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LSDeep1_scaffold_41_prodigal-single.1__X__X__00057

Bact-Vir

LSDeep1_scaffold_41_prodigal-single.1__X__X__00057

Identity

Kingdom:
phage

Quality

83.1 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 125-202
PDB
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1kk1A02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.54 44.0 3.86e-01 100.0% 61.3%
4tkoB02 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.53 41.0 4.35e-01 100.0% 100.0%
2j3vA02 3.90.176.10 Alpha Beta › Alpha-Beta Complex › Toxin ADP-ribosyltransferase; Chain A, domain 1 › Toxin ADP-ribosyltransferase; Chain A, domain 1 0.51 44.0 3.32e-01 100.0% 62.3%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3602381 4.1.1.403 beta barrels › SH3 › SH3 › SH3 › UPF0179 0.59 50.0 5.12e-01 100.0% 96.0%
4952573 1.1.13.74 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › UPF0179 0.58 49.0 5.06e-01 100.0% 96.0%
5040464 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 39.0 3.69e-01 100.0% 57.9%
4050976 1.1.9.30 beta barrels › cradle loop barrel › RIFT-related › PUA domain › UPF0179 0.57 48.0 4.91e-01 100.0% 96.0%
3281705 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.56 44.0 4.02e-01 100.0% 65.0%
4440715 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 36.0 3.85e-01 100.0% 80.0%
5036886 1.1.13.74 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › UPF0179 0.55 46.0 4.69e-01 100.0% 96.0%
4204828 1.1.9.30 beta barrels › cradle loop barrel › RIFT-related › PUA domain › UPF0179 0.54 43.0 4.49e-01 93.6% 95.7%
3826545 4.1.1.158 beta barrels › SH3 › SH3 › SH3 › DUF3444 0.54 44.0 4.02e-01 92.3% 82.9%
3965955 325.1.7.21 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › BSH_RND 0.54 43.0 4.48e-01 100.0% 97.1%
3972515 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.53 37.0 4.12e-01 92.3% 96.7%
4449102 1.1.7.70 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Beta-barrel_GLAA-B_II 0.51 41.0 3.91e-01 98.7% 74.4%
4009668 325.1.7.0 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.51 41.0 4.35e-01 100.0% 98.6%
1562394 1.1.8.6 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GlxA 0.51 39.0 3.59e-01 100.0% 61.1%
4059260 325.1.7.21 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › BSH_RND 0.51 42.0 4.31e-01 100.0% 97.3%
2723599 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.51 42.0 3.60e-01 100.0% 57.4%
D2 medium residues 13-88
PDB
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ms4A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.69 55.0 4.05e-01 85.5% 63.4%
1dp4C02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.68 56.0 4.11e-01 90.8% 58.3%
4ms4B02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.67 53.0 4.06e-01 86.8% 62.8%
1yu0A01 2.10.10.30 Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › 0.66 43.0 5.02e-01 80.3% 100.0%
1jdpA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.66 52.0 4.02e-01 88.2% 65.9%
2cs0A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.64 45.0 4.19e-01 73.7% 68.4%
2oq1A03 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.60 44.0 4.05e-01 77.6% 67.0%
1wquA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.59 41.0 3.71e-01 73.7% 72.8%
2oap202 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 48.0 3.33e-01 92.1% 47.3%
8djfA01 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.58 46.0 3.22e-01 89.5% 54.7%
2qe8A00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.58 46.0 3.02e-01 86.8% 65.0%
3v7dD02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.58 47.0 3.12e-01 93.4% 51.9%
1npeA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.57 45.0 3.22e-01 89.5% 52.1%
3mmyA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 45.0 3.03e-01 92.1% 48.0%
1ob8A00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.56 41.0 3.56e-01 77.6% 94.1%
1s3iA02 3.10.25.10 Alpha Beta › Roll › Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 › Formyl transferase, C-terminal domain 0.56 40.0 3.70e-01 77.6% 100.0%
1ijqA01 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.54 43.0 3.14e-01 90.8% 65.7%
2rbcA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.54 44.0 3.05e-01 94.7% 53.9%
2p4oA01 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.54 42.0 2.97e-01 89.5% 46.2%
1k32A01 2.120.10.60 Mainly Beta › 6 Propeller › Neuraminidase › Tricorn protease N-terminal domain 0.54 43.0 3.07e-01 92.1% 54.8%
3c5mA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 45.0 2.93e-01 94.7% 47.1%
4gc1A01 2.90.10.10 Mainly Beta › Orthogonal Prism › Agglutinin, subunit A › Bulb-type lectin domain 0.54 39.0 3.54e-01 76.3% 85.6%
1c5kA02 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.54 43.0 3.07e-01 92.1% 55.3%
8f5pE01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 43.0 2.80e-01 92.1% 56.1%
1k32A02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 43.0 2.87e-01 94.7% 66.0%
5c2vB00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 40.0 2.72e-01 90.8% 70.7%
5m8cB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 40.0 2.66e-01 88.2% 54.0%
1gofA02 2.130.10.80 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Galactose oxidase/kelch, beta-propeller 0.51 42.0 2.73e-01 94.7% 61.1%
3fgbA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 41.0 2.70e-01 90.8% 59.0%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3505544 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.70 56.0 3.83e-01 85.5% 86.2%
