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LC788703.1__BEU75278.1__RNIID_0660__00066

Bact-Vir

LC788703.1__BEU75278.1__RNIID_0660__00066

Identity

Accession:
LC788703 ↗
Kingdom:
phage

Quality

77.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Herelleviridae› Silviavirus› Staphylococcus_phage_phiRNIID

TaxID: 3092518

Cluster

Singleton — not in a non-trivial cluster

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 3-37
PDB
Domain cluster: representative
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1cptA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.64 47.0 2.70e-01 85.7% 59.0%
2pg4A00 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 0.63 44.0 3.29e-01 97.1% 28.6%
4hs5A00 3.30.920.10 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Frataxin/CyaY 0.63 46.0 3.32e-01 77.1% 69.5%
2gukA00 3.30.2190.10 Alpha Beta › 2-Layer Sandwich › PG1857-like › PG1857-like 0.62 45.0 3.20e-01 80.0% 49.5%
1js3A03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.62 46.0 3.44e-01 85.7% 60.8%
3ltoA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.61 48.0 3.28e-01 91.4% 38.1%
6qpqB00 1.10.10.580 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Structural maintenance of chromosome 1. Chain E 0.60 48.0 3.83e-01 100.0% 61.7%
3cuqA03 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 0.59 49.0 3.84e-01 100.0% 48.8%
5ly3A02 3.30.420.570 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.59 44.0 2.78e-01 85.7% 71.4%
3jcmH04 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.58 50.0 3.90e-01 100.0% 68.8%
2v79A00 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 0.58 50.0 3.48e-01 100.0% 35.7%
5yk4A04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.58 43.0 2.97e-01 85.7% 45.6%
5f7qC01 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 0.58 49.0 3.96e-01 100.0% 51.4%
2i4lA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.58 47.0 2.74e-01 94.3% 42.1%
3eyyA01 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 0.57 48.0 3.75e-01 100.0% 46.3%
1u5tA03 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 0.57 46.0 3.83e-01 100.0% 52.1%
2dy1A03 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.57 45.0 3.54e-01 88.6% 69.7%
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 0.57 48.0 3.51e-01 100.0% 34.6%
4tzmB00 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.57 45.0 2.81e-01 94.3% 63.4%
4rayA01 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 0.57 48.0 3.70e-01 100.0% 48.2%
1oyiA00 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 0.57 45.0 3.94e-01 100.0% 75.8%
1n8jA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.57 41.0 2.63e-01 94.3% 15.1%
1k8rB00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.57 47.0 3.70e-01 100.0% 56.1%
3uoxB01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 45.0 2.66e-01 91.4% 39.3%
6v9qH01 3.30.70.2540 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › CRISPR-associated endoribonuclease Cas6/Csy4 0.56 43.0 2.99e-01 91.4% 42.1%
3ez2A01 1.10.1660.30 Mainly Alpha › Orthogonal Bundle › Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 › 0.55 42.0 3.55e-01 94.3% 64.3%
1c0gA03 3.90.640.10 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 0.55 44.0 3.43e-01 100.0% 67.4%
4y66F01 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 0.55 46.0 3.83e-01 100.0% 59.1%
6ui4A01 1.20.120.720 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Myosin VI head, motor domain, U50 subdomain 0.55 44.0 3.32e-01 91.4% 56.8%
4e1oA03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.55 45.0 3.31e-01 94.3% 72.4%
1ku9B01 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 0.54 44.0 3.44e-01 100.0% 42.5%
2ntxA01 1.20.58.2010 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › PRONE domain, subdomain 1 0.54 45.0 2.83e-01 100.0% 70.0%
1mdoA02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.53 42.0 2.92e-01 91.4% 63.5%
2xzn800 3.30.63.20 Alpha Beta › 2-Layer Sandwich › Guanylate Kinase phosphate binding domain › 0.53 38.0 2.90e-01 80.0% 38.7%
1s2oA02 3.90.1070.10 Alpha Beta › Alpha-Beta Complex › Hypothetical Protein Ta0175; Chain: A, domain 2 › 0.53 40.0 3.45e-01 100.0% 97.2%
6juvB01 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 0.52 43.0 3.47e-01 100.0% 46.7%
2r6fA06 1.20.1580.10 Mainly Alpha › Up-down Bundle › ABC transporter ATPase like fold › ABC transporter ATPase like domain 0.52 40.0 2.85e-01 100.0% 86.2%
4v1al00 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.51 36.0 2.49e-01 77.1% 24.8%
1p5hA01 3.40.50.10540 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Crotonobetainyl-coa:carnitine coa-transferase; domain 1 0.51 42.0 2.50e-01 100.0% 77.3%
2hqyA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 42.0 2.96e-01 100.0% 42.3%
1vlrA01 3.30.200.40 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Scavenger mRNA decapping enzyme, N-terminal domain 0.50 40.0 3.01e-01 97.1% 37.8%
