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LD_Run2_08_scaffold_35_prodigal-single.1__X__X__00062

Bact-Vir

LD_Run2_08_scaffold_35_prodigal-single.1__X__X__00062

Identity

Kingdom:
phage

Quality

91.8 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 12-77
PDB
CATH (51)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4qblE00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.95 84.0 6.52e-01 100.0% 48.4%
4qboA00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.80 64.0 5.68e-01 100.0% 62.0%
2bonA01 3.40.50.10330 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Probable inorganic polyphosphate/atp-NAD kinase; domain 1 0.73 51.0 4.14e-01 74.2% 42.2%
4jgiB02 3.40.50.280 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cobalamin-binding domain 0.72 53.0 4.28e-01 77.3% 42.9%
3lteD00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.71 49.0 4.05e-01 90.9% 39.0%
4hh3C02 3.40.50.280 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cobalamin-binding domain 0.67 50.0 4.06e-01 81.8% 41.7%
1jr2A01 3.40.50.10090 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.66 46.0 3.78e-01 72.7% 40.0%
1reqA02 3.40.50.280 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cobalamin-binding domain 0.65 53.0 3.95e-01 89.4% 36.6%
3qq5A02 3.40.50.11420 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.65 51.0 4.39e-01 95.5% 53.2%
3m1yC01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.64 48.0 3.74e-01 81.8% 60.8%
4oc8A02 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.63 50.0 3.87e-01 93.9% 67.4%
1wu7A03 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.62 46.0 4.15e-01 87.9% 55.7%
1t9hA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 56.0 4.31e-01 100.0% 56.2%
1p3y100 3.40.50.1950 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavin prenyltransferase-like 0.61 54.0 4.01e-01 100.0% 91.8%
6kmoB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.60 52.0 3.36e-01 100.0% 49.1%
4wy5A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.60 52.0 3.38e-01 100.0% 50.9%
1n0uA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.60 51.0 3.61e-01 97.0% 91.4%
2p4gA00 3.40.430.10 Alpha Beta › 3-Layer(aba) Sandwich › Dihydrofolate Reductase, subunit A › Dihydrofolate Reductase, subunit A 0.60 51.0 3.54e-01 100.0% 42.7%
6h4dA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 52.0 4.01e-01 100.0% 52.6%
3l4eA00 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.59 43.0 3.15e-01 80.3% 27.7%
3egcA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.59 46.0 3.77e-01 90.9% 44.4%
5swvC02 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.59 42.0 3.46e-01 80.3% 39.0%
4impA02 3.40.50.11460 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 50.0 3.56e-01 100.0% 75.8%
3dv9A01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.58 49.0 3.65e-01 95.5% 49.4%
3vs8H00 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.58 49.0 3.02e-01 100.0% 16.1%
2yweA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.58 49.0 3.79e-01 100.0% 92.6%
3lzdA03 3.40.50.11860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Diphthamide synthesis DPH1/DPH2 domain 3 0.57 45.0 3.99e-01 98.5% 57.8%
1auoA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 48.0 3.42e-01 100.0% 47.2%
7atrA01 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.56 45.0 3.06e-01 87.9% 67.1%
1qydA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 49.0 3.55e-01 100.0% 52.9%
3lftB02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.56 46.0 3.65e-01 97.0% 42.9%
4njmA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 49.0 3.87e-01 100.0% 86.1%
3lkkB00 3.40.1160.10 Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like 0.55 47.0 3.28e-01 100.0% 94.1%
7essA01 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.54 45.0 3.65e-01 93.9% 96.2%
1npyA01 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.54 41.0 3.73e-01 87.9% 92.0%
4ombA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.54 39.0 3.04e-01 78.8% 55.2%
2hszA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.54 45.0 3.54e-01 97.0% 60.0%
2qi2A03 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.53 42.0 3.73e-01 86.4% 72.3%
2z8fA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.53 42.0 3.28e-01 92.4% 80.4%
3il6A01 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.53 46.0 3.47e-01 100.0% 41.2%
3fbtA01 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.52 39.0 3.21e-01 86.4% 40.7%
1g19A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 45.0 3.08e-01 100.0% 27.7%
1udxA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 44.0 3.34e-01 100.0% 94.8%
3qyfA01 3.40.50.10770 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Hypothetical protein VC1899 like domain (Restriction endonuclease-like) 0.52 42.0 3.18e-01 90.9% 91.5%
3fg2P02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 44.0 3.59e-01 97.0% 69.0%
3bblA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 44.0 3.55e-01 100.0% 85.5%
1mzjB01 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.51 43.0 3.32e-01 100.0% 40.1%
3fd3A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 35.0 3.10e-01 72.7% 48.1%
1ixcA02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 37.0 3.32e-01 80.3% 85.0%
4f2gA01 3.40.50.1370 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase 0.51 44.0 3.43e-01 100.0% 70.1%
2b4lA02 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.50 42.0 3.31e-01 98.5% 75.8%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1349404 2008.1.1.31 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › VRR_NUC 0.95 84.0 6.61e-01 100.0% 50.0%
