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LSDeep1_scaffold_41_prodigal-single.1__X__X__00521

Bact-Vir

LSDeep1_scaffold_41_prodigal-single.1__X__X__00521

Identity

Kingdom:
phage

Quality

83.9 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 1-91
PDB
Domain cluster: representative
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3p34A02 3.30.1120.30 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › POLO box domain 0.67 41.0 4.00e-01 78.0% 56.7%
1ekgA00 3.30.920.10 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Frataxin/CyaY 0.67 61.0 5.56e-01 100.0% 79.8%
5upiA01 2.70.98.30 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Golgi alpha-mannosidase II; domain 4 0.64 47.0 3.65e-01 75.8% 85.1%
3mswA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.62 46.0 3.97e-01 78.0% 69.8%
6u1oA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.59 53.0 5.03e-01 100.0% 97.2%
3bc8A03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.59 54.0 4.66e-01 100.0% 84.8%
2xvlA01 2.60.40.1760 Mainly Beta › Sandwich › Immunoglobulin-like › glycosyl hydrolase (family 31) 0.58 52.0 3.88e-01 100.0% 96.6%
4r7rA00 3.30.1490.410 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Uncharacterised protein PF16224, DUF4883 0.57 40.0 3.67e-01 73.6% 78.7%
2v43A01 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.57 42.0 3.39e-01 78.0% 91.3%
4upiA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.55 45.0 2.84e-01 89.0% 86.0%
3b8bA01 3.30.540.10 Alpha Beta › 2-Layer Sandwich › Fructose-1,6-Bisphosphatase; Chain A, domain 1 › Fructose-1,6-Bisphosphatase, subunit A, domain 1 0.55 47.0 3.95e-01 94.5% 86.2%
3v5nB02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.55 43.0 3.45e-01 84.6% 82.6%
2ftxA00 3.30.457.50 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › Chromosome segregation protein Spc25 0.54 43.0 4.34e-01 87.9% 87.6%
2vqrA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.54 44.0 2.78e-01 87.9% 89.7%
4py5A01 3.30.310.10 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein 0.54 36.0 3.95e-01 94.5% 87.5%
1xfdA01 2.140.10.30 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Dipeptidylpeptidase IV, N-terminal domain 0.53 45.0 2.89e-01 94.5% 43.1%
1yqfB00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.53 47.0 3.74e-01 96.7% 68.4%
4nsxA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 45.0 3.20e-01 96.7% 97.4%
2giaB00 2.30.31.40 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › 0.53 40.0 3.40e-01 79.1% 72.6%
3ot2A00 3.90.1570.10 Alpha Beta › Alpha-Beta Complex › tt1808, chain A › tt1808, chain A 0.53 46.0 3.75e-01 100.0% 72.6%
3jv1A00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.52 45.0 3.61e-01 95.6% 68.7%
1ukfA00 3.90.70.20 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.52 42.0 3.32e-01 89.0% 42.0%
1tfkA00 3.10.450.200 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 34.0 3.41e-01 75.8% 63.8%
1cruA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.51 42.0 2.75e-01 93.4% 73.2%
2w4yA00 2.40.160.220 Mainly Beta › Beta Barrel › Porin › 0.50 43.0 3.93e-01 96.7% 93.4%
2z4hA01 2.40.128.300 Mainly Beta › Beta Barrel › Lipocalin › NlpE, N-terminal domain 0.50 37.0 3.90e-01 92.3% 88.6%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3244243 207.1.1.81 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.67 43.0 3.31e-01 83.5% 30.3%
3704327 292.2.1.0 a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain 0.66 41.0 4.64e-01 78.0% 81.4%
4530314 375.13.1.0 few secondary structure elements › Rubredoxin-like › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Mycobacterium tuberculosis Topoisomerase I C-terminal domain 0.66 39.0 4.62e-01 72.5% 91.4%
4951147 881.4.1.0 a+b three layers › Mog1p/PsbP-like › C-terminal domain in sigma-E factor regulatory protein rseB › C-terminal domain in sigma-E factor regulatory protein rseB 0.65 38.0 3.48e-01 73.6% 43.3%
