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NC_042082.1__YP_009619908.1__FDJ07_gp013__00013

Bact-Vir

NC_042082.1__YP_009619908.1__FDJ07_gp013__00013

Identity

Accession:
NC_042082 ↗
Kingdom:
phage

Quality

64.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Delepquintavirus› Stenotrophomonas_phage_vB_SmaS_DLP_5

TaxID: 2044561

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 7-51
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23843.3 best DUF7210 32.5 6.60e-08 84.4% 100.0%
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3anwB00 1.20.58.2050 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.83 66.0 4.48e-01 100.0% 24.7%
4v19I01 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.74 57.0 5.40e-01 95.6% 70.2%
6f0cA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.74 50.0 2.92e-01 71.1% 15.7%
3anwA02 3.40.5.50 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.73 62.0 5.82e-01 100.0% 87.9%
4tpoA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.73 50.0 2.88e-01 71.1% 15.3%
2e9xB01 3.40.5.50 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.73 62.0 5.57e-01 100.0% 75.8%
2hvfA00 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.73 56.0 5.44e-01 95.6% 76.9%
6bldA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.71 49.0 2.82e-01 71.1% 14.7%
4apyA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.69 48.0 2.77e-01 71.1% 14.7%
1vw4G00 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.68 54.0 5.17e-01 100.0% 76.4%
4dnjA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.67 45.0 2.65e-01 71.1% 15.0%
2hjqA01 3.40.5.20 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › YqbF domain 0.66 53.0 5.35e-01 100.0% 100.0%
1u3oA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.66 50.0 4.59e-01 86.7% 95.2%
7bjkA02 3.55.40.20 Alpha Beta › 3-Layer(bab) Sandwich › minor pseudopilin epsh fold › Iron/manganese superoxide dismutase, C-terminal domain 0.61 43.0 3.36e-01 100.0% 31.0%
3pe0A03 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.59 50.0 4.55e-01 100.0% 82.8%
2hpuA02 3.30.70.2050 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 44.0 4.03e-01 97.8% 61.9%
3l9aX01 3.30.720.180 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.56 39.0 3.45e-01 100.0% 46.7%
1y7xA01 2.30.30.550 Mainly Beta › Roll › SH3 type barrels. › Major Vault Protein repeat 0.56 43.0 4.34e-01 100.0% 89.4%
2cs4A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.53 38.0 3.16e-01 100.0% 38.9%
7vufD01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 40.0 2.72e-01 88.9% 75.6%
1eupA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.53 46.0 2.67e-01 100.0% 25.3%
4cbgD02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 37.0 2.73e-01 82.2% 44.1%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.52 43.0 3.75e-01 100.0% 71.1%
1goiA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.51 42.0 3.50e-01 100.0% 96.7%
6jptA00 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.51 36.0 2.72e-01 75.6% 79.3%
ECOD (64)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5010674 4076.3.1.11 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PF25865 0.85 75.0 7.01e-01 100.0% 80.0%
3296816 4076.3.1.6 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › GINS_N 0.81 71.0 6.47e-01 100.0% 83.3%
5042275 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 68.0 6.40e-01 95.6% 89.1%
4025911 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.78 68.0 6.21e-01 97.8% 83.3%
4144346 4076.3.1.6 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › GINS_N 0.78 67.0 5.95e-01 97.8% 75.4%
4991614 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.76 63.0 5.99e-01 95.6% 80.0%
4927873 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.76 66.0 5.99e-01 97.8% 76.7%
4981952 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.75 65.0 6.31e-01 100.0% 96.0%
4956746 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.75 63.0 6.16e-01 97.8% 100.0%
3977355 4076.3.1.1 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Packaging_FI 0.75 64.0 6.09e-01 100.0% 94.4%
5035786 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.75 62.0 6.07e-01 97.8% 100.0%
3601134 4076.1.1.0 ↗ a+b two layers › L9 N-domain-like › L9 N-domain-like › L9 N-domain-like 0.74 60.0 5.27e-01 97.8% 60.0%
5083883 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.74 64.0 6.43e-01 100.0% 97.8%
3716713 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.74 61.0 5.96e-01 95.6% 96.0%
4935547 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.74 64.0 6.20e-01 100.0% 96.0%
5045837 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.73 64.0 5.87e-01 100.0% 81.7%
4994655 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.73 60.0 5.84e-01 95.6% 98.0%
