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js4906-25-2-S21_Prophage_curated_prodigal-single.1__X__X__00213

Bact-Vir

js4906-25-2-S21_Prophage_curated_prodigal-single.1__X__X__00213

Identity

Kingdom:
phage

Quality

86.2 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 11-145
PDB
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hxlA02 2.60.40.4290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.63 32.0 3.79e-01 99.3% 71.1%
2ffgA00 3.30.720.20 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Protein of unknown function DUF1797 0.61 34.0 4.35e-01 99.3% 92.5%
1cbyA00 3.40.198.10 Alpha Beta › 3-Layer(aba) Sandwich › Delta-endotoxin CytB › Delta-endotoxin CytB-like 0.59 41.0 3.42e-01 70.4% 83.7%
4l9cA00 3.40.1000.30 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › 0.57 51.0 4.91e-01 96.3% 90.0%
3bk5A00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.56 43.0 3.61e-01 80.7% 90.2%
4mxtA00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.55 43.0 3.83e-01 80.7% 86.6%
3o2uA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.55 39.0 3.69e-01 71.9% 66.7%
6j8yC00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.54 39.0 3.16e-01 74.1% 42.7%
1e3uD00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 45.0 3.71e-01 90.4% 77.3%
7xr9E01 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.53 39.0 3.46e-01 77.0% 53.8%
3sc7X01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.53 47.0 3.58e-01 100.0% 70.8%
3buuB00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.52 42.0 3.64e-01 87.4% 91.8%
4r8oA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.52 36.0 4.12e-01 89.6% 98.0%
4gn2A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.52 42.0 3.53e-01 88.1% 82.5%
4r03A00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.52 37.0 4.05e-01 92.6% 91.7%
3p02A02 2.40.128.440 Mainly Beta › Beta Barrel › Lipocalin › Uncharacterised protein PF14274, DUF4361 0.50 35.0 3.33e-01 71.1% 85.7%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5024241 330.2.1.5 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.67 46.0 5.33e-01 100.0% 100.0%
5029238 330.2.1.0 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.65 45.0 5.13e-01 99.3% 96.0%
5080980 330.2.1.1 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › Ribosomal_S30AE 0.65 44.0 4.77e-01 82.2% 83.6%
4937410 330.2.1.0 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.65 44.0 5.08e-01 97.8% 97.9%
4943626 330.2.1.0 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.65 45.0 4.77e-01 98.5% 80.8%
4982298 330.2.1.1 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › Ribosomal_S30AE 0.64 44.0 4.85e-01 100.0% 87.2%
3515197 4051.1.1.2 a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F-actin_cap_A 0.62 51.0 4.70e-01 86.7% 78.2%
5056130 330.2.1.0 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.62 43.0 4.91e-01 97.0% 100.0%
3684661 4099.1.1.1 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › MAD 0.60 37.0 3.67e-01 88.1% 57.9%
5016199 330.2.1.0 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.57 47.0 4.73e-01 98.5% 86.7%
3719143 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.57 41.0 4.15e-01 74.1% 85.2%
4024473 243.3.1.20 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › AKAP28 0.57 43.0 4.58e-01 88.1% 88.3%
3204821 314.1.1.3 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2d 0.55 47.0 3.48e-01 90.4% 48.1%
3309970 5.1.3.118 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.54 43.0 3.28e-01 87.4% 55.0%
3203106 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.53 43.0 3.55e-01 88.9% 87.1%
3915628 5.1.4.12 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Sema 0.53 47.0 3.30e-01 100.0% 86.2%
166794 71.1.1.8 beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolA_like 0.53 43.0 3.64e-01 87.4% 90.2%