1169937 71.1.1.4 beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › MucB_RseB 0.63 44.0 3.51e-01 73.6% 87.3%
3219284 2484.1.1.190 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FBA_2 0.62 44.0 3.14e-01 82.4% 25.3%
3224967 207.1.1.81 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.61 44.0 3.18e-01 83.5% 26.7%
5067782 331.1.1.0 a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.61 40.0 4.43e-01 95.6% 87.1%
3057485 71.1.1.10 beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolA_3 0.61 45.0 3.81e-01 79.1% 47.4%
5014724 295.1.1.51 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › FtsQ_DivIB_C 0.58 36.0 3.51e-01 83.5% 57.0%
3970026 5.1.3.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.58 49.0 3.43e-01 95.6% 91.0%
4985368 331.1.1.1 a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › TBP 0.57 34.0 4.07e-01 81.3% 90.0%
3928306 223.2.1.1 a+b three layers › Profilin-like › profilin-like › profilin-like › Profilin 0.57 41.0 3.60e-01 76.9% 51.8%
3313320 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.56 44.0 4.13e-01 97.8% 68.7%
3209295 223.2.1.1 a+b three layers › Profilin-like › profilin-like › profilin-like › Profilin 0.55 40.0 3.53e-01 76.9% 59.3%
4007747 3735.1.1.14 beta meanders › Rearrangement hotspot (RHS) repeats protein › Rearrangement hotspot (RHS) repeats protein › Rearrangement hotspot (RHS) repeats protein › TEN_YD-shell 0.55 47.0 2.67e-01 95.6% 51.0%
4100064 5.1.3.192 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › DUF5050 0.54 47.0 3.42e-01 98.9% 91.6%
3224579 207.1.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.54 45.0 3.04e-01 90.1% 25.5%
3387155 298.1.1.24 a+b two layers › FwdE/GAPDH domain-like › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › GFO_IDH_MocA_C3 0.54 45.0 3.56e-01 92.3% 88.2%
3246217 214.1.1.1 a+b two layers › SH2 › SH2 › SH2 › SH2 0.54 45.0 4.06e-01 96.7% 85.9%
3254948 633.23.1.0 alpha bundles › Bromodomain-like › Claudin › Claudin 0.53 36.0 2.78e-01 70.3% 69.3%
4027220 331.23.1.0 a+b two layers › TBP-like › Integrator IntS9/IntS11 C-terminal domain › Integrator IntS9/IntS11 C-terminal domain 0.52 40.0 4.25e-01 94.5% 93.8%
3475065 5.1.4.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.52 44.0 2.88e-01 94.5% 90.3%
3616765 10.1.1.17 beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.52 39.0 2.99e-01 80.2% 79.5%
3400083 5.1.5.18 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › Vps16_N 0.51 42.0 3.04e-01 94.5% 98.7%
3237575 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.51 40.0 2.91e-01 100.0% 28.6%
4030804 2004.1.1.159 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.51 44.0 3.17e-01 100.0% 41.7%
3497302 10.1.1.0 beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.50 41.0 3.55e-01 89.0% 72.9%
3242234 206.1.1.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.50 44.0 2.73e-01 96.7% 40.6%
D2 high residues 94-136
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1xf1A05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 53.0 4.23e-01 100.0% 61.4%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.66 54.0 4.36e-01 100.0% 93.5%
2w82A01 3.10.20.480 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Antirestriction protein ArdA, domain 1 0.65 52.0 4.86e-01 100.0% 96.6%
7whgG02 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.63 51.0 4.17e-01 100.0% 48.9%
3holA01 2.40.128.250 Mainly Beta › Beta Barrel › Lipocalin › 0.62 48.0 4.00e-01 90.7% 96.4%
5t89Y06 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 43.0 3.49e-01 79.1% 85.9%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.60 46.0 3.99e-01 93.0% 68.4%
4r8tB02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.59 48.0 4.23e-01 100.0% 74.0%
3ddcB00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.59 45.0 3.35e-01 93.0% 32.3%
4hscX04 2.60.40.1430 Mainly Beta › Sandwich › Immunoglobulin-like › Perfringolysin, domain 4 0.59 48.0 3.72e-01 100.0% 63.6%
