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putative_DNA-binding_protein

Euk-Vir

Emiliania_huxleyi_virus_86

putative_DNA-binding_protein__YP_293937__Emiliania_huxleyi_virus_86__181082

Identity

Accession:
YP_293937 ↗
Protein ID:
putative_DNA-binding_protein
Kingdom:
euk

Quality

82.0 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 41-147_412-433
PDB
Domain cluster: rep: OP056089.1__UYD72102.1__X__00002__D5-102
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM01 3.90.75.20 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › 0.78 60.0 6.59e-01 82.9% 96.2%
1a73A00 3.90.75.10 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A 0.58 45.0 4.17e-01 80.6% 88.3%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3586841 378.1.1.7 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › NUMOD4,HNH_3 0.77 62.0 6.56e-01 82.9% 99.1%
3965202 378.1.1.19 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH_3 0.70 55.0 5.97e-01 82.2% 100.0%
4945288 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 19.0 3.05e-01 73.6% 86.0%
4941425 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.52 25.0 3.04e-01 80.6% 70.0%
D2 high residues 151-207
PDB
Domain cluster: rep: OL505084.1__UIE13765.1__X__00060__D15-63
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM02 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 0.89 81.0 7.57e-01 100.0% 82.4%
4yrdA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.61 42.0 3.30e-01 100.0% 34.5%
2oyzA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.59 37.0 3.18e-01 93.0% 38.3%
3kyfA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 42.0 3.43e-01 78.9% 82.5%
2hn1A01 3.30.460.20 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › CorA soluble domain-like 0.57 46.0 3.54e-01 91.2% 88.7%
3lqmA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 42.0 3.45e-01 100.0% 45.1%
7zxkB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 41.0 3.50e-01 100.0% 48.4%
1bquA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 42.0 3.40e-01 94.7% 42.6%
7eebI01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.54 41.0 2.92e-01 80.7% 32.0%
4e6xB00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 40.0 2.60e-01 84.2% 81.7%
1y6kR01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 42.0 3.45e-01 94.7% 47.1%
3ffyA00 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.53 39.0 3.20e-01 94.7% 40.2%
2e3vA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 40.0 3.33e-01 94.7% 45.6%
1tc5C00 3.50.80.10 Alpha Beta › 3-Layer(bba) Sandwich › D-tyrosyl-trna(Tyr) Deacylase; Chain: A; › D-tyrosyl-tRNA(Tyr) deacylase 0.53 38.0 2.78e-01 80.7% 83.3%
1oeyA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 40.0 3.70e-01 89.5% 98.8%
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.52 42.0 3.64e-01 93.0% 64.1%
3puaA01 2.60.120.650 Mainly Beta › Sandwich › Jelly Rolls › Cupin 0.51 41.0 2.69e-01 93.0% 33.2%
1x5fA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 39.0 3.11e-01 86.0% 53.3%
2o6cA00 2.60.40.2480 Mainly Beta › Sandwich › Immunoglobulin-like › Periplasmic metal-binding protein Tp34-type 0.50 40.0 3.00e-01 91.2% 55.7%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2876 101.1.14.2 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › I-HmuI_NUMOD-like 0.89 81.0 7.53e-01 100.0% 81.2%
4384880 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.81 72.0 6.31e-01 100.0% 68.2%
4414927 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.76 67.0 6.34e-01 100.0% 87.0%
3587703 101.1.14.0 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases 0.75 57.0 5.95e-01 86.0% 94.0%
3192481 12.6.1.3 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycoside hydrolase family 127 middle domain-related › Glycoside hydrolase family 127 middle domain-related › Bac_rhamnosid_C 0.66 41.0 3.41e-01 94.7% 35.0%
3518173 206.1.3.57 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › FAM91_C 0.63 43.0 2.81e-01 93.0% 16.4%
5066729 632.3.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain 0.63 44.0 3.77e-01 93.0% 46.7%
