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OK040790.1__UDL15881.1__SEA_PUMPERNICKEL_90__00090

Bact-Vir

OK040790.1__UDL15881.1__SEA_PUMPERNICKEL_90__00090

Identity

Accession:
OK040790 ↗
Kingdom:
phage

Quality

92.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pumpernickelvirus› Microbacterium_phage_Pumpernickel

TaxID: 2885983

Cluster

View cluster (351 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 40-167
PDB
Domain cluster: rep: NC_024392.1__YP_009045168.1__LP114_114__00113__D16-138
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5ajiB03 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.76 40.0 4.58e-01 79.7% 68.4%
4noiA01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.75 44.0 4.89e-01 98.4% 72.8%
2gjvA00 3.30.2000.10 Alpha Beta › 2-Layer Sandwich › STM4215-like › Phage tail protein-like 0.73 59.0 5.79e-01 100.0% 80.1%
4bfiB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.73 36.0 4.26e-01 85.9% 67.8%
3fz2A00 3.30.70.1700 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Phage minor tail protein U 0.70 56.0 5.61e-01 100.0% 84.4%
4bbyA05 3.30.300.330 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.69 41.0 4.41e-01 92.2% 68.5%
1o51A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 33.0 3.90e-01 91.4% 68.5%
6ofsA04 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.65 42.0 3.76e-01 95.3% 45.1%
3tupA02 3.30.70.380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain 0.65 36.0 4.09e-01 77.3% 71.9%
3ce8A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 34.0 3.97e-01 91.4% 73.0%
4r6uA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 36.0 3.96e-01 99.2% 69.9%
4hudA01 3.30.2000.40 Alpha Beta › 2-Layer Sandwich › STM4215-like › Myoviridae tail sheath stabiliser 0.61 56.0 4.75e-01 100.0% 71.9%
2petA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 39.0 4.13e-01 99.2% 72.4%
6ofsA02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.60 41.0 3.46e-01 96.1% 40.6%
2nyiA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.60 32.0 3.70e-01 89.8% 72.2%
3qkbA00 3.30.110.70 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Hypothetical protein apc22750. Chain B 0.59 39.0 4.39e-01 75.8% 89.4%
2c5dC01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 36.0 3.99e-01 98.4% 76.0%
3cfuA00 2.60.40.1240 Mainly Beta › Sandwich › Immunoglobulin-like › 0.58 45.0 4.33e-01 96.9% 72.9%
3rkxA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.57 51.0 4.35e-01 100.0% 61.5%
3fbqA01 2.60.40.1630 Mainly Beta › Sandwich › Immunoglobulin-like › bacillus anthracis domain 0.57 39.0 3.74e-01 94.5% 61.1%
3byqA00 3.30.1330.110 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › BB2672 0.57 52.0 4.51e-01 99.2% 87.4%
2pmeA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 50.0 3.79e-01 100.0% 76.5%
4gafB03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 38.0 4.06e-01 100.0% 80.0%
1hxdA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 49.0 4.27e-01 96.9% 75.6%
3o4oB03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 39.0 4.19e-01 88.3% 85.3%
4cvuA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 34.0 3.54e-01 99.2% 65.5%
6gdxA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 35.0 3.81e-01 89.1% 77.6%
2vneA01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 35.0 3.26e-01 78.1% 51.5%
3rt0C00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 36.0 3.33e-01 79.7% 51.7%
1vs3A02 3.30.70.660 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Pseudouridine synthase I, catalytic domain, C-terminal subdomain 0.54 36.0 3.47e-01 78.1% 60.4%
5wy8B03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 38.0 4.07e-01 100.0% 84.8%
4fomA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 38.0 4.28e-01 99.2% 96.0%