3591072 4321.1.1.1 a+b two layers › Peptidoglycan deacetylase N-terminal noncatalytic region › Peptidoglycan deacetylase N-terminal noncatalytic region › Peptidoglycan deacetylase N-terminal noncatalytic region › DUF3298 0.52 42.0 3.63e-01 86.7% 85.8%
4012015 2011.1.1.0 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases 0.52 44.0 3.36e-01 92.6% 86.5%
4980680 225.1.1.0 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.52 44.0 3.98e-01 91.1% 85.6%
3736781 7579.1.1.36 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_3 0.52 44.0 3.32e-01 94.8% 81.7%
4014340 314.1.1.0 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.52 44.0 3.26e-01 90.4% 41.5%
4031724 225.1.1.0 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.51 39.0 4.09e-01 79.3% 94.2%
3977348 225.1.1.3 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.51 41.0 4.09e-01 86.7% 96.4%
None 0.51 43.0 3.35e-01 94.8% 85.0%
4381659 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.50 44.0 3.36e-01 97.8% 84.2%
4968257 225.1.1.0 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.50 38.0 3.79e-01 79.3% 96.4%
3227990 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.50 43.0 2.91e-01 92.6% 33.4%
3608130 225.1.1.0 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.50 40.0 4.07e-01 84.4% 83.7%
D2 high residues 151-243
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3jtzA00 3.30.160.390 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Integrase, DNA-binding domain 0.66 43.0 4.65e-01 95.7% 80.5%
1flgA00 2.140.10.10 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Quinoprotein alcohol dehydrogenase-like superfamily 0.63 50.0 3.08e-01 87.1% 25.4%
2m3xC02 2.40.10.360 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.62 40.0 4.62e-01 87.1% 88.4%
2ogqA01 3.30.1120.30 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › POLO box domain 0.62 47.0 4.18e-01 84.9% 57.9%
1ospO02 3.90.930.1 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.62 47.0 4.07e-01 84.9% 52.1%
4fr9A00 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 52.0 4.50e-01 91.4% 81.6%
5cxbA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.59 42.0 2.83e-01 74.2% 36.0%
4fnvA02 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.59 51.0 3.60e-01 94.6% 83.3%
7dd9A02 2.70.98.30 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Golgi alpha-mannosidase II; domain 4 0.59 51.0 3.67e-01 94.6% 92.2%
1bagA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.58 40.0 4.33e-01 92.5% 87.2%
4n9jA02 3.30.1120.130 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.56 41.0 3.99e-01 86.0% 67.3%
1iv8A05 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.56 35.0 3.96e-01 92.5% 87.9%
2ymsC00 2.40.10.480 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.55 38.0 4.18e-01 87.1% 86.7%
1mufA01 2.20.110.10 Mainly Beta › Single Sheet › Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain › Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain 0.55 45.0 4.19e-01 87.1% 74.3%
3dsoA00 2.40.10.300 Mainly Beta › Beta Barrel › Thrombin, subunit H › Copper resistance protein K 0.55 33.0 3.85e-01 77.4% 84.8%
2w18A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 40.0 2.73e-01 83.9% 23.2%
2ymsB00 2.40.10.480 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.54 37.0 4.17e-01 87.1% 90.5%
2pn2A00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.52 35.0 3.10e-01 76.3% 46.0%
2ymsA00 2.40.128.630 Mainly Beta › Beta Barrel › Lipocalin › 0.52 38.0 3.47e-01 83.9% 58.1%
2in5A00 2.40.360.10 Mainly Beta › Beta Barrel › YmcC-like fold › YmcC-like 0.52 41.0 3.32e-01 88.2% 92.8%
2xu7A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 39.0 2.67e-01 80.6% 43.3%
1xipA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 43.0 2.94e-01 94.6% 54.8%
4gq1A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 41.0 2.85e-01 88.2% 64.6%
4g7nA01 3.30.1120.120 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.51 40.0 3.71e-01 84.9% 75.2%
4hdjA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 41.0 2.85e-01 90.3% 46.2%
