Back to structures

js4906-26-2_S25_scaffold_55_prodigal-single.1__X__X__00314

Bact-Vir

js4906-26-2_S25_scaffold_55_prodigal-single.1__X__X__00314

Identity

Kingdom:
phage

Quality

75.3 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 high residues 19-80
PDB
Domain cluster: representative
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mgtA01 3.30.160.70 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Methylated DNA-protein cysteine methyltransferase domain 0.77 52.0 4.57e-01 90.3% 48.9%
1huxA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.77 60.0 4.86e-01 90.3% 44.5%
2dmwA01 3.30.450.50 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Longin domain 0.71 51.0 4.22e-01 90.3% 41.4%
6h5bB01 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.70 52.0 4.25e-01 91.9% 42.0%
2f9wA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.69 49.0 3.87e-01 87.1% 35.9%
1j3wC00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.69 53.0 4.12e-01 85.5% 39.1%
6j9eJ00 3.30.160.560 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.68 53.0 5.20e-01 85.5% 80.3%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.68 52.0 4.45e-01 100.0% 50.5%
2ywqA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.67 55.0 4.95e-01 93.5% 64.8%
7yh1A01 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.67 48.0 4.00e-01 90.3% 42.1%
4bg8A01 3.30.420.430 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.67 50.0 4.07e-01 83.9% 51.9%
2l2nA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.66 55.0 5.28e-01 100.0% 81.7%
7oufB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.65 51.0 3.89e-01 87.1% 100.0%
2rs7A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.62 49.0 4.65e-01 88.7% 82.4%
7z0sE02 1.10.645.10 Mainly Alpha › Orthogonal Bundle › Cytochrome-c3 Hydrogenase; chain B › Cytochrome-c3 Hydrogenase, chain B 0.61 50.0 3.28e-01 96.8% 57.4%
3bs4A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.60 49.0 3.30e-01 91.9% 33.5%
4rs6A01 3.30.1120.30 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › POLO box domain 0.60 40.0 3.29e-01 90.3% 36.4%
1ti2A01 2.20.25.340 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.59 41.0 4.04e-01 72.6% 86.4%
2db2A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.59 51.0 4.52e-01 100.0% 64.9%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.59 51.0 4.93e-01 100.0% 87.3%
7r97A02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 47.0 4.59e-01 100.0% 86.8%
4tyzA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 40.0 3.40e-01 90.3% 43.1%
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.56 45.0 4.43e-01 95.2% 84.5%
4ig1A00 3.10.520.10 Alpha Beta › Roll › T-fold › ApbE-like domains 0.56 46.0 2.89e-01 90.3% 53.4%
1bakA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 39.0 3.24e-01 88.7% 39.5%
3a0oA03 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.54 43.0 2.93e-01 95.2% 80.8%
3qitB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 45.0 3.00e-01 98.4% 25.4%
4bubA02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.53 47.0 3.20e-01 100.0% 50.4%
1qw2A00 3.30.1980.10 Alpha Beta › 2-Layer Sandwich › Hypothetical protein Ta1206 fold › Hypothetical protein YunC 0.53 46.0 3.97e-01 100.0% 81.4%
3c19A02 3.10.20.300 Alpha Beta › Roll › Ubiquitin-like (UB roll) › mk0293 like domain 0.53 35.0 3.37e-01 74.2% 56.4%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 37.0 3.11e-01 79.0% 39.7%
2r41A00 3.10.450.150 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › enterococcus faecalis protein 0.52 37.0 3.23e-01 90.3% 47.6%
3pvlA04 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 36.0 3.17e-01 90.3% 46.5%
1z47A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 35.0 3.77e-01 87.1% 91.8%
4e5xG00 2.60.40.3530 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 41.0 3.68e-01 96.8% 62.6%
1j8bA00 3.30.1310.10 Alpha Beta › 2-Layer Sandwich › Ybab; Chain: A; › Nucleoid-associated protein YbaB-like domain 0.51 44.0 3.88e-01 96.8% 70.7%
2mhdA00 2.40.128.370 Mainly Beta › Beta Barrel › Lipocalin › 0.50 37.0 3.19e-01 88.7% 46.4%
ECOD (74)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4977899 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.77 56.0 4.60e-01 88.7% 43.6%
3680934 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.76 48.0 5.64e-01 90.3% 100.0%
4950038 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.73 56.0 5.19e-01 90.3% 65.0%
3461881 223.2.1.15 a+b three layers › Profilin-like › profilin-like › profilin-like › Longin 0.73 53.0 4.25e-01 91.9% 39.2%
5000609 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.72 53.0 4.24e-01 90.3% 39.2%
4975639 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.72 53.0 4.18e-01 90.3% 37.7%
5076068 223.2.1.3 a+b three layers › Profilin-like › profilin-like › profilin-like › Clat_adaptor_s 0.71 52.0 4.40e-01 91.9% 46.7%
4996048 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.71 57.0 4.49e-01 90.3% 42.3%
5079402 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.71 52.0 4.11e-01 90.3% 37.7%
3935131 2484.1.1.9 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.70 53.0 3.98e-01 96.8% 32.1%
5063657 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.69 50.0 4.06e-01 90.3% 40.3%
4976003 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.69 50.0 4.00e-01 90.3% 37.7%
4996848 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.69 52.0 4.25e-01 95.2% 43.3%
3510695 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.68 53.0 4.91e-01 100.0% 66.3%
5000374 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.67 49.0 3.81e-01 90.3% 35.0%
3281830 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.67 52.0 4.06e-01 87.1% 39.3%
5076907 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.67 49.0 3.84e-01 90.3% 36.3%
