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PHAGE-A4--js4906-25-3_S22_scaffold_24_curated_closed_complete_prodigal-single.1__X__X__00211

Bact-Vir

PHAGE-A4--js4906-25-3_S22_scaffold_24_curated_closed_complete_prodigal-single.1__X__X__00211

Identity

Kingdom:
phage

Quality

74.6 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 37-92
PDB
Domain cluster: representative
CATH (46)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5ejrA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.80 48.0 4.23e-01 92.9% 42.5%
3d89A00 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.68 54.0 4.11e-01 89.3% 64.0%
2c9wA01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.65 50.0 3.99e-01 83.9% 61.9%
6ruiB04 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.65 52.0 3.66e-01 89.3% 63.2%
2ablA02 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.64 50.0 4.17e-01 85.7% 67.0%
4adiA02 3.30.67.20 Alpha Beta › 2-Layer Sandwich › Viral Envelope Glycoprotein; domain 2 › Rubella membrane glycoprotein E1, domain 2 0.63 54.0 4.75e-01 100.0% 87.5%
2dx0B01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.62 45.0 4.16e-01 78.6% 77.3%
4aghA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.61 44.0 3.99e-01 78.6% 70.0%
1kmdA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.59 47.0 3.89e-01 96.4% 92.3%
7pluA01 1.20.58.530 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 40.0 3.22e-01 71.4% 99.1%
2o8bA04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.58 41.0 3.63e-01 100.0% 50.6%
3frnA01 3.10.129.70 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › 0.57 40.0 3.03e-01 75.0% 48.9%
2i2lA01 2.10.70.50 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.57 39.0 4.09e-01 73.2% 80.8%
3u97A00 3.10.450.530 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Ribonuclease toxin, BrnT, of type II toxin-antitoxin system 0.56 42.0 3.90e-01 100.0% 61.0%
2lc4A00 2.30.30.830 Mainly Beta › Roll › SH3 type barrels. › 0.56 42.0 3.43e-01 82.1% 61.3%
3lq6A02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.55 44.0 3.60e-01 92.9% 95.6%
1wi5A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 45.0 4.18e-01 96.4% 86.7%
2wb8A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 46.0 3.40e-01 100.0% 80.7%
5hmaA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.54 45.0 3.90e-01 92.9% 93.1%
1l8rA00 3.10.260.20 Alpha Beta › Roll › Mlu1-box Binding Protein; DNA-binding Domain › Ski 0.54 42.0 3.64e-01 92.9% 87.1%
3tu3A00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.54 43.0 3.44e-01 89.3% 75.6%
7b9cA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 37.0 2.30e-01 75.0% 34.8%
4trtA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.53 43.0 3.51e-01 98.2% 87.7%
1bm8A00 3.10.260.10 Alpha Beta › Roll › Mlu1-box Binding Protein; DNA-binding Domain › Transcription regulator HTH, APSES-type DNA-binding domain 0.53 42.0 3.48e-01 87.5% 70.7%
1bbuA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 46.0 3.47e-01 100.0% 72.9%
1uebA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 44.0 4.31e-01 94.6% 84.1%
4rnyA03 2.70.70.10 Mainly Beta › Distorted Sandwich › Glucose Permease (Domain IIA) › Glucose Permease (Domain IIA) 0.53 46.0 3.57e-01 100.0% 52.3%
4btfA03 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.53 44.0 3.65e-01 100.0% 76.8%
1mk1A00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.53 39.0 2.79e-01 82.1% 94.7%
4ynmB00 2.170.270.10 Mainly Beta › Beta Complex › Beta-clip-like › SET domain 0.52 45.0 3.14e-01 100.0% 70.4%
2kheA00 3.30.2310.20 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › RelE-like 0.52 43.0 3.83e-01 100.0% 88.8%
1mdaH00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 40.0 2.48e-01 87.5% 18.2%
2hjjA00 3.30.160.130 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › ykff protein like domains 0.52 40.0 3.85e-01 89.3% 71.2%
2fm8B00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.52 40.0 3.19e-01 87.5% 73.6%
