←Back to structures

NC_054725.1__YP_010059410.1__KHQ85_gp160__00160

Bact-Vir

NC_054725.1__YP_010059410.1__KHQ85_gp160__00160

Identity

Accession:
NC_054725 ↗
Kingdom:
phage

Quality

75.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Skogvirus› Gordonia_phage_Skog

TaxID: 2704033

Cluster

View cluster (2 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 144-234
PDB
Domain cluster: rep: ON526981.1__USH45528.1__SEA_PHABULOSO_33__00033__D270-320_334-361
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vw3C01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.75 65.0 5.74e-01 100.0% 65.6%
2xzlA02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.73 58.0 6.20e-01 100.0% 97.5%
3w1eA03 2.40.10.410 Mainly Beta › Beta Barrel › Thrombin, subunit H › FlgT, C-terminal domain 0.66 56.0 5.66e-01 100.0% 95.5%
1e62A01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.65 59.0 5.24e-01 100.0% 89.8%
6k2lA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.65 58.0 5.46e-01 100.0% 94.6%
1xqbA01 2.40.30.70 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › YaeB-like 0.63 57.0 5.37e-01 100.0% 81.7%
5tr9A01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.62 56.0 5.54e-01 100.0% 94.8%
2ok7A01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.62 56.0 5.23e-01 100.0% 89.3%
2qtlA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.58 53.0 5.04e-01 100.0% 98.1%
3kf8A00 2.40.50.1040 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.57 38.0 2.87e-01 100.0% 30.0%
5gxuB01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.56 51.0 4.61e-01 100.0% 85.2%
3kl0D01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.56 38.0 3.68e-01 100.0% 61.3%
4jgwA01 1.20.870.10 Mainly Alpha › Up-down Bundle › Son of sevenless (SoS) protein; Chain S, domain 1 › Son of sevenless (SoS) protein Chain: S domain 1 0.55 27.0 2.29e-01 85.7% 27.6%
4dqlB01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.55 49.0 4.68e-01 100.0% 91.7%
3wcyA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 38.0 3.88e-01 100.0% 76.7%
2wliA02 2.60.40.1400 Mainly Beta › Sandwich › Immunoglobulin-like › G protein-activated inward rectifier potassium channel 1 0.54 47.0 3.96e-01 100.0% 64.0%
1loxA02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.53 36.0 3.45e-01 93.4% 57.7%
2ekjA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 39.0 3.80e-01 100.0% 68.6%
8owfA01 2.60.40.290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 46.0 4.32e-01 100.0% 91.0%
2jllA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 40.0 3.95e-01 100.0% 77.6%
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 38.0 4.01e-01 100.0% 90.0%
1n26A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 40.0 3.87e-01 100.0% 74.8%
1orvA02 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 33.0 2.41e-01 96.7% 23.3%
5nfiB02 2.60.40.2090 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 38.0 3.47e-01 93.4% 56.4%
1jz7A04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 39.0 3.73e-01 100.0% 72.6%
4wtxA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 39.0 3.91e-01 100.0% 80.4%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3740846 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.71 65.0 5.99e-01 100.0% 85.2%
3299532 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.66 61.0 5.70e-01 100.0% 91.8%
3273358 1.1.7.13 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › TrmO 0.65 59.0 5.14e-01 100.0% 82.6%
1005534 1.1.7.37 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FlgT_C 0.65 56.0 5.64e-01 100.0% 95.6%
3786133 1.1.7.24 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_8 0.65 58.0 5.66e-01 100.0% 90.0%
3384073 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.65 60.0 5.40e-01 100.0% 95.0%
3805340 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.65 58.0 5.15e-01 100.0% 91.5%
3548451 1.1.7.4 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_1 0.61 56.0 4.70e-01 100.0% 84.0%
4047081 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.60 43.0 4.47e-01 100.0% 80.0%
3795742 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 46.0 4.24e-01 100.0% 76.0%
5040939 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.53 36.0 3.70e-01 100.0% 72.2%
4945637 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 41.0 4.07e-01 98.9% 81.0%
4963491 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 39.0 3.92e-01 100.0% 80.0%
5001251 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 40.0 4.10e-01 100.0% 85.6%
5056751 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 42.0 4.11e-01 100.0% 81.9%
3708492 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.51 35.0 3.36e-01 100.0% 61.9%
5083030 11.1.1.284 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PKD_4 0.50 34.0 3.82e-01 100.0% 91.4%
4001868 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 42.0 3.99e-01 98.9% 79.1%
D2 high residues 252-342
PDB
Domain cluster: rep: IMGVR_UViG_3300017746_000056-3300017746-Ga0181389_10000689__D582-686
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ztnA02 2.40.30.190 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.75 66.0 5.73e-01 97.8% 87.9%
1v0fB03 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.69 60.0 6.21e-01 96.7% 100.0%
2v31A01 2.40.30.180 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Ubiquitin-activating enzyme E1, FCCH domain 0.68 59.0 5.86e-01 96.7% 88.7%
3gqbA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.67 48.0 5.32e-01 94.5% 97.2%
6oqrA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.66 47.0 4.81e-01 95.6% 76.7%
2gpjA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.64 56.0 5.46e-01 95.6% 99.0%
4wqmA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.64 56.0 5.54e-01 96.7% 94.9%
4xotA03 2.40.30.250 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.63 50.0 5.16e-01 97.8% 90.7%
2dpyA00 3.40.50.12240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.63 48.0 3.11e-01 94.5% 17.5%
3dclA02 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.62 54.0 5.45e-01 97.8% 95.6%
1qfjA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.62 53.0 5.39e-01 93.4% 96.7%
