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MN988534.1__QIG73996.1__EVC06_221__00221

Bact-Vir

MN988534.1__QIG73996.1__EVC06_221__00221

Identity

Accession:
MN988534 ↗
Kingdom:
phage

Quality

89.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Trinifflemingvirus› Rhizobium_phage_RHph_N34

TaxID: 2509586

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 2-64
PDB
Domain cluster: representative
CATH (44)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2yn5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.72 45.0 4.17e-01 100.0% 50.6%
1qr4A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.71 45.0 4.07e-01 100.0% 47.1%
4kncA02 2.60.120.1380 Mainly Beta › Sandwich › Jelly Rolls › C-terminal carbohydrate-binding module 0.70 52.0 4.22e-01 100.0% 42.7%
1o5uA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.68 38.0 3.43e-01 100.0% 39.8%
6b9tF01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.67 37.0 2.98e-01 100.0% 27.2%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.67 49.0 4.16e-01 100.0% 45.9%
6m3aA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 44.0 4.42e-01 100.0% 66.7%
1tq5A02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.65 38.0 3.01e-01 100.0% 28.8%
4gi3C00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.65 39.0 4.09e-01 100.0% 66.7%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.64 49.0 4.31e-01 100.0% 55.2%
2i45D00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.62 36.0 3.12e-01 100.0% 35.4%
2dlgA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 41.0 3.90e-01 100.0% 55.0%
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.62 47.0 3.78e-01 100.0% 39.4%
1u9pA00 1.10.1220.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant › Met repressor-like 0.61 49.0 4.31e-01 90.5% 93.8%
2f4nB02 2.40.30.90 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Bacterial fluorinating enzyme like 0.60 53.0 4.67e-01 100.0% 68.1%
1mt1B00 3.50.20.10 Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Pyruvoyl-Dependent Histidine Decarboxylase, subunit B 0.60 52.0 4.34e-01 100.0% 58.9%
2k57A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.60 45.0 4.87e-01 100.0% 92.7%
1u1sA00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.60 41.0 4.12e-01 100.0% 69.7%
3vzbB02 2.60.200.40 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.59 51.0 3.62e-01 98.4% 95.4%
1kq1H00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.58 41.0 4.11e-01 100.0% 71.2%
3nrnA02 3.90.660.50 Alpha Beta › Alpha-Beta Complex › Polyamine Oxidase; Chain A, domain 2 › 0.58 50.0 3.69e-01 100.0% 46.6%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.57 39.0 3.67e-01 100.0% 57.9%
1ji6A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.57 46.0 3.38e-01 100.0% 34.0%
4ewtA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 45.0 3.80e-01 90.5% 93.9%
3i6sA03 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.56 49.0 3.93e-01 100.0% 96.9%
2n17A00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.55 35.0 3.67e-01 100.0% 71.4%
5c9iD01 1.10.439.10 Mainly Alpha › Orthogonal Bundle › Penicillin Amidohydrolase; domain 1 › Penicillin Amidohydrolase, domain 1 0.55 41.0 3.15e-01 82.5% 68.9%
3icyA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 34.0 2.79e-01 74.6% 33.1%
2jz6A01 2.30.170.40 Mainly Beta › Roll › Ribosomal Protein L24e; Chain: T; › Ribosomal protein L28/L24 0.55 32.0 3.42e-01 100.0% 68.0%
3r4cA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.54 37.0 3.27e-01 73.0% 99.0%
1ywlA00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.54 40.0 3.50e-01 100.0% 52.1%
3cjlA00 3.10.20.850 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Protein of unknown function DUF3861 0.54 42.0 3.86e-01 90.5% 76.1%
2z8lA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.54 46.0 3.83e-01 100.0% 78.6%
1u3eM02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 41.0 3.98e-01 100.0% 75.0%
1olmC01 3.40.525.10 Alpha Beta › 3-Layer(aba) Sandwich › Phosphatidylinositol Transfer Protein Sec14p › CRAL-TRIO lipid binding domain 0.53 37.0 2.50e-01 84.1% 17.0%
3h1qA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 44.0 3.74e-01 100.0% 76.5%
1ca1A02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.52 46.0 3.77e-01 100.0% 75.0%
1wh2A01 3.30.1490.40 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › GYF domain 0.51 32.0 3.25e-01 98.4% 62.3%
1y96A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.51 41.0 3.66e-01 100.0% 62.8%
1o54A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.51 42.0 4.04e-01 100.0% 79.2%
4bg8A01 3.30.420.430 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.50 42.0 3.47e-01 100.0% 74.4%
2lw3A00 2.60.40.2880 Mainly Beta › Sandwich › Immunoglobulin-like › MmpS1-5, C-terminal soluble domain 0.50 32.0 2.90e-01 100.0% 44.4%