1sjdB01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 43.0 3.33e-01 94.6% 83.2%
7d27A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.51 42.0 2.92e-01 100.0% 40.0%
3nemA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 43.0 3.61e-01 100.0% 85.7%
1xkwA01 2.170.130.10 Mainly Beta › Beta Complex › Ferric Hydroxamate Uptake Protein; Chain A, domain 1 › TonB-dependent receptor, plug domain 0.51 42.0 3.58e-01 98.2% 89.0%
3bpqD00 3.30.2310.20 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › RelE-like 0.51 42.0 3.73e-01 100.0% 62.8%
2pn2A00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.51 35.0 2.77e-01 75.0% 89.1%
1jssA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 40.0 2.96e-01 100.0% 86.4%
4uy9A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 42.0 3.71e-01 100.0% 91.1%
1sbxA00 3.10.260.20 Alpha Beta › Roll › Mlu1-box Binding Protein; DNA-binding Domain › Ski 0.51 41.0 3.45e-01 96.4% 83.0%
1stzA03 3.30.390.60 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Heat-inducible transcription repressor hrca homolog; domain 3 0.51 40.0 3.56e-01 91.1% 93.3%
1u5qA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.50 43.0 3.67e-01 100.0% 86.5%
1u5kA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.50 41.0 3.74e-01 96.4% 72.0%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4962459 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 46.0 4.00e-01 73.2% 81.8%
4943079 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 49.0 3.54e-01 82.1% 44.5%
3981109 206.1.1.97 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › ABC1, WaaY 0.64 50.0 3.30e-01 85.7% 61.7%
3246217 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.63 53.0 4.04e-01 94.6% 55.6%
4474942 4337.1.1.0 ↗ a+b two layers › DNA mismatch repair protein MutL dimerization subdomain › DNA mismatch repair protein MutL dimerization subdomain › DNA mismatch repair protein MutL dimerization subdomain 0.63 53.0 4.86e-01 96.4% 92.0%
3587270 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.63 45.0 3.61e-01 80.4% 37.4%
3714752 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 47.0 2.92e-01 82.1% 38.9%
4971601 241.14.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › SARS-unique domain-C › SARS-unique domain-C 0.62 46.0 4.36e-01 82.1% 81.4%
3697550 284.2.1.0 ↗ a+b two layers › FKBP-like › Chitinase insertion domain › Chitinase insertion domain 0.62 47.0 4.23e-01 83.9% 58.7%
4146531 4056.1.1.0 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein 0.61 44.0 4.03e-01 80.4% 57.3%
3308663 601.3.1.11 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain › PHD_Oberon 0.60 44.0 3.42e-01 83.9% 48.3%
6288 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.59 47.0 3.89e-01 96.4% 92.3%
3619623 101.1.9.4 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain › Ski_Sno 0.58 46.0 4.53e-01 94.6% 84.6%
3429387 386.1.1.6 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › ARS2 0.58 40.0 4.31e-01 83.9% 88.9%
3570680 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.58 46.0 2.79e-01 87.5% 20.8%
3935486 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.58 49.0 3.88e-01 98.2% 45.6%
3675412 386.1.1.6 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › ARS2 0.58 41.0 3.70e-01 91.1% 53.8%
4945344 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 43.0 2.73e-01 83.9% 29.8%
4032291 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.58 48.0 4.59e-01 91.1% 84.6%
4483173 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.57 48.0 4.59e-01 94.6% 80.0%
5069121 4.6.1.0 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain 0.56 48.0 4.80e-01 100.0% 93.3%
3883532 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.56 45.0 3.25e-01 87.5% 50.6%
3787893 206.1.1.70 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, ABC1 0.56 48.0 3.04e-01 100.0% 30.4%
4945895 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.56 47.0 3.88e-01 94.6% 61.0%
