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NC_021559.1__YP_008130117.1__PRAG_00191__00184

Bact-Vir

NC_021559.1__YP_008130117.1__PRAG_00191__00184

Identity

Accession:
NC_021559 ↗
Kingdom:
phage

Quality

85.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Ronodorvirus› Prochlorococcus_phage_P-SSM3

TaxID: 536453

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 3-60
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1qqgA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.75 56.0 4.59e-01 81.0% 44.7%
2yztA00 3.30.160.250 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.73 55.0 5.29e-01 93.1% 71.2%
1wp0A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.72 52.0 3.78e-01 77.6% 88.1%
2k49A00 2.30.29.80 Mainly Beta › Roll › PH-domain like › 0.70 57.0 4.58e-01 91.4% 45.8%
3fm8D03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.69 56.0 4.57e-01 89.7% 51.9%
2d9xA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.66 49.0 3.97e-01 84.5% 41.8%
3fmwC03 3.40.30.120 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.66 46.0 3.80e-01 75.9% 63.2%
2r0cA03 3.40.30.120 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.65 47.0 3.79e-01 77.6% 66.4%
2b7jB01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.65 48.0 3.54e-01 79.3% 85.0%
2yf0A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.65 47.0 4.14e-01 79.3% 51.7%
2z7bA00 3.40.225.10 Alpha Beta › 3-Layer(aba) Sandwich › L-fuculose-1-phosphate Aldolase › Class II aldolase/adducin N-terminal domain 0.65 51.0 3.42e-01 87.9% 71.3%
3ihgA03 3.40.30.120 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.64 47.0 3.58e-01 79.3% 63.4%
6brdA03 3.40.30.120 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.63 44.0 3.86e-01 75.9% 67.4%
4k2xA03 3.40.30.120 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.63 44.0 3.67e-01 75.9% 68.8%
2dsyD00 3.30.160.250 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.63 52.0 4.79e-01 100.0% 72.8%
2lw7A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.62 47.0 3.81e-01 82.8% 85.1%
4fo5A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.62 43.0 3.34e-01 74.1% 82.4%
3ha9A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.61 43.0 3.24e-01 77.6% 78.3%
1yw5A01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.59 35.0 3.50e-01 79.3% 54.0%
2hjjA00 3.30.160.130 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › ykff protein like domains 0.59 43.0 4.19e-01 79.3% 80.3%
4cy8A03 3.40.30.120 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.58 45.0 3.43e-01 91.4% 44.3%
1q67A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 45.0 3.42e-01 86.2% 74.3%
7lscA01 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.56 41.0 3.22e-01 84.5% 49.0%
3gveA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.56 41.0 2.57e-01 98.3% 14.1%
3dcxA00 2.30.29.50 Mainly Beta › Roll › PH-domain like › Bacterial Pleckstrin homology domain 0.56 41.0 3.40e-01 82.8% 43.6%
3hi0A03 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.54 40.0 2.79e-01 79.3% 88.6%
1nr4C00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 37.0 3.61e-01 70.7% 65.2%
3kkjA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 43.0 3.29e-01 93.1% 98.7%
1u2kA02 1.10.420.10 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 2 › Peroxidase, domain 2 0.54 40.0 3.10e-01 79.3% 41.4%
2olsA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.54 42.0 3.11e-01 84.5% 67.8%
3rpjA00 3.30.310.230 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Sigma factor-binding protein Crl monomer 0.53 38.0 2.92e-01 75.9% 58.7%
3ieyA02 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.53 36.0 3.14e-01 72.4% 81.0%
3mz2A00 3.20.20.190 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphatidylinositol (PI) phosphodiesterase 0.53 45.0 2.88e-01 96.6% 82.1%
1es6A02 2.60.510.10 Mainly Beta › Sandwich › EV matrix protein fold › EV matrix protein 0.52 41.0 3.53e-01 87.9% 61.6%
4ls9B02 3.10.310.30 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › 0.52 42.0 3.41e-01 93.1% 82.1%
2bjoA01 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.52 35.0 3.99e-01 82.8% 100.0%
1eqtA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.50 33.0 3.27e-01 75.9% 61.2%
4py5A01 3.30.310.10 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein 0.50 37.0 3.45e-01 79.3% 97.2%
ECOD (57)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3976684 7089.1.1.0 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD 0.78 60.0 5.38e-01 87.9% 60.0%
3233139 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.75 55.0 4.30e-01 79.3% 77.6%
3189844 2485.1.1.12 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › SCO1-SenC 0.73 53.0 3.62e-01 77.6% 68.8%
4966809 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.72 49.0 4.40e-01 70.7% 100.0%
3685086 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.72 52.0 3.83e-01 77.6% 82.6%
4098661 2485.1.1.105 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › PF29430 0.70 50.0 3.82e-01 77.6% 69.0%
3261962 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.70 49.0 3.63e-01 82.8% 29.7%
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 0.70 50.0 5.51e-01 81.0% 97.8%
