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NC_053236.1__YP_010001774.1__J1763_gp65__00065

Bact-Vir

NC_053236.1__YP_010001774.1__J1763_gp65__00065

Identity

Accession:
NC_053236 ↗
Kingdom:
phage

Quality

90.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Stackebrandtviridae› Kroosvirus› Gordonia_phage_YorkOnyx

TaxID: 2762402

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 3-57
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2vugA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.68 54.0 5.03e-01 100.0% 69.4%
3e8vA00 2.60.40.1120 Mainly Beta › Sandwich › Immunoglobulin-like › Carboxypeptidase-like, regulatory domain 0.67 52.0 4.60e-01 100.0% 57.3%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.66 53.0 3.79e-01 89.1% 49.7%
3au4A02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.66 50.0 4.25e-01 94.5% 48.9%
2qyxA02 3.30.70.1360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › mj0159-like 0.65 54.0 4.45e-01 100.0% 83.2%
1es6A02 2.60.510.10 Mainly Beta › Sandwich › EV matrix protein fold › EV matrix protein 0.63 51.0 4.32e-01 96.4% 99.0%
1pzxA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.62 57.0 4.32e-01 100.0% 72.1%
8gk4C02 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.62 44.0 3.80e-01 78.2% 100.0%
3u7vA02 2.60.220.20 Mainly Beta › Sandwich › Chondroitinase Ac; Chain A, domain 3 › putative beta-Galactosidase from caulobacter crescentus 0.62 44.0 3.29e-01 89.1% 29.2%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.61 51.0 4.46e-01 100.0% 94.6%
2i44B00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.61 45.0 2.90e-01 83.6% 73.7%
3am2A02 2.60.120.1050 Mainly Beta › Sandwich › Jelly Rolls › 0.61 44.0 3.55e-01 87.3% 37.6%
2xf1A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.61 50.0 3.98e-01 100.0% 43.4%
2g9gA00 2.60.120.1020 Mainly Beta › Sandwich › Jelly Rolls › PAW domain 0.61 41.0 2.86e-01 89.1% 20.6%
2jjuA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 53.0 4.36e-01 100.0% 61.9%
2mv2A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.61 51.0 3.84e-01 100.0% 45.9%
2kt4B01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.60 43.0 3.38e-01 81.8% 93.7%
2hvzA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.60 45.0 4.16e-01 80.0% 100.0%
1m4jA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.60 50.0 3.92e-01 100.0% 46.6%
2pw9C03 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.60 49.0 3.80e-01 98.2% 68.8%
1jmtA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.59 51.0 4.24e-01 98.2% 100.0%
1d3yB02 3.40.1360.10 Alpha Beta › 3-Layer(aba) Sandwich › Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 › 0.59 42.0 2.99e-01 83.6% 77.4%
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.58 44.0 4.55e-01 89.1% 96.0%
2mgzA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.58 47.0 4.03e-01 92.7% 87.2%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.57 46.0 4.07e-01 100.0% 91.5%
2xepB02 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.57 48.0 3.20e-01 100.0% 63.7%
2mzsA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.56 42.0 3.61e-01 85.5% 79.8%
4ggmX02 3.40.140.80 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › LpxI C-terminal catalytic domain 0.56 47.0 3.55e-01 100.0% 68.7%
2pk0A00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.56 45.0 3.08e-01 98.2% 65.2%
2wadA02 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.56 44.0 3.43e-01 96.4% 42.6%
7a6pB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 46.0 3.41e-01 90.9% 75.4%
2c60A01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.55 43.0 4.04e-01 100.0% 94.9%
2v72A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 40.0 3.14e-01 87.3% 33.6%
1t3yA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.54 46.0 3.60e-01 100.0% 42.0%
7vjvA01 2.60.120.590 Mainly Beta › Sandwich › Jelly Rolls › Alpha-ketoglutarate-dependent dioxygenase AlkB-like 0.53 39.0 2.79e-01 85.5% 82.6%
5g5gC03 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.53 39.0 3.33e-01 81.8% 47.3%
1nxmA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.53 40.0 2.81e-01 85.5% 33.0%
3bt7A02 2.40.50.1070 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 44.0 3.32e-01 98.2% 42.8%
2pjyC00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.52 42.0 3.86e-01 100.0% 94.9%
4ehoB03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.51 38.0 2.84e-01 89.1% 33.0%
2cs4A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 41.0 3.61e-01 100.0% 78.9%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.51 40.0 3.65e-01 85.5% 72.4%
