Back to structures

NC_062746.1__YP_010356729.1__M1M24_gp40__00040

Bact-Vir

NC_062746.1__YP_010356729.1__M1M24_gp40__00040

Identity

Accession:
NC_062746 ↗
Kingdom:
phage

Quality

94.4 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 3-41
PDB
Domain cluster: representative
CATH (46)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mgpA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.74 62.0 4.46e-01 100.0% 43.8%
3noyB02 3.30.413.10 Alpha Beta › 2-Layer Sandwich › Sulfite Reductase Hemoprotein; domain 1 › Sulfite Reductase Hemoprotein, domain 1 0.71 59.0 4.47e-01 97.4% 38.9%
4o2zA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.69 50.0 3.41e-01 100.0% 20.9%
7mi4A02 3.100.10.20 Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › CRISPR-associated endonuclease Cas1, N-terminal domain 0.68 48.0 3.95e-01 76.9% 43.2%
3fogA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.68 53.0 4.18e-01 100.0% 73.5%
1e2tA02 3.30.1120.150 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.67 46.0 3.64e-01 71.8% 43.0%
4emtA02 3.40.50.12100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Stimulator of interferon genes protein 0.67 57.0 3.98e-01 100.0% 84.3%
8d3lA01 3.100.10.20 Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › CRISPR-associated endonuclease Cas1, N-terminal domain 0.67 47.0 3.67e-01 76.9% 36.4%
2p1jA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.66 47.0 3.32e-01 79.5% 57.2%
3d6wB02 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.64 46.0 4.68e-01 79.5% 87.2%
3df7A02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.64 44.0 3.00e-01 71.8% 34.3%
1iv0A00 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.64 52.0 4.04e-01 97.4% 49.0%
1jcfA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.63 49.0 3.99e-01 97.4% 48.3%
7kfuC01 3.100.10.20 Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › CRISPR-associated endonuclease Cas1, N-terminal domain 0.63 44.0 3.67e-01 76.9% 42.7%
3bexA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.63 50.0 3.75e-01 94.9% 77.7%
1h10A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 53.0 3.82e-01 100.0% 37.6%
2wm1A00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.62 51.0 3.03e-01 100.0% 45.2%
3pesA00 3.30.300.260 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.61 44.0 3.57e-01 82.1% 66.3%
5mu3B00 3.40.50.12050 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.61 49.0 3.37e-01 100.0% 70.6%
1lucA00 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.61 51.0 3.06e-01 100.0% 96.0%
3orqA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.60 46.0 3.05e-01 97.4% 85.8%
1hztA00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.60 45.0 3.17e-01 84.6% 65.4%
1lucB00 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.59 46.0 2.77e-01 89.7% 96.9%
3cxbB00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.59 51.0 3.78e-01 100.0% 40.8%
1o9yC00 2.30.330.10 Mainly Beta › Roll › Surface presentation of antigens (SPOA) › SpoA-like 0.59 45.0 3.85e-01 92.3% 86.1%
4mybA00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.58 49.0 3.13e-01 100.0% 36.4%
4epkB00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.58 46.0 2.75e-01 100.0% 45.8%
5ddtA00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.57 50.0 3.15e-01 100.0% 53.4%
5j3tA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 45.0 3.23e-01 100.0% 28.6%
3fehA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 48.0 3.46e-01 100.0% 37.1%
3uh0A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.57 45.0 3.37e-01 100.0% 35.5%
4jqtA01 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.56 42.0 2.72e-01 79.5% 17.4%
3rklA00 6.10.140.1640 Special › Helix non-globular › Helix Hairpins › 0.55 42.0 3.27e-01 82.1% 77.5%
2felA00 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.55 47.0 2.76e-01 100.0% 59.9%
2pfmA02 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.55 45.0 2.83e-01 100.0% 83.6%
4khbD02 2.30.29.220 Mainly Beta › Roll › PH-domain like › Structure-specific recognition protein (SSRP1) 0.55 40.0 3.36e-01 84.6% 76.5%
1dhkB00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.55 45.0 2.97e-01 97.4% 35.4%
3abzA01 3.20.20.300 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycoside hydrolase, family 3, N-terminal domain 0.55 46.0 2.72e-01 100.0% 78.1%
4e1pA00 3.30.60.230 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › Lsr2, dimerisation domain 0.54 40.0 3.64e-01 82.1% 78.2%
4n06A01 3.100.10.20 Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › CRISPR-associated endonuclease Cas1, N-terminal domain 0.53 38.0 3.13e-01 79.5% 37.8%
2hqvA00 3.40.1570.10 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › HemS/ChuS/ChuX like domains 0.53 44.0 2.94e-01 97.4% 35.5%
4zyaB00 3.30.1910.20 Alpha Beta › 2-Layer Sandwich › so0334 like fold › asparaginyl-tRNA synthetase, N-terminal domain 0.52 43.0 3.57e-01 97.4% 96.1%
1y0mA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.52 35.0 3.18e-01 71.8% 47.5%
2mkyA00 3.30.70.1530 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Hypothetical protein rpa1041 0.51 40.0 3.66e-01 94.9% 96.6%
3v4rA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 39.0 2.47e-01 94.9% 52.0%
2kcwA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.50 39.0 2.85e-01 100.0% 56.5%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4073461 2484.1.1.12 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Acetate_kinase 0.76 62.0 4.06e-01 100.0% 22.1%
