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MN988486.1__QIG68129.1__EVB55_194__00194

Bact-Vir

MN988486.1__QIG68129.1__EVB55_194__00194

Identity

Accession:
MN988486 ↗
Kingdom:
phage

Quality

69.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Trinifflemingvirus› Rhizobium_phage_RHph_Y68

TaxID: 2509787

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 medium residues 32-92
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3fvyA03 3.30.70.2600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 54.0 5.05e-01 86.9% 74.7%
4pg4B03 3.30.70.3100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 44.0 4.11e-01 90.2% 53.3%
2f1fA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.62 44.0 4.11e-01 77.0% 59.5%
2j8aA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.58 44.0 3.99e-01 90.2% 58.6%
2ltsA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.58 39.0 3.52e-01 70.5% 72.1%
2l66A00 2.10.260.10 Mainly Beta › Ribbon › Pemi-like Protein 1; Chain: D › 0.56 37.0 3.88e-01 73.8% 75.5%
2vfrA03 3.30.70.2530 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 37.0 3.36e-01 77.0% 47.1%
4oa3A00 3.10.310.50 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › 0.55 46.0 3.52e-01 91.8% 72.3%
1k8kA04 3.90.640.10 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 0.55 42.0 3.78e-01 86.9% 79.3%
4pbdA00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 44.0 3.85e-01 93.4% 62.7%
4c0dB00 2.30.30.1020 Mainly Beta › Roll › SH3 type barrels. › CCR4-NOT complex subunit 2/3/5, C-terminal domain 0.55 39.0 2.83e-01 78.7% 42.9%
2bopA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 41.0 3.69e-01 82.0% 75.3%
1y0hB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 39.0 3.38e-01 77.0% 50.0%
1k0rA01 3.30.1480.10 Alpha Beta › 2-Layer Sandwich › N Utilization Substance Protein A; Chain:P; domain 4 › NusA, N-terminal domain 0.54 45.0 3.89e-01 95.1% 64.6%
4hl9A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 39.0 3.40e-01 77.0% 53.2%
4ivkA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 45.0 2.72e-01 91.8% 90.8%
4nohA01 3.30.70.3060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 39.0 3.73e-01 82.0% 66.2%
2fdoA00 3.30.1970.10 Alpha Beta › 2-Layer Sandwich › AF2331-like fold › AF2331-like 0.54 36.0 3.21e-01 70.5% 66.7%
4lrjA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.54 37.0 3.38e-01 73.8% 51.7%
2dulA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 42.0 2.71e-01 86.9% 20.8%
1aw8B00 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.54 40.0 3.65e-01 85.2% 89.0%
5wb7E00 2.10.25.10 Mainly Beta › Ribbon › Laminin › Laminin 0.54 35.0 3.79e-01 83.6% 85.1%
4k3cA01 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.53 42.0 3.87e-01 96.7% 65.9%
3venA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 44.0 3.10e-01 98.4% 61.0%
1tr0A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 40.0 3.35e-01 82.0% 55.7%
3og5A01 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.53 43.0 3.88e-01 95.1% 64.7%
3n0vA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.53 37.0 3.44e-01 77.0% 61.9%
8d3mI01 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.52 39.0 2.73e-01 80.3% 59.9%
3nrbB01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.52 38.0 3.53e-01 82.0% 59.0%
2go8A01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 37.0 3.49e-01 77.0% 62.2%
2nvmA00 3.30.310.110 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › XisI-like 0.52 37.0 3.19e-01 93.4% 46.2%
2bbeA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 38.0 3.30e-01 82.0% 51.5%
4dpoB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 38.0 3.29e-01 82.0% 52.5%
3bguA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 37.0 3.30e-01 80.3% 55.2%
2lydA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 40.0 3.25e-01 91.8% 59.0%
3fgvA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 40.0 3.49e-01 86.9% 74.2%
