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NC_052972.1__YP_009997385.1__JT314_gp04__00004

Bact-Vir

NC_052972.1__YP_009997385.1__JT314_gp04__00004

Identity

Accession:
NC_052972 ↗
Kingdom:
phage

Quality

78.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Casjensviridae› Ruegeria_phage_vB_RpoS-V7

TaxID: 2218620

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 6-52
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5vmzA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.75 55.0 5.88e-01 100.0% 97.4%
4ijdA02 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.74 46.0 5.39e-01 83.0% 96.8%
2rsiA02 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.73 45.0 5.09e-01 70.2% 100.0%
3mpxA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.71 55.0 4.38e-01 95.7% 42.3%
2incA00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.70 48.0 2.73e-01 72.3% 10.2%
2yztA00 3.30.160.250 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.70 55.0 4.98e-01 100.0% 63.6%
7febA03 3.40.50.12790 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › FHIPEP family, domain 4 0.68 40.0 3.23e-01 85.1% 30.4%
3pp2A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.67 58.0 4.37e-01 100.0% 41.1%
4h63Q04 3.90.1150.120 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.66 51.0 3.87e-01 100.0% 35.3%
4ztkA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.64 51.0 3.23e-01 91.5% 67.5%
7oslA02 3.40.50.12790 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › FHIPEP family, domain 4 0.63 38.0 2.98e-01 85.1% 28.0%
1pjqA02 3.30.160.110 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Sirohaem synthase, central domain 0.62 45.0 4.92e-01 78.7% 100.0%
3n5oA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.61 49.0 4.13e-01 95.7% 97.8%
2eggB01 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.61 45.0 3.31e-01 85.1% 50.7%
2v25A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.61 45.0 3.28e-01 78.7% 41.5%
1eazA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 48.0 3.80e-01 91.5% 45.6%
2ctdA00 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.60 45.0 3.70e-01 100.0% 42.7%
2x48A00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.59 38.0 3.78e-01 93.6% 57.4%
4fshA01 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.58 45.0 3.44e-01 93.6% 43.8%
2kqrA01 3.30.1910.20 Alpha Beta › 2-Layer Sandwich › so0334 like fold › asparaginyl-tRNA synthetase, N-terminal domain 0.57 42.0 3.67e-01 100.0% 51.4%
3d6wB01 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 39.0 3.50e-01 91.5% 50.0%
4m7xA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 42.0 3.51e-01 93.6% 45.1%
3rbtD01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.56 46.0 3.53e-01 100.0% 63.2%
3oqgA00 3.40.1440.50 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › 0.55 40.0 2.71e-01 78.7% 59.7%
2v1nA01 1.10.10.2030 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › DNA/RNA-binding protein Kin17, conserved domain 0.55 34.0 2.70e-01 93.6% 28.7%
1qhoA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.53 45.0 2.64e-01 95.7% 12.5%
4v02C00 2.160.20.70 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › 0.52 35.0 2.70e-01 70.2% 41.0%
1qo2A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.52 41.0 2.76e-01 100.0% 89.2%
3zq4D03 3.10.20.580 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.52 42.0 3.50e-01 100.0% 62.1%
5trdA01 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 0.51 45.0 3.70e-01 97.9% 91.7%
3aleA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.51 43.0 3.14e-01 100.0% 81.8%
5ucoA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.50 42.0 3.03e-01 100.0% 77.1%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4112122 386.1.1.81 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › DUF1391 0.85 61.0 6.55e-01 93.6% 90.0%
4007827 386.1.1.81 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › DUF1391 0.84 60.0 6.46e-01 97.9% 90.0%
5018724 872.3.1.0 ↗ a+b two layers › Dodecin subunit-like › YbjQ-like › YbjQ-like 0.81 67.0 5.28e-01 100.0% 45.3%
3721997 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.81 62.0 6.08e-01 95.7% 78.0%
3570260 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.79 49.0 4.55e-01 78.7% 50.0%
