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NC_054454.1__YP_010052259.1__KD933_gp52__00052

Bact-Vir

NC_054454.1__YP_010052259.1__KD933_gp52__00052

Identity

Accession:
NC_054454 ↗
Kingdom:
phage

Quality

82.8 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 22-79
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1lzwA00 3.30.1390.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS 0.73 58.0 5.05e-01 87.9% 89.0%
1xmbA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.73 58.0 4.91e-01 89.7% 96.0%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.72 60.0 4.38e-01 96.6% 51.5%
4iyqA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 59.0 4.83e-01 94.8% 85.0%
4yjmC00 3.30.1390.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS 0.70 57.0 5.09e-01 91.4% 100.0%
3ramA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 56.0 4.53e-01 91.4% 95.8%
2ypyA00 3.30.70.390 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Epstein Barr virus nuclear antigen-1, DNA-binding domain 0.67 56.0 4.32e-01 94.8% 67.2%
4mmoA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 53.0 3.80e-01 86.2% 97.6%
5uejA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 52.0 4.24e-01 87.9% 98.2%
1s7hA01 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 54.0 4.89e-01 94.8% 100.0%
1rlhA02 3.40.1520.10 Alpha Beta › 3-Layer(aba) Sandwich › hypothetical protein tt1634 › Ta1353-like 0.65 48.0 4.10e-01 82.8% 100.0%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.64 48.0 4.11e-01 79.3% 85.9%
1tdjA03 3.40.1020.10 Alpha Beta › 3-Layer(aba) Sandwich › Biosynthetic Threonine Deaminase; domain 3 › Biosynthetic Threonine Deaminase; Domain 3 0.64 48.0 3.55e-01 82.8% 49.1%
2iboA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 54.0 4.69e-01 94.8% 95.5%
3pvlA02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.64 54.0 4.60e-01 100.0% 58.3%
3fgtA01 2.10.70.60 Mainly Beta › Ribbon › Complement Module; domain 1 › Phospholipase B-like, domain 1 0.64 40.0 4.16e-01 96.6% 67.3%
4ah6A03 3.30.1360.30 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › GAD-like domain 0.63 43.0 3.21e-01 70.7% 71.1%
1lxnA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 51.0 4.36e-01 93.1% 94.9%
3tupA02 3.30.70.380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain 0.62 44.0 3.83e-01 77.6% 94.8%
1s7hA02 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 50.0 4.57e-01 94.8% 97.6%
4kpnA00 3.90.245.10 Alpha Beta › Alpha-Beta Complex › Inosine-uridine Nucleoside N-ribohydrolase; Chain A › Ribonucleoside hydrolase-like 0.61 49.0 3.09e-01 89.7% 54.1%
2djwA01 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.61 45.0 4.29e-01 84.5% 100.0%
1yqhA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 50.0 4.23e-01 94.8% 87.5%
1wvqA00 3.40.1520.10 Alpha Beta › 3-Layer(aba) Sandwich › hypothetical protein tt1634 › Ta1353-like 0.61 47.0 3.57e-01 91.4% 63.2%
1vk8A00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 49.0 4.31e-01 96.6% 93.5%
1lxjA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 49.0 4.12e-01 94.8% 90.3%
2hpuA02 3.30.70.2050 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 39.0 3.89e-01 82.8% 65.1%
3t8iA00 3.90.245.10 Alpha Beta › Alpha-Beta Complex › Inosine-uridine Nucleoside N-ribohydrolase; Chain A › Ribonucleoside hydrolase-like 0.58 46.0 2.98e-01 89.7% 52.9%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.58 46.0 4.03e-01 91.4% 59.6%
3eqvA02 3.30.450.330 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.56 41.0 3.13e-01 77.6% 60.2%
3pz8C00 2.40.240.130 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › 0.56 37.0 3.49e-01 89.7% 51.9%
4zkdA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 37.0 2.53e-01 70.7% 81.5%
3ue3A02 3.30.450.330 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.55 40.0 3.03e-01 77.6% 62.7%
2y8yA02 3.30.70.1210 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Crispr-associated protein; domain 2 0.55 40.0 3.41e-01 84.5% 95.7%
3eipA00 3.10.50.20 Alpha Beta › Roll › Chitinase A; domain 3 › Cloacin immunity protein 0.55 44.0 3.98e-01 91.4% 98.8%
1vs5I00 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.55 41.0 3.25e-01 82.8% 48.8%
2wyoD02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.55 38.0 3.08e-01 100.0% 35.5%
2zw2A00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.54 43.0 3.88e-01 91.4% 100.0%
1gtdA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.54 41.0 3.77e-01 87.9% 100.0%
1va9A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 44.0 3.64e-01 100.0% 75.4%
1o51A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 44.0 3.96e-01 100.0% 97.8%
1t8rA01 3.30.1730.10 Alpha Beta › 2-Layer Sandwich › amp nucleosidase, domain 1 › AMP nucleoside phosphorylase, N-terminal domain 0.53 42.0 3.35e-01 100.0% 69.5%
1ukfA00 3.90.70.20 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.53 45.0 3.22e-01 96.6% 38.8%
3rgzA02 3.30.1490.310 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.52 43.0 4.26e-01 96.6% 96.7%
1t4aA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.52 38.0 3.55e-01 84.5% 100.0%
2a90A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.52 42.0 3.72e-01 100.0% 96.9%
2hgsA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.51 44.0 3.63e-01 100.0% 53.2%
2rilA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 39.0 3.51e-01 93.1% 95.8%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3615104 245.1.1.1 a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.75 51.0 4.30e-01 100.0% 43.2%
3619035 245.1.1.0 a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.75 50.0 4.28e-01 100.0% 43.2%