1d5aA01 3.30.342.10 Alpha Beta › 2-Layer Sandwich › DNA Polymerase; Chain A, domain 1 › DNA Polymerase, chain B, domain 1 0.53 35.0 3.33e-01 80.5% 57.0%
2ek0A00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.53 36.0 4.15e-01 90.6% 100.0%
3lvtA03 2.60.40.2210 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 36.0 3.67e-01 100.0% 69.8%
3r75B01 3.60.120.10 Alpha Beta › 4-Layer Sandwich › Anthranilate synthase › Anthranilate synthase 0.52 47.0 3.35e-01 100.0% 35.5%
1vr4E00 3.30.110.70 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Hypothetical protein apc22750. Chain B 0.52 34.0 3.93e-01 75.8% 93.5%
3p9vA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 38.0 3.58e-01 78.1% 65.2%
2cjaA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.51 46.0 3.44e-01 99.2% 71.0%
2bkyX00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.51 34.0 3.99e-01 93.8% 100.0%
2vf9A00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.51 33.0 3.35e-01 100.0% 64.1%
3icaB00 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.51 46.0 3.91e-01 99.2% 92.2%
1hw7A01 3.55.30.10 Alpha Beta › 3-Layer(bab) Sandwich › Hsp33 domain › Hsp33 domain 0.50 41.0 3.77e-01 89.1% 99.4%
ECOD (59)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3211894 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.72 44.0 4.90e-01 85.2% 77.0%
3934458 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.72 35.0 4.04e-01 81.2% 63.2%
4934927 304.19.1.0 ↗ a+b two layers › Alpha-beta plaits › eIF-2-alpha, C-terminal domain › eIF-2-alpha, C-terminal domain 0.71 34.0 4.16e-01 82.8% 69.4%
3964886 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.68 61.0 5.93e-01 99.2% 87.1%
3627282 872.3.1.0 ↗ a+b two layers › Dodecin subunit-like › YbjQ-like › YbjQ-like 0.68 46.0 5.16e-01 75.8% 89.0%
4342449 305.1.1.1 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.67 45.0 4.61e-01 88.3% 71.7%
3589403 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.66 49.0 5.06e-01 98.4% 82.5%
4028741 304.20.1.1 ↗ a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP_RNA-bind 0.65 38.0 3.79e-01 81.2% 54.1%
4983523 4081.1.1.17 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › DUF7345 0.65 38.0 3.71e-01 87.5% 51.0%
984477 878.1.1.1 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.64 39.0 4.33e-01 77.3% 77.8%
3970985 304.124.1.9 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_tail_terminator_9 0.63 55.0 5.37e-01 100.0% 85.7%
3552777 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.63 46.0 2.92e-01 93.8% 14.7%
4952750 872.3.1.0 ↗ a+b two layers › Dodecin subunit-like › YbjQ-like › YbjQ-like 0.62 44.0 4.77e-01 75.8% 89.4%
3599466 304.42.1.0 ↗ a+b two layers › Alpha-beta plaits › Molybdenum cofactor biosynthesis protein C, MoaC › Molybdenum cofactor biosynthesis protein C, MoaC 0.62 43.0 4.06e-01 71.9% 63.2%
4940026 4081.1.1.17 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › DUF7345 0.61 47.0 4.29e-01 99.2% 60.0%
3863526 11.1.1.108 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_2 0.60 39.0 4.15e-01 100.0% 73.0%
4319533 305.1.1.1 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.60 48.0 4.70e-01 91.4% 77.1%
3183905 880.1.1.1 ↗ a+b duplicates or obligate multimers › ADC synthase › ADC synthase › ADC synthase › Chorismate_bind 0.60 55.0 3.47e-01 97.7% 70.2%
3472250 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.59 44.0 3.75e-01 100.0% 48.3%
4945287 314.1.1.6 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › BPL_LplA_LipB 0.59 53.0 4.59e-01 98.4% 67.0%
3997493 314.1.1.0 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.59 53.0 4.35e-01 97.7% 89.8%
4174584 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.58 37.0 3.79e-01 91.4% 65.8%
1725 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.58 36.0 3.98e-01 100.0% 75.7%
4025112 304.114.1.2 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain › POL3_N 0.57 34.0 3.78e-01 80.5% 74.0%
