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js4906-29-5_S40_scaffold_90_prodigal-single.1__X__X__00057

Bact-Vir

js4906-29-5_S40_scaffold_90_prodigal-single.1__X__X__00057

Identity

Kingdom:
phage

Quality

76.8 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 203-274
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vwxS01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.64 46.0 4.72e-01 76.4% 85.9%
2hiyA01 3.30.70.1280 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › SP0830-like domains 0.60 46.0 4.36e-01 84.7% 96.6%
1vwxS02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.58 49.0 4.88e-01 100.0% 88.2%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.58 43.0 4.45e-01 83.3% 86.6%
1ctfA00 3.30.1390.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS 0.55 38.0 3.92e-01 73.6% 100.0%
6k2eA01 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 39.0 4.00e-01 76.4% 95.6%
2w82A01 3.10.20.480 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Antirestriction protein ArdA, domain 1 0.54 38.0 4.04e-01 86.1% 94.9%
3eipA00 3.10.50.20 Alpha Beta › Roll › Chitinase A; domain 3 › Cloacin immunity protein 0.53 38.0 3.65e-01 76.4% 92.9%
3n77A00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.52 42.0 3.45e-01 93.1% 95.0%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4937773 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.70 50.0 5.51e-01 75.0% 98.3%
4967222 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.66 48.0 5.16e-01 76.4% 96.7%
4939739 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.65 47.0 5.07e-01 76.4% 98.3%
5012895 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.60 43.0 4.72e-01 76.4% 100.0%
5449 304.121.1.1 a+b two layers › Alpha-beta plaits › SP0830-like › SP0830-like › DUF1697 0.60 46.0 4.27e-01 84.7% 90.4%
4151900 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.60 47.0 3.78e-01 88.9% 43.1%
223776 3115.4.1.1 a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 › DUF1543 0.57 43.0 4.41e-01 88.9% 83.1%
5067865 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.57 48.0 4.89e-01 100.0% 95.7%
4969863 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.57 48.0 4.73e-01 100.0% 89.3%
5074648 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.57 48.0 4.77e-01 100.0% 89.3%
3356117 210.1.3.5 a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_7 0.56 47.0 3.10e-01 93.1% 52.3%
3738592 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.56 45.0 3.51e-01 88.9% 78.2%
3968966 7523.1.1.32 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › NMT1_3 0.54 46.0 3.80e-01 97.2% 100.0%
5079581 7523.1.1.32 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › NMT1_3 0.54 46.0 3.82e-01 98.6% 96.3%
3651649 3397.1.1.1 a+b complex topology › Tic22 › Tic22 › Tic22 › Tic22 0.53 46.0 4.01e-01 100.0% 89.6%
4090279 304.36.1.1 a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › DUF520 0.53 38.0 3.62e-01 75.0% 98.8%
4671238 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.53 44.0 3.18e-01 91.7% 75.2%
3462782 219.1.1.71 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › PDDEXK_6 0.52 40.0 3.16e-01 87.5% 63.4%
3815036 3397.1.1.0 a+b complex topology › Tic22 › Tic22 › Tic22 0.52 44.0 3.79e-01 100.0% 71.2%
3193224 219.1.1.23 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › MINDY_DUB 0.52 39.0 2.78e-01 87.5% 91.8%
4233743 2002.1.1.29 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DHDPS 0.52 40.0 2.79e-01 90.3% 84.1%
4948555 316.1.1.2 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.51 37.0 3.33e-01 77.8% 81.9%
D2 medium residues 1-131
PDB
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vbkA01 3.30.70.1510 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › THUMP domain-like 0.64 35.0 4.25e-01 71.8% 83.1%
1ul7A00 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.61 38.0 4.30e-01 87.0% 81.4%
1ni9A01 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 0.59 48.0 4.60e-01 86.3% 90.1%
1gjwA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.59 28.0 3.68e-01 78.6% 83.8%
1kafA00 3.90.1150.20 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Transcription regulator MotA, C-terminal domain 0.59 45.0 4.88e-01 80.9% 100.0%
2kd2A01 2.40.128.180 Mainly Beta › Beta Barrel › Lipocalin › 0.58 36.0 4.42e-01 84.0% 98.8%
4nkbA01 3.30.1120.120 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.57 41.0 4.41e-01 90.8% 86.0%
1mpgA01 3.30.310.20 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › DNA-3-methyladenine glycosylase AlkA, N-terminal domain 0.57 33.0 3.59e-01 86.3% 66.1%
1ob8A00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.56 43.0 4.46e-01 80.2% 100.0%
4ncbA01 3.30.530.60 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.55 43.0 4.21e-01 83.2% 79.5%
1j0hA04 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.55 32.0 3.85e-01 84.7% 89.2%
4nogA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.55 42.0 3.84e-01 86.3% 62.0%
2cjgA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.54 39.0 3.70e-01 84.0% 63.0%
5ee2A00 2.40.160.90 Mainly Beta › Beta Barrel › Porin › 0.54 39.0 4.08e-01 85.5% 81.1%
4hbrA00 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 37.0 3.71e-01 71.0% 74.3%
3w9kA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 42.0 4.22e-01 83.2% 80.7%
5gv0A00 2.40.160.110 Mainly Beta › Beta Barrel › Porin › 0.54 41.0 3.83e-01 80.2% 77.8%
5tseA00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.53 42.0 4.14e-01 81.7% 88.2%
