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NC_004112.1__NP_680540.1__A2p61__00058

Bact-Vir

NC_004112.1__NP_680540.1__A2p61__00058

Identity

Accession:
NC_004112 ↗
Kingdom:
phage

Quality

66.3 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 68-139
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3gkuA03 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.75 62.0 6.24e-01 97.2% 94.4%
2pt7G02 3.30.1370.180 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.73 61.0 6.26e-01 95.8% 98.5%
2fphX01 3.30.1370.160 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.73 59.0 5.83e-01 94.4% 84.4%
3pieA02 3.30.1370.250 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.71 62.0 5.62e-01 100.0% 76.0%
2dchX01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.68 52.0 4.75e-01 86.1% 62.4%
2b3tA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.67 58.0 4.30e-01 98.6% 44.8%
1ug8A00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.67 58.0 5.49e-01 100.0% 85.1%
3keyA02 3.30.1370.230 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Stn1, C-terminal wHTH domain 0.66 57.0 5.38e-01 97.2% 92.0%
7dswA01 1.20.1530.20 Mainly Alpha › Up-down Bundle › Na+/H+ antiporter like fold › 0.66 54.0 3.39e-01 91.7% 76.3%
1whrA00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.66 52.0 4.38e-01 94.4% 50.8%
7agpA01 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.65 38.0 4.08e-01 75.0% 68.9%
4lrjA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.64 49.0 4.91e-01 86.1% 80.8%
2cdqA03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.64 50.0 4.79e-01 95.8% 73.8%
3c0wA02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.62 54.0 4.76e-01 94.4% 75.7%
3mahA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.62 41.0 4.16e-01 90.3% 70.0%
2qmwA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.61 48.0 4.43e-01 87.5% 66.7%
3g3zA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.60 46.0 4.86e-01 87.5% 95.3%
3r4qA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.59 46.0 3.76e-01 83.3% 68.2%
2kkhA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 37.0 3.69e-01 72.2% 60.0%
3dxqA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.58 42.0 4.05e-01 81.9% 66.3%
3v8hC00 3.30.572.10 Alpha Beta › 2-Layer Sandwich › Thymidylate Synthase; Chain A › Thymidylate synthase/dCMP hydroxymethylase domain 0.58 46.0 3.19e-01 88.9% 71.2%
1jyoA00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.58 40.0 3.28e-01 70.8% 46.2%
3juwA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.58 48.0 3.74e-01 100.0% 40.7%
2r7hB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.58 48.0 3.82e-01 95.8% 84.9%
2joeA01 3.30.1830.10 Alpha Beta › 2-Layer Sandwich › YehR-like fold › YehR-like 0.57 45.0 3.76e-01 86.1% 54.7%
3c1mA02 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.57 49.0 3.82e-01 97.2% 87.8%
1u6mA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 44.0 3.41e-01 97.2% 33.9%
2cpjA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.56 39.0 3.54e-01 76.4% 52.5%
2rt3A00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.56 40.0 3.70e-01 87.5% 56.7%
5f7qC01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 48.0 4.94e-01 100.0% 98.6%
5h20A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 49.0 4.40e-01 100.0% 72.8%
3fmbA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 40.0 3.61e-01 76.4% 82.0%
1kyzA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.55 41.0 3.75e-01 83.3% 67.0%
7ovuA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 48.0 3.59e-01 100.0% 54.9%
1nv8A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 44.0 3.33e-01 91.7% 48.2%
4jzjC02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 43.0 3.89e-01 100.0% 61.5%
3fncB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 46.0 3.63e-01 97.2% 85.1%
2jx2A00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 41.0 3.93e-01 83.3% 69.0%
1whxA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 39.0 3.40e-01 84.7% 48.6%
1xb4B02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 44.0 4.43e-01 93.1% 98.7%
4d9uA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 40.0 3.78e-01 80.6% 71.6%
4r78A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 40.0 3.69e-01 80.6% 62.5%
2yweA03 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.54 41.0 3.93e-01 80.6% 97.6%
7xc2A02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 42.0 3.79e-01 88.9% 69.8%
6abqB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 45.0 4.07e-01 100.0% 69.8%
2k4jA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.52 41.0 3.73e-01 88.9% 65.7%
2af6A01 3.30.70.3180 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 44.0 3.74e-01 100.0% 84.0%
4lq0A02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.52 45.0 3.65e-01 100.0% 54.4%
4v1al00 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.52 44.0 3.70e-01 98.6% 55.6%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5019545 328.5.1.1 a+b two layers › IF3-like › SirA-like › SirA-like › TusA 0.80 65.0 6.42e-01 91.7% 84.0%
4228350 320.1.1.1 a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.79 62.0 6.52e-01 91.7% 95.4%
3236950 320.1.1.0 a+b two layers › R3H domain-like › R3H domain › R3H domain 0.77 62.0 6.32e-01 94.4% 90.0%
4017553 320.1.1.0 a+b two layers › R3H domain-like › R3H domain › R3H domain 0.72 58.0 5.37e-01 94.4% 68.4%
