Back to structures

NC_049471.1__YP_009884565.1__HYQ01_gp080__00080

Bact-Vir

NC_049471.1__YP_009884565.1__HYQ01_gp080__00080

Identity

Accession:
NC_049471 ↗
Kingdom:
phage

Quality

75.8 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 1-118
PDB
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h8zA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.68 36.0 4.77e-01 80.5% 95.3%
1wjsA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.60 39.0 3.84e-01 78.0% 61.4%
4ic5A02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.59 37.0 3.91e-01 72.9% 70.2%
2gpjA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 41.0 4.41e-01 71.2% 98.0%
3a2yA00 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.55 40.0 3.44e-01 74.6% 60.0%
2vobB02 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.55 46.0 3.76e-01 89.0% 69.6%
5tr9A01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.54 39.0 4.25e-01 72.9% 100.0%
1a8pA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.54 38.0 4.15e-01 72.0% 100.0%
1ts9A00 2.30.30.210 Mainly Beta › Roll › SH3 type barrels. › Ribonuclease P/MRP, subunit p29 0.54 31.0 3.36e-01 72.0% 67.3%
4ecnA01 2.60.40.3540 Mainly Beta › Sandwich › Immunoglobulin-like › Domain of unknown function DUF4458 0.53 32.0 3.44e-01 70.3% 68.0%
7ylrA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.53 36.0 3.80e-01 70.3% 99.0%
3kyfA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 35.0 3.62e-01 73.7% 71.1%
3dnhA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 36.0 3.32e-01 70.3% 57.0%
2eixA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.51 36.0 3.77e-01 72.0% 92.5%
5utkA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 28.0 3.23e-01 70.3% 74.7%
2hq9B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.50 32.0 3.10e-01 70.3% 54.7%
1tdqA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 34.0 3.78e-01 72.0% 91.1%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3619619 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.62 36.0 4.53e-01 75.4% 95.7%
3246086 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.61 37.0 4.15e-01 77.1% 75.8%
3841414 4.1.1.42 beta barrels › SH3 › SH3 › SH3 › Agenet 0.61 36.0 4.60e-01 80.5% 100.0%
4572937 4.1.1.34 beta barrels › SH3 › SH3 › SH3 › MBT 0.59 40.0 3.55e-01 76.3% 48.2%
3890336 4.1.1.34 beta barrels › SH3 › SH3 › SH3 › MBT 0.59 40.0 3.03e-01 76.3% 29.8%
3572964 4.1.1.9 beta barrels › SH3 › SH3 › SH3 › TUDOR 0.59 36.0 3.18e-01 77.1% 43.6%
3774803 4.1.1.34 beta barrels › SH3 › SH3 › SH3 › MBT 0.59 40.0 2.82e-01 76.3% 23.1%
3276599 6.1.1.0 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil 0.58 40.0 3.28e-01 70.3% 89.1%
3257642 6.1.1.4 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › Ricin_B_lectin 0.58 40.0 3.36e-01 71.2% 83.9%
3229867 1.1.17.8 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › DUF316 0.58 41.0 3.15e-01 73.7% 74.1%
3502085 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.57 38.0 4.11e-01 72.0% 80.0%
3275615 4.1.1.42 beta barrels › SH3 › SH3 › SH3 › Agenet 0.56 40.0 3.95e-01 82.2% 69.0%
4012802 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.55 38.0 3.96e-01 71.2% 90.0%
3518700 1.1.17.1 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.55 38.0 3.14e-01 71.2% 89.0%
5041801 4.15.1.0 beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like 0.55 35.0 4.04e-01 70.3% 90.6%
4273561 1.1.7.91 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25940 0.55 37.0 3.59e-01 70.3% 77.0%
3972868 1.1.7.7 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.54 38.0 4.07e-01 71.2% 96.0%
3781180 1.1.2.0 beta barrels › cradle loop barrel › RIFT-related › double psi 0.54 37.0 3.88e-01 70.3% 98.2%
3290160 4.1.1.323 beta barrels › SH3 › SH3 › SH3 › WYL 0.54 35.0 4.14e-01 71.2% 97.5%
4463104 1.1.5.11 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › UbiD 0.54 44.0 3.55e-01 87.3% 52.0%
3719639 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.54 39.0 3.83e-01 74.6% 100.0%