4011188 11.1.4.92 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › VPS13_VAB 0.59 41.0 3.33e-01 93.0% 41.0%
4527994 12.1.1.52 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › GLGE_C 0.59 40.0 3.34e-01 94.7% 41.0%
3891509 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.57 40.0 3.41e-01 94.7% 44.2%
3400352 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.57 42.0 4.34e-01 98.2% 85.2%
3518250 822.2.1.0 ↗ a+b two layers › GYF/BRK domain-like › BRK domain-like › BRK domain-like 0.55 35.0 3.89e-01 93.0% 92.5%
3405188 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.53 40.0 3.36e-01 96.5% 47.0%
77927 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.52 42.0 3.67e-01 94.7% 63.8%
3722166 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.51 46.0 3.66e-01 100.0% 64.3%
3918983 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.51 41.0 3.42e-01 100.0% 50.0%
3223734 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.51 43.0 3.54e-01 93.0% 54.0%
3399954 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.50 40.0 3.38e-01 91.2% 59.0%
D3 high residues 220-317
PDB
Domain cluster: rep: OP056089.1__UYD72102.1__X__00002__D5-102
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM01 3.90.75.20 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › 0.81 72.0 7.05e-01 100.0% 86.8%
1a73A00 3.90.75.10 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A 0.63 56.0 4.69e-01 96.9% 72.2%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3266965 378.1.2.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › Inactive Tox-GHH domain of teneurin › HNH_3 0.83 52.0 6.32e-01 70.4% 96.9%
5053631 378.1.1.19 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH_3 0.80 55.0 5.29e-01 70.4% 84.5%
3586841 378.1.1.7 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › NUMOD4,HNH_3 0.75 69.0 6.56e-01 100.0% 92.2%
3965202 378.1.1.19 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH_3 0.72 66.0 6.31e-01 98.0% 94.5%
3539740 378.1.1.19 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH_3 0.70 57.0 5.23e-01 86.7% 69.6%
89916 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.63 56.0 4.71e-01 96.9% 72.2%
8233 378.1.1.6 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › zf-His_Me_endon 0.63 56.0 4.69e-01 96.9% 72.2%
3695527 378.1.1.6 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › zf-His_Me_endon 0.61 54.0 5.06e-01 98.0% 90.0%
4006493 4032.1.1.3 ↗ beta complex topology › barrel domains in phase 1 flagellin › barrel domains in phase 1 flagellin › barrel domains in phase 1 flagellin › FLIC_barrel 0.58 33.0 3.95e-01 73.5% 90.0%
3590122 4999.1.1.1 ↗ beta barrels › YopX, C-terminal domain-like › YopX, C-terminal domain-like › YopX, C-terminal domain-like › YopX 0.53 27.0 3.13e-01 91.8% 66.2%
D4 high residues 338-398
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM02 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 0.87 68.0 6.51e-01 100.0% 73.5%
1a0iA01 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.70 45.0 4.12e-01 100.0% 49.4%
2xubA01 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 0.64 42.0 3.91e-01 98.4% 53.8%
2oqgB00 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 0.63 42.0 3.46e-01 96.7% 38.9%
3cuoD00 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 0.59 41.0 3.57e-01 96.7% 46.8%
6uvuA01 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 0.59 40.0 3.40e-01 96.7% 41.3%
6j0eB01 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 0.58 41.0 3.30e-01 96.7% 38.5%
1sfuA00 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 40.0 3.87e-01 96.7% 65.7%
4dqnA01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.56 48.0 3.65e-01 100.0% 83.5%
2rdpA00 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 39.0 3.07e-01 96.7% 32.9%
3cuqB03 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 39.0 3.84e-01 95.1% 66.7%
4b8vA03 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.53 38.0 4.14e-01 77.0% 93.9%
3zgzD04 2.20.28.290 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.53 38.0 3.83e-01 100.0% 77.4%
2mkxA00 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.53 37.0 4.02e-01 82.0% 90.2%
