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NC_060137.1__YP_010246662.1__L3Y25_gp003__00003

Bact-Vir

NC_060137.1__YP_010246662.1__L3Y25_gp003__00003

Identity

Accession:
NC_060137 ↗
Kingdom:
phage

Quality

81.0 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 6-92
PDB
Domain cluster: representative
CATH (53)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2d73A01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.73 60.0 4.12e-01 88.5% 94.0%
4jocA00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.72 49.0 3.19e-01 70.1% 94.9%
2o5nA02 3.30.500.30 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › 0.70 48.0 3.89e-01 71.3% 71.3%
3l9rA01 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 0.70 50.0 3.94e-01 74.7% 74.3%
3holA02 2.40.160.90 Mainly Beta › Beta Barrel › Porin › 0.68 47.0 3.76e-01 71.3% 59.6%
3loyA01 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.67 48.0 4.59e-01 74.7% 80.2%
2ciuA00 3.10.450.320 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Mitochondrial import inner membrane translocase subunit Tim21 0.67 54.0 4.81e-01 87.4% 91.1%
3doaA01 2.30.310.10 Mainly Beta › Roll › ibrinogen binding protein from staphylococcus aureus fold › ibrinogen binding protein from staphylococcus aureus domain 0.67 49.0 4.09e-01 94.3% 44.4%
5ay6A01 2.60.98.20 Mainly Beta › Sandwich › Tick-borne Encephalitis virus Glycoprotein; domain 1 › Flagellar hook protein FlgE 0.65 53.0 4.28e-01 88.5% 67.3%
4q8gA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.65 46.0 3.02e-01 72.4% 80.8%
4g59C02 3.30.500.30 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › 0.65 47.0 3.81e-01 74.7% 72.8%
1v2bB00 3.40.1000.10 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich 0.65 51.0 4.21e-01 82.8% 53.0%
3esiA00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.65 47.0 4.18e-01 75.9% 94.4%
4u13A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.64 43.0 4.05e-01 70.1% 92.7%
1tp6A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.64 45.0 3.99e-01 73.6% 96.0%
3kg7B00 3.10.129.110 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Polyketide synthase dehydratase 0.64 43.0 3.03e-01 70.1% 75.8%
7x7zA01 2.40.480.10 Mainly Beta › Beta Barrel › AOC barrel-like › Allene oxide cyclase-like 0.64 55.0 4.70e-01 95.4% 95.0%
3nqzA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.63 46.0 4.69e-01 75.9% 89.3%
2ebkA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.63 56.0 4.96e-01 100.0% 78.9%
2lexA00 2.20.25.80 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › WRKY domain 0.63 44.0 5.06e-01 96.6% 100.0%
4j8tA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.63 45.0 3.99e-01 75.9% 94.5%
3f40A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.63 45.0 4.18e-01 75.9% 89.2%
3gd6A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.62 42.0 3.63e-01 70.1% 83.8%
3fssA01 2.30.29.120 Mainly Beta › Roll › PH-domain like › 0.61 44.0 3.77e-01 74.7% 60.3%
2nlkA02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.61 51.0 3.60e-01 89.7% 46.5%
3ec9A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 43.0 3.83e-01 74.7% 72.9%
1ygaA00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.60 53.0 3.56e-01 98.9% 88.4%
2bngC00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.60 43.0 3.69e-01 75.9% 82.1%
1uzxA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.59 50.0 4.40e-01 100.0% 75.0%
8fkmA01 3.30.1460.50 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.58 51.0 4.21e-01 100.0% 95.7%
2qguA01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.57 43.0 4.15e-01 82.8% 95.0%
4eg9A00 2.50.20.40 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › 0.56 45.0 3.37e-01 88.5% 95.2%
7t4dA01 2.70.240.10 Mainly Beta › Distorted Sandwich › Leukocidin-like › Leukocidin/porin MspA 0.56 43.0 3.01e-01 81.6% 71.3%
3fljA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.56 46.0 3.94e-01 89.7% 93.6%
7zghA01 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.56 41.0 2.73e-01 79.3% 97.8%
1gesA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.56 40.0 3.75e-01 77.0% 77.0%
