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NC_052972.1__YP_009997389.1__JT314_gp08__00008

Bact-Vir

NC_052972.1__YP_009997389.1__JT314_gp08__00008

Identity

Accession:
NC_052972 ↗
Kingdom:
phage

Quality

74.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Casjensviridae› Ruegeria_phage_vB_RpoS-V7

TaxID: 2218620

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 2-84
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2zyzC00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.73 50.0 4.81e-01 71.1% 85.4%
3ajvC02 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.71 49.0 4.79e-01 71.1% 92.3%
1uwvA03 2.40.50.1070 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.64 44.0 3.67e-01 100.0% 42.3%
1xmxA01 3.40.50.10770 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Hypothetical protein VC1899 like domain (Restriction endonuclease-like) 0.64 50.0 4.27e-01 86.7% 90.8%
3lgdA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.62 50.0 3.15e-01 90.4% 73.2%
1ycoA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.59 51.0 3.65e-01 100.0% 59.8%
3ieyB00 3.40.1350.150 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.57 49.0 4.02e-01 94.0% 88.2%
2o2zA00 3.40.50.10680 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › CofD-like domains 0.57 41.0 2.85e-01 78.3% 41.3%
2q07A01 3.40.50.10630 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Uracil-DNA glycosylase-like 0.56 44.0 3.85e-01 91.6% 84.2%
1g41A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 44.0 3.39e-01 86.7% 85.5%
1pfkA01 3.40.50.450 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 43.0 3.43e-01 89.2% 88.9%
2pnqA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.55 42.0 2.79e-01 84.3% 85.1%
4k6nA02 3.20.10.10 Alpha Beta › Alpha-Beta Barrel › D-amino Acid Aminotransferase; Chain A, domain 2 › D-amino Acid Aminotransferase, subunit A, domain 2 0.54 39.0 3.31e-01 78.3% 94.1%
1a80A00 3.20.20.100 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › NADP-dependent oxidoreductase domain 0.54 43.0 3.05e-01 89.2% 87.4%
2r47A01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 42.0 3.71e-01 90.4% 88.4%
3op6A00 3.90.960.10 Alpha Beta › Alpha-Beta Complex › YbaK protein › YbaK/aminoacyl-tRNA synthetase-associated domain 0.54 46.0 3.89e-01 98.8% 71.9%
5cecA02 3.50.80.20 Alpha Beta › 3-Layer(bba) Sandwich › D-tyrosyl-trna(Tyr) Deacylase; Chain: A; › D-Ala-D-Ala carboxypeptidase C, peptidase S13 0.53 46.0 3.77e-01 100.0% 98.2%
3tssA02 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 36.0 3.89e-01 96.4% 83.1%
3e6qA00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.52 42.0 3.71e-01 89.2% 87.3%
1aj6A00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.52 45.0 3.50e-01 100.0% 86.1%
1ii2A03 3.90.228.20 Alpha Beta › Alpha-Beta Complex › Phosphoenolpyruvate Carboxykinase; domain 3 › 0.52 43.0 3.21e-01 100.0% 76.6%
1q0sA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.52 42.0 3.55e-01 91.6% 85.6%
6l4lA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.51 41.0 3.77e-01 91.6% 97.4%
2otnB01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.51 39.0 3.36e-01 86.7% 85.6%
5u3fA02 3.20.10.10 Alpha Beta › Alpha-Beta Barrel › D-amino Acid Aminotransferase; Chain A, domain 2 › D-amino Acid Aminotransferase, subunit A, domain 2 0.51 43.0 3.45e-01 100.0% 45.5%
3g7kA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.51 40.0 3.26e-01 92.8% 92.6%
6rqxA02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.50 35.0 2.56e-01 72.3% 66.3%
3r1kA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.50 43.0 3.70e-01 100.0% 59.4%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4947849 2008.2.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.71 49.0 4.68e-01 71.1% 94.7%
4240799 299.1.1.0 ↗ a+b complex topology › YbaK/ProRS associated domain › YbaK/ProRS associated domain › YbaK/ProRS associated domain 0.69 59.0 4.78e-01 94.0% 82.6%
3994678 4045.1.1.1 ↗ a+b two layers › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › Aminotran_4 0.68 42.0 3.09e-01 92.8% 24.9%
3409623 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.66 46.0 4.31e-01 71.1% 91.0%
4271018 2003.1.5.53 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr 0.64 42.0 2.76e-01 100.0% 15.3%
5042728 7514.1.1.1 ↗ a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › NAD_binding_1 0.61 50.0 4.18e-01 91.6% 84.5%
4486112 7592.1.1.3 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › DUF6293_N 0.60 49.0 4.30e-01 89.2% 99.2%
3832641 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.60 42.0 2.47e-01 73.5% 52.7%
4990485 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 41.0 3.32e-01 73.5% 75.4%
