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LSDeep1_scaffold_42_prodigal-single.1__X__X__00438

Bact-Vir

LSDeep1_scaffold_42_prodigal-single.1__X__X__00438

Identity

Kingdom:
phage

Quality

90.5 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 medium residues 1-84_148-173
PDB
Domain cluster: representative
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2diuA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.66 31.0 3.74e-01 71.8% 65.8%
3ofgB00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.63 34.0 3.81e-01 72.7% 66.7%
1lfwA03 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 33.0 3.57e-01 80.9% 71.6%
3hz7A00 3.30.110.40 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › TusA-like domain 0.53 34.0 4.00e-01 76.4% 97.3%
1r89A03 3.30.70.590 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Poly(A) polymerase predicted RNA binding domain 0.53 38.0 3.62e-01 76.4% 93.3%
6ttrA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.51 41.0 3.52e-01 88.2% 75.7%
3hvaA00 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.50 41.0 3.63e-01 88.2% 87.0%
1ndbA02 3.30.559.70 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Choline/Carnitine o-acyltransferase, domain 2 0.50 43.0 3.21e-01 99.1% 73.6%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4959193 304.39.1.0 a+b two layers › Alpha-beta plaits › Mechanosensitive channel protein MscS (YggB), C-terminal domain › Mechanosensitive channel protein MscS (YggB), C-terminal domain 0.67 35.0 3.96e-01 72.7% 65.9%
4957337 304.28.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.59 35.0 3.83e-01 71.8% 72.9%
4416593 304.28.1.4 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › SecD_1st 0.58 32.0 3.49e-01 71.8% 64.4%
4942434 304.28.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.57 35.0 3.70e-01 73.6% 68.4%
3781460 206.1.1.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.57 47.0 3.63e-01 91.8% 70.0%
4974602 304.57.1.1 a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.56 31.0 3.16e-01 73.6% 53.6%
4994641 304.19.1.1 a+b two layers › Alpha-beta plaits › eIF-2-alpha, C-terminal domain › eIF-2-alpha, C-terminal domain › EIF_2_alpha 0.56 31.0 3.28e-01 71.8% 60.0%
3794633 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.55 46.0 3.27e-01 91.8% 52.4%
4025755 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.55 46.0 3.49e-01 92.7% 63.9%
4931425 304.57.1.1 a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.54 31.0 3.15e-01 71.8% 54.5%
3518086 246.3.1.4 a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like › Exo_endo_phos2 0.54 38.0 2.89e-01 73.6% 33.7%
3503585 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.52 43.0 2.81e-01 92.7% 30.1%
5051083 328.7.1.1 a+b two layers › IF3-like › Smr domain › Smr domain › Smr 0.51 37.0 4.09e-01 75.5% 100.0%
3245395 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 42.0 3.03e-01 91.8% 55.1%
3504203 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 42.0 3.18e-01 92.7% 55.9%
D2 medium residues 85-147
PDB
Domain cluster: representative
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2e0zC03 3.30.2320.10 Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › hypothetical protein PF0899 domain 0.82 74.0 6.40e-01 100.0% 83.3%
2pk8A00 3.30.2320.10 Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › hypothetical protein PF0899 domain 0.81 69.0 6.01e-01 93.7% 77.7%
6vu9A02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.77 68.0 4.42e-01 100.0% 35.0%
1vk3A02 3.30.1330.10 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › PurM-like, N-terminal domain 0.72 63.0 4.95e-01 98.4% 67.4%
4ohxA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.67 50.0 3.46e-01 82.5% 80.7%
2rb9A01 3.30.1330.10 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › PurM-like, N-terminal domain 0.65 54.0 4.28e-01 96.8% 61.8%
2zf8A02 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.65 55.0 4.94e-01 98.4% 97.8%
2mzbA00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.64 55.0 3.93e-01 98.4% 43.4%
4rhaA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.63 53.0 4.30e-01 98.4% 91.6%