3194602 2008.1.1.31 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › VRR_NUC 0.79 56.0 3.76e-01 83.3% 20.9%
4976255 2007.1.3.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › B12-binding 0.77 58.0 4.56e-01 80.3% 41.5%
3269087 2008.1.1.31 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › VRR_NUC 0.72 56.0 3.82e-01 83.3% 27.7%
3597780 2008.1.1.31 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › VRR_NUC 0.71 55.0 3.63e-01 81.8% 28.0%
3592079 7590.1.1.0 a/b three-layered sandwiches › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs 0.70 54.0 4.00e-01 95.5% 32.9%
3205969 2003.1.1.3 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.69 52.0 4.06e-01 81.8% 38.6%
3687742 7579.1.1.36 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_3 0.69 52.0 3.29e-01 81.8% 20.0%
2889549 2007.1.3.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › B12-binding 0.67 47.0 3.93e-01 75.8% 43.0%
3593046 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.66 56.0 4.39e-01 98.5% 62.0%
1397696 2003.1.11.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Formate/glycerate dehydrogenase catalytic domain-like › 2-Hacid_dh 0.65 45.0 3.83e-01 72.7% 44.5%
3723832 7579.1.1.36 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_3 0.65 50.0 3.29e-01 89.4% 21.8%
4878449 7579.1.1.17 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S15 0.64 48.0 4.18e-01 81.8% 67.0%
4995781 2008.1.1.17 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF559 0.62 50.0 4.51e-01 100.0% 64.2%
4028819 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.61 54.0 4.66e-01 100.0% 69.5%
4411724 2007.1.6.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Aminoacid dehydrogenase-like, N-terminal domain › Shikimate_dh_N 0.61 43.0 3.82e-01 75.8% 54.0%
4038226 7502.1.1.1 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.61 46.0 4.16e-01 86.4% 57.0%
4406429 2005.1.1.8 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Arginosuc_synth 0.60 46.0 3.41e-01 83.3% 64.0%
4930870 2007.1.1.21 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › PylD_N 0.60 47.0 3.89e-01 90.9% 47.5%
3782271 2007.1.1.1 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › GATase 0.60 40.0 2.78e-01 77.3% 18.1%
5079561 7574.1.1.5 a/b three-layered sandwiches › Thiamin diphosphate-binding fold (THDP-binding) › Thiamin diphosphate-binding fold (THDP-binding) › Thiamin diphosphate-binding fold (THDP-binding) › TPP_enzyme_C 0.60 47.0 3.11e-01 95.5% 18.7%
4033614 7523.1.1.3 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_5 0.59 41.0 2.91e-01 74.2% 65.6%
4373132 2007.1.1.34 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › OST48_N 0.59 43.0 2.99e-01 80.3% 22.9%
5026111 2007.1.16.1 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Iron-sulphur enzyme Dph2 › Diphthamide_syn 0.58 46.0 3.90e-01 93.9% 50.4%
3878424 2007.1.6.2 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Aminoacid dehydrogenase-like, N-terminal domain › THF_DHG_CYH 0.58 46.0 3.74e-01 90.9% 48.6%
3953416 129.1.1.70 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › SpnB_Rossmann 0.58 49.0 3.47e-01 98.5% 72.7%
3785896 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 0.58 40.0 3.82e-01 80.3% 61.3%
4958578 2007.1.14.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like 0.57 50.0 4.00e-01 100.0% 96.3%
3470214 2006.1.6.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like 0.57 49.0 3.48e-01 100.0% 91.2%
4021412 301.1.1.5 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › SpoU_sub_bind 0.56 42.0 3.60e-01 81.8% 60.9%
3183222 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 0.56 42.0 3.84e-01 81.8% 66.7%
5000239 7523.1.1.3 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_5 0.56 44.0 2.70e-01 87.9% 31.7%
4961408 7523.1.1.3 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_5 0.56 44.0 2.99e-01 87.9% 55.8%
4386055 2005.1.1.47 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase, tRNA_Me_trans 0.55 46.0 3.22e-01 100.0% 40.4%
4073364 2005.1.1.38 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTU2 0.55 48.0 3.12e-01 100.0% 42.9%
3255931 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.54 44.0 3.30e-01 93.9% 93.7%
1763075 7523.1.1.17 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › OpuAC 0.54 40.0 3.67e-01 83.3% 60.5%
5005063 7523.1.1.30 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_11 0.53 39.0 3.18e-01 80.3% 74.1%
5081615 316.1.1.2 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.53 44.0 3.91e-01 100.0% 71.4%
4968084 2004.1.1.343 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_14 0.53 44.0 3.15e-01 97.0% 51.4%
5083672 7523.1.1.3 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_5 0.52 43.0 2.88e-01 92.4% 65.6%
169716 2007.1.6.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Aminoacid dehydrogenase-like, N-terminal domain › Shikimate_dh_N 0.52 38.0 3.48e-01 89.4% 55.4%
4955982 7523.1.1.3 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_5 0.52 43.0 3.02e-01 98.5% 63.5%
3480410 2003.1.14.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Aspartate/ornithine carbamoyltransferase 0.51 42.0 3.30e-01 93.9% 61.3%
4961520 7523.1.1.3 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_5 0.51 42.0 3.04e-01 98.5% 62.7%
3700337 2004.1.1.14 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › GTP_EFTU 0.51 40.0 2.82e-01 89.4% 74.7%
4931800 2003.1.14.2 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Aspartate/ornithine carbamoyltransferase › OTCace_N 0.51 43.0 3.40e-01 97.0% 63.4%
4663708 7523.1.1.15 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › LysR_substrate 0.50 38.0 3.46e-01 89.4% 85.7%
5039570 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.50 41.0 3.54e-01 100.0% 65.8%