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PHAGE-A4--js4906-25-3_S22_scaffold_24_curated_closed_complete_prodigal-single.1__X__X__00173

Bact-Vir

PHAGE-A4--js4906-25-3_S22_scaffold_24_curated_closed_complete_prodigal-single.1__X__X__00173

Identity

Kingdom:
phage

Quality

68.2 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 17-120
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4mfzA02 3.40.630.120 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › 0.67 50.0 4.48e-01 79.8% 100.0%
3tt2A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.66 51.0 3.63e-01 81.7% 83.2%
2fl4A02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.64 49.0 4.94e-01 81.7% 99.0%
1y9kA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.63 47.0 4.59e-01 86.5% 71.7%
1ufhA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.63 49.0 4.23e-01 81.7% 54.8%
1xe4A01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.63 48.0 4.13e-01 81.7% 70.1%
3d8pB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.62 47.0 4.10e-01 80.8% 71.9%
3efaA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.61 47.0 4.21e-01 81.7% 70.5%
2zyzC00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.61 40.0 4.13e-01 88.5% 70.8%
1lrzA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.61 47.0 4.22e-01 81.7% 64.3%
3lodA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.60 46.0 4.14e-01 81.7% 72.4%
4fvaC00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.59 45.0 3.41e-01 80.8% 51.0%
2q3fA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 45.0 3.82e-01 85.6% 81.0%
7n3yC01 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.56 43.0 2.94e-01 80.8% 59.4%
2ppyA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.56 50.0 4.01e-01 99.0% 81.9%
1nxuA02 3.30.1370.60 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain 0.56 41.0 3.64e-01 76.9% 97.3%
3qreA00 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.56 48.0 3.85e-01 93.3% 61.6%
3kxqA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 45.0 3.48e-01 88.5% 54.4%
3pbkA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.55 40.0 4.04e-01 76.9% 85.2%
2i0fA00 3.40.50.960 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Lumazine/riboflavin synthase 0.54 41.0 3.68e-01 79.8% 88.4%
4bv4R00 3.80.10.10 Alpha Beta › Alpha-Beta Horseshoe › Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) › Ribonuclease Inhibitor 0.54 40.0 2.69e-01 78.8% 23.0%
5ewtA00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.54 41.0 3.16e-01 80.8% 57.5%
1wdkA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.54 48.0 3.45e-01 100.0% 94.2%
2h9fA02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.54 40.0 3.35e-01 78.8% 67.7%
4arnA00 3.80.10.10 Alpha Beta › Alpha-Beta Horseshoe › Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) › Ribonuclease Inhibitor 0.54 39.0 2.92e-01 76.9% 36.5%
4b3hB01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.54 46.0 3.30e-01 96.2% 91.0%
1dciA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.54 46.0 3.71e-01 96.2% 83.5%
3gkbA00 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.54 46.0 3.47e-01 97.1% 93.1%
3zwbA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.54 45.0 3.33e-01 92.3% 91.4%
2wtbA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.54 45.0 3.34e-01 94.2% 51.9%
6lpmA00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.54 40.0 3.11e-01 80.8% 57.8%
1qy9A02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.53 46.0 3.98e-01 95.2% 84.0%
3l3sA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.53 45.0 3.70e-01 93.3% 81.5%
3peaF00 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.53 47.0 3.58e-01 100.0% 87.8%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.53 32.0 3.76e-01 90.4% 88.7%
6j4nC01 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.52 40.0 2.81e-01 82.7% 88.3%
3ux3A01 3.30.300.130 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › Fe-S cluster assembly (FSCA) 0.52 40.0 4.16e-01 97.1% 89.7%
2q34A01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.52 44.0 3.76e-01 96.2% 88.3%
4mi2B01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.52 44.0 3.61e-01 96.2% 81.8%
1hr6A01 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.51 41.0 3.35e-01 89.4% 75.7%
3r6hA00 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.51 43.0 3.50e-01 98.1% 94.2%
1wz8A01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.51 44.0 3.58e-01 99.0% 83.0%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.50 41.0 3.64e-01 89.4% 78.9%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3716378 327.6.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like 0.66 55.0 4.95e-01 91.3% 94.5%