5028408 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.73 61.0 5.98e-01 97.8% 100.0%
4230268 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.73 57.0 5.75e-01 88.9% 100.0%
3962059 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.72 49.0 2.97e-01 71.1% 23.3%
4932084 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.72 61.0 5.96e-01 100.0% 100.0%
4358525 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.72 61.0 5.99e-01 97.8% 90.0%
4269273 4076.4.1.1 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain › PriS_C 0.72 56.0 5.66e-01 88.9% 100.0%
3957920 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.72 48.0 2.88e-01 71.1% 18.2%
5069341 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.71 57.0 5.63e-01 95.6% 96.0%
5011186 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.71 61.0 5.60e-01 100.0% 80.0%
4956454 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.71 60.0 5.67e-01 100.0% 83.6%
4956745 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.70 57.0 5.63e-01 95.6% 96.0%
4031645 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.70 60.0 5.88e-01 100.0% 100.0%
4939413 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.70 58.0 5.64e-01 97.8% 100.0%
5063665 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.70 59.0 5.94e-01 95.6% 97.8%
3806748 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.69 47.0 2.83e-01 71.1% 24.6%
4967982 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.69 54.0 5.47e-01 91.1% 100.0%
3454403 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.68 46.0 2.76e-01 71.1% 22.2%
4081421 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.68 57.0 5.61e-01 100.0% 98.0%
4934987 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.68 53.0 5.35e-01 88.9% 95.6%
3327949 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.67 45.0 2.81e-01 71.1% 25.8%
4932061 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.66 55.0 5.55e-01 97.8% 100.0%
5009 4076.3.1.2 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › YqbF 0.66 54.0 5.31e-01 100.0% 91.8%
3868927 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.66 44.0 2.72e-01 71.1% 22.4%
3458617 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.66 45.0 2.74e-01 71.1% 24.7%
4613882 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.65 54.0 5.33e-01 100.0% 92.0%
5033467 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.64 54.0 5.35e-01 97.8% 97.9%
4397359 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.64 43.0 2.60e-01 71.1% 21.2%
3515342 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.64 44.0 2.68e-01 71.1% 22.2%
3396897 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.63 53.0 4.84e-01 100.0% 95.2%
4032281 268.2.1.1 ↗ a+b two layers › Sterol carrier protein-like › LytR-Cps2A-Psr (LCP) enzymes › LytR-Cps2A-Psr (LCP) enzymes › LytR_cpsA_psr 0.62 52.0 3.26e-01 100.0% 21.1%
5023430 3529.1.1.0 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain 0.61 51.0 4.75e-01 100.0% 85.0%
3902139 4.1.1.99 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_10 0.59 49.0 4.37e-01 100.0% 80.0%
3481344 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 49.0 4.44e-01 97.8% 87.7%
3929801 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.57 48.0 3.77e-01 100.0% 44.2%
3174687 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.57 44.0 3.85e-01 91.1% 90.7%
2794885 807.1.1.1 ↗ a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › CpcD 0.57 46.0 4.26e-01 100.0% 76.6%
3941732 3115.6.1.0 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon 0.56 44.0 4.38e-01 100.0% 86.0%
3958220 149.1.1.0 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 0.54 47.0 2.93e-01 100.0% 37.9%
3236725 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.54 42.0 2.76e-01 100.0% 54.2%
4867394 3820.1.1.1 ↗ a+b complex topology › CRISPR-associated endonuclease Cas9 C-terminal domain › CRISPR-associated endonuclease Cas9 C-terminal domain › CRISPR-associated endonuclease Cas9 C-terminal domain › Cas9_PI 0.54 45.0 3.60e-01 100.0% 59.6%
4826872 2010.1.1.4 ↗ a/b three-layered sandwiches › EDD domain › EDD domain › EDD domain › FakA-like_C 0.54 47.0 3.64e-01 100.0% 93.2%
3252771 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.54 46.0 3.82e-01 100.0% 60.0%
4464132 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.54 45.0 4.08e-01 93.3% 80.0%
None — 0.52 36.0 2.29e-01 77.8% 82.1%
4350668 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.51 36.0 3.29e-01 100.0% 52.9%
3846043 219.1.1.15 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › OTU 0.50 39.0 2.41e-01 95.6% 36.9%
4270226 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.50 39.0 3.76e-01 93.3% 85.5%