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NC_053505.1__YP_010012696.1__J4T94_gp071__00110

Bact-Vir

NC_053505.1__YP_010012696.1__J4T94_gp071__00110

Identity

Accession:
NC_053505 ↗
Kingdom:
phage

Quality

85.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vilmaviridae› Lumosvirus› Mycobacterium_phage_Krypton555

TaxID: 2015885

Cluster

View cluster (20 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 3-74
PDB
Domain cluster: rep: NC_041951.1__YP_009603449.1__FDH68_gp76__00076__D2-59
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4m1xD00 3.30.1360.240 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.75 44.0 4.42e-01 100.0% 58.3%
1wosA04 2.40.30.110 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains 0.68 49.0 4.64e-01 91.7% 64.0%
3prbA02 2.40.10.330 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.68 41.0 5.02e-01 80.6% 100.0%
2pp6A02 2.40.10.210 Mainly Beta › Beta Barrel › Thrombin, subunit H › Phage tail proteins (gpFII-like) 0.64 45.0 4.78e-01 84.7% 85.7%
1feuA01 2.40.240.10 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Ribosomal Protein L25; Chain P 0.62 48.0 4.52e-01 86.1% 76.9%
4m01A02 3.10.20.320 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Putative peptidoglycan bound protein (lpxtg motif) 0.61 48.0 4.70e-01 84.7% 98.7%
1uqwA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.60 46.0 3.91e-01 100.0% 51.8%
4iupA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.59 41.0 4.19e-01 73.6% 91.7%
3r2uB01 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.59 42.0 2.86e-01 75.0% 50.8%
6dddH00 2.40.240.10 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Ribosomal Protein L25; Chain P 0.58 45.0 4.20e-01 86.1% 74.2%
6n36A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.58 41.0 2.81e-01 75.0% 54.7%
1dfuP00 2.40.240.10 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Ribosomal Protein L25; Chain P 0.58 45.0 4.18e-01 86.1% 75.5%
4ge6A00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.58 44.0 2.92e-01 81.9% 38.0%
3f13B00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.58 49.0 4.05e-01 100.0% 56.6%
1r5bA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.57 51.0 4.75e-01 100.0% 80.9%
4hpqB00 2.60.270.60 Mainly Beta › Sandwich › Mutm (Fpg) Protein; Chain: A, domain 2 › Autophagy-related protein 31 0.57 46.0 4.02e-01 91.7% 73.0%
2zo4A01 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.56 42.0 2.92e-01 80.6% 80.2%
3x2xA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.56 41.0 2.97e-01 79.2% 66.1%
1qh5A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.56 41.0 2.86e-01 79.2% 60.4%
3p26B02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.56 49.0 4.39e-01 98.6% 79.2%
2yweA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.56 48.0 4.40e-01 100.0% 83.0%
1k28D03 2.40.30.150 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Bacteriophage T4, Gp27, baseplate hub, domain 3 0.56 45.0 4.17e-01 90.3% 82.1%
2b9kA00 2.20.20.70 Mainly Beta › Single Sheet › Anthopleurin-A › 0.56 34.0 3.96e-01 90.3% 93.6%
6u10A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.56 41.0 2.82e-01 79.2% 53.2%
1g7sA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.56 47.0 4.19e-01 97.2% 74.1%
4g6iB01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.55 47.0 4.45e-01 97.2% 82.0%
4wsqB00 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.54 44.0 2.95e-01 90.3% 48.1%
4gqzA00 2.60.40.3700 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 43.0 3.39e-01 88.9% 62.8%
4ad9A01 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.53 40.0 2.91e-01 80.6% 81.4%
1m4wA00 2.60.120.180 Mainly Beta › Sandwich › Jelly Rolls › Glycoside hydrolase family 11/12, catalytic domain 0.52 40.0 3.04e-01 87.5% 40.1%
1zu0A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.52 47.0 3.49e-01 100.0% 58.5%
6a5gA01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 43.0 3.64e-01 100.0% 95.6%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5042402 239.1.1.0 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like 0.71 55.0 5.90e-01 86.1% 98.3%
3802388 239.1.1.0 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like 0.70 57.0 5.44e-01 87.5% 80.7%
5042815 239.1.1.15 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › CPxCG_zf 0.67 55.0 5.37e-01 88.9% 87.5%
5019594 239.1.1.0 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like 0.67 53.0 5.55e-01 88.9% 95.4%
3961706 4.1.1.161 ↗ beta barrels › SH3 › SH3 › SH3 › DUF4178 0.67 46.0 4.81e-01 70.8% 92.3%
