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js4906-29-5_S40_scaffold_13_prodigal-single.1__X__X__00040

Bact-Vir

js4906-29-5_S40_scaffold_13_prodigal-single.1__X__X__00040

Identity

Kingdom:
phage

Quality

71.1 mean pLDDT

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 21-70
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7q5yB01 3.30.460.80 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › NADH:ubiquinone oxidoreductase Nqo5 subunit 0.77 66.0 5.06e-01 100.0% 70.0%
1nf2A02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.77 65.0 5.14e-01 98.0% 92.5%
1zr6A01 3.30.43.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 0.75 64.0 5.31e-01 98.0% 96.7%
3gr0D01 3.30.70.1780 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.75 53.0 5.64e-01 76.0% 100.0%
4alzA03 3.30.70.1770 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.74 63.0 5.89e-01 100.0% 96.9%
4qgrA02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.74 58.0 4.39e-01 88.0% 61.5%
4zevA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.73 61.0 4.87e-01 100.0% 90.7%
2e0gA00 3.30.300.180 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › DnaA, N-terminal domain 0.71 61.0 4.83e-01 100.0% 69.2%
3r4cA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.70 60.0 4.84e-01 100.0% 90.1%
4alzA01 3.30.1340.30 Alpha Beta › 2-Layer Sandwich › Histidine-containing Protein; Chain: A; › 0.68 55.0 5.30e-01 100.0% 91.9%
5u89A01 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.67 56.0 4.71e-01 100.0% 68.5%
2wmmA02 3.30.70.3500 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › MukB, hinge domain 0.66 53.0 4.25e-01 98.0% 59.3%
3awmA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.64 49.0 2.96e-01 88.0% 26.5%
1wpqA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.64 53.0 3.62e-01 96.0% 93.2%
1itpA00 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.64 53.0 4.74e-01 100.0% 70.1%
6nqbC01 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.62 49.0 4.29e-01 100.0% 76.9%
1zbrA00 3.75.10.10 Alpha Beta › 5-stranded Propeller › L-arginine/glycine Amidinotransferase; Chain A › L-arginine/glycine Amidinotransferase; Chain A 0.61 50.0 3.11e-01 98.0% 90.6%
2rbkA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.61 50.0 4.19e-01 100.0% 95.0%
3k96A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.61 50.0 3.46e-01 96.0% 87.7%
2e3tB03 3.30.43.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 0.61 43.0 4.09e-01 76.0% 91.8%
2bh1X00 3.30.300.160 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › Type II secretion system, protein E, N-terminal domain 0.61 49.0 4.61e-01 100.0% 76.5%
7r0kA02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.61 43.0 2.99e-01 100.0% 22.9%
8gtzA03 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.59 49.0 3.45e-01 100.0% 47.5%
2cvzA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 51.0 3.64e-01 100.0% 55.8%
4uhwA03 3.30.43.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 0.58 40.0 3.76e-01 76.0% 83.6%
5khaB01 3.60.110.10 Alpha Beta › 4-Layer Sandwich › Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase › Carbon-nitrogen hydrolase 0.58 41.0 2.67e-01 78.0% 15.0%
8dpkD01 3.75.10.10 Alpha Beta › 5-stranded Propeller › L-arginine/glycine Amidinotransferase; Chain A › L-arginine/glycine Amidinotransferase; Chain A 0.58 48.0 3.09e-01 100.0% 34.3%
2qdsA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.57 46.0 3.11e-01 98.0% 34.8%
2dewX03 3.75.10.10 Alpha Beta › 5-stranded Propeller › L-arginine/glycine Amidinotransferase; Chain A › L-arginine/glycine Amidinotransferase; Chain A 0.57 46.0 2.85e-01 100.0% 90.3%
1xizB00 3.40.930.10 Alpha Beta › 3-Layer(aba) Sandwich › Mannitol-specific EII; Chain A › Mannitol-specific EII; Chain A 0.56 46.0 3.38e-01 100.0% 56.4%
2d4oA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 46.0 3.48e-01 94.0% 58.9%
1iftA01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.55 46.0 3.23e-01 98.0% 28.7%
1htwA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 44.0 3.14e-01 90.0% 43.7%
