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MN988490.1__QIG68370.1__EVB59_036__00036

Bact-Vir

MN988490.1__QIG68370.1__EVB59_036__00036

Identity

Accession:
MN988490 ↗
Kingdom:
phage

Quality

78.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_RHph_Y3_1

TaxID: 2509775

Cluster

View cluster (5 members)

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 3-46
PDB
Domain cluster: representative
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3anwA02 3.40.5.50 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.81 72.0 6.56e-01 100.0% 79.3%
2e9xD02 3.40.5.60 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.80 70.0 6.37e-01 100.0% 85.0%
2hjqA01 3.40.5.20 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › YqbF domain 0.75 60.0 5.94e-01 100.0% 89.1%
2e9xB01 3.40.5.50 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.71 61.0 5.39e-01 100.0% 68.2%
3jc6C00 1.20.58.2050 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 56.0 3.88e-01 100.0% 28.9%
3pp9B00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.62 48.0 3.28e-01 88.6% 62.6%
4jn3A01 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.62 49.0 3.22e-01 93.2% 67.0%
3agjF01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.61 47.0 3.56e-01 93.2% 88.2%
2fyiC01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.59 43.0 3.27e-01 84.1% 37.8%
2q3fA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 41.0 2.81e-01 75.0% 35.2%
5eqjB01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.58 43.0 3.79e-01 84.1% 60.6%
8es5A01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 42.0 3.19e-01 93.2% 89.1%
3fwlA02 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.56 46.0 2.75e-01 100.0% 48.2%
1mdbA02 3.40.50.980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.56 40.0 2.74e-01 79.5% 56.3%
3tm8B00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.54 41.0 2.56e-01 88.6% 31.6%
2z5bB01 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.54 41.0 3.15e-01 88.6% 71.4%
3ihlB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 40.0 2.66e-01 88.6% 82.1%
1nz8A00 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.54 42.0 3.31e-01 100.0% 79.8%
1kfiA04 3.30.310.50 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Alpha-D-phosphohexomutase, C-terminal domain 0.53 41.0 3.25e-01 100.0% 96.0%
6lxgA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.53 42.0 3.77e-01 100.0% 98.6%
4huqA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 42.0 2.66e-01 97.7% 22.5%
4jklA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 41.0 2.90e-01 100.0% 49.7%
2yz2B00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 41.0 2.66e-01 97.7% 24.3%
4melA02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 38.0 3.15e-01 88.6% 60.6%
2dziA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.50 36.0 3.19e-01 86.4% 81.5%
3wisA00 3.40.50.1950 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavin prenyltransferase-like 0.50 37.0 2.53e-01 84.1% 19.4%
2mizA00 2.60.40.2900 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 37.0 2.73e-01 88.6% 78.8%
ECOD (68)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5000438 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.89 77.0 6.61e-01 100.0% 61.4%
4967982 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.89 81.0 8.11e-01 100.0% 97.7%
5069341 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.88 80.0 7.63e-01 100.0% 90.0%
4981952 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.87 76.0 7.35e-01 100.0% 86.0%
4939413 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.86 79.0 7.52e-01 100.0% 96.0%
3716713 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.86 77.0 7.40e-01 100.0% 90.0%
5024995 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.85 77.0 7.26e-01 100.0% 83.0%
4956745 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.85 76.0 7.32e-01 100.0% 90.0%
5069643 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 77.0 7.19e-01 100.0% 84.9%
5066664 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 71.0 7.11e-01 97.7% 93.3%
4927873 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 73.0 6.58e-01 100.0% 71.7%
4932061 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.84 73.0 7.27e-01 100.0% 95.6%
5028408 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.84 75.0 7.25e-01 100.0% 92.0%
5055750 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 76.0 7.26e-01 100.0% 90.0%
5045837 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 75.0 6.72e-01 100.0% 75.0%
5011186 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 74.0 6.68e-01 100.0% 73.3%
4951589 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.83 76.0 7.24e-01 100.0% 90.0%
5044096 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 73.0 7.06e-01 97.7% 88.0%
4982789 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 73.0 6.41e-01 100.0% 67.7%
