.1 ↗ a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Aminotran_1_2 0.88 78.0 4.34e-01 100.0% 8.6%
3943133 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.88 76.0 7.17e-01 100.0% 82.2%
4569255 2007.1.2.9 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › DUF3798 0.87 71.0 4.95e-01 91.9% 29.6%
3249191 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.85 68.0 4.17e-01 91.9% 15.1%
4433184 130.1.1.3 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.85 73.0 6.44e-01 100.0% 67.3%
3254598 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.84 74.0 5.98e-01 100.0% 52.9%
4959048 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.84 73.0 6.59e-01 97.3% 72.0%
3739606 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.84 70.0 5.42e-01 97.3% 43.8%
3724166 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.83 71.0 5.97e-01 100.0% 56.9%
3568558 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.83 71.0 6.15e-01 100.0% 61.7%
3813837 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.81 57.0 4.42e-01 73.0% 44.0%
3214333 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 0.80 54.0 3.71e-01 70.3% 22.6%
3507079 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.80 68.0 6.67e-01 100.0% 92.5%
3702706 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.79 54.0 4.19e-01 73.0% 86.3%
3298325 3846.1.1.0 ↗ alpha bundles › IcmR › IcmR › IcmR 0.78 55.0 5.18e-01 75.7% 75.6%
3282638 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.78 55.0 3.69e-01 75.7% 22.2%
56801 150.6.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › SO2669-like › SO2669-like 0.78 55.0 4.54e-01 75.7% 46.9%
3995535 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.77 52.0 3.95e-01 70.3% 46.3%
4974358 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.76 58.0 4.29e-01 89.2% 31.4%
5003241 102.7.1.1 ↗ alpha arrays › HhH/H2TH › Baseplate wedge protein gp7 domain IV › Baseplate wedge protein gp7 domain IV › Tail_P2_I 0.75 62.0 4.42e-01 100.0% 31.3%
4961346 3805.1.1.1 ↗ alpha bundles › Hypothetical protein TTHB059 › Hypothetical protein TTHB059 › Hypothetical protein TTHB059 › DUF3209 0.74 50.0 3.48e-01 70.3% 60.0%
3655557 148.1.1.25 ↗ alpha arrays › Histone-like › Histone-related › Histone › Tim17 0.74 55.0 3.82e-01 83.8% 26.4%
4499267 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.72 51.0 3.38e-01 75.7% 22.0%
3972191 101.1.9.82 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain › MerR-DNA-bind, MerR_1 0.72 54.0 3.59e-01 86.5% 21.4%
5052725 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.70 51.0 4.02e-01 89.2% 40.0%
3961960 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.70 54.0 4.03e-01 83.8% 37.8%
3291724 101.1.3.0 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like 0.69 57.0 4.44e-01 100.0% 41.1%
3769015 130.1.1.2 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › LEM 0.69 55.0 5.14e-01 100.0% 72.0%
3482354 283.1.1.1 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › Creatinase/aminopeptidase › Creatinase/aminopeptidase › Peptidase_M24 0.68 57.0 3.70e-01 94.6% 33.7%
3600020 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.68 50.0 2.82e-01 81.1% 13.3%
3609066 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.67 51.0 3.61e-01 83.8% 27.0%
4986734 103.8.1.1 ↗ alpha arrays › RuvA-C › Hypothetical protein AF0491, middle domain › Hypothetical protein AF0491, middle domain › SBDS_domain_II 0.65 53.0 4.35e-01 100.0% 75.0%
3651198 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.64 52.0 4.56e-01 94.6% 60.0%
3245021 110.1.1.0 ↗ alpha arrays › DEATH domain › DEATH domain › DEATH domain 0.64 48.0 3.95e-01 100.0% 43.3%
4010451 3788.1.1.15 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › PF27202 0.63 57.0 4.44e-01 100.0% 80.0%
3573038 4207.1.1.99 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › PF28139 0.63 57.0 4.21e-01 100.0% 100.0%
3480954 130.1.1.2 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › LEM 0.63 49.0 4.79e-01 100.0% 82.2%
3256882 103.8.1.1 ↗ alpha arrays › RuvA-C › Hypothetical protein AF0491, middle domain › Hypothetical protein AF0491, middle domain › SBDS_domain_II 0.62 48.0 4.14e-01 97.3% 82.9%
3384197 101.1.17.40 ↗ alpha arrays › HTH › HTH › FF domain › FF, FF_PRPF40A 0.59 51.0 3.63e-01 100.0% 58.2%
4300120 605.1.1.108 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › GrpE 0.57 49.0 4.19e-01 91.9% 61.8%
4242982 4120.1.1.1 ↗ few secondary structure elements › Tim10/DDP › Tim10/DDP › Tim10/DDP › zf-Tim10_DDP 0.56 50.0 4.02e-01 100.0% 60.0%
4025873 4120.1.1.1 ↗ few secondary structure elements › Tim10/DDP › Tim10/DDP › Tim10/DDP › zf-Tim10_DDP 0.55 47.0 3.79e-01 94.6% 87.1%