5026139 304.25.1.1 a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.73 57.0 4.64e-01 86.2% 100.0%
4383381 304.25.1.1 a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.68 53.0 4.38e-01 87.9% 100.0%
3840416 4323.1.1.1 alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › V_ATPase_I 0.66 54.0 4.80e-01 94.8% 90.0%
3895104 304.24.1.7 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › V_ATPase_I 0.66 55.0 4.47e-01 94.8% 64.3%
3566248 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.66 54.0 4.79e-01 94.8% 81.1%
5000967 304.5.1.3 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.66 55.0 4.65e-01 98.3% 88.6%
1116587 304.26.1.2 a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like › Ykof 0.65 54.0 4.78e-01 96.6% 91.0%
3271498 304.121.1.1 a+b two layers › Alpha-beta plaits › SP0830-like › SP0830-like › DUF1697 0.65 52.0 4.58e-01 91.4% 94.4%
5048109 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 0.65 52.0 4.53e-01 89.7% 98.9%
5081920 304.160.1.1 a+b two layers › Alpha-beta plaits › Gas vesicle protein GvpF › Gas vesicle protein GvpF › GvpL_GvpF 0.64 53.0 4.10e-01 93.1% 99.3%
3937857 245.1.1.0 a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.64 43.0 3.85e-01 100.0% 48.2%
4929491 304.5.1.13 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF3574 0.64 54.0 4.49e-01 100.0% 98.2%
3225952 304.5.1.23 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › V_ATPase_I 0.63 51.0 4.47e-01 94.8% 74.7%
4948080 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.63 50.0 4.55e-01 93.1% 96.5%
5045103 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.63 47.0 4.43e-01 86.2% 100.0%
3285401 3986.2.1.0 a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.63 50.0 4.65e-01 89.7% 69.3%
5069565 304.26.1.0 a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like 0.62 51.0 4.45e-01 94.8% 96.8%
3928208 304.163.1.0 a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.62 47.0 4.47e-01 87.9% 100.0%
3312666 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.62 50.0 4.80e-01 96.6% 78.6%
3953647 304.26.1.1 a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like › Thiamine_BP 0.61 51.0 4.38e-01 94.8% 96.8%
4179371 1119.1.1.1 a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.61 50.0 3.34e-01 93.1% 24.1%
4057352 1119.1.1.1 a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.61 51.0 3.39e-01 96.6% 23.9%
5054411 304.19.1.0 a+b two layers › Alpha-beta plaits › eIF-2-alpha, C-terminal domain › eIF-2-alpha, C-terminal domain 0.60 46.0 4.19e-01 86.2% 98.8%
4122400 1119.1.1.1 a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.60 49.0 3.28e-01 93.1% 25.7%
4654177 1119.1.1.1 a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.60 48.0 3.25e-01 93.1% 23.3%
3670198 221.1.1.4 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.60 47.0 4.02e-01 96.6% 51.4%
4033553 304.26.1.1 a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like › Thiamine_BP 0.59 48.0 4.08e-01 94.8% 92.4%
4928621 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.59 49.0 3.86e-01 100.0% 52.1%
5049794 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.58 49.0 3.78e-01 100.0% 50.3%
5063823 304.55.2.0 a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like 0.58 45.0 4.07e-01 94.8% 96.8%
3471370 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.56 43.0 3.73e-01 96.6% 52.0%
3333290 10.32.1.203 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.56 48.0 3.44e-01 100.0% 69.4%
3600134 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.56 45.0 3.86e-01 100.0% 54.0%
3519830 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 43.0 3.45e-01 94.8% 99.3%
1236096 11.1.5.44 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › MatB 0.55 44.0 3.29e-01 98.3% 67.0%
3251743 4357.1.1.1 beta barrels › WWE domain › WWE domain › WWE domain › WWE 0.55 45.0 4.14e-01 100.0% 98.8%
4977431 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.54 43.0 4.23e-01 89.7% 80.0%
3683581 7512.1.1.32 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_trans_1_4 0.54 40.0 2.72e-01 82.8% 37.3%
5010290 304.100.1.1 a+b two layers › Alpha-beta plaits › PurS-like › PurS-like › PurS 0.53 42.0 3.70e-01 89.7% 94.4%
4433786 382.1.1.1 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › UPAR_LY6 0.53 41.0 3.82e-01 94.8% 94.1%
5065436 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.53 41.0 4.03e-01 91.4% 95.3%
3374802 7512.1.1.0 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase 0.53 36.0 2.62e-01 72.4% 32.8%
4939340 223.8.1.0 a+b three layers › Profilin-like › LapD periplasmic domain › LapD periplasmic domain 0.53 45.0 3.77e-01 100.0% 54.4%
4015453 212.1.1.12 a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › UPF0029 0.52 39.0 3.05e-01 81.0% 65.4%
4011483 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 39.0 3.33e-01 89.7% 83.5%
3835461 207.1.1.223 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1, LRRNT_2, LRR_8, Island 0.52 43.0 2.45e-01 100.0% 8.1%
2106285 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.52 39.0 3.36e-01 89.7% 55.6%
3199908 11.1.1.207 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › AMPK1_CBM 0.52 40.0 3.35e-01 91.4% 61.7%
2443967 70.4.1.4 beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_decoration 0.51 37.0 2.99e-01 84.5% 89.0%
None 0.51 38.0 2.57e-01 79.3% 69.6%
5012895 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.50 39.0 4.00e-01 89.7% 100.0%
4969863 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.50 39.0 3.67e-01 91.4% 77.3%
5067865 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.50 38.0 3.67e-01 89.7% 85.7%