1go4A00 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.55 44.0 3.09e-01 100.0% 56.1%
3tt2A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 39.0 2.48e-01 82.0% 23.5%
4mo0A00 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.54 44.0 3.94e-01 100.0% 64.6%
2czrA01 3.40.1350.70 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › TBP-interacting protein, N-terminal domain 0.54 40.0 3.30e-01 86.0% 74.5%
6ll8A02 3.10.310.20 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › DHHA2 domain 0.54 36.0 2.85e-01 82.0% 29.2%
7l9pK01 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.54 44.0 3.49e-01 98.0% 95.8%
4uhiA01 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.54 45.0 2.67e-01 100.0% 23.4%
4qt4A00 3.40.50.1470 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidyl-tRNA hydrolase 0.54 42.0 2.92e-01 90.0% 49.2%
8e83B01 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.54 40.0 2.40e-01 88.0% 27.2%
3qz1D00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.53 41.0 2.50e-01 94.0% 78.1%
3p8aA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.51 35.0 2.61e-01 74.0% 90.6%
3ejbB01 3.30.43.20 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › 0.51 35.0 3.13e-01 76.0% 71.1%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3984450 327.13.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif I in type III secretion system › Ring-building motif I in type III secretion system › PrgH 0.78 67.0 6.73e-01 96.0% 100.0%
2105092 3012.1.1.4 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › Hydrolase_3 0.78 67.0 5.12e-01 98.0% 85.2%
4048312 4272.1.1.1 a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.78 65.0 4.35e-01 98.0% 49.5%
4309637 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.77 67.0 5.63e-01 98.0% 83.3%
3941592 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.75 64.0 4.99e-01 98.0% 95.5%
4010106 3012.1.1.4 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › Hydrolase_3 0.75 63.0 4.97e-01 98.0% 95.5%
3386759 3433.1.2.0 a+b duplicates or obligate multimers › ParB dimerization domain › ParB dimerization domain › Chromosome-encoded ParB dimerization domain 0.74 54.0 5.71e-01 82.0% 100.0%
1851173 3261.1.1.4 a+b two layers › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › Yop-YscD_ppl_3rd 0.74 63.0 5.90e-01 100.0% 96.9%
3980816 3261.1.1.0 a+b two layers › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb 0.73 62.0 5.56e-01 100.0% 81.3%
4392601 304.36.1.1 a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › DUF520 0.73 63.0 5.64e-01 100.0% 78.1%
4681738 4272.1.1.1 a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.73 61.0 4.34e-01 100.0% 52.7%
5029665 327.7.1.0 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.72 60.0 5.85e-01 94.0% 98.2%
3986529 327.13.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif I in type III secretion system › Ring-building motif I in type III secretion system › PrgH 0.71 59.0 4.94e-01 100.0% 65.3%
4129523 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.71 50.0 4.64e-01 76.0% 58.5%
3969124 3261.1.1.2 a+b two layers › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › Yop-YscD_ppl_1st 0.71 58.0 5.74e-01 98.0% 100.0%
4046801 327.10.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DnaA_N 0.69 59.0 5.19e-01 98.0% 96.0%
4400635 327.1.1.1 a+b two layers › Alpha-lytic protease prodomain-like › Alpha-lytic protease prodomain › Alpha-lytic protease prodomain › Pro_Al_protease 0.68 58.0 5.38e-01 100.0% 87.7%
4973518 327.3.1.0 a+b two layers › Alpha-lytic protease prodomain-like › GMP synthetase C-terminal dimerisation domain › GMP synthetase C-terminal dimerisation domain 0.68 55.0 4.77e-01 96.0% 70.6%
4149158 327.10.1.11 a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DNA_pol3_a_NII 0.68 57.0 4.96e-01 98.0% 90.0%
4055694 327.10.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DnaA_N 0.67 57.0 5.10e-01 100.0% 97.3%
4411713 327.1.1.1 a+b two layers › Alpha-lytic protease prodomain-like › Alpha-lytic protease prodomain › Alpha-lytic protease prodomain › Pro_Al_protease 0.67 54.0 5.05e-01 100.0% 84.3%