3222053 2484.1.1.200 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FTH 0.76 60.0 3.68e-01 87.2% 16.4%
3958912 296.1.1.0 a+b three layers › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 0.74 63.0 4.64e-01 94.9% 37.0%
4058896 296.1.1.3 a+b three layers › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › PF26540 0.73 63.0 4.61e-01 97.4% 38.1%
4443103 296.1.1.3 a+b three layers › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › PF26540 0.73 60.0 4.37e-01 97.4% 33.6%
4612008 2485.1.1.6 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › FHIPEP 0.72 58.0 4.44e-01 100.0% 84.8%
4251998 296.1.1.3 a+b three layers › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › PF26540 0.71 57.0 4.50e-01 100.0% 41.1%
4086202 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.70 48.0 4.07e-01 100.0% 44.6%
4989457 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.68 56.0 5.32e-01 100.0% 82.0%
4369577 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.68 47.0 4.11e-01 100.0% 48.3%
3742310 5.1.4.38 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › ANAPC1 0.67 57.0 3.40e-01 100.0% 20.3%
5038438 3407.1.1.0 mixed a+b and a/b › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.67 51.0 3.74e-01 87.2% 47.0%
3542422 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.67 49.0 4.89e-01 94.9% 87.5%
4583884 296.1.1.3 a+b three layers › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › PF26540 0.67 57.0 4.04e-01 97.4% 35.2%
4973040 3407.1.1.0 mixed a+b and a/b › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.67 48.0 3.73e-01 100.0% 35.3%
4108971 296.1.1.3 a+b three layers › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › PF26540 0.67 57.0 4.14e-01 97.4% 38.3%
4974887 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.66 50.0 3.53e-01 87.2% 31.1%
4983508 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.66 52.0 4.51e-01 97.4% 98.6%
3671443 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 50.0 4.29e-01 87.2% 66.2%
4029844 220.1.1.10 beta barrels › PH domain-like › PH domain-like › PH domain-like › SSrecog 0.65 48.0 3.81e-01 84.6% 71.8%
4584323 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.64 46.0 4.00e-01 100.0% 50.0%
3945385 219.1.1.6 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Acetyltransf_2 0.64 44.0 2.93e-01 71.8% 20.6%
5058744 3407.1.1.2 mixed a+b and a/b › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Nop5_56-rel_N_Arc 0.64 47.0 3.64e-01 89.7% 52.4%
4215069 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.63 54.0 4.22e-01 100.0% 86.7%
4028480 2485.1.1.1 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.63 50.0 3.74e-01 94.9% 78.2%
4968411 3407.1.1.0 mixed a+b and a/b › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.63 46.0 3.48e-01 87.2% 47.0%
5008130 213.1.1.35 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_CG 0.62 45.0 3.46e-01 79.5% 55.8%
5023957 101.1.2.280 alpha arrays › HTH › HTH › winged helix domain › HTH_12 0.62 48.0 3.76e-01 100.0% 41.2%
5051102 2004.1.1.5 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.61 49.0 3.45e-01 94.9% 37.9%
3515993 220.1.1.13 beta barrels › PH domain-like › PH domain-like › PH domain-like › DCP1 0.61 43.0 3.09e-01 76.9% 30.0%
4649506 3239.1.1.1 alpha complex topology › Cas1 › Cas1 › Cas1 › Cas_Cas1 0.60 51.0 2.98e-01 97.4% 86.0%
3940847 220.1.1.22 beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.60 41.0 3.16e-01 76.9% 33.6%
4335502 2.8.1.2 beta barrels › OB-fold › mu transposases-C › mu transposases-C › Mu-transpos_C_2 0.60 50.0 3.91e-01 100.0% 42.2%
3414272 220.1.1.22 beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.60 49.0 3.70e-01 100.0% 37.9%
3995338 10.1.1.17 beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.60 47.0 3.29e-01 97.4% 39.4%
3388895 220.1.1.170 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_alsin 0.60 48.0 3.55e-01 100.0% 32.7%
4294910 4263.2.1.1 a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain › FtsH_ext 0.59 42.0 3.80e-01 76.9% 61.8%
4484289 633.23.1.9 alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 0.58 42.0 2.74e-01 79.5% 16.8%
2897753 220.1.1.10 beta barrels › PH domain-like › PH domain-like › PH domain-like › SSrecog 0.58 43.0 3.62e-01 84.6% 83.1%
4580548 109.4.1.211 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_19,TPR_20 0.58 43.0 2.76e-01 84.6% 17.7%
5074749 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.57 40.0 3.43e-01 79.5% 42.9%
5016928 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.57 47.0 3.01e-01 100.0% 68.2%
4107115 304.111.1.1 a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like › AIRS_C 0.56 46.0 2.92e-01 100.0% 91.5%
2516891 2002.1.1.134 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_2 0.56 44.0 2.64e-01 100.0% 45.8%
2507513 210.1.2.1 a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain › Penicil_amidase 0.56 45.0 2.92e-01 100.0% 48.8%
3375924 2004.1.1.308 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_21 0.55 43.0 2.91e-01 94.9% 29.5%
4028871 2.1.1.10 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.54 40.0 3.51e-01 92.3% 64.4%
3276072 220.1.1.7 beta barrels › PH domain-like › PH domain-like › PH domain-like › IRS 0.54 45.0 3.25e-01 92.3% 80.0%
3528398 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 45.0 2.86e-01 100.0% 22.6%
3214083 10.1.1.0 beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.52 42.0 2.94e-01 100.0% 32.9%
4990709 7516.1.1.1 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › NTP_transferase 0.51 43.0 2.75e-01 100.0% 86.6%