5015232 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 74.0 6.87e-01 100.0% 80.0%
4983060 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 71.0 5.86e-01 100.0% 53.8%
4081421 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.83 75.0 7.23e-01 100.0% 90.0%
4935547 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 74.0 7.12e-01 100.0% 90.0%
4932084 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 74.0 7.12e-01 100.0% 90.0%
4973337 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 74.0 6.84e-01 100.0% 81.8%
4993371 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.82 71.0 6.86e-01 100.0% 86.0%
5019734 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.82 74.0 7.07e-01 100.0% 90.0%
4956454 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 67.0 6.29e-01 100.0% 74.5%
4999890 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.82 74.0 6.64e-01 100.0% 73.3%
4358525 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.82 72.0 6.89e-01 100.0% 86.0%
4933005 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 72.0 6.49e-01 100.0% 75.0%
5036149 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 70.0 6.98e-01 100.0% 95.6%
4934987 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 67.0 6.68e-01 97.7% 91.1%
4994655 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 72.0 6.93e-01 100.0% 92.0%
3600426 4076.3.1.3 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › SLD5_C 0.81 71.0 6.61e-01 100.0% 87.3%
4536596 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 70.0 6.86e-01 100.0% 89.6%
4944185 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 72.0 6.28e-01 100.0% 67.7%
5031576 4076.3.1.8 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PSF2_N 0.81 70.0 6.49e-01 97.7% 80.0%
3691283 4076.3.1.9 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PSF1_C 0.80 70.0 6.79e-01 100.0% 88.0%
4946969 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.80 71.0 6.86e-01 100.0% 92.0%
4230268 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.80 69.0 6.94e-01 97.7% 95.6%
4280403 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.80 67.0 6.74e-01 97.7% 93.3%
4169249 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.79 68.0 6.69e-01 100.0% 89.6%
4641420 4076.4.1.1 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain › PriS_C 0.77 66.0 5.22e-01 100.0% 47.8%
4269273 4076.4.1.1 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain › PriS_C 0.76 65.0 6.51e-01 97.7% 95.6%
3265780 3529.1.1.1 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Vault 0.76 65.0 5.82e-01 100.0% 70.0%
4025149 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.75 64.0 5.84e-01 100.0% 88.3%
4304365 4076.3.1.8 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PSF2_N 0.75 64.0 5.56e-01 100.0% 64.3%
5038458 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.74 62.0 5.99e-01 95.5% 92.0%
3873942 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 60.0 5.37e-01 100.0% 86.2%
3918340 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.70 58.0 5.12e-01 100.0% 80.0%
3510029 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.67 56.0 5.14e-01 97.7% 95.0%
3509345 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.67 55.0 4.30e-01 97.7% 54.3%
3557677 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.66 55.0 4.88e-01 100.0% 85.7%
3711002 3075.1.1.0 ↗ a+b two layers › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA 0.62 47.0 4.25e-01 86.4% 84.6%
3237292 209.1.1.0 ↗ a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like 0.62 48.0 3.84e-01 88.6% 57.9%
3534068 101.1.2.593 ↗ alpha arrays › HTH › HTH › winged helix domain › PheRS_DBD3, PheRS_DBD2 0.61 52.0 3.90e-01 97.7% 97.3%
4971406 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.58 49.0 4.13e-01 100.0% 85.0%
3988189 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.57 46.0 3.98e-01 100.0% 83.7%
3601608 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.55 40.0 2.65e-01 81.8% 19.0%
3800293 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.55 40.0 3.42e-01 90.9% 72.0%
4991377 1075.1.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain 0.54 38.0 2.43e-01 77.3% 35.3%
4975562 217.1.1.0 ↗ a+b complex topology › FAD-binding domain-like › FAD-binding domain › FAD-binding domain 0.54 39.0 2.47e-01 79.5% 27.0%
5022463 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.53 42.0 3.84e-01 97.7% 89.2%
3199589 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 41.0 3.47e-01 100.0% 75.6%
4448936 558.1.1.0 ↗ alpha duplicates or obligate multimers › Lis-homology dimerization domain › Lis-homology dimerization domain › Lis-homology dimerization domain 0.52 38.0 2.23e-01 79.5% 39.3%
4390215 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.52 40.0 3.60e-01 100.0% 76.0%
3253067 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.51 37.0 3.01e-01 81.8% 77.0%