5032509 4100.1.1.0 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.69 53.0 5.15e-01 100.0% 75.4%
3721997 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.68 53.0 5.66e-01 89.7% 96.0%
3729598 65.1.1.0 ↗ beta sandwiches › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases 0.68 49.0 4.92e-01 77.6% 83.3%
1518906 2485.1.1.45 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_8 0.67 46.0 3.54e-01 72.4% 82.6%
3797728 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.67 49.0 4.32e-01 82.8% 52.9%
3624498 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.67 49.0 3.78e-01 82.8% 36.0%
4586179 2485.1.1.56 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Rng_hyd_C 0.67 46.0 3.55e-01 72.4% 62.3%
3233071 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.66 49.0 4.04e-01 84.5% 43.8%
3271442 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.66 46.0 3.41e-01 77.6% 28.7%
3866966 386.1.1.236 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › PF26743 0.66 48.0 4.78e-01 79.3% 93.3%
5062306 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.66 48.0 4.24e-01 81.0% 96.7%
1835053 2485.1.1.56 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Rng_hyd_C 0.65 47.0 3.87e-01 77.6% 71.3%
3720463 2485.1.1.56 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Rng_hyd_C 0.65 48.0 3.67e-01 79.3% 60.0%
3520218 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.65 48.0 3.80e-01 82.8% 38.3%
4486447 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.65 52.0 3.06e-01 91.4% 69.7%
3704939 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 46.0 4.08e-01 82.8% 52.2%
3548274 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.62 51.0 4.05e-01 91.4% 86.7%
3486058 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.62 51.0 3.44e-01 100.0% 22.7%
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 0.61 48.0 4.33e-01 86.2% 63.7%
5080692 298.4.1.1 ↗ a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E › vATP-synt_E 0.61 54.0 3.88e-01 100.0% 64.2%
4365268 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.61 49.0 2.87e-01 89.7% 40.4%
3923731 220.1.1.35 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › IQ_SEC7_PH 0.61 46.0 3.39e-01 82.8% 30.6%
3514692 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 46.0 3.77e-01 82.8% 46.1%
4098787 136.1.1.1 ↗ alpha complex topology › Heme-dependent peroxidases › Heme-dependent peroxidases › Heme-dependent peroxidases › peroxidase 0.59 43.0 2.42e-01 77.6% 7.0%
3291339 2485.1.1.56 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Rng_hyd_C 0.58 42.0 3.61e-01 77.6% 72.0%
3222762 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.58 48.0 4.42e-01 98.3% 78.8%
5042381 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.58 43.0 2.64e-01 84.5% 12.1%
3874175 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.58 43.0 3.48e-01 82.8% 44.0%
3800448 3922.1.1.129 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › SMC_N 0.58 40.0 2.32e-01 70.7% 19.4%
3566455 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.58 43.0 3.71e-01 84.5% 51.0%
3956669 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.57 43.0 3.08e-01 82.8% 51.7%
4969228 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.57 42.0 3.49e-01 82.8% 72.7%
3656728 252.1.1.0 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD 0.56 42.0 4.21e-01 87.9% 81.4%
3953675 330.7.1.0 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain 0.56 41.0 4.00e-01 79.3% 81.5%
3399731 3016.1.1.21 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › PDXDC1-like_cen 0.56 41.0 3.06e-01 79.3% 98.7%
4067567 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.56 48.0 4.14e-01 100.0% 77.9%
5059099 241.2.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › Frataxin-like › Frataxin-like 0.55 42.0 3.73e-01 91.4% 55.7%
3958672 2485.1.1.56 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Rng_hyd_C 0.54 41.0 3.92e-01 87.9% 74.3%
4047302 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.53 45.0 3.85e-01 100.0% 76.0%
5031046 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.53 39.0 3.32e-01 79.3% 85.4%
3176989 601.19.1.40 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › PF28954 0.52 45.0 3.35e-01 100.0% 45.6%
4618205 604.1.1.150 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF28954 0.52 45.0 3.61e-01 100.0% 60.8%
4640808 136.1.1.1 ↗ alpha complex topology › Heme-dependent peroxidases › Heme-dependent peroxidases › Heme-dependent peroxidases › peroxidase 0.52 44.0 2.52e-01 100.0% 37.3%
3236774 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.51 42.0 2.74e-01 96.6% 22.8%
5075801 298.1.1.24 ↗ a+b two layers › FwdE/GAPDH domain-like › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › GFO_IDH_MocA_C3 0.51 40.0 2.86e-01 86.2% 79.2%
4658740 220.1.1.82 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_6 0.51 37.0 3.44e-01 79.3% 80.0%
3218159 389.1.1.9 ↗ few secondary structure elements › EGF-like › EGF-related › EGF/Laminin › EGF_2 0.51 28.0 3.21e-01 72.4% 72.5%
5083210 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.50 42.0 3.49e-01 96.6% 63.6%
3757443 223.1.1.71 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › VGCC_alpha2 0.50 44.0 2.71e-01 100.0% 98.4%