3738229 213.1.1.31 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_10 0.65 50.0 4.42e-01 80.8% 69.3%
1176053 213.1.1.27 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_7 0.65 48.0 4.29e-01 76.9% 65.8%
5006836 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.64 47.0 4.05e-01 86.5% 50.0%
3703858 207.1.1.22 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_6 0.64 47.0 3.26e-01 79.8% 23.1%
4591342 2003.1.5.5 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › UPF0020 0.63 44.0 3.11e-01 76.0% 23.1%
5013472 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.63 47.0 4.35e-01 77.9% 69.2%
4928402 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.62 47.0 4.55e-01 78.8% 85.2%
3937689 2496.1.1.2 ↗ a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like › STAS 0.62 45.0 4.02e-01 76.0% 67.3%
None — 0.62 43.0 3.09e-01 76.9% 23.7%
3279428 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.61 47.0 4.13e-01 81.7% 69.5%
4980226 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.61 46.0 4.17e-01 81.7% 76.6%
3860136 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.60 45.0 3.07e-01 79.8% 26.4%
3643512 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.60 45.0 3.64e-01 85.6% 40.0%
3723138 7574.1.1.2 ↗ a/b three-layered sandwiches › Thiamin diphosphate-binding fold (THDP-binding) › Thiamin diphosphate-binding fold (THDP-binding) › Thiamin diphosphate-binding fold (THDP-binding) › E1_dh 0.60 42.0 2.75e-01 73.1% 45.1%
3457337 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.59 39.0 3.55e-01 72.1% 49.3%
3613954 2486.1.1.1 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase › ECH_1 0.59 51.0 3.79e-01 94.2% 91.1%
4475641 2003.1.5.363 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › UPF0020, Methyltransf_11, Methyltrans_SAM 0.59 42.0 2.69e-01 76.9% 14.3%
3838750 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.59 42.0 3.80e-01 76.0% 53.8%
5043433 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.59 41.0 4.03e-01 73.1% 80.0%
4565386 327.10.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › RBFA 0.58 43.0 4.20e-01 78.8% 88.7%
4285425 2486.1.1.7 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase › Peptidase_S41 0.58 41.0 3.36e-01 74.0% 68.5%
4275412 327.10.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › RBFA 0.57 47.0 4.63e-01 90.4% 90.9%
3257065 2486.1.1.11 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase › ECH_2 0.57 50.0 3.45e-01 99.0% 44.7%
4501142 2486.1.1.1 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase › ECH_1 0.57 51.0 3.64e-01 100.0% 95.8%
None — 0.57 49.0 3.65e-01 96.2% 88.7%
4071667 213.1.1.24 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › GNAT_acetyltran 0.56 38.0 3.81e-01 88.5% 67.6%
4639416 2003.1.5.74 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltrans_SAM 0.56 41.0 2.89e-01 76.9% 29.1%
3614532 2486.1.1.1 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase › ECH_1 0.56 49.0 3.60e-01 96.2% 86.2%
3592548 309.1.1.0 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase 0.56 43.0 3.35e-01 82.7% 67.1%
3707585 309.1.1.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16 0.56 42.0 3.37e-01 82.7% 71.3%
4986386 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.55 38.0 3.49e-01 73.1% 62.8%
1018858 2486.1.1.1 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase › ECH_1 0.55 48.0 3.64e-01 99.0% 63.9%
4186341 2486.1.1.1 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase › ECH_1 0.55 48.0 3.68e-01 100.0% 86.0%
3915267 328.8.1.1 ↗ a+b two layers › IF3-like › Schlafen 8 › Schlafen 8 › SLFN_AlbA_2 0.54 40.0 3.92e-01 77.9% 71.8%
3611613 7574.1.1.2 ↗ a/b three-layered sandwiches › Thiamin diphosphate-binding fold (THDP-binding) › Thiamin diphosphate-binding fold (THDP-binding) › Thiamin diphosphate-binding fold (THDP-binding) › E1_dh 0.54 39.0 2.58e-01 76.0% 29.7%
None — 0.54 47.0 3.57e-01 98.1% 62.6%
11397 2486.1.1.1 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase › ECH_1 0.54 48.0 3.46e-01 100.0% 95.2%
3962955 2486.1.1.0 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase 0.54 46.0 3.47e-01 94.2% 63.8%
3594151 2486.1.1.0 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase 0.54 47.0 3.49e-01 98.1% 94.3%
4124225 2003.1.5.138 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › UPF0020+Methyltrans_SAM 0.53 42.0 2.76e-01 88.5% 75.7%
3781580 5104.1.1.2 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › CDC45 0.53 44.0 4.27e-01 91.3% 82.4%
3255450 2486.1.1.11 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase › ECH_2 0.52 47.0 3.92e-01 100.0% 74.6%
3992229 610.2.1.2 ↗ alpha arrays › ERP29 C domain-like › Helical domain of Sec23/24 › Helical domain of Sec23/24 › Gelsolin, Sec23_helical 0.50 40.0 3.10e-01 86.5% 97.1%