1kqfA02 3.40.50.740 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 45.0 3.12e-01 100.0% 70.7%
6s2wA01 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.53 46.0 4.17e-01 100.0% 70.7%
5trdA01 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 40.0 3.65e-01 96.7% 61.9%
2jv2A00 3.10.330.10 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.51 39.0 3.67e-01 100.0% 68.4%
1h0hA02 3.40.50.740 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.50 40.0 2.88e-01 100.0% 69.9%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4414927 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.76 59.0 5.69e-01 100.0% 73.9%
3171408 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.73 56.0 6.05e-01 98.4% 100.0%
4992529 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 44.0 3.86e-01 96.7% 47.8%
5041009 101.1.2.530 ↗ alpha arrays › HTH › HTH › winged helix domain › HVO_A0114 0.64 45.0 3.76e-01 96.7% 42.9%
4937088 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 45.0 4.17e-01 96.7% 57.5%
4961283 101.1.2.935 ↗ alpha arrays › HTH › HTH › winged helix domain › HVO_B0008_C 0.62 46.0 3.83e-01 80.3% 76.1%
4988069 101.1.2.14 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.62 41.0 3.54e-01 96.7% 44.2%
5062256 101.1.2.673 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_HVO_0163_N 0.61 41.0 3.57e-01 98.4% 45.3%
3278292 101.1.2.136 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_20 0.61 41.0 3.59e-01 96.7% 45.3%
3951460 101.30.1.3 ↗ alpha arrays › HTH › Rv2175c › Rv2175c › Rv2175c_wHTH 0.60 40.0 3.50e-01 100.0% 46.7%
4991174 101.1.2.63 ↗ alpha arrays › HTH › HTH › winged helix domain › FaeA 0.60 41.0 3.84e-01 96.7% 57.3%
4968475 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 41.0 3.96e-01 96.7% 61.4%
4993306 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 42.0 3.68e-01 96.7% 50.0%
4977845 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 40.0 3.92e-01 96.7% 64.6%
4928469 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 42.0 3.87e-01 96.7% 58.7%
5057644 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 40.0 3.91e-01 96.7% 64.3%
2511580 101.1.2.14 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.58 41.0 3.23e-01 96.7% 36.0%
5038398 101.1.2.673 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_HVO_0163_N 0.57 40.0 3.77e-01 96.7% 60.0%
4941666 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.57 40.0 3.43e-01 96.7% 45.5%
4123283 284.1.1.0 ↗ a+b two layers › FKBP-like › FKBP-like › FKBP-like 0.57 45.0 4.27e-01 93.4% 78.8%
4929744 101.1.2.141 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.56 39.0 3.83e-01 96.7% 67.7%
4967809 101.1.2.110 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_IclR 0.56 39.0 3.79e-01 96.7% 64.3%
3603379 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.56 37.0 3.46e-01 96.7% 53.8%
3413357 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.55 43.0 4.13e-01 85.2% 77.1%
5040337 101.1.2.673 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_HVO_0163_N 0.54 38.0 3.44e-01 96.7% 51.1%
3395053 101.1.2.57 ↗ alpha arrays › HTH › HTH › winged helix domain › EAP30 0.54 37.0 3.60e-01 96.7% 62.9%
5054374 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 36.0 3.78e-01 96.7% 75.9%
5070231 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 39.0 3.83e-01 96.7% 71.0%
4940141 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.54 39.0 3.76e-01 96.7% 67.1%
5024958 101.1.2.142 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_Crp_2 0.52 39.0 3.50e-01 96.7% 55.6%
4498369 101.1.2.135 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR_2 0.52 38.0 3.47e-01 96.7% 55.6%
3989372 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.52 35.0 3.67e-01 100.0% 86.0%
5010731 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.52 37.0 2.80e-01 96.7% 29.4%
4993968 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 41.0 3.74e-01 98.4% 66.3%
3063602 101.1.2.22 ↗ alpha arrays › HTH › HTH › winged helix domain › PCI 0.50 42.0 4.15e-01 93.4% 90.9%
4940202 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 41.0 2.97e-01 96.7% 31.1%