3403871 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.70 57.0 4.16e-01 89.5% 73.7%
3265025 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.69 57.0 4.33e-01 90.8% 58.3%
3917110 2007.1.2.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.69 56.0 4.15e-01 90.8% 59.0%
4989790 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.68 55.0 4.22e-01 89.5% 64.0%
3412045 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.67 56.0 4.19e-01 90.8% 61.6%
3524397 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.67 56.0 4.07e-01 92.1% 59.0%
3899247 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.67 55.0 4.12e-01 89.5% 57.8%
3934930 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.66 56.0 4.08e-01 90.8% 64.5%
4957015 2007.1.2.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.66 52.0 3.93e-01 86.8% 65.8%
3493958 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.66 54.0 3.96e-01 89.5% 80.5%
3247100 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.65 53.0 3.72e-01 90.8% 73.2%
3516546 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.64 53.0 3.99e-01 90.8% 63.7%
3800769 2007.1.2.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.64 52.0 3.77e-01 90.8% 82.2%
2495545 207.2.1.22 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › Beta_helix 0.63 53.0 3.24e-01 90.8% 30.1%
3474700 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.63 51.0 3.73e-01 90.8% 74.0%
3506773 214.1.1.9 a+b two layers › SH2 › SH2 › SH2 › DUF7063 0.62 46.0 3.96e-01 78.9% 57.5%
3477642 214.1.1.1 a+b two layers › SH2 › SH2 › SH2 › SH2 0.62 49.0 4.26e-01 88.2% 60.0%
5029609 2004.1.1.42 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.60 50.0 3.13e-01 92.1% 33.7%
3777778 214.1.1.1 a+b two layers › SH2 › SH2 › SH2 › SH2 0.60 43.0 3.05e-01 77.6% 26.3%
3591951 11.2.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.60 45.0 3.76e-01 80.3% 77.7%
4999472 101.1.8.1 alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.60 45.0 3.41e-01 81.6% 81.1%
5055415 2004.1.1.42 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.59 48.0 3.00e-01 92.1% 27.4%
3648728 5.1.3.144 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › b-prop_At3g26010-like 0.59 44.0 2.89e-01 80.3% 41.3%
3465957 5.1.4.504 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › b-prop_At3g26010-like 0.58 47.0 3.00e-01 88.2% 47.6%
3463667 5.1.3.144 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › b-prop_At3g26010-like 0.58 46.0 3.07e-01 88.2% 68.2%
195810 5.1.3.11 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › MRJP 0.58 46.0 3.02e-01 86.8% 65.0%
4016284 219.1.1.9 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C12 0.57 44.0 3.26e-01 84.2% 80.5%
4928895 79.1.1.0 beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain 0.56 44.0 3.07e-01 86.8% 30.2%
3517136 5.1.3.2 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Ldl_recept_b 0.56 45.0 3.25e-01 90.8% 53.1%
3536338 5.1.3.145 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Ldl_recept_b, DUF5050 0.55 44.0 3.05e-01 86.8% 58.1%
4526577 5.1.3.2 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Ldl_recept_b 0.55 43.0 3.13e-01 90.8% 52.5%
4984579 2004.1.1.42 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.55 45.0 2.79e-01 92.1% 24.7%
3624954 5.1.3.2 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Ldl_recept_b 0.55 45.0 3.09e-01 92.1% 50.2%
3551297 5.1.3.2 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Ldl_recept_b 0.55 45.0 3.14e-01 92.1% 47.4%
4939442 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.55 46.0 3.06e-01 92.1% 56.4%
4015863 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.55 43.0 2.79e-01 84.2% 40.3%
3710725 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.54 42.0 2.70e-01 85.5% 37.9%
3962065 5.1.3.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.54 44.0 3.20e-01 94.7% 48.0%
5033616 246.2.1.1 a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.54 44.0 3.12e-01 92.1% 66.7%
5077254 2004.1.1.42 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.54 46.0 2.87e-01 98.7% 69.5%
4618792 5.1.4.307 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PF29630 0.53 43.0 2.81e-01 97.4% 53.5%
3314585 5.1.5.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40 0.53 43.0 3.08e-01 92.1% 71.0%
3568964 11.1.1.99 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › V-set 0.52 37.0 3.51e-01 80.3% 62.2%
3989853 77.1.1.13 beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › CFSR 0.52 44.0 3.02e-01 100.0% 96.8%
3175018 871.1.1.1 a+b two layers › SSo0622-like (Pfam 02676) › SSo0622-like (Pfam 02676) › SSo0622-like (Pfam 02676) › TYW3 0.51 42.0 3.17e-01 92.1% 76.0%
1693983 5.1.4.64 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › YNCE 0.51 40.0 2.71e-01 90.8% 70.7%
5052953 246.2.1.1 a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.51 38.0 2.76e-01 84.2% 63.4%
5037203 2004.1.1.42 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.51 43.0 2.73e-01 100.0% 78.3%
4937420 2004.1.1.42 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.51 42.0 2.61e-01 94.7% 25.9%
3601107 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 41.0 2.56e-01 92.1% 67.5%
5079783 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.50 42.0 2.64e-01 100.0% 63.0%