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KR053199.1__AKJ72283.1__GMA4_8__00008

Bact-Vir

KR053199.1__AKJ72283.1__GMA4_8__00008

Identity

Accession:
KR053199 ↗
Kingdom:
phage

Quality

76.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Gordonia_phage_GMA4

TaxID: 1647471

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 2-46
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ultB01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.64 45.0 2.62e-01 75.6% 15.5%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.62 49.0 3.94e-01 91.1% 59.4%
2y3aA01 3.10.20.770 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.62 49.0 3.06e-01 91.1% 22.9%
2v1yA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.62 49.0 4.02e-01 91.1% 71.9%
4avaA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.60 42.0 3.06e-01 77.8% 83.3%
2kjwA00 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.60 50.0 4.01e-01 100.0% 68.8%
2w5fB01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.59 47.0 3.34e-01 93.3% 44.7%
2r7rA04 3.30.70.2480 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 50.0 3.51e-01 100.0% 44.6%
4jn3A01 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.58 47.0 3.18e-01 100.0% 68.4%
2askA00 2.10.90.10 Mainly Beta › Ribbon › Cystine Knot Cytokines, subunit B › Cystine-knot cytokines 0.58 30.0 2.31e-01 75.6% 20.8%
1js3A03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.58 49.0 3.89e-01 100.0% 89.7%
5h5oA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 45.0 3.32e-01 86.7% 94.4%
6kghA03 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.58 46.0 3.16e-01 100.0% 88.7%
1fjrA02 2.170.180.11 Mainly Beta › Beta Complex › Methuselah ectodomain, domain 2 › Methuselah ectodomain, domain 2 0.57 48.0 3.62e-01 100.0% 94.4%
2dlbA00 3.10.20.330 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Protein of unknown function YopT 0.57 32.0 2.77e-01 100.0% 30.0%
3c7aA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 40.0 2.65e-01 75.6% 21.0%
7ylrA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.56 44.0 3.44e-01 88.9% 81.0%
2arpF02 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.56 35.0 2.99e-01 95.6% 31.9%
1mpyA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.56 41.0 2.84e-01 80.0% 59.7%
1qmeA01 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.56 42.0 3.46e-01 88.9% 63.5%
1vw3C01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.55 47.0 3.47e-01 100.0% 60.3%
7x4nE01 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.55 45.0 2.77e-01 97.8% 99.1%
5xc5A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 42.0 2.92e-01 86.7% 98.8%
1vypX00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 42.0 2.51e-01 88.9% 10.8%
1wx9A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.54 41.0 3.48e-01 88.9% 72.1%
6hj2A00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.54 41.0 2.58e-01 84.4% 75.5%
1vwxg01 6.20.370.70 Special › Other non-globular › Rhinovirus 14, subunit 4 › 0.54 32.0 3.51e-01 86.7% 54.1%
3cobC00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.54 43.0 2.68e-01 97.8% 88.5%
2g23K04 2.60.40.420 Mainly Beta › Sandwich › Immunoglobulin-like › Cupredoxins - blue copper proteins 0.54 43.0 2.98e-01 100.0% 55.3%
2yg3A02 3.90.660.10 Alpha Beta › Alpha-Beta Complex › Polyamine Oxidase; Chain A, domain 2 › 0.53 40.0 2.88e-01 91.1% 43.9%
2z2mD01 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.53 39.0 3.68e-01 84.4% 91.5%
2dziA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 40.0 3.42e-01 88.9% 79.0%
3b70A01 3.90.180.10 Alpha Beta › Alpha-Beta Complex › Quinone Oxidoreductase; Chain A, domain 1 › Medium-chain alcohol dehydrogenases, catalytic domain 0.52 43.0 2.95e-01 93.3% 61.7%
7trwA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.52 40.0 3.26e-01 93.3% 88.1%
2v0uA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 45.0 3.16e-01 100.0% 44.5%
1nz8A00 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.52 39.0 3.13e-01 95.6% 75.6%
3uxuA00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.52 38.0 2.59e-01 80.0% 71.7%
3iuzA00 3.10.180.50 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 0.52 43.0 2.63e-01 100.0% 51.2%
2kinA00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.51 42.0 2.71e-01 100.0% 25.2%
5yzzC00 2.40.330.10 Mainly Beta › Beta Barrel › At1g16640 B3 domain › DNA-binding pseudobarrel domain 0.51 37.0 2.93e-01 84.4% 83.8%
1v9kA00 3.30.2350.10 Alpha Beta › 2-Layer Sandwich › Pseudouridine synthase › Pseudouridine synthase 0.50 43.0 2.78e-01 100.0% 62.6%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4935547 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.77 64.0 6.21e-01 95.6% 84.0%
4994655 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.77 62.0 6.05e-01 93.3% 86.0%
4932084 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.75 62.0 6.01e-01 95.6% 84.0%