3al9A01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 41.0 2.66e-01 90.3% 42.4%
6vp6A03 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.50 39.0 2.77e-01 86.0% 31.3%
3v9fA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.50 37.0 2.57e-01 87.1% 23.7%
3aihB01 2.70.130.10 Mainly Beta › Distorted Sandwich › Cation-dependent Mannose-6-phosphate Receptor; Chain A › Mannose-6-phosphate receptor binding domain 0.50 39.0 3.81e-01 87.1% 92.5%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3647663 5.1.10.8 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed › ANAPC4_WD40 0.67 37.0 4.62e-01 84.9% 86.7%
4890644 12.3.1.53 beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › DUF608, Glyco_hydr_116N 0.64 46.0 3.01e-01 75.3% 93.0%
1141859 5.1.10.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed › DUF6849 0.62 40.0 4.52e-01 87.1% 84.7%
3259296 71.1.1.0 beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.61 47.0 3.99e-01 80.6% 80.7%
3776456 5.1.10.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed 0.60 37.0 3.96e-01 81.7% 70.2%
3930913 5.1.4.39 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › ANAPC4_WD40 0.58 48.0 3.21e-01 87.1% 26.9%
3660003 5.1.10.8 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed › ANAPC4_WD40 0.56 39.0 4.24e-01 86.0% 85.0%
3584922 5.1.4.39 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › ANAPC4_WD40 0.55 45.0 3.23e-01 86.0% 33.6%
3590274 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.55 33.0 3.34e-01 84.9% 58.9%
3716389 77.3.1.0 beta meanders › open-sided beta-meander › CPAP G-box domain › CPAP G-box domain 0.55 48.0 3.22e-01 94.6% 91.0%
4104948 5.1.3.39 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › TrAA12 0.54 40.0 2.69e-01 92.5% 20.6%
3605675 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.54 47.0 3.08e-01 100.0% 29.7%
3994442 5.1.2.34 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › PQQ_2 0.54 41.0 3.50e-01 100.0% 50.7%
3772396 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.53 43.0 2.85e-01 97.8% 21.9%
3787812 5.1.5.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.53 44.0 2.95e-01 94.6% 34.7%
3492330 5.1.4.116 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › IKI3 0.53 42.0 2.79e-01 86.0% 32.0%
4027850 5.1.4.6 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40,ANAPC4_WD40 0.52 43.0 2.85e-01 92.5% 25.0%
3840061 4991.1.1.0 extended segments › Lag-3 N-terminal region › Lag-3 N-terminal region › Lag-3 N-terminal region 0.52 41.0 2.86e-01 91.4% 29.5%
3917795 5.1.4.173 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_WDR75_2nd 0.52 39.0 2.59e-01 86.0% 20.8%
3504014 5.1.5.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40 0.51 42.0 2.99e-01 92.5% 45.9%
3947013 9.1.1.0 beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.51 38.0 3.87e-01 90.3% 81.1%
3734800 5.1.4.39 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › ANAPC4_WD40 0.51 42.0 2.79e-01 94.6% 52.7%
3574360 5.1.3.25 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Mcl1_mid 0.51 44.0 3.10e-01 95.7% 70.2%
3593185 5.1.5.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.51 41.0 2.90e-01 90.3% 46.2%
3576925 5.1.4.40 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PQQ_2 0.51 42.0 2.88e-01 91.4% 29.8%
3168539 109.4.1.69 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › IKI3 0.51 41.0 2.86e-01 87.1% 42.0%
3557192 5.1.4.48 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › BBS1 0.51 37.0 2.43e-01 83.9% 19.5%
3444546 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.50 42.0 3.06e-01 95.7% 63.1%
3692403 5.1.4.378 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PF27702 0.50 41.0 2.69e-01 92.5% 82.4%
3232146 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.50 41.0 2.91e-01 92.5% 58.1%
4965574 247.1.1.12 a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B_3 0.50 41.0 3.15e-01 92.5% 63.4%