3391921 508.1.1.0 ↗ a+b three layers › Protein interacting with HSP90 1 (Pih1) N-terminal domain › Protein interacting with HSP90 1 (Pih1) N-terminal domain › Protein interacting with HSP90 1 (Pih1) N-terminal domain 0.59 49.0 4.08e-01 91.6% 82.1%
5013509 7531.1.1.1 ↗ a/b three-layered sandwiches › Carbamate kinase-like › Carbamate kinase-like › Carbamate kinase-like › AA_kinase 0.59 50.0 3.62e-01 97.6% 94.8%
4245798 508.1.1.1 ↗ a+b three layers › Protein interacting with HSP90 1 (Pih1) N-terminal domain › Protein interacting with HSP90 1 (Pih1) N-terminal domain › Protein interacting with HSP90 1 (Pih1) N-terminal domain › PIH1 0.58 48.0 4.03e-01 89.2% 85.7%
4247735 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.58 42.0 2.46e-01 77.1% 22.1%
5039733 7592.1.1.0 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains 0.58 50.0 4.29e-01 94.0% 93.1%
3272800 508.1.1.1 ↗ a+b three layers › Protein interacting with HSP90 1 (Pih1) N-terminal domain › Protein interacting with HSP90 1 (Pih1) N-terminal domain › Protein interacting with HSP90 1 (Pih1) N-terminal domain › PIH1 0.57 48.0 4.12e-01 91.6% 86.9%
3420651 109.4.1.1521 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, DYW_deaminase, Eplus_motif, E_motif 0.57 38.0 2.53e-01 100.0% 16.8%
4520708 2003.1.5.53 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr 0.57 36.0 2.42e-01 100.0% 15.1%
3487736 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.57 43.0 3.31e-01 80.7% 57.2%
3339265 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.57 38.0 2.24e-01 100.0% 8.7%
None — 0.56 41.0 2.78e-01 78.3% 96.9%
3678845 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.56 38.0 2.28e-01 100.0% 9.3%
3816405 109.4.1.1383 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.56 38.0 2.29e-01 100.0% 9.5%
3333061 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.56 38.0 2.28e-01 100.0% 9.5%
3351960 109.4.1.2979 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.56 37.0 2.25e-01 100.0% 9.3%
3382877 109.4.1.3024 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif 0.56 38.0 2.39e-01 100.0% 13.0%
3671030 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.56 38.0 2.28e-01 100.0% 9.8%
3320228 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.56 38.0 2.26e-01 100.0% 9.4%
3453417 2492.1.1.39 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › DYW_deaminase 0.56 38.0 3.27e-01 100.0% 43.7%
3348902 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.56 38.0 2.28e-01 100.0% 10.2%
3808939 109.4.1.619 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DYW_deaminase 0.56 38.0 3.22e-01 100.0% 43.0%
4462824 2003.1.5.174 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr, Methyltransf_15 0.56 36.0 2.39e-01 100.0% 15.0%
3329759 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.56 38.0 2.21e-01 100.0% 8.2%
3354291 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.55 38.0 2.56e-01 100.0% 18.8%
3831659 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.55 37.0 2.23e-01 100.0% 8.7%
3335071 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.55 38.0 2.30e-01 100.0% 10.6%
5035363 7514.1.1.0 ↗ a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain 0.55 44.0 3.75e-01 91.6% 83.4%
2815886 10.32.1.22 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › CFA20_dom 0.54 42.0 3.24e-01 83.1% 59.4%
4392521 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.54 45.0 3.11e-01 91.6% 53.1%
3435214 109.4.1.2064 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif, TPR_24 0.54 37.0 2.23e-01 71.1% 15.7%
3837823 109.4.1.1383 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.54 39.0 2.28e-01 100.0% 9.1%
3390767 10.32.1.22 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › CFA20_dom 0.54 42.0 3.27e-01 84.3% 60.0%
4954737 7514.1.1.0 ↗ a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain 0.54 44.0 3.70e-01 92.8% 77.8%
3698218 4045.1.1.1 ↗ a+b two layers › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › Aminotran_4 0.53 42.0 3.20e-01 90.4% 70.2%
3443843 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.53 39.0 2.38e-01 78.3% 21.4%
3702364 4045.1.1.1 ↗ a+b two layers › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › Aminotran_4 0.53 41.0 3.25e-01 89.2% 85.9%
None — 0.52 42.0 2.82e-01 91.6% 40.6%
3322777 109.4.1.1738 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.51 37.0 2.49e-01 78.3% 33.2%
None — 0.51 41.0 2.76e-01 90.4% 44.5%
3646564 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.51 38.0 2.35e-01 80.7% 20.0%
4102412 101.1.2.1 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_1 0.50 32.0 3.20e-01 100.0% 58.9%
3349809 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.50 37.0 2.29e-01 79.5% 23.3%
3683857 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.50 37.0 2.24e-01 80.7% 20.1%