4978275 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.74 62.0 5.87e-01 95.6% 78.2%
4951589 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.74 61.0 5.92e-01 95.6% 84.0%
4973337 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.74 61.0 5.72e-01 95.6% 76.4%
4982789 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.74 59.0 5.29e-01 95.6% 63.1%
5019734 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.73 59.0 5.81e-01 95.6% 84.0%
3977412 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.69 56.0 5.48e-01 93.3% 91.8%
3402509 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.67 50.0 4.28e-01 88.9% 75.3%
4183435 7531.1.1.1 ↗ a/b three-layered sandwiches › Carbamate kinase-like › Carbamate kinase-like › Carbamate kinase-like › AA_kinase 0.67 48.0 3.01e-01 77.8% 15.5%
4081797 3860.1.1.158 ↗ alpha bundles › Myosin VI lever arm › Myosin VI lever arm › Myosin VI lever arm › ThrE 0.65 38.0 2.64e-01 97.8% 18.6%
3740041 2004.1.1.325 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TRAPPC-Trs85 0.63 40.0 2.54e-01 88.9% 11.2%
3311237 304.52.1.1 ↗ a+b two layers › Alpha-beta plaits › YbeD/HP0495-like › YbeD/HP0495-like › DUF493 0.63 51.0 4.26e-01 100.0% 81.1%
4279139 3819.2.1.1 ↗ alpha complex topology › CRISPR-associated endonuclease Cas9 alpha-helical lobe › F. novicida CRISPR-associated endonuclease Cas9 alpha-helical lobe › F. novicida CRISPR-associated endonuclease Cas9 alpha-helical lobe › Csx12 0.62 39.0 2.15e-01 88.9% 3.6%
3178264 109.4.1.1588 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF27584, PF27595, PF30849 0.60 41.0 2.24e-01 73.3% 11.7%
4072334 218.1.1.8 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.60 40.0 3.09e-01 91.1% 31.0%
4965204 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.60 46.0 3.47e-01 86.7% 64.2%
3410353 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 40.0 2.55e-01 73.3% 23.0%
4989936 304.51.1.7 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR_Cas6 0.58 46.0 3.46e-01 100.0% 90.7%
1877618 330.15.1.1 ↗ a+b two layers › dsRBD-like › VtrA protein periplasmic domain › VtrA protein periplasmic domain › VtrA_C 0.57 37.0 3.04e-01 100.0% 32.2%
4931686 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.57 43.0 3.23e-01 86.7% 66.9%
3925890 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.57 37.0 3.03e-01 100.0% 30.5%
3656521 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.56 43.0 3.52e-01 91.1% 60.0%
5074448 2003.1.2.300 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › GGR_cat 0.56 48.0 2.81e-01 100.0% 75.3%
3935753 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.55 39.0 2.62e-01 80.0% 29.5%
4439247 7523.1.1.15 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › LysR_substrate 0.55 44.0 3.52e-01 97.8% 86.7%
3785339 3294.1.1.1 ↗ alpha complex topology › FAS type I helical domain › FAS type I helical domain › FAS type I helical domain › FAS_I_H 0.55 43.0 2.61e-01 88.9% 39.1%
4073485 218.1.1.8 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.55 43.0 3.41e-01 91.1% 49.5%
4298574 3019.1.1.1 ↗ beta sandwiches › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › Flagellin_IN 0.54 46.0 3.63e-01 100.0% 93.0%
5055211 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.54 45.0 2.79e-01 100.0% 68.8%
5051610 2003.1.2.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.54 45.0 2.69e-01 100.0% 77.1%
3483771 101.1.2.394 ↗ alpha arrays › HTH › HTH › winged helix domain › eWH_GTF3C1 0.54 38.0 3.03e-01 75.6% 91.6%
3430929 198.1.1.4 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › DUF3456 0.54 43.0 3.04e-01 91.1% 28.0%
4313114 378.1.1.30 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › PF30178 0.53 44.0 3.29e-01 95.6% 75.0%
3240822 7523.1.1.20 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Lig_chan-Glu_bd 0.53 40.0 2.74e-01 84.4% 54.2%
3560843 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 39.0 3.02e-01 84.4% 64.5%
5078994 2003.1.2.300 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › GGR_cat 0.52 45.0 2.63e-01 100.0% 74.6%
4958814 3457.1.1.3 ↗ alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Arc_PepC_II 0.52 42.0 2.58e-01 88.9% 16.2%
3410614 320.1.1.0 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain 0.52 38.0 2.95e-01 80.0% 36.2%
3653800 377.12.1.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › RPL34 › RPL34 › Ribosomal_L34e 0.52 42.0 3.48e-01 95.6% 52.9%
3987428 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.51 42.0 3.26e-01 91.1% 42.0%
4999507 330.7.1.2 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain › HicA_toxin 0.51 36.0 3.13e-01 75.6% 84.3%
4093401 4187.2.1.1 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 › NAGPA 0.51 34.0 2.68e-01 95.6% 33.7%
4472559 2005.1.1.30 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › BshC 0.50 42.0 2.54e-01 100.0% 28.2%
3193726 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.50 41.0 2.86e-01 91.1% 30.3%