4069560 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.54 33.0 3.98e-01 72.0% 96.0%
5063188 1.1.5.33 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.53 38.0 3.13e-01 74.6% 70.2%
4956280 4.1.1.301 beta barrels › SH3 › SH3 › SH3 › MJ1316 0.53 33.0 3.87e-01 71.2% 96.0%
2455725 1.1.7.7 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.52 36.0 3.85e-01 71.2% 91.4%
3448643 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.52 38.0 3.14e-01 74.6% 78.0%
1167973 1.1.5.11 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › UbiD 0.52 42.0 3.56e-01 88.1% 57.1%
2832896 1.1.5.11 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › UbiD 0.52 42.0 3.51e-01 88.1% 53.2%
4993962 1.1.5.11 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › UbiD 0.52 42.0 3.44e-01 86.4% 56.7%
3377696 1.1.17.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.52 38.0 3.13e-01 75.4% 80.0%
4943438 1.1.5.11 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › UbiD 0.51 41.0 3.46e-01 88.1% 53.3%
3689576 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.51 36.0 3.31e-01 73.7% 61.3%
3167605 1.1.5.11 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › UbiD 0.50 41.0 3.43e-01 88.1% 56.3%
D2 medium residues 119-190
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1wmhA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.63 46.0 4.45e-01 79.2% 88.0%
3aeiA00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 40.0 3.71e-01 100.0% 50.0%
3afhA02 3.90.800.10 Alpha Beta › Alpha-Beta Complex › Glutamyl-tRNA Synthetase; domain 3 › Glutamyl-tRNA Synthetase; Domain 3 0.61 52.0 4.68e-01 97.2% 87.5%
3m1cA04 2.60.40.3190 Mainly Beta › Sandwich › Immunoglobulin-like › Herpesvirus glycoprotein H, C-terminal domain 0.58 51.0 4.17e-01 97.2% 57.6%
2aq6A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.56 45.0 3.72e-01 91.7% 91.6%
1wi0A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.56 43.0 3.72e-01 83.3% 74.3%
3h8hA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.56 41.0 3.80e-01 79.2% 82.6%
2xqyA03 2.60.40.3190 Mainly Beta › Sandwich › Immunoglobulin-like › Herpesvirus glycoprotein H, C-terminal domain 0.56 48.0 3.97e-01 98.6% 57.9%
2arzA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 44.0 3.59e-01 91.7% 83.3%
2vugA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.55 46.0 4.61e-01 95.8% 100.0%
3gasB02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 44.0 3.44e-01 91.7% 76.8%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.54 38.0 3.35e-01 73.6% 60.2%
4p6bB00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 46.0 2.98e-01 100.0% 69.7%
2i51B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 43.0 3.25e-01 91.7% 79.6%
6kjcA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.53 46.0 2.90e-01 100.0% 65.9%
1d0nA06 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.53 38.0 3.22e-01 76.4% 73.2%
1sfxB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 30.0 2.71e-01 86.1% 35.6%
5tgfD00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.52 44.0 2.97e-01 100.0% 64.5%
1nzjA02 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.52 40.0 3.35e-01 87.5% 60.9%
4clcA00 3.30.450.150 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Haem-degrading domain 0.52 43.0 3.29e-01 91.7% 78.7%
2bhgA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.52 36.0 3.39e-01 75.0% 58.7%
3vpbA02 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.51 39.0 4.03e-01 84.7% 100.0%
1tvgA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 44.0 3.66e-01 100.0% 88.2%
4wd3A02 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.51 38.0 3.81e-01 80.6% 96.0%
1va0B02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.51 41.0 3.49e-01 90.3% 88.7%
3tiiA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.51 39.0 4.05e-01 86.1% 100.0%
1pjqB05 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.51 39.0 3.37e-01 87.5% 73.0%