3795927 314.1.1.0 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.57 52.0 3.92e-01 100.0% 66.6%
6981 301.11.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › BB2672-like › BB2672-like › AA_synth 0.57 52.0 4.51e-01 99.2% 87.4%
3490212 314.1.1.6 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › BPL_LplA_LipB 0.57 50.0 3.98e-01 99.2% 78.5%
5047867 314.1.1.6 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › BPL_LplA_LipB 0.56 51.0 4.35e-01 100.0% 64.3%
3971453 314.1.1.6 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › BPL_LplA_LipB 0.56 50.0 4.32e-01 98.4% 65.9%
3515349 314.1.1.0 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.56 50.0 3.90e-01 100.0% 71.7%
4953222 314.1.1.6 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › BPL_LplA_LipB 0.56 50.0 4.25e-01 97.7% 77.6%
None — 0.56 38.0 2.89e-01 100.0% 29.5%
4057787 872.3.1.1 ↗ a+b two layers › Dodecin subunit-like › YbjQ-like › YbjQ-like › YbjQ_1 0.56 40.0 4.39e-01 75.8% 96.2%
4229976 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.55 50.0 4.20e-01 100.0% 86.8%
3955529 872.3.1.1 ↗ a+b two layers › Dodecin subunit-like › YbjQ-like › YbjQ-like › YbjQ_1 0.55 40.0 4.43e-01 78.9% 97.0%
3164250 880.1.1.1 ↗ a+b duplicates or obligate multimers › ADC synthase › ADC synthase › ADC synthase › Chorismate_bind 0.55 48.0 3.57e-01 94.5% 55.3%
3948250 304.124.1.9 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_tail_terminator_9 0.55 49.0 4.63e-01 100.0% 81.9%
3923148 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.54 43.0 3.66e-01 100.0% 51.4%
3499933 273.1.1.0 ↗ a+b three layers › PR-1-like › PR-1-like › PR-1-like 0.54 36.0 3.60e-01 93.8% 65.4%
4957376 314.1.1.6 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › BPL_LplA_LipB 0.54 49.0 4.12e-01 98.4% 78.6%
3605908 304.31.1.3 ↗ a+b two layers › Alpha-beta plaits › HMG-CoA reductase › NAD-binding domain of HMG-CoA reductase › FAZ1_cons 0.54 36.0 3.68e-01 78.1% 70.8%
5044328 304.109.1.0 ↗ a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e 0.54 46.0 3.84e-01 100.0% 52.6%
5042257 256.1.1.0 ↗ a+b two layers › MTH1598-like › MTH1598-like › MTH1598-like 0.54 46.0 4.67e-01 93.0% 95.2%
3217135 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.54 42.0 3.64e-01 100.0% 52.7%
4478726 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.53 48.0 3.99e-01 100.0% 87.0%
3576847 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.53 42.0 3.48e-01 100.0% 47.0%
3795498 7.1.1.0 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain 0.53 44.0 4.33e-01 89.1% 97.0%
3619547 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.52 42.0 3.52e-01 100.0% 50.0%
4957562 1.1.13.76 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › DUF6046 0.52 41.0 4.43e-01 96.1% 97.3%
2388936 11.12.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD,Neur_chan_memb 0.52 41.0 3.26e-01 100.0% 40.2%
3798241 11.12.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like 0.52 42.0 3.49e-01 100.0% 49.5%
3936858 11.12.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD,Neur_chan_memb 0.52 42.0 2.90e-01 100.0% 25.1%
5018915 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.51 47.0 4.40e-01 100.0% 88.7%
3713199 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.51 44.0 3.69e-01 93.0% 90.2%
3222273 11.12.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like 0.51 39.0 3.51e-01 100.0% 57.8%
3992575 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.51 43.0 3.99e-01 100.0% 72.1%
3622783 11.12.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like 0.51 46.0 3.81e-01 100.0% 63.1%
3903625 11.1.1.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.50 38.0 4.10e-01 100.0% 95.2%
3500525 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.50 38.0 3.44e-01 82.8% 58.8%