4lgvD02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.53 42.0 3.38e-01 84.7% 98.9%
1p32B00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.53 40.0 3.65e-01 78.6% 65.5%
2fyxA00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.52 37.0 3.78e-01 72.5% 77.7%
2aaaA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.52 33.0 3.68e-01 85.5% 81.4%
4akmB00 2.40.160.110 Mainly Beta › Beta Barrel › Porin › 0.52 39.0 3.69e-01 78.6% 79.0%
1iugA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 38.0 4.04e-01 85.5% 89.2%
1eurA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.52 42.0 3.06e-01 87.0% 52.1%
3rbyA02 2.40.128.310 Mainly Beta › Beta Barrel › Lipocalin › Protein HRI1, C-terminal domain 0.51 33.0 3.80e-01 80.2% 90.5%
2p4bB02 3.30.200.100 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › MucB/RseB, C-terminal domain 0.51 35.0 4.00e-01 70.2% 96.9%
4kcaA02 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.51 45.0 3.28e-01 100.0% 98.2%
4clfA02 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.51 42.0 3.78e-01 89.3% 72.8%
6phxA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 31.0 3.61e-01 81.7% 85.3%
2zzeA04 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.50 34.0 3.87e-01 71.8% 93.7%
2nvnA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.50 31.0 3.22e-01 89.3% 63.3%
1cgtA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.50 31.0 3.51e-01 80.2% 84.0%
2it9A00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.50 30.0 3.16e-01 89.3% 62.5%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4939731 512.1.1.1 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.72 37.0 5.06e-01 81.7% 100.0%
5074419 512.1.1.1 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.70 36.0 4.96e-01 77.9% 100.0%
4228206 708.1.1.0 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.69 37.0 4.69e-01 71.0% 87.5%
5004346 331.19.1.0 a+b two layers › TBP-like › Toxin RnlA N-terminal domains › Toxin RnlA N-terminal domains 0.68 39.0 4.75e-01 85.5% 87.1%
5014277 274.1.1.0 a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.66 37.0 4.52e-01 93.1% 84.7%
3519601 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.60 49.0 5.15e-01 92.4% 95.8%
3484575 4099.1.1.0 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.60 50.0 5.23e-01 96.9% 97.5%
3837990 3675.1.1.0 a+b complex topology › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain 0.60 34.0 3.51e-01 87.0% 56.2%
4122018 4099.1.1.10 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med1 0.59 44.0 4.91e-01 96.2% 100.0%
5013018 274.1.1.0 a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.59 42.0 4.24e-01 90.1% 73.1%
3738183 4099.1.1.10 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med1 0.59 48.0 4.97e-01 100.0% 92.0%
3492352 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.59 43.0 4.75e-01 93.1% 96.2%
3875620 883.1.1.1 a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like › LBP_BPI_CETP 0.58 44.0 3.87e-01 77.9% 92.6%
3602709 241.15.1.6 a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › PF27355 0.58 49.0 4.62e-01 91.6% 98.1%
3328470 4099.1.1.0 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.58 49.0 4.98e-01 91.6% 96.2%
3368132 4099.1.1.4 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › CENP-O 0.58 49.0 5.09e-01 91.6% 99.2%
5045322 331.6.1.0 a+b two layers › TBP-like › MoaD-related protein, C-terminal domain › MoaD-related protein, C-terminal domain 0.57 35.0 3.59e-01 89.3% 61.6%
3784412 5.1.4.44 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › RCC1_2 0.57 40.0 2.74e-01 72.5% 48.1%
3168452 331.10.2.3 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase › Med1 0.56 43.0 4.70e-01 100.0% 100.0%
5074323 331.10.2.0 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.56 41.0 4.42e-01 81.7% 87.8%
3962450 9.27.1.0 beta barrels › Lipocalins/Streptavidin › LpqH › LpqH 0.55 37.0 4.15e-01 71.0% 85.7%
4970968 331.10.2.0 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.55 38.0 4.07e-01 86.3% 81.4%
3191832 12.3.1.36 beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › DUF5127 0.55 43.0 3.34e-01 80.9% 87.6%
4240410 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.55 47.0 4.51e-01 92.4% 80.0%
5014493 331.3.1.12 a+b two layers › TBP-like › Bet v1-like › Bet v1-like › STK_08120-like 0.55 42.0 3.51e-01 81.7% 47.4%
5036898 881.1.1.0 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.55 43.0 4.25e-01 84.7% 80.6%
3953943 9.27.1.1 beta barrels › Lipocalins/Streptavidin › LpqH › LpqH › Myco_19_kDa 0.54 38.0 4.08e-01 75.6% 85.5%
3583988 10.1.1.17 beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.53 31.0 3.39e-01 93.9% 67.3%
4569249 9.14.1.1 beta barrels › Lipocalins/Streptavidin › Uncharacterized protein YLR301W › Uncharacterized protein YLR301W › HRI1 0.53 33.0 3.93e-01 74.8% 91.1%
4974181 331.3.1.74 a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PF27226 0.52 37.0 4.17e-01 96.9% 97.0%
4011809 206.1.1.11 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › APH 0.52 41.0 2.88e-01 83.2% 27.5%
4941640 211.1.1.0 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.52 36.0 3.39e-01 86.3% 58.7%
None 0.51 41.0 2.59e-01 85.5% 18.7%
5046173 4252.1.1.7 beta barrels › AttH-like › AttH-like › AttH-like › Tocopherol_cycl 0.51 41.0 3.95e-01 85.5% 95.2%
4310253 9.1.1.14 beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › CpeS 0.50 40.0 3.70e-01 83.2% 95.2%
D3 medium residues 136-198
PDB