4r78A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.50 38.0 3.09e-01 100.0% 94.8%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5012277 101.1.2.904 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_38 0.68 45.0 3.52e-01 100.0% 32.0%
3933404 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.65 45.0 3.05e-01 77.1% 20.7%
3630462 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.65 44.0 3.00e-01 71.4% 20.0%
3718200 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.64 44.0 3.10e-01 71.4% 28.0%
4463557 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.63 43.0 3.29e-01 71.4% 33.7%
4029803 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.62 44.0 3.05e-01 77.1% 23.1%
3771989 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.62 42.0 2.92e-01 71.4% 20.7%
4025655 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.62 44.0 3.29e-01 77.1% 31.6%
4410759 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.62 43.0 3.12e-01 77.1% 25.2%
3303322 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.62 50.0 4.00e-01 94.3% 45.7%
3538408 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.61 42.0 3.19e-01 71.4% 30.5%
5078958 101.1.2.1 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_1 0.61 47.0 3.40e-01 100.0% 29.5%
4934340 101.1.2.1 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_1 0.61 45.0 3.32e-01 82.9% 45.0%
3865234 7581.1.1.22 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Thiolase_N, ketoacyl-synt 0.60 48.0 2.86e-01 91.4% 30.0%
3229643 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.60 42.0 2.98e-01 71.4% 21.7%
3457354 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.59 41.0 2.83e-01 77.1% 36.6%
3710532 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.59 41.0 3.03e-01 77.1% 38.1%
4968041 101.1.2.26 ↗ alpha arrays › HTH › HTH › winged helix domain › HxlR 0.59 43.0 2.97e-01 85.7% 21.4%
4033043 616.1.1.41 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Terminase_4 0.58 39.0 3.02e-01 100.0% 26.7%
4961046 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 49.0 3.67e-01 100.0% 37.9%
3589863 101.1.2.92 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_11 0.58 49.0 3.72e-01 100.0% 41.1%
3947618 7581.1.1.1 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Thiolase_N 0.58 47.0 2.87e-01 94.3% 34.0%
3989790 3433.1.2.1 ↗ a+b duplicates or obligate multimers › ParB dimerization domain › ParB dimerization domain › Chromosome-encoded ParB dimerization domain › ParB_dimer 0.58 45.0 4.01e-01 94.3% 60.0%
4936127 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.58 46.0 3.74e-01 94.3% 78.7%
4527101 101.1.2.31 ↗ alpha arrays › HTH › HTH › winged helix domain › TFIIE_alpha 0.56 47.0 3.11e-01 100.0% 23.1%
3386295 3079.1.1.0 ↗ extended segments › RNA polymerase PB2 N-terminal fragment › RNA polymerase PB2 N-terminal fragment › RNA polymerase PB2 N-terminal fragment 0.56 39.0 4.20e-01 88.6% 86.7%
4370843 7524.1.1.2 ↗ a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › Histidinol_dh 0.56 39.0 2.47e-01 85.7% 42.9%
3686838 387.1.5.0 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like 0.56 46.0 4.49e-01 100.0% 82.5%
3188665 223.2.1.34 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › NPR2 0.56 43.0 2.93e-01 100.0% 49.4%
3940520 223.2.1.34 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › NPR2 0.55 41.0 2.88e-01 100.0% 37.4%
5051070 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.55 46.0 3.07e-01 100.0% 71.6%
4972761 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 40.0 2.51e-01 91.4% 87.8%
4955571 101.1.2.1 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_1 0.54 41.0 2.93e-01 85.7% 69.6%
3782903 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 38.0 2.69e-01 100.0% 38.9%
4044429 1197.1.1.1 ↗ alpha bundles › Integral membrane glycerol 3-phosphate acyltransferase PlsY › Integral membrane glycerol 3-phosphate acyltransferase PlsY › Integral membrane glycerol 3-phosphate acyltransferase PlsY › G3P_acyltransf 0.53 46.0 2.83e-01 100.0% 39.6%
3844118 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 46.0 2.79e-01 100.0% 27.4%
4954067 101.1.2.92 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_11 0.52 46.0 3.78e-01 100.0% 58.7%
3589866 101.1.2.66 ↗ alpha arrays › HTH › HTH › winged helix domain › Mga 0.52 42.0 3.34e-01 100.0% 43.5%
3644183 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.52 42.0 3.57e-01 94.3% 87.5%
3528137 3636.1.1.0 ↗ a+b two layers › XPD arch domain › XPD arch domain › XPD arch domain 0.52 42.0 2.71e-01 100.0% 57.4%
4031357 101.1.2.39 ↗ alpha arrays › HTH › HTH › winged helix domain › SMC_ScpA 0.52 43.0 3.57e-01 100.0% 55.7%
4025072 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.51 36.0 2.67e-01 77.1% 27.0%
5076133 101.1.2.55 ↗ alpha arrays › HTH › HTH › winged helix domain › SMC_ScpB 0.51 40.0 3.24e-01 94.3% 56.2%
3538243 1128.1.1.1 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.51 43.0 3.26e-01 94.3% 45.0%
3219380 387.1.5.0 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like 0.51 40.0 3.96e-01 100.0% 84.2%
3893811 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.51 43.0 3.14e-01 100.0% 51.0%