2l2mA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 42.0 4.59e-01 95.4% 100.0%
6nvxB02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.55 35.0 3.67e-01 93.1% 71.4%
3eliA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.55 47.0 4.08e-01 100.0% 77.8%
4bs9A05 3.30.160.660 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 42.0 3.89e-01 100.0% 64.0%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.54 42.0 3.73e-01 83.9% 69.6%
2b02A01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 37.0 3.55e-01 72.4% 94.2%
6kjuB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 38.0 3.52e-01 75.9% 86.3%
1t3qB04 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.54 43.0 3.48e-01 93.1% 60.8%
1e69A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 42.0 3.01e-01 85.1% 42.2%
4n6tA00 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 37.0 3.83e-01 72.4% 89.9%
1aqbA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 41.0 3.33e-01 90.8% 43.4%
1pn2B01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.52 39.0 3.30e-01 80.5% 70.9%
3hrdB01 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.52 39.0 3.26e-01 82.8% 61.0%
2gj3A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.51 36.0 3.33e-01 74.7% 82.4%
6hmjA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.51 37.0 3.50e-01 77.0% 96.2%
6canA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 41.0 2.88e-01 89.7% 84.8%
3dgtA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 43.0 3.12e-01 98.9% 76.6%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3783000 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.78 56.0 5.48e-01 74.7% 80.0%
3276558 12.3.1.0 beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich 0.71 59.0 3.99e-01 88.5% 95.7%
4195996 222.1.1.0 a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.71 49.0 4.05e-01 71.3% 83.3%
4545039 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.71 50.0 5.52e-01 73.6% 100.0%
1678533 243.3.1.10 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › YPEB_PepSY1-2 0.69 50.0 5.54e-01 74.7% 95.7%
4642457 12.3.1.50 beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › PF28395 0.69 56.0 3.79e-01 88.5% 80.3%
3577955 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.69 55.0 3.83e-01 85.1% 96.7%
3596331 243.1.1.2 a+b two layers › Cystatin-like › NTF2-like › NTF2-like › NTF2 0.68 48.0 4.28e-01 74.7% 87.5%
3272662 12.3.1.0 beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich 0.68 56.0 3.84e-01 89.7% 98.0%
3744012 5.1.4.16 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CPSF_A 0.67 47.0 3.09e-01 72.4% 30.6%
1169934 71.1.1.5 beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › DUF576 0.67 46.0 4.21e-01 71.3% 59.3%
4937710 243.1.1.18 a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.67 46.0 4.20e-01 71.3% 96.5%
3829563 897.1.1.0 a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 0.67 59.0 4.78e-01 97.7% 61.8%
4011390 243.1.1.0 a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.67 47.0 4.00e-01 73.6% 88.3%
1162187 233.1.1.8 a+b two layers › MHC antigen-recognition domain › MHC antigen-recognition domain › MHC antigen-recognition domain › M157_N_1 0.66 47.0 3.69e-01 74.7% 66.1%
3742459 243.1.1.12 a+b two layers › Cystatin-like › NTF2-like › NTF2-like › TIM21 0.65 56.0 5.40e-01 93.1% 97.0%
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 0.65 58.0 4.68e-01 100.0% 70.6%
3169357 331.4.1.0 a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.65 57.0 5.21e-01 97.7% 74.5%
5053256 331.9.1.0 a+b two layers › TBP-like › Subdomain of clathrin and coatomer appendage domain › Subdomain of clathrin and coatomer appendage domain 0.65 52.0 4.59e-01 100.0% 60.0%
3820010 881.1.1.1 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PsbP 0.64 52.0 4.25e-01 87.4% 64.4%
3484227 4051.1.1.0 a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz 0.64 56.0 4.53e-01 98.9% 70.0%
4505397 5087.1.1.0 beta meanders › Lipovitellin-phosvitin complex › Lipovitellin LV-2 › Lipovitellin LV-2 0.64 54.0 3.96e-01 94.3% 48.3%