4037316 327.10.1.11 a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DNA_pol3_a_NII 0.66 55.0 4.76e-01 98.0% 85.9%
4577243 327.10.1.11 a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DNA_pol3_a_NII 0.66 54.0 4.84e-01 96.0% 97.3%
4536808 327.10.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DnaA_N 0.66 54.0 4.88e-01 98.0% 97.3%
4413472 327.10.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DnaA_N 0.66 57.0 5.03e-01 100.0% 96.0%
5054331 327.7.1.0 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.66 52.0 5.15e-01 94.0% 94.5%
4129776 327.10.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DnaA_N 0.66 55.0 4.89e-01 98.0% 96.0%
4377027 131.1.1.15 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › Ppx-GppA_III 0.65 52.0 3.70e-01 100.0% 52.1%
4679174 2007.1.7.2 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Rossmann-like domain in dehydroquinate synthase-like enzymes › DHQ_synthase 0.65 46.0 3.16e-01 76.0% 94.7%
4959479 327.7.1.2 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › FKBP26_C 0.64 53.0 4.78e-01 100.0% 84.0%
3588308 327.10.1.11 a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DNA_pol3_a_NII 0.63 51.0 4.62e-01 98.0% 98.7%
3603362 327.3.1.0 a+b two layers › Alpha-lytic protease prodomain-like › GMP synthetase C-terminal dimerisation domain › GMP synthetase C-terminal dimerisation domain 0.62 51.0 4.73e-01 98.0% 88.6%
1565126 3261.1.1.7 a+b two layers › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › CdsD_PD1 0.62 51.0 4.82e-01 100.0% 89.2%
4122987 5104.1.1.1 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.62 46.0 3.68e-01 88.0% 37.4%
1563558 3261.1.1.1 a+b two layers › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › BON 0.62 50.0 4.45e-01 100.0% 74.1%
2075062 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.61 50.0 4.19e-01 100.0% 95.0%
5044613 3261.1.1.1 a+b two layers › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › BON 0.61 50.0 4.62e-01 100.0% 87.1%
4985405 5104.1.1.1 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.61 46.0 3.59e-01 88.0% 35.2%
5043684 5104.1.1.1 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.61 45.0 3.53e-01 86.0% 36.0%
3968611 327.8.1.1 a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.61 49.0 4.23e-01 98.0% 60.0%
4117010 5104.1.1.0 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases 0.60 44.0 3.53e-01 82.0% 39.1%
4542368 327.1.1.7 a+b two layers › Alpha-lytic protease prodomain-like › Alpha-lytic protease prodomain › Alpha-lytic protease prodomain › PF28778 0.60 49.0 4.73e-01 100.0% 88.3%
3088103 131.1.1.16 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › Ppx_C 0.60 49.0 3.49e-01 100.0% 36.3%
1854374 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 0.60 45.0 3.41e-01 88.0% 32.6%
3449511 207.1.1.103 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_R13L1-DRL21 0.59 49.0 3.01e-01 100.0% 16.1%
2554795 131.1.1.15 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › Ppx-GppA_III 0.59 49.0 3.44e-01 100.0% 31.9%
3969775 327.8.1.2 a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › GSPE_N1E 0.58 47.0 4.46e-01 98.0% 76.9%
4234478 5104.1.1.1 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.58 43.0 3.46e-01 88.0% 40.4%
2770746 149.1.1.1 alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.57 44.0 2.65e-01 88.0% 23.6%
5046734 247.1.1.30 a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Anti-Pycsar_Apyc1 0.57 43.0 2.78e-01 84.0% 33.9%
4250586 5104.1.1.1 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.57 41.0 3.32e-01 82.0% 40.9%
4951627 327.11.1.0 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.57 49.0 4.43e-01 100.0% 82.9%
3482727 246.2.1.0 a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases 0.56 44.0 2.73e-01 96.0% 82.5%
4945782 5104.1.1.0 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases 0.55 41.0 3.21e-01 88.0% 41.9%
4995246 5104.1.1.1 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.54 39.0 3.20e-01 88.0% 38.2%
3468641 109.4.1.2213 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF29032 0.51 45.0 2.90e-01 100.0% 37.4%