3n40P02 2.60.40.3200 Mainly Beta › Sandwich › Immunoglobulin-like › Alphavirus E2 glycoprotein, A domain 0.51 43.0 3.14e-01 100.0% 47.9%
1id2A00 2.60.40.420 Mainly Beta › Sandwich › Immunoglobulin-like › Cupredoxins - blue copper proteins 0.50 39.0 3.50e-01 87.5% 72.6%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4952123 3986.2.1.0 a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.75 51.0 5.56e-01 70.8% 96.7%
3325376 221.1.1.4 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.62 46.0 4.67e-01 79.2% 100.0%
3464866 1.1.5.33 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.62 44.0 3.44e-01 75.0% 51.3%
3528684 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.60 44.0 4.12e-01 80.6% 80.0%
3523019 221.1.1.4 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.60 44.0 4.22e-01 79.2% 90.6%
3836597 221.1.1.4 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.60 45.0 3.77e-01 80.6% 66.4%
3489385 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.60 47.0 3.97e-01 87.5% 62.4%
3573560 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.60 45.0 4.06e-01 81.9% 77.0%
3405682 7579.1.1.2 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Lipase 0.59 47.0 3.11e-01 90.3% 22.4%
3493732 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.58 43.0 3.97e-01 80.6% 88.4%
3429643 221.1.1.4 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.58 46.0 4.17e-01 90.3% 78.1%
5037837 1056.1.1.1 a+b two layers › tRNA pseudouridine synthase TruD insertion domain › tRNA pseudouridine synthase TruD insertion domain › tRNA pseudouridine synthase TruD insertion domain › TruD 0.57 45.0 3.42e-01 93.1% 100.0%
5004573 1.1.5.8 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.57 44.0 3.61e-01 88.9% 83.9%
4952973 4.15.1.0 beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like 0.56 42.0 4.03e-01 84.7% 96.7%
4067342 5069.1.1.15 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cytochrom_C_asm 0.56 39.0 2.52e-01 72.2% 99.4%
3996439 224.1.1.2 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.56 39.0 3.34e-01 73.6% 77.5%
4992755 4.15.1.2 beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.56 42.0 3.98e-01 83.3% 90.0%
4982722 4.15.1.2 beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.56 42.0 4.03e-01 83.3% 95.3%
3603402 4.15.1.2 beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.55 43.0 4.04e-01 84.7% 91.1%
3237233 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.55 40.0 3.96e-01 79.2% 93.8%
3730205 221.1.1.4 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.55 43.0 4.18e-01 86.1% 86.3%
3404828 1.1.5.8 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.54 43.0 3.31e-01 91.7% 72.1%
4234527 2006.1.1.11 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase_3 0.53 42.0 2.93e-01 88.9% 43.0%
4197453 1137.1.1.1 a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain › TP_methylase 0.53 42.0 3.51e-01 87.5% 76.2%
3581135 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.53 43.0 3.67e-01 91.7% 80.8%
4073610 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.53 42.0 3.68e-01 90.3% 99.1%
3438348 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 38.0 3.79e-01 80.6% 100.0%
4489065 1137.1.1.1 a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain › TP_methylase 0.52 39.0 3.39e-01 86.1% 73.6%
3603835 304.122.1.1 a+b two layers › Alpha-beta plaits › Nitrogen repressor-like proteins › Nitrogen repressor-like proteins › NRD1_2 0.51 38.0 3.45e-01 83.3% 89.5%
4061211 2484.1.1.2 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.51 38.0 2.66e-01 86.1% 54.2%
3496497 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.51 36.0 2.70e-01 76.4% 42.0%
6800 224.1.1.1 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.50 34.0 2.86e-01 72.2% 66.2%
3617550 4342.1.1.0 alpha complex topology › Tex N-terminal region-like › Tex N-terminal region-like › Tex N-terminal region-like 0.50 41.0 3.15e-01 100.0% 90.0%