3byqA00 3.30.1330.110 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › BB2672 0.63 53.0 3.90e-01 100.0% 84.8%
5m38C00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.62 52.0 4.41e-01 98.4% 97.4%
3khnB00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.62 52.0 4.01e-01 98.4% 82.8%
1ltqA02 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.61 47.0 3.67e-01 85.7% 39.9%
2xbuA00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.61 47.0 3.36e-01 85.7% 57.0%
3oonA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.60 51.0 4.31e-01 98.4% 98.2%
2b8tA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.60 42.0 3.36e-01 76.2% 40.3%
3wj7A00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 49.0 3.14e-01 98.4% 51.5%
2j6pA00 3.40.250.10 Alpha Beta › 3-Layer(aba) Sandwich › Oxidized Rhodanese; domain 1 › Rhodanese-like domain 0.58 42.0 3.33e-01 81.0% 46.9%
5bqpD00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.57 47.0 3.50e-01 95.2% 62.5%
4mnnA00 3.40.30.80 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.57 45.0 3.36e-01 90.5% 33.3%
6g62A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.56 48.0 4.06e-01 100.0% 79.1%
4rrfA01 3.50.80.10 Alpha Beta › 3-Layer(bba) Sandwich › D-tyrosyl-trna(Tyr) Deacylase; Chain: A; › D-tyrosyl-tRNA(Tyr) deacylase 0.56 48.0 3.80e-01 98.4% 89.7%
1nyrA03 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 45.0 3.04e-01 100.0% 31.3%
4m7xA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 45.0 4.04e-01 92.1% 64.8%
2z6oA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.55 46.0 3.53e-01 100.0% 78.9%
3v3tA02 3.30.1330.150 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › 0.54 43.0 3.92e-01 98.4% 75.8%
3e1sA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 46.0 3.27e-01 100.0% 50.5%
2p6rA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 44.0 3.27e-01 100.0% 66.0%
5supC01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 38.0 2.75e-01 81.0% 40.4%
3obyA03 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.52 43.0 3.82e-01 98.4% 73.7%
2i6dA01 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.52 43.0 3.83e-01 95.2% 67.0%
2x5kP02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.52 40.0 3.18e-01 93.7% 95.2%
3d22A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 44.0 3.60e-01 100.0% 82.9%
1ggpA01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.51 44.0 3.40e-01 100.0% 81.9%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5011908 2485.3.1.2 a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 0.84 77.0 5.06e-01 100.0% 34.6%
5083777 2485.3.1.3 a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid 0.83 75.0 4.73e-01 100.0% 30.3%
4091867 314.1.1.2 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.79 69.0 4.27e-01 100.0% 26.2%
3361769 3617.1.1.0 a+b three layers › Thioredoxin-like domain in RNase E › Thioredoxin-like domain in RNase E › Thioredoxin-like domain in RNase E 0.77 64.0 5.54e-01 93.7% 82.0%
3423646 3008.1.1.0 a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.76 64.0 5.49e-01 93.7% 82.0%
3975504 298.4.1.0 a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E 0.75 62.0 5.67e-01 95.2% 69.4%
4125320 298.4.1.2 a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E › FliH 0.73 61.0 5.59e-01 95.2% 75.3%
5033325 298.4.1.1 a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E › vATP-synt_E 0.72 57.0 4.95e-01 95.2% 55.0%
4982289 298.4.1.0 a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E 0.71 57.0 5.34e-01 93.7% 71.2%
4974331 298.2.1.0 a+b two layers › FwdE/GAPDH domain-like › FwdE-like › FwdE-like 0.67 56.0 4.57e-01 93.7% 55.5%
5062666 298.4.1.1 a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E › vATP-synt_E 0.67 55.0 4.57e-01 95.2% 54.2%
3590038 301.10.1.1 a+b three layers › Bacillus chorismate mutase-like › YueI-like › YueI-like › DUF1694 0.66 57.0 4.91e-01 100.0% 72.4%
5060196 7528.1.1.3 a/b three-layered sandwiches › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains › PGM_PMM_III 0.66 53.0 4.43e-01 90.5% 68.7%