5022325 239.1.1.15 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › CPxCG_zf 0.67 54.0 4.82e-01 86.1% 72.0%
4959950 239.1.1.15 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › CPxCG_zf 0.67 54.0 5.13e-01 87.5% 84.7%
3191369 239.1.1.5 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › tRNA-synt_1c_C 0.65 53.0 4.36e-01 88.9% 87.7%
5041151 239.1.1.15 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › CPxCG_zf 0.64 51.0 5.18e-01 84.7% 95.7%
5041150 239.1.1.15 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › CPxCG_zf 0.64 51.0 5.19e-01 86.1% 95.7%
3253514 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.63 50.0 4.52e-01 86.1% 73.0%
4945213 239.1.1.6 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › tRNA-synt_1c_C2 0.63 53.0 4.70e-01 93.1% 92.4%
3747587 239.3.1.0 ↗ beta barrels › Ribosomal protein L25-like › FAS1 domain › FAS1 domain 0.63 57.0 4.79e-01 100.0% 74.2%
3183652 239.1.1.5 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › tRNA-synt_1c_C 0.63 53.0 4.60e-01 91.7% 90.9%
5019872 239.1.1.15 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › CPxCG_zf 0.62 49.0 4.63e-01 84.7% 87.1%
3582045 391.1.1.7 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › Fn1_2 0.62 30.0 4.06e-01 83.3% 94.3%
3319602 239.1.1.5 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › tRNA-synt_1c_C 0.62 52.0 4.54e-01 93.1% 90.9%
4951496 239.1.1.15 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › CPxCG_zf 0.62 49.0 4.68e-01 87.5% 88.2%
3923528 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.61 47.0 3.10e-01 81.9% 35.3%
4344650 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.61 48.0 4.37e-01 87.5% 74.0%
3221209 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.61 46.0 3.01e-01 81.9% 32.9%
4139867 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.60 49.0 4.50e-01 88.9% 74.7%
5054413 5090.1.1.0 ↗ beta complex topology › Viral glycoprotein, central and dimerisation domains-like › Viral glycoprotein, central and dimerisation domains › Viral glycoprotein, central and dimerisation domains 0.60 44.0 3.95e-01 77.8% 74.8%
4169889 239.1.1.15 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › CPxCG_zf 0.60 51.0 5.22e-01 93.1% 97.1%
4259249 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.60 48.0 4.40e-01 87.5% 76.8%
4231034 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.60 47.0 4.28e-01 87.5% 72.0%
3933549 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.60 41.0 2.63e-01 72.2% 28.1%
4065090 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.59 46.0 4.30e-01 87.5% 75.8%
4197235 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.59 46.0 4.28e-01 87.5% 74.7%
4145938 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.58 46.0 4.19e-01 87.5% 71.0%
3969414 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.58 50.0 4.60e-01 100.0% 90.0%
4069101 239.1.1.3 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal_L25p 0.58 46.0 4.17e-01 87.5% 72.0%
4028218 1.1.7.19 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › GTP_EFTU_D2 0.58 49.0 4.11e-01 97.2% 61.5%
3730835 4.8.1.10 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › MSL3_chromo-like 0.58 40.0 3.63e-01 70.8% 63.2%
None — 0.57 50.0 4.51e-01 98.6% 77.0%
3558025 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.57 39.0 2.50e-01 70.8% 26.4%
4205494 1.1.7.19 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › GTP_EFTU_D2 0.57 49.0 4.23e-01 100.0% 70.8%
4070992 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.56 48.0 4.30e-01 100.0% 80.0%
3185910 2003.1.9.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.55 46.0 2.88e-01 90.3% 44.4%
3609057 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.55 46.0 3.77e-01 97.2% 79.3%
1694860 3363.1.1.0 ↗ beta sandwiches › avirulence protein AvrPiz-t homologs › avirulence protein AvrPiz-t homologs › avirulence protein AvrPiz-t homologs 0.55 38.0 3.75e-01 98.6% 67.1%
3873066 206.1.1.71 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, Kdo 0.54 41.0 2.53e-01 80.6% 26.9%
4963049 4.1.1.486 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7098 0.54 44.0 4.34e-01 93.1% 88.7%
3502375 391.1.2.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related 0.53 31.0 3.82e-01 83.3% 93.3%
5028249 5090.1.1.0 ↗ beta complex topology › Viral glycoprotein, central and dimerisation domains-like › Viral glycoprotein, central and dimerisation domains › Viral glycoprotein, central and dimerisation domains 0.53 40.0 3.58e-01 86.1% 95.6%