3489236 243.1.1.12 a+b two layers › Cystatin-like › NTF2-like › NTF2-like › TIM21 0.63 53.0 5.00e-01 92.0% 94.3%
4991694 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.62 47.0 3.21e-01 80.5% 39.9%
3248437 267.1.1.3 a+b complex topology › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Cation_ATPase 0.62 52.0 3.87e-01 90.8% 74.8%
3234838 243.1.1.28 a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF4440 0.62 43.0 3.92e-01 73.6% 95.8%
3989856 11.1.5.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.61 47.0 3.96e-01 80.5% 77.9%
3735671 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.61 51.0 4.92e-01 100.0% 79.0%
3699994 243.1.1.0 a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.61 55.0 4.72e-01 98.9% 92.6%
1678532 243.3.1.3 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › PepSY 0.60 41.0 4.55e-01 74.7% 87.1%
3782746 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.60 51.0 4.76e-01 93.1% 96.4%
3865129 5.1.4.394 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_FAM234A_B 0.60 47.0 2.93e-01 83.9% 24.0%
4858377 9.13.1.5 beta barrels › Lipocalins/Streptavidin › AOC barrel-like › AOC barrel-like › AOC_like 0.60 49.0 4.79e-01 90.8% 90.4%
3243473 5087.1.1.0 beta meanders › Lipovitellin-phosvitin complex › Lipovitellin LV-2 › Lipovitellin LV-2 0.59 47.0 3.41e-01 86.2% 60.8%
3517117 2484.1.1.48 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MutS_II 0.59 46.0 3.53e-01 82.8% 84.7%
3663874 2484.1.1.157 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF4371 0.59 41.0 2.62e-01 72.4% 61.1%
3801624 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.58 48.0 4.58e-01 98.9% 77.0%
3789856 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.58 45.0 4.16e-01 100.0% 64.3%
3375268 5084.5.1.3 beta barrels › Outer membrane meander beta-barrels › Porins › Porin › Porin_3 0.58 47.0 3.47e-01 87.4% 36.4%
5044807 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.58 41.0 4.33e-01 74.7% 92.5%
5033737 71.1.1.0 beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.57 46.0 3.64e-01 88.5% 41.0%
5035440 244.2.1.1 a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › Pyr_redox_dim 0.56 43.0 3.77e-01 82.8% 61.5%
4931757 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.56 41.0 3.72e-01 77.0% 77.5%
5055705 3110.1.1.3 a/b three-layered sandwiches › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › AglB_core-like 0.56 44.0 3.05e-01 86.2% 57.4%
3825504 330.1.1.5 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DND1_DSRM 0.56 46.0 4.62e-01 100.0% 88.9%
3243587 2484.1.1.200 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FTH 0.55 40.0 2.77e-01 86.2% 21.3%
3259407 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.55 45.0 4.60e-01 100.0% 91.8%
3704403 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.55 49.0 4.84e-01 100.0% 98.9%
3992540 79.1.1.24 beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Mlf1IP 0.55 42.0 4.16e-01 82.8% 96.8%
3723348 10.1.1.73 beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › PF26113 0.55 47.0 3.31e-01 93.1% 96.3%
3246034 216.1.1.2 a+b two layers › UBC-like › UBC-like › UBC-like › Autophagy_act_C 0.55 46.0 3.79e-01 89.7% 54.0%
4508852 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.54 49.0 4.45e-01 100.0% 85.2%
5016199 330.2.1.0 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.53 47.0 4.11e-01 100.0% 74.1%
4115838 814.1.1.1 a+b two layers › Chorismate lyase › Chorismate lyase › Chorismate lyase › Rv2949c-like 0.53 46.0 3.75e-01 97.7% 82.4%
3739446 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.52 44.0 4.36e-01 100.0% 86.3%
5047296 223.1.1.25 a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.52 37.0 3.47e-01 77.0% 86.1%
4015435 2.1.1.44 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Dna2 0.52 41.0 4.02e-01 86.2% 84.2%
5026243 2484.1.1.59 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.51 41.0 2.92e-01 89.7% 52.5%
4442643 330.1.1.25 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › PF26980 0.51 45.0 4.53e-01 97.7% 94.4%
3663088 2484.1.1.157 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF4371 0.50 41.0 3.19e-01 96.6% 41.7%