4b3fX02 2.40.30.270 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.62 53.0 5.18e-01 93.4% 96.9%
1ep3B01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.61 54.0 5.28e-01 95.6% 100.0%
4a6fA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 42.0 4.04e-01 72.5% 82.9%
5gxuB01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.60 53.0 4.77e-01 96.7% 93.4%
1a8pA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 51.0 5.06e-01 95.6% 100.0%
3myxA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 44.0 4.11e-01 96.7% 64.3%
4kbxA01 2.40.37.30 Mainly Beta › Beta Barrel › Lyase, Ornithine Decarboxylase; Chain A, domain 1 › 0.58 52.0 3.88e-01 100.0% 84.3%
2xzlA02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.58 46.0 4.94e-01 91.2% 100.0%
2qf4A02 2.40.10.350 Mainly Beta › Beta Barrel › Thrombin, subunit H › Rod shape-determining protein MreC, domain 2 0.57 44.0 4.41e-01 81.3% 82.4%
1wqsA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.57 36.0 4.05e-01 82.4% 82.9%
1wi1A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 40.0 3.77e-01 73.6% 81.1%
4jzjC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 35.0 3.90e-01 95.6% 84.3%
1x31A02 3.30.1360.120 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1 0.53 41.0 2.71e-01 84.6% 30.7%
1k85A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 38.0 3.92e-01 98.9% 80.7%
4i1kA00 2.40.330.10 Mainly Beta › Beta Barrel › At1g16640 B3 domain › DNA-binding pseudobarrel domain 0.52 44.0 4.10e-01 95.6% 73.7%
2covG00 2.60.40.2450 Mainly Beta › Sandwich › Immunoglobulin-like › Beta-1,3-xylanase, CBM31 domain 0.52 36.0 3.67e-01 91.2% 76.1%
3wcyA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 37.0 3.84e-01 97.8% 83.7%
3f7pD01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 38.0 3.87e-01 98.9% 81.3%
1hn0A01 2.60.120.430 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding lectin 0.51 43.0 3.54e-01 98.9% 82.1%
1k3iA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.50 43.0 3.72e-01 100.0% 93.5%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4028468 1.1.7.35 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › E1_FCCH 0.72 62.0 5.88e-01 97.8% 80.0%
3332862 1.1.7.35 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › E1_FCCH 0.71 61.0 6.06e-01 96.7% 89.5%
4943639 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.69 59.0 6.06e-01 96.7% 97.6%
1030933 1.1.7.29 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › End_beta_barrel 0.68 60.0 6.09e-01 97.8% 96.6%
199114 1.1.7.35 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › E1_FCCH 0.68 59.0 5.55e-01 96.7% 76.8%
3103203 1.1.7.35 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › E1_FCCH 0.67 60.0 6.03e-01 100.0% 100.0%
4854958 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.67 49.0 4.86e-01 97.8% 74.0%
4047241 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.66 48.0 4.80e-01 96.7% 73.7%
4060488 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.66 52.0 5.46e-01 100.0% 96.2%
4883589 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.66 48.0 4.75e-01 93.4% 72.9%
4453032 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.64 57.0 5.50e-01 96.7% 96.0%
3842233 1.1.7.69 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › MOV-10_beta-barrel 0.64 56.0 5.63e-01 96.7% 100.0%
3387360 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.64 51.0 5.28e-01 98.9% 94.1%
3272448 11.21.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Ig-like domain in tailspike protein › Ig-like domain in tailspike protein 0.63 55.0 5.43e-01 96.7% 89.5%
3614391 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.63 56.0 5.47e-01 97.8% 99.0%
3978877 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.63 53.0 5.35e-01 100.0% 92.2%
4429352 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.63 52.0 5.26e-01 98.9% 92.2%
4319764 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.62 50.0 4.75e-01 98.9% 72.7%
5011498 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.62 54.0 5.48e-01 94.5% 100.0%
3893654 1.1.7.69 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › MOV-10_beta-barrel 0.62 55.0 5.09e-01 97.8% 81.7%
3291083 11.21.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Ig-like domain in tailspike protein › Ig-like domain in tailspike protein 0.60 53.0 5.39e-01 98.9% 98.9%
3415428 1.1.7.69 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › MOV-10_beta-barrel 0.60 53.0 5.06e-01 98.9% 91.4%
3369214 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.59 53.0 5.03e-01 100.0% 100.0%
4173804 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.59 50.0 5.06e-01 92.3% 96.7%
3250056 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.59 53.0 4.80e-01 100.0% 92.0%
3273490 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.59 53.0 4.86e-01 100.0% 100.0%
4205165 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.58 49.0 5.03e-01 97.8% 100.0%
4939996 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.58 50.0 4.79e-01 95.6% 93.3%
3542883 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.58 51.0 4.49e-01 98.9% 99.3%
4963598 1.1.7.150 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF26503 0.57 41.0 4.46e-01 82.4% 92.0%
4936008 1.1.7.28 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › HAS-barrel 0.57 48.0 4.77e-01 93.4% 100.0%
3219381 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 42.0 4.24e-01 91.2% 78.9%
4159881 220.1.1.197 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF28623 0.56 38.0 3.82e-01 71.4% 89.5%
3226290 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 41.0 3.66e-01 93.4% 54.1%
3965822 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.54 47.0 4.73e-01 95.6% 98.9%
3525543 11.1.1.991 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF28112 0.53 43.0 4.08e-01 93.4% 73.6%
3273204 11.1.1.802 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF8390 0.53 40.0 4.02e-01 93.4% 80.0%
3964888 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.52 42.0 3.29e-01 96.7% 39.5%
1220925 11.1.1.47 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › CBM_48 0.50 37.0 3.19e-01 89.0% 47.0%
D3 medium residues 553-713_727-740
PDB
D4 medium residues 741-810
PDB