4uzgA01 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 43.0 3.31e-01 100.0% 40.4%
1icrA00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.50 40.0 2.97e-01 100.0% 59.3%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4945546 10.7.1.0 ↗ beta sandwiches › jelly-roll › Hypothetical protein TM1070 › Hypothetical protein TM1070 0.75 49.0 4.08e-01 100.0% 40.0%
4958689 821.1.1.14 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › DUF2797 0.75 44.0 4.55e-01 100.0% 61.7%
4158495 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.67 48.0 4.28e-01 100.0% 53.3%
3266103 10.12.1.13 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Pirin 0.65 38.0 3.14e-01 100.0% 32.7%
3415617 379.1.1.1 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors › Kazal_1 0.64 39.0 4.26e-01 100.0% 78.0%
5054262 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.64 40.0 3.56e-01 100.0% 45.6%
3567640 4187.2.1.0 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 0.63 36.0 3.97e-01 100.0% 70.0%
5014273 169.1.1.3 ↗ alpha complex topology › Aldehyde ferredoxin oxidoreductase-C › Aldehyde ferredoxin oxidoreductase-C › Aldehyde ferredoxin oxidoreductase-C › AFOR_N 0.62 52.0 3.03e-01 100.0% 16.7%
4961835 377.9.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › HIT/MYND zinc finger-like › HIT/MYND zinc finger-like 0.62 42.0 4.03e-01 100.0% 61.6%
5047427 75.1.1.4 ↗ beta barrels › Cyclophilin-like › Cyclophilin-like › Cyclophilin-like › Cyclophil_like 0.62 55.0 4.44e-01 100.0% 100.0%
5041088 11.1.1.103 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › CARDB 0.61 44.0 3.74e-01 100.0% 45.7%
3730254 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.61 51.0 3.84e-01 96.8% 69.1%
3421509 2487.1.1.0 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" 0.60 51.0 4.02e-01 98.4% 97.1%
4624043 11.1.1.1201 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF27413 0.59 52.0 4.24e-01 100.0% 83.3%
3526348 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 40.0 3.44e-01 100.0% 42.9%
3929781 11.1.1.813 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › INTS4_C 0.59 48.0 3.69e-01 100.0% 39.3%
5025086 101.1.11.0 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix 0.58 44.0 4.65e-01 96.8% 94.5%
3668540 2487.1.1.0 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" 0.58 49.0 3.71e-01 98.4% 95.9%
3285052 304.139.1.4 ↗ a+b two layers › Alpha-beta plaits › Cas7-related › CRISPR-associated protein Cas7/Csa2-related › Cas_CT1975 0.58 48.0 3.18e-01 96.8% 48.5%
3783481 11.1.1.642 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig-like_Pom152_1 0.58 51.0 4.13e-01 100.0% 51.7%
3475431 133.1.1.0 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) 0.58 40.0 2.69e-01 71.4% 85.4%
3400250 379.1.1.3 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors › Kazal_2 0.58 38.0 4.09e-01 100.0% 84.0%
5037556 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.58 50.0 3.41e-01 100.0% 71.4%
3368065 11.1.1.813 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › INTS4_C 0.58 44.0 3.61e-01 100.0% 43.2%
4566976 375.14.2.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS2) 0.58 33.0 3.87e-01 98.4% 87.5%
4978421 1.1.2.16 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › MacB_PCD 0.57 43.0 3.56e-01 84.1% 46.7%
3630069 223.1.1.101 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PF30734 0.56 43.0 2.57e-01 88.9% 68.3%
3988557 2003.1.5.12 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › N6_N4_Mtase 0.55 42.0 2.91e-01 92.1% 78.5%
3609079 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 41.0 3.28e-01 85.7% 97.2%
3217778 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.54 44.0 3.72e-01 100.0% 52.7%
3603549 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 44.0 4.13e-01 100.0% 73.1%
3924084 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 46.0 4.01e-01 98.4% 98.0%
4971386 210.1.3.0 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases 0.54 48.0 3.06e-01 100.0% 21.1%
3622958 304.127.1.2 ↗ a+b two layers › Alpha-beta plaits › Notch heterodimerization domain › Notch heterodimerization domain › NOD,NODP 0.53 46.0 3.61e-01 100.0% 93.1%
1841043 7579.1.1.48 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Obc1_C 0.53 45.0 2.89e-01 98.4% 21.2%
3215161 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 40.0 3.66e-01 100.0% 63.1%
3670307 2487.1.1.0 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" 0.52 42.0 3.50e-01 98.4% 97.7%
4951893 219.1.1.76 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › DUF553 0.51 42.0 3.00e-01 100.0% 47.0%
3520893 109.4.1.1812 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RYDR_ITPR, RIH_assoc 0.51 41.0 2.18e-01 98.4% 3.3%