1fsuA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.51 40.0 2.47e-01 85.2% 35.8%
1q8bA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 38.0 3.36e-01 91.8% 54.8%
3qxyA01 3.90.1410.10 Alpha Beta › Alpha-Beta Complex › set domain protein methyltransferase, domain 1 › set domain protein methyltransferase, domain 1 0.50 37.0 2.54e-01 85.2% 19.8%
6u7tA03 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.50 37.0 3.04e-01 82.0% 43.0%
1g0hA01 3.30.540.10 Alpha Beta › 2-Layer Sandwich › Fructose-1,6-Bisphosphatase; Chain A, domain 1 › Fructose-1,6-Bisphosphatase, subunit A, domain 1 0.50 38.0 3.15e-01 91.8% 62.8%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3697768 872.4.1.0 ↗ a+b two layers › Dodecin subunit-like › YdgH-like › YdgH-like 0.70 44.0 4.97e-01 72.1% 86.7%
3004432 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.65 51.0 4.31e-01 83.6% 100.0%
3214977 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.64 43.0 4.05e-01 70.5% 76.0%
3193779 312.1.1.11 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › Ap4A_phos_N 0.62 43.0 3.19e-01 72.1% 51.0%
3211665 387.1.5.0 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like 0.62 41.0 4.32e-01 82.0% 82.0%
1517806 7518.1.1.1 ↗ a/b three-layered sandwiches › PK C-terminal domain-like › PK C-terminal domain-like › PK C-terminal domain-like › PK_C 0.62 42.0 3.32e-01 73.8% 33.9%
5032935 304.8.1.112 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › MazE_antitoxin 0.61 41.0 3.20e-01 75.4% 31.1%
4930285 1.1.3.0 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB 0.60 40.0 4.31e-01 70.5% 88.0%
3724441 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.59 47.0 4.63e-01 100.0% 81.5%
3816749 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.59 51.0 3.23e-01 95.1% 40.9%
4190223 2004.1.1.455 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › UvrD-helicase, UvrD_C, UvrD_C_2 0.59 40.0 2.24e-01 70.5% 41.0%
3993716 327.7.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.59 46.0 4.51e-01 90.2% 90.0%
3423942 304.8.1.45 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant 0.58 48.0 4.50e-01 93.4% 96.0%
3193792 2008.2.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.57 45.0 3.36e-01 86.9% 84.5%
5029727 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.56 40.0 3.11e-01 86.9% 31.3%
4861745 305.1.1.0 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase 0.55 36.0 3.60e-01 72.1% 64.5%
None — 0.54 37.0 2.57e-01 73.8% 20.9%
3278261 304.28.1.13 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › MMPL 0.53 42.0 3.33e-01 91.8% 53.8%
4638770 601.48.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › vWA2 C-terminal domain › vWA2 C-terminal domain 0.53 36.0 3.18e-01 90.2% 47.8%
3204533 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.52 35.0 3.39e-01 82.0% 58.7%
4544770 2492.1.1.1 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › dCMP_cyt_deam_1 0.52 40.0 3.18e-01 88.5% 38.6%
3992658 5.1.4.149 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WDR54 0.52 37.0 2.63e-01 78.7% 41.8%
3625473 70.3.1.0 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like 0.51 42.0 2.80e-01 100.0% 63.2%
3838596 2008.1.1.85 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_TdeIII 0.51 43.0 2.94e-01 91.8% 66.8%
3962339 4014.1.1.0 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase 0.51 41.0 3.09e-01 100.0% 37.8%
3602244 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 38.0 2.89e-01 80.3% 40.3%
3670395 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.50 40.0 3.78e-01 100.0% 71.2%
3275992 859.1.1.0 ↗ a+b two layers › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 0.50 39.0 2.78e-01 83.6% 95.2%
396210 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.50 41.0 2.88e-01 100.0% 29.2%
5066011 7584.1.1.1 ↗ a/b three-layered sandwiches › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › AMP-binding 0.50 37.0 2.97e-01 77.0% 39.2%