7ejoB01 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.59 46.0 3.96e-01 100.0% 90.4%
1goiA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.59 46.0 3.73e-01 90.7% 98.9%
5mybA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 46.0 3.75e-01 97.7% 57.3%
5j3uA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 45.0 3.39e-01 93.0% 34.7%
1pqzA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 46.0 3.72e-01 100.0% 62.4%
3ir9A02 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.57 46.0 3.43e-01 95.3% 40.8%
1d0nA06 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.57 43.0 3.35e-01 100.0% 70.1%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.55 46.0 3.53e-01 100.0% 55.6%
3eb7A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 41.0 2.97e-01 93.0% 56.1%
2hn1A01 3.30.460.20 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › CorA soluble domain-like 0.54 41.0 3.11e-01 100.0% 76.8%
2m83A00 2.60.40.2440 Mainly Beta › Sandwich › Immunoglobulin-like › Carbohydrate binding type-21 domain 0.54 41.0 3.14e-01 100.0% 46.8%
3c9aA03 2.20.20.160 Mainly Beta › Single Sheet › Anthopleurin-A › 0.53 43.0 3.69e-01 93.0% 77.5%
4ac9C04 2.40.10.190 Mainly Beta › Beta Barrel › Thrombin, subunit H › translation elongation factor selb, chain A, domain 4 0.53 37.0 3.24e-01 79.1% 56.2%
1i7dA03 2.70.20.10 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › Topoisomerase I, domain 3 0.53 40.0 2.99e-01 93.0% 92.2%
3h41A02 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.53 40.0 3.71e-01 100.0% 76.5%
6a97C01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.52 44.0 3.21e-01 100.0% 64.1%
3j26N01 2.60.120.1100 Mainly Beta › Sandwich › Jelly Rolls › 0.52 39.0 2.86e-01 100.0% 51.8%
3b4vD01 3.90.290.10 Alpha Beta › Alpha-Beta Complex › Extracellular Matrix Fibrillin › TGF-beta binding (TB) domain 0.51 38.0 3.52e-01 100.0% 82.9%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4956457 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.66 53.0 5.13e-01 93.0% 86.0%
4390313 224.1.1.2 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.62 51.0 3.87e-01 100.0% 40.0%
2530280 284.2.1.0 a+b two layers › FKBP-like › Chitinase insertion domain › Chitinase insertion domain 0.61 47.0 4.35e-01 90.7% 100.0%
3744599 7056.1.1.0 few secondary structure elements › Zinc binding domain of metalloprotease Spartan › Zinc binding domain of metalloprotease Spartan › Zinc binding domain of metalloprotease Spartan 0.61 47.0 4.82e-01 88.4% 100.0%
3930206 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 48.0 3.83e-01 100.0% 58.0%
3508836 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 47.0 3.55e-01 100.0% 56.0%
3485866 221.1.1.6 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.58 43.0 3.56e-01 93.0% 42.2%
3437290 1.1.17.3 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.57 46.0 3.06e-01 100.0% 31.2%
3377609 4.1.1.75 beta barrels › SH3 › SH3 › SH3 › NdhS 0.57 43.0 4.29e-01 93.0% 82.2%
3895786 224.1.1.2 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.56 45.0 3.45e-01 100.0% 50.8%
3755511 11.1.5.12 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › STAT_bind 0.54 44.0 3.46e-01 100.0% 74.3%
3466470 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.53 42.0 3.16e-01 95.3% 70.0%
5024617 4.15.1.2 beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.53 40.0 3.29e-01 93.0% 65.3%
3394885 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.53 41.0 3.29e-01 100.0% 60.0%
5026284 4.15.1.2 beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.51 39.0 3.19e-01 93.0% 65.3%
3990889 2007.1.2.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.51 38.0 2.82e-01 100.0% 55.9%
5048177 375.1.3.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Hypothetical protein MTH1184 0.51 40.0 3.77e-01 97.7% 83.3%
3843400 11.1.1.127 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › IL6Ra-bind 0.51 38.0 3.08e-01 100.0% 65.0%