4952469 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.71 58.0 5.37e-01 88.9% 71.1%
4580031 2003.1.5.55 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › PrmA 0.71 54.0 3.96e-01 91.7% 29.2%
4161632 2003.1.5.55 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › PrmA 0.70 54.0 3.99e-01 90.3% 31.3%
4992652 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.70 52.0 5.04e-01 87.5% 71.2%
None 0.70 53.0 3.91e-01 90.3% 30.0%
4620729 2003.1.5.46 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › MTS 0.69 60.0 4.30e-01 97.2% 40.0%
3825121 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.69 56.0 5.46e-01 98.6% 78.8%
3266091 2003.1.5.82 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_31 0.69 60.0 4.19e-01 98.6% 39.1%
3824278 101.1.2.132 alpha arrays › HTH › HTH › winged helix domain › DUF3591 0.68 59.0 5.61e-01 100.0% 80.0%
3781365 320.1.1.0 a+b two layers › R3H domain-like › R3H domain › R3H domain 0.68 53.0 5.30e-01 88.9% 82.7%
3970545 310.3.1.2 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related › T2SSM 0.67 55.0 5.38e-01 90.3% 81.0%
3866072 207.1.1.22 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_6 0.66 49.0 2.71e-01 90.3% 4.8%
4385003 2003.1.5.25 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › GidB 0.66 51.0 3.63e-01 87.5% 26.5%
3351908 320.1.1.7 a+b two layers › R3H domain-like › R3H domain › R3H domain › PUS7L_N 0.66 53.0 5.19e-01 93.1% 92.5%
3595128 320.1.1.0 a+b two layers › R3H domain-like › R3H domain › R3H domain 0.66 49.0 5.13e-01 93.1% 92.3%
4155057 242.1.1.2 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_2 0.65 55.0 4.97e-01 90.3% 74.7%
3221919 246.3.1.0 a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like 0.65 54.0 3.45e-01 95.8% 19.8%
4987106 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.65 52.0 4.74e-01 86.1% 73.7%
4972476 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.65 48.0 4.57e-01 84.7% 67.1%
4651438 2003.1.5.46 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › MTS 0.65 57.0 4.16e-01 98.6% 42.0%
3188029 320.1.1.0 a+b two layers › R3H domain-like › R3H domain › R3H domain 0.65 51.0 5.20e-01 87.5% 98.6%
4044410 186.1.1.1 alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 0.65 53.0 4.55e-01 90.3% 80.9%
3251044 242.1.1.2 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_2 0.64 57.0 4.44e-01 98.6% 53.2%
4658611 242.1.1.2 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_2 0.64 56.0 5.01e-01 95.8% 74.0%
5001828 2003.1.5.81 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.63 52.0 3.87e-01 95.8% 98.0%
3735563 101.1.2.267 alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.63 54.0 4.33e-01 97.2% 94.7%
3467470 2003.1.5.154 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_29, Methyltransf_11 0.63 49.0 3.34e-01 88.9% 25.2%
4771543 327.3.1.0 a+b two layers › Alpha-lytic protease prodomain-like › GMP synthetase C-terminal dimerisation domain › GMP synthetase C-terminal dimerisation domain 0.63 51.0 5.20e-01 93.1% 97.1%
5083386 304.12.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 0.61 42.0 3.87e-01 72.2% 54.7%
2420845 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.61 51.0 4.40e-01 100.0% 85.7%
3003835 3016.1.1.0 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.61 43.0 3.78e-01 75.0% 56.9%
3802175 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.60 42.0 3.88e-01 73.6% 63.2%
3405387 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.60 40.0 4.32e-01 81.9% 90.9%
137913 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.59 37.0 3.42e-01 72.2% 47.4%
5013279 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.59 45.0 4.47e-01 88.9% 80.0%
4852533 3016.1.1.0 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.59 41.0 3.84e-01 75.0% 60.6%
3964731 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.58 44.0 4.00e-01 81.9% 67.0%
3799570 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.58 46.0 3.81e-01 91.7% 83.4%
3279987 213.1.1.28 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_8 0.58 48.0 3.63e-01 97.2% 36.9%
3178012 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.58 43.0 3.84e-01 84.7% 55.2%
3632479 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.57 49.0 3.79e-01 100.0% 42.3%
4682574 3016.1.1.1 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_1_2 0.57 41.0 3.85e-01 76.4% 63.3%
4979991 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.56 48.0 4.31e-01 95.8% 81.0%
4993554 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 47.0 3.83e-01 100.0% 51.4%
4927944 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 42.0 3.83e-01 87.5% 62.0%
3386369 3747.1.1.0 a+b two layers › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain 0.54 48.0 3.92e-01 100.0% 63.0%
303762 304.4.1.5 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Dyp_perox_N 0.53 41.0 3.41e-01 86.1% 65.7%
3487202 209.1.1.0 a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like 0.53 42.0 3.43e-01 93.1% 87.1%
3944955 213.1.1.27 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_7 0.53 44.0 3.65e-01 98.6% 81.4%
3475612 209.1.1.1 a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like › Lectin_C 0.52 42.0 3.36e-01 93.1% 83.7%
3381288 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.51 42.0 3.98e-01 90.3% 95.3%