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MN988531.1__QIG73382.1__EVC03_074__00073

Bact-Vir

MN988531.1__QIG73382.1__EVC03_074__00073

Identity

Accession:
MN988531 ↗
Kingdom:
phage

Quality

54.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_RHph_Y5A

TaxID: 2509784

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 88-141
PDB
Domain cluster: rep: MH727593.1__AXY83340.1__X__00023__D71-122
CATH (53)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ej9A02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.69 48.0 5.08e-01 74.1% 100.0%
3mb5A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.69 49.0 4.69e-01 75.9% 98.4%
4a53A01 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.68 49.0 4.74e-01 77.8% 88.7%
4a0tA03 2.60.320.30 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › 0.67 57.0 4.91e-01 100.0% 87.8%
1dq3A01 2.170.16.10 Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain 0.67 48.0 3.36e-01 77.8% 94.4%
5owvD01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.66 47.0 3.20e-01 77.8% 29.3%
2fb7A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.66 45.0 3.91e-01 70.4% 87.5%
2e12A00 2.30.30.720 Mainly Beta › Roll › SH3 type barrels. › Protein of unknown function (DUF3247) 0.66 55.0 4.59e-01 92.6% 81.7%
6v4xC01 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.66 52.0 4.24e-01 87.0% 74.0%
3hfnA00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.65 51.0 5.00e-01 87.0% 98.3%
2eqjA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.63 46.0 4.35e-01 79.6% 80.3%
2piaA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.62 53.0 4.38e-01 100.0% 89.4%
2bvfA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.62 53.0 4.00e-01 100.0% 68.8%
3bcwA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.62 49.0 4.09e-01 100.0% 48.1%
1dyoA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.61 52.0 3.82e-01 100.0% 94.2%
2fhqA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.60 40.0 3.12e-01 72.2% 65.9%
7ylrA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 50.0 4.12e-01 100.0% 98.1%
2vfrA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.59 50.0 3.88e-01 100.0% 73.1%
1o54A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.58 46.0 4.24e-01 88.9% 97.2%
1hskA01 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.58 49.0 3.84e-01 100.0% 70.1%
3fkfD00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.57 39.0 2.96e-01 72.2% 71.5%
2yvsA01 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.57 48.0 3.87e-01 100.0% 83.3%
4kncA02 2.60.120.1380 Mainly Beta › Sandwich › Jelly Rolls › C-terminal carbohydrate-binding module 0.57 49.0 3.86e-01 100.0% 66.7%
3p42A03 3.10.560.10 Alpha Beta › Roll › Outer membrane lipoprotein wza fold like › Outer membrane lipoprotein wza domain like 0.57 48.0 4.41e-01 100.0% 94.6%
2d93A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.57 47.0 3.67e-01 100.0% 41.8%
1wp5A00 2.120.10.90 Mainly Beta › 6 Propeller › Neuraminidase › DNA gyrase/topoisomerase IV, subunit A, C-terminal 0.56 45.0 2.88e-01 96.3% 28.0%
5kcoA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.56 42.0 4.17e-01 83.3% 98.3%
2budA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.56 41.0 3.52e-01 79.6% 68.5%
6vtmB00 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.55 46.0 3.96e-01 100.0% 92.7%
1f39A00 2.10.109.10 Mainly Beta › Ribbon › Umud Fragment, subunit A › Umud Fragment, subunit A 0.55 48.0 3.96e-01 100.0% 54.5%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 40.0 3.45e-01 83.3% 71.4%
4pqqA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 45.0 3.40e-01 100.0% 75.6%
4h8wC02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 42.0 3.83e-01 87.0% 81.3%
1wmhB00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.54 45.0 4.06e-01 100.0% 90.2%
1yn3A00 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.54 45.0 3.86e-01 100.0% 92.9%
3bn6A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 45.0 3.35e-01 100.0% 93.7%
2id4A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 44.0 3.44e-01 100.0% 91.3%
2vm9A01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 44.0 3.32e-01 100.0% 91.6%
5eb9A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 44.0 3.61e-01 100.0% 82.1%
2ldmA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.53 38.0 3.88e-01 75.9% 92.5%
2e6nA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.53 45.0 3.72e-01 100.0% 54.8%
4j2gA00 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.53 41.0 2.90e-01 92.6% 75.7%
4xuoA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 42.0 3.24e-01 100.0% 90.4%
6m3aA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 41.0 3.89e-01 90.7% 77.3%
1p8jA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 43.0 3.37e-01 100.0% 87.9%
3wdhA01 2.60.40.2320 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 41.0 3.58e-01 98.1% 74.0%
6j0qA02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.51 41.0 3.46e-01 100.0% 92.7%
7cfdA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.51 44.0 4.04e-01 100.0% 75.3%
2q7nA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 38.0 3.50e-01 88.9% 76.5%
4o1nD01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.51 41.0 3.40e-01 100.0% 77.4%