5004725 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.79 71.0 5.37e-01 100.0% 54.3%
3392271 386.1.1.26 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_6 0.78 48.0 5.51e-01 76.6% 96.7%
3498926 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.78 50.0 5.62e-01 89.4% 88.6%
3516025 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.76 68.0 5.18e-01 100.0% 44.8%
3907166 386.1.1.24 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_4 0.75 47.0 4.39e-01 80.9% 51.7%
3996291 4351.1.1.1 ↗ alpha arrays › ATP12-like › ATP12-like › ATP12-like › ATP12 0.75 55.0 3.57e-01 100.0% 17.3%
3874221 220.1.1.145 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_RASGAP 0.73 63.0 4.94e-01 100.0% 47.4%
3857959 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.73 59.0 5.83e-01 100.0% 86.0%
3527580 220.1.1.145 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_RASGAP 0.73 63.0 5.98e-01 100.0% 81.8%
3861324 386.1.1.1 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2 0.73 55.0 5.43e-01 95.7% 78.0%
3774381 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.72 58.0 5.06e-01 95.7% 60.0%
3248516 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.71 62.0 4.85e-01 100.0% 47.0%
3215898 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.71 52.0 4.92e-01 78.7% 67.3%
3766449 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.70 59.0 4.51e-01 100.0% 40.9%
3259130 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.70 59.0 4.61e-01 100.0% 45.0%
3866936 386.1.1.1 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2 0.70 52.0 4.44e-01 83.0% 50.7%
3540261 376.1.2.28 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › zf-FCS 0.69 56.0 5.40e-01 93.6% 92.7%
4192693 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.69 61.0 5.02e-01 100.0% 55.3%
3737151 3561.1.1.1 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 17 › Mediator of RNA polymerase II transcription subunit 17 › Mediator of RNA polymerase II transcription subunit 17 › Med17 0.69 57.0 3.32e-01 100.0% 10.1%
3264176 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.68 54.0 4.09e-01 93.6% 39.2%
5026090 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.65 56.0 4.79e-01 100.0% 60.0%
4890983 6110.1.1.0 ↗ alpha superhelices › Linker domain of cytoplasmic dynein heavy chain › Linker domain of cytoplasmic dynein heavy chain › Linker domain of cytoplasmic dynein heavy chain 0.62 41.0 2.38e-01 83.0% 7.4%
3494276 5104.1.1.4 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › UPF0160 0.62 44.0 3.25e-01 76.6% 94.4%
4429847 3675.1.1.1 ↗ a+b complex topology › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › GyrB_insert 0.61 48.0 3.30e-01 87.2% 100.0%
3945660 101.1.2.1 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_1 0.61 44.0 3.59e-01 100.0% 42.4%
None — 0.61 52.0 3.33e-01 100.0% 33.3%
934 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.60 48.0 3.80e-01 91.5% 45.6%
996932 2007.1.6.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Aminoacid dehydrogenase-like, N-terminal domain › Shikimate_dh_N 0.60 41.0 3.09e-01 72.3% 39.3%
3530014 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.59 49.0 2.77e-01 100.0% 47.7%
3311409 2485.1.1.39 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › GST_N_2 0.59 51.0 4.18e-01 100.0% 88.9%
4936961 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.59 50.0 4.11e-01 100.0% 52.9%
426290 2485.1.1.40 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › GST_N_3 0.58 46.0 3.75e-01 93.6% 80.4%
4488509 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.57 47.0 3.46e-01 100.0% 33.3%
3506704 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.56 45.0 3.47e-01 93.6% 95.7%
3595258 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.56 45.0 3.66e-01 93.6% 83.2%
3740887 102.1.2.10 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase › Q_salvage 0.55 43.0 2.64e-01 93.6% 12.3%
3478704 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 41.0 3.70e-01 91.5% 58.5%
4444947 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 0.53 42.0 3.51e-01 95.7% 49.5%
5015831 2008.1.1.107 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NERD 0.53 41.0 3.21e-01 97.9% 86.7%