5xbfA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.50 39.0 3.57e-01 98.2% 95.4%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5059796 4326.1.1.0 ↗ a+b two layers › ERH-like › ERH-like › ERH-like 0.73 61.0 5.73e-01 100.0% 75.4%
3816405 109.4.1.1383 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.69 48.0 2.74e-01 74.5% 19.6%
3328266 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.67 54.0 4.52e-01 90.9% 79.0%
4529646 304.8.1.62 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › CitX 0.65 55.0 3.91e-01 98.2% 52.8%
3173372 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.64 48.0 4.11e-01 80.0% 86.7%
4999682 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.63 48.0 4.46e-01 87.3% 97.3%
3994958 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.62 53.0 4.08e-01 100.0% 70.4%
2629457 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.62 51.0 3.98e-01 100.0% 45.7%
3177860 11.1.5.98 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › SPT23_MGA2_DBD 0.61 52.0 3.57e-01 100.0% 54.0%
3723396 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.61 52.0 4.68e-01 100.0% 81.2%
3224222 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.61 55.0 4.65e-01 100.0% 82.2%
3620456 221.1.1.64 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Formin_GBD_N 0.60 47.0 3.79e-01 87.3% 43.6%
3842874 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.60 45.0 3.84e-01 89.1% 46.7%
3486197 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.59 43.0 3.72e-01 89.1% 47.8%
3761694 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.59 48.0 4.12e-01 94.5% 72.6%
3933905 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.58 48.0 3.73e-01 100.0% 41.4%
3420651 109.4.1.1521 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, DYW_deaminase, Eplus_motif, E_motif 0.58 47.0 2.87e-01 89.1% 36.5%
4962335 3115.5.1.1 ↗ a+b two layers › GP2-like › phenylacetate-CoA oxygenase subunit PaaB › phenylacetate-CoA oxygenase subunit PaaB › PaaB 0.58 46.0 4.44e-01 94.5% 84.6%
3286213 327.6.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like 0.58 46.0 3.79e-01 94.5% 100.0%
3312666 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.58 45.0 4.21e-01 89.1% 74.3%
4930766 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.57 45.0 3.63e-01 98.2% 80.0%
5080205 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.57 42.0 4.29e-01 87.3% 94.0%
3786112 317.1.1.0 ↗ a+b two layers › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase 0.57 46.0 3.45e-01 100.0% 59.4%
5048876 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.56 45.0 4.43e-01 100.0% 87.7%
3922539 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.56 42.0 2.71e-01 83.6% 83.4%
4954188 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.56 45.0 3.49e-01 98.2% 63.8%
3553704 382.1.1.1 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › UPAR_LY6 0.56 46.0 4.04e-01 98.2% 93.3%
3213999 210.2.1.1 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C 0.55 42.0 2.62e-01 90.9% 89.7%
3473057 4357.1.1.3 ↗ beta barrels › WWE domain › WWE domain › WWE domain › WWE_2 0.55 42.0 3.70e-01 92.7% 95.8%
3916476 221.1.1.73 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RASSF8-10_RA 0.55 44.0 4.01e-01 100.0% 89.4%
3727963 247.1.1.0 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase 0.55 45.0 2.81e-01 94.5% 34.8%
3407846 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.54 41.0 3.48e-01 85.5% 47.0%
3315515 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.53 42.0 3.34e-01 90.9% 40.8%
3780612 221.1.1.9 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PI3K_rbd,PIK3CG_ABD 0.53 42.0 2.82e-01 100.0% 28.5%
5075866 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.53 43.0 3.96e-01 98.2% 98.8%
3237024 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.53 43.0 3.51e-01 100.0% 69.2%
5017559 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.53 38.0 3.67e-01 81.8% 100.0%
4867320 221.1.1.66 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PIK3CG_ABD 0.53 45.0 3.73e-01 98.2% 92.2%
None — 0.52 38.0 2.38e-01 78.2% 36.5%
3533173 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.52 41.0 3.84e-01 100.0% 93.8%
5050610 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.52 46.0 4.29e-01 100.0% 94.3%
4941987 329.1.1.2 ↗ a+b two layers › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › DUF4443 0.51 39.0 3.32e-01 92.7% 47.3%
3560843 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.51 40.0 3.38e-01 96.4% 84.5%
None — 0.50 36.0 2.37e-01 81.8% 83.9%
3307527 109.4.1.619 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DYW_deaminase 0.50 40.0 3.21e-01 100.0% 88.9%