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NC_054912.1__YP_010068722.1__KMC04_gp237__00237

Bact-Vir

NC_054912.1__YP_010068722.1__KMC04_gp237__00237

Identity

Accession:
NC_054912 ↗
Kingdom:
phage

Quality

72.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Straboviridae› Tequatrovirus› Escherichia_phage_vB_EcoM_F1

TaxID: 2750846

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 4-54
PDB
Domain cluster: representative
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF01541.31 best GIY-YIG 39.3 9.30e-10 100.0% 62.8%
PF20987.4 I-TevI_DNA-bd 47.7 1.60e-12 66.7% 45.1%
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.73 60.0 5.08e-01 100.0% 53.3%
4obmA00 3.40.630.190 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › LCP protein 0.59 48.0 3.18e-01 100.0% 89.5%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.58 42.0 3.53e-01 100.0% 43.5%
1e1hA00 3.90.1240.10 Alpha Beta › Alpha-Beta Complex › Zincin-like › "Metalloproteases (""zincins""), catalytic domain like" 0.57 41.0 2.66e-01 74.5% 80.9%
3p2aA01 2.30.30.380 Mainly Beta › Roll › SH3 type barrels. › Zn-finger domain of Sec23/24 0.57 37.0 4.06e-01 98.0% 94.4%
5r0dB01 2.60.34.20 Mainly Beta › Sandwich › Substrate Binding Domain Of DNAk; Chain A, domain 1 › 0.57 39.0 2.89e-01 96.1% 25.9%
4nnaA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.57 40.0 2.46e-01 74.5% 83.9%
2pe4A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.56 38.0 2.27e-01 70.6% 83.2%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.56 39.0 3.85e-01 76.5% 75.4%
4p6zM01 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.56 42.0 3.22e-01 80.4% 50.4%
2gukA00 3.30.2190.10 Alpha Beta › 2-Layer Sandwich › PG1857-like › PG1857-like 0.56 39.0 3.22e-01 80.4% 42.3%
3fdfA02 6.10.140.550 Special › Helix non-globular › Helix Hairpins › 0.55 36.0 3.60e-01 100.0% 64.3%
1d7bA00 2.60.40.1210 Mainly Beta › Sandwich › Immunoglobulin-like › Cellobiose dehydrogenase, cytochrome domain 0.54 42.0 3.01e-01 94.1% 63.8%
4mtnA01 3.30.1480.10 Alpha Beta › 2-Layer Sandwich › N Utilization Substance Protein A; Chain:P; domain 4 › NusA, N-terminal domain 0.54 38.0 3.21e-01 76.5% 92.6%
1gpqB00 3.40.1420.10 Alpha Beta › 3-Layer(aba) Sandwich › Inhibitor of vertebrate lysozyme, Ivy › Inhibitor of vertebrate lysozyme 0.52 35.0 2.70e-01 70.6% 79.7%
2bm0A03 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.52 32.0 3.26e-01 80.4% 56.9%
1vw4H00 3.90.1180.10 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L13p; Chain: A; › Ribosomal protein L13 0.52 37.0 2.70e-01 76.5% 73.0%
1neiA00 3.30.160.220 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › YoaG 0.51 44.0 4.26e-01 100.0% 91.7%
7r0kA02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.50 39.0 2.92e-01 96.1% 59.0%
3ar4A04 3.40.1110.10 Alpha Beta › 3-Layer(aba) Sandwich › Calcium-transporting ATPase, cytoplasmic domain N › Calcium-transporting ATPase, cytoplasmic domain N 0.50 39.0 2.55e-01 86.3% 32.8%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3496147 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.71 61.0 4.97e-01 100.0% 59.0%
4929347 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.64 45.0 4.44e-01 98.0% 70.9%
3970701 560.1.1.0 ↗ few secondary structure elements › H-NS histone-like proteins, C-terminal domain › H-NS histone-like proteins, C-terminal domain › H-NS histone-like proteins, C-terminal domain 0.62 37.0 4.14e-01 100.0% 77.5%
3784067 320.1.1.0 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain 0.62 44.0 3.38e-01 76.5% 81.7%
4142311 109.4.1.1297 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TIMELESS, PF27570 0.60 41.0 2.32e-01 70.6% 10.8%
1144695 268.2.1.0 ↗ a+b two layers › Sterol carrier protein-like › LytR-Cps2A-Psr (LCP) enzymes › LytR-Cps2A-Psr (LCP) enzymes 0.59 48.0 3.18e-01 100.0% 89.5%
3946510 803.1.1.0 ↗ a+b duplicates or obligate multimers › Hypothetical protein YoaG › Hypothetical protein YoaG › Hypothetical protein YoaG 0.58 44.0 4.58e-01 100.0% 95.6%
5006512 3012.1.1.0 ↗ a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.58 33.0 3.21e-01 76.5% 45.0%
3641337 2485.1.1.1 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.57 39.0 3.22e-01 72.5% 55.0%
3253565 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.56 36.0 3.94e-01 100.0% 97.1%
3738283 109.4.1.356 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans 0.55 39.0 2.32e-01 78.4% 16.1%
3596174 3075.1.1.0 ↗ a+b two layers › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA 0.55 37.0 3.47e-01 100.0% 52.9%
5010744 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.54 45.0 4.25e-01 100.0% 90.8%
4016050 2490.2.1.1 ↗ a/b three-layered sandwiches › Ribosomal protein L13/L15p/L18e/L32e › Ribosomal protein L13 and L16-A › Ribosomal protein L13 and L16-A › Ribosomal_L13 0.54 38.0 2.57e-01 72.5% 67.4%
4981338 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 38.0 2.23e-01 98.0% 7.8%
4141047 593.1.1.0 ↗ alpha bundles › GroEL equatorial domain-like › GroEL equatorial domain-like › GroEL equatorial domain-like 0.52 43.0 2.86e-01 100.0% 79.2%
4374416 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 41.0 2.32e-01 100.0% 9.3%
4991835 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.51 40.0 4.06e-01 98.0% 90.0%
3238459 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.51 35.0 3.37e-01 76.5% 100.0%
4663376 3593.1.1.1 ↗ a+b complex topology › Oncogenic effector CagA meander beta sheet domain › Oncogenic effector CagA meander beta sheet domain › Oncogenic effector CagA meander beta sheet domain › CagA_N 0.51 40.0 2.47e-01 94.1% 26.4%
5077058 304.51.1.1 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › Cas_Cas6_C 0.51 37.0 2.89e-01 82.4% 91.2%
3360654 376.1.3.57 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › zf_ULT1 0.50 40.0 4.00e-01 94.1% 87.3%
4075176 167.1.1.1 ↗ alpha arrays › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal_S7 0.50 42.0 2.99e-01 94.1% 73.8%
3748911 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.50 39.0 2.37e-01 86.3% 67.8%