4100221 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.56 46.0 4.43e-01 94.6% 80.0%
3223544 9.3.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Quinohemoprotein amine dehydrogenase A chain, domain 3-like › Quinohemoprotein amine dehydrogenase A chain, domain 3-like 0.55 43.0 3.60e-01 92.9% 78.3%
3523669 9.3.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Quinohemoprotein amine dehydrogenase A chain, domain 3-like › Quinohemoprotein amine dehydrogenase A chain, domain 3-like 0.55 44.0 3.77e-01 87.5% 75.6%
4568123 219.1.1.79 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core2 0.55 48.0 3.42e-01 100.0% 59.4%
3307718 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.55 40.0 3.23e-01 80.4% 53.3%
3948516 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.55 45.0 4.32e-01 91.1% 87.7%
4966955 330.7.1.2 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain › HicA_toxin 0.55 41.0 3.91e-01 89.3% 67.1%
3786534 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.55 45.0 3.31e-01 100.0% 84.4%
4950404 330.7.1.2 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain › HicA_toxin 0.55 42.0 3.82e-01 89.3% 62.7%
3309686 206.1.1.15 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Fructosamin_kin 0.54 48.0 3.02e-01 100.0% 30.0%
3933098 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 43.0 4.18e-01 92.9% 84.6%
3484263 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.54 46.0 3.18e-01 100.0% 50.0%
4119533 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.54 45.0 4.47e-01 94.6% 88.3%
3500153 219.1.1.27 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Menin 0.54 47.0 3.22e-01 100.0% 52.3%
4678731 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.54 45.0 4.34e-01 94.6% 83.1%
4434149 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.53 45.0 4.30e-01 94.6% 81.5%
3971872 241.1.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone 0.53 42.0 3.36e-01 91.1% 69.9%
4590724 3291.1.1.163 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Pescadillo_N 0.53 40.0 3.04e-01 83.9% 64.1%
3370517 109.1.1.6 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C_2 0.53 39.0 2.97e-01 85.7% 66.9%
3509127 2004.1.1.361 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › UTP25_NTPase-like 0.53 39.0 2.47e-01 87.5% 34.0%
4030291 70.3.1.1 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like › SET 0.53 45.0 3.14e-01 100.0% 70.0%
3742632 5.1.4.16 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CPSF_A 0.52 40.0 2.63e-01 87.5% 25.2%
3638387 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.52 43.0 2.70e-01 100.0% 40.3%
3616471 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.52 42.0 2.65e-01 92.9% 24.4%
2229 5.1.4.25 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Me-amine-dh_H 0.52 40.0 2.48e-01 87.5% 18.2%
4216985 331.19.1.2 ↗ a+b two layers › TBP-like › Toxin RnlA N-terminal domains › Toxin RnlA N-terminal domains › RnlA_toxin_N 0.52 43.0 3.80e-01 94.6% 72.9%
4066623 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.52 42.0 4.19e-01 92.9% 90.0%
3475103 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.52 41.0 2.66e-01 100.0% 30.3%
4425795 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.52 44.0 4.19e-01 94.6% 84.6%
5065528 330.7.1.0 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain 0.51 40.0 3.76e-01 87.5% 72.9%
3189211 70.3.1.1 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like › SET 0.51 43.0 2.88e-01 98.2% 70.8%
3826272 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.51 44.0 2.75e-01 98.2% 79.1%
4993341 4312.1.1.0 ↗ a+b two layers › RelE-like › RelE-like › RelE-like 0.51 41.0 3.85e-01 100.0% 72.9%
4183857 325.1.7.30 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › Peptidase_M23 0.51 41.0 3.80e-01 92.9% 78.7%
4167626 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.50 42.0 4.04e-01 96.4% 81.5%
4050524 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.50 40.0 3.86e-01 91.1% 86.2%