1iw4A00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.51 39.0 3.92e-01 100.0% 94.5%
2j4xA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.51 41.0 3.33e-01 100.0% 76.6%
4a42A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.50 41.0 3.30e-01 100.0% 79.5%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
146288 4187.2.1.0 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 0.69 56.0 5.78e-01 100.0% 94.1%
3698553 4012.3.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 0.68 46.0 4.62e-01 70.4% 96.4%
4646501 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.68 50.0 3.64e-01 81.5% 34.8%
3741160 284.1.1.5 ↗ a+b two layers › FKBP-like › FKBP-like › FKBP-like › Gcd10p 0.67 48.0 3.52e-01 77.8% 100.0%
3507639 4.1.1.219 ↗ beta barrels › SH3 › SH3 › SH3 › LSM12_LSM 0.65 55.0 5.10e-01 96.3% 94.3%
3907190 4.1.1.219 ↗ beta barrels › SH3 › SH3 › SH3 › LSM12_LSM 0.65 50.0 4.13e-01 83.3% 66.3%
4321108 4187.2.1.0 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 0.64 54.0 5.44e-01 100.0% 96.4%
4132165 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.63 54.0 4.43e-01 100.0% 88.6%
4350337 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.62 52.0 4.80e-01 100.0% 96.0%
5051788 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.61 51.0 4.27e-01 100.0% 65.7%
3227731 10.12.1.101 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › JmjC, Cupin_8 0.61 48.0 2.96e-01 88.9% 13.2%
3635320 4027.1.1.0 ↗ beta barrels › all-beta domain in DNA topoisomerase IV alpha subunit › all-beta domain in DNA topoisomerase IV alpha subunit › all-beta domain in DNA topoisomerase IV alpha subunit 0.60 41.0 4.37e-01 70.4% 84.4%
3334173 217.1.1.1 ↗ a+b complex topology › FAD-binding domain-like › FAD-binding domain › FAD-binding domain › FAD_binding_5 0.60 49.0 3.49e-01 100.0% 56.5%
4022833 4027.1.1.0 ↗ beta barrels › all-beta domain in DNA topoisomerase IV alpha subunit › all-beta domain in DNA topoisomerase IV alpha subunit › all-beta domain in DNA topoisomerase IV alpha subunit 0.59 40.0 4.50e-01 70.4% 95.0%
4020238 1.1.7.4 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_1 0.59 49.0 3.70e-01 100.0% 86.0%
3367439 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.58 48.0 3.23e-01 100.0% 31.2%
4493828 5.2.1.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-pinwheel › beta-pinwheel › DNA_gyraseA_C 0.57 47.0 3.07e-01 100.0% 84.5%
4617844 7579.1.1.2 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Lipase 0.57 39.0 2.45e-01 74.1% 22.9%
3532264 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.57 48.0 3.56e-01 100.0% 36.8%
3678413 10.32.1.198 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › PP2 0.57 47.0 3.25e-01 100.0% 39.5%
3970673 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 45.0 4.34e-01 94.4% 81.5%
2179 5.2.1.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-pinwheel › beta-pinwheel › DNA_gyraseA_C 0.56 45.0 2.87e-01 96.3% 27.9%
4243030 210.2.1.2 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › SpoIIE 0.56 45.0 2.97e-01 92.6% 61.3%
3180565 2485.1.1.4 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › AhpC-TSA 0.56 40.0 2.74e-01 75.9% 48.3%
3822637 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.56 45.0 3.92e-01 98.1% 80.0%
3223001 10.4.1.9 ↗ beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain › CUB_2 0.56 48.0 3.85e-01 100.0% 56.5%
3492162 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.55 46.0 3.45e-01 100.0% 37.3%
4609257 5.2.1.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-pinwheel › beta-pinwheel › DNA_gyraseA_C 0.55 46.0 2.90e-01 98.1% 32.4%
3494269 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.55 45.0 2.85e-01 100.0% 16.2%
2716345 1.4.1.1 ↗ beta barrels › cradle loop barrel › N-terminal domain of poxin › N-terminal domain of poxin › Baculo_p26 0.54 45.0 3.37e-01 100.0% 73.6%
5005784 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 45.0 3.67e-01 98.1% 78.2%
5056535 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 44.0 3.96e-01 98.1% 81.2%
4538670 221.1.4.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Nqo1 middle domain-like 0.53 43.0 3.83e-01 100.0% 82.2%
3227155 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.53 44.0 3.61e-01 100.0% 100.0%
3196947 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.53 42.0 2.48e-01 100.0% 13.2%
3407855 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.53 42.0 3.61e-01 88.9% 67.8%
3877478 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.52 46.0 3.79e-01 100.0% 62.0%
4055256 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.52 46.0 3.88e-01 100.0% 61.1%
3769507 4.1.1.31 ↗ beta barrels › SH3 › SH3 › SH3 › Spin-Ssty 0.52 37.0 3.47e-01 77.8% 80.0%
4013853 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.52 41.0 2.56e-01 100.0% 16.8%
4028554 10.30.1.0 ↗ beta sandwiches › jelly-roll › Latrophilin 1 gal_lectin domain › Latrophilin 1 gal_lectin domain 0.51 41.0 3.76e-01 100.0% 96.4%
3570700 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.51 44.0 3.52e-01 100.0% 48.7%
4060102 2.1.1.48 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Elong-fact-P_C 0.51 34.0 3.38e-01 83.3% 65.5%
D2 medium residues 1-59
PDB