4971822 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.67 52.0 3.86e-01 88.7% 53.7%
3716107 2484.2.1.0 mixed a+b and a/b › Ribonuclease H-like › Methylated DNA-protein cysteine methyltransferase domain › Methylated DNA-protein cysteine methyltransferase domain 0.67 46.0 4.52e-01 100.0% 68.2%
4976809 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.66 48.0 3.87e-01 90.3% 37.7%
5075537 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.66 51.0 4.14e-01 87.1% 42.7%
5042876 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.66 49.0 3.99e-01 91.9% 41.7%
4980137 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.66 51.0 4.13e-01 87.1% 42.7%
4972549 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.66 51.0 4.10e-01 87.1% 43.1%
5072371 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.66 47.0 4.13e-01 91.9% 49.0%
4950075 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.65 47.0 3.94e-01 90.3% 42.6%
4972248 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.65 49.0 3.99e-01 88.7% 40.8%
3234330 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.65 50.0 4.19e-01 100.0% 48.2%
3519032 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.65 52.0 4.57e-01 93.5% 61.0%
3515884 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 45.0 3.67e-01 98.4% 39.2%
5065002 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.64 49.0 3.96e-01 85.5% 42.4%
4481632 2484.1.1.21 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › BcrAD_BadFG 0.64 50.0 4.28e-01 90.3% 54.5%
5008246 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.63 43.0 3.86e-01 90.3% 48.9%
4946587 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.62 45.0 3.60e-01 90.3% 36.9%
3620870 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.62 47.0 4.11e-01 87.1% 53.0%
3224950 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.62 43.0 3.68e-01 96.8% 43.8%
3482713 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 44.0 3.47e-01 85.5% 34.8%
3515207 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.61 50.0 4.52e-01 100.0% 64.4%
3184922 330.1.1.3 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dicer_dimer 0.61 49.0 4.05e-01 90.3% 59.1%
4093535 220.1.1.1 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 44.0 3.52e-01 96.8% 36.9%
4931141 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.61 39.0 3.91e-01 90.3% 63.1%
3929135 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 42.0 3.57e-01 72.6% 59.0%
3670605 330.1.1.3 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dicer_dimer 0.60 52.0 4.64e-01 100.0% 71.1%
5036411 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 42.0 3.35e-01 74.2% 58.5%
5810 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.59 51.0 4.43e-01 100.0% 62.6%
3700289 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.59 50.0 4.01e-01 100.0% 46.9%
3789602 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 43.0 3.51e-01 96.8% 40.0%
3921576 220.1.1.1 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.58 44.0 3.44e-01 96.8% 36.4%
3584264 220.1.1.1 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.58 43.0 3.50e-01 96.8% 40.0%
3591459 220.1.1.8 beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.57 43.0 3.89e-01 90.3% 58.8%
4012071 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 41.0 2.61e-01 96.8% 12.7%
3299579 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.57 47.0 4.53e-01 91.9% 88.6%
3593110 898.1.1.0 a+b two layers › a+b domain in Ribosomal protein L1 › a+b domain in Ribosomal protein L1 › a+b domain in Ribosomal protein L1 0.57 44.0 3.61e-01 85.5% 73.1%
5038289 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.57 45.0 3.69e-01 96.8% 100.0%
4890129 220.1.1.44 beta barrels › PH domain-like › PH domain-like › PH domain-like › POB3_N 0.56 40.0 3.54e-01 96.8% 47.1%
3671668 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.56 47.0 3.43e-01 95.2% 58.9%
4674129 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 40.0 3.54e-01 98.4% 48.6%
3219484 220.1.1.44 beta barrels › PH domain-like › PH domain-like › PH domain-like › POB3_N 0.55 39.0 3.49e-01 96.8% 49.0%
3462961 5.1.4.122 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › DUF295 0.54 44.0 2.97e-01 93.5% 23.9%
5001324 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 39.0 3.39e-01 96.8% 46.7%
3810543 220.1.1.20 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_TFIIH 0.54 39.0 3.32e-01 90.3% 44.5%
4600223 616.1.1.33 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › UPF0262 0.54 43.0 3.46e-01 96.8% 62.1%
4932458 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.54 37.0 2.47e-01 82.3% 15.6%
3473908 220.1.1.157 beta barrels › PH domain-like › PH domain-like › PH domain-like › PF29715 0.53 43.0 3.30e-01 95.2% 72.7%
4203238 220.1.1.217 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH, GRAM 0.53 38.0 2.70e-01 100.0% 20.8%
3956336 245.2.1.0 a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB 0.51 42.0 3.36e-01 88.7% 47.5%
4067487 245.2.1.1 a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.51 45.0 3.91e-01 98.4% 69.5%
5056316 2002.1.1.120 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.51 42.0 2.72e-01 100.0% 99.4%
4472467 245.2.1.1 a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.51 45.0 4.05e-01 98.4% 76.5%
4567436 245.2.1.1 a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.51 44.0 4.01e-01 96.8% 77.6%
3960596 245.2.1.0 a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB 0.51 44.0 3.99e-01 96.8% 76.5%
4139864 245.2.1.1 a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.50 44.0 3.84e-01 98.4% 66.3%
3589881 245.2.1.1 a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.50 44.0 3.86e-01 98.4% 71.6%
4168230 245.2.1.1 a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.50 44.0 3.82e-01 98.4% 76.8%