4122989 298.4.1.1 a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E › vATP-synt_E 0.66 55.0 4.06e-01 96.8% 35.8%
4961484 7570.1.1.5 a/b three-layered sandwiches › MurD-like peptide ligases, peptide-binding domain › MurD-like peptide ligases, peptide-binding domain › MurD-like peptide ligases, peptide-binding domain › PF31156 0.65 50.0 3.88e-01 87.3% 76.7%
3783332 2484.3.1.4 mixed a+b and a/b › Ribonuclease H-like › Creatinase/prolidase N-terminal domain › Creatinase/prolidase N-terminal domain › Creatinase_N_2 0.64 49.0 3.81e-01 84.1% 52.4%
4679436 298.4.1.1 a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E › vATP-synt_E 0.63 48.0 3.63e-01 95.2% 31.4%
4191373 298.4.1.0 a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E 0.63 51.0 4.49e-01 96.8% 65.7%
4024556 2004.1.1.30 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.62 45.0 3.37e-01 77.8% 43.5%
1253075 2007.1.2.2 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › Peripla_BP_1 0.61 45.0 3.94e-01 84.1% 52.6%
4548971 2003.1.1.3 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.61 45.0 3.05e-01 84.1% 47.9%
5016820 7516.1.1.24 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › NTP_transf_3 0.60 52.0 3.66e-01 100.0% 44.9%
5057726 7516.1.1.2 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.60 50.0 3.49e-01 95.2% 31.8%
4319924 2003.1.1.20 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Epimerase 0.60 50.0 3.21e-01 98.4% 55.3%
4994706 301.1.1.1 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › Ribosomal_L7Ae 0.60 52.0 4.51e-01 100.0% 77.0%
3597683 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.59 46.0 3.31e-01 87.3% 66.0%
4975562 217.1.1.0 a+b complex topology › FAD-binding domain-like › FAD-binding domain › FAD-binding domain 0.59 41.0 2.72e-01 73.0% 93.3%
4991620 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.58 49.0 4.15e-01 100.0% 75.7%
4997788 2485.1.1.166 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › YoaP 0.57 39.0 3.48e-01 95.2% 48.4%
1125616 2485.1.1.57 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_17 0.57 45.0 4.15e-01 90.5% 65.5%
5046403 2003.1.1.20 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Epimerase 0.56 47.0 3.06e-01 98.4% 51.4%
4286843 7512.1.1.10 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_28 0.56 48.0 3.41e-01 98.4% 38.5%
4100589 2004.1.1.30 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.56 43.0 2.99e-01 85.7% 80.4%
4114089 7512.1.1.10 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_28 0.55 47.0 3.42e-01 98.4% 45.4%
4390105 2003.1.1.64 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Staph_opine_DH 0.55 41.0 3.01e-01 85.7% 57.6%
3519842 223.1.1.3 a+b three layers › Profilin-like › sensor domains › sensor domains › GAF 0.55 47.0 3.42e-01 100.0% 73.8%
3955553 2003.1.1.20 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Epimerase 0.55 45.0 2.96e-01 98.4% 55.6%
1178308 301.6.1.6 a+b three layers › Bacillus chorismate mutase-like › Tubulin C-terminal domain-like › Tubulin C-terminal domain-like › TubZ_C_3 0.54 43.0 3.71e-01 98.4% 60.0%
3627917 226.1.1.1 a+b two layers › POZ domain › POZ domain › POZ domain › BTB 0.54 38.0 2.87e-01 77.8% 40.0%
3981253 2003.1.1.31 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › CbiJ 0.53 44.0 3.51e-01 96.8% 44.4%
3226348 209.1.1.14 a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like › PF29411 0.53 44.0 3.37e-01 100.0% 85.3%
3970664 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.52 44.0 3.58e-01 96.8% 89.2%
3478463 2007.2.5.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase › Rhodanese 0.52 40.0 3.06e-01 84.1% 85.2%
3996378 2485.1.1.93 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like_DJC16_2nd 0.52 43.0 3.61e-01 100.0% 94.4%
3865294 217.1.1.2 a+b complex topology › FAD-binding domain-like › FAD-binding domain › FAD-binding domain › FAD_binding_4 0.52 41.0 3.02e-01 88.9% 85.6%
3206220 323.1.1.0 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.51 41.0 3.38e-01 95.2% 47.2%
3936118 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.50 42.0 3.46e-01 93.7% 67.8%