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exonuclease

Euk-Vir

Micromonas_pusilla_virus_12T

exonuclease__YP_007676078__Micromonas_pusilla_virus_12T__755272

Identity

Accession:
YP_007676078 ↗
Protein ID:
exonuclease
Kingdom:
euk

Quality

79.2 mean pLDDT

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 12-194
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00929.32 best RNase_T 49.4 1.10e-12 97.3% 100.0%
D2 high residues 322-446
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF12705.14 best PDDEXK_1 23.9 5.30e-05 89.6% 23.5%
D3 medium residues 245-321
PDB
Domain cluster: representative
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2uubT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.71 54.0 5.00e-01 81.8% 72.7%
1tzvA00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.70 60.0 4.89e-01 94.8% 52.5%
6dv2G02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.69 49.0 3.64e-01 72.7% 32.6%
4l8iB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.69 56.0 4.96e-01 88.3% 93.8%
4uurA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.69 59.0 4.95e-01 90.9% 100.0%
4zvaA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.68 62.0 4.94e-01 100.0% 92.6%
2wy4A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.68 60.0 5.00e-01 100.0% 100.0%
4c0nA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.68 61.0 4.86e-01 98.7% 87.3%
2ig3A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.68 56.0 4.74e-01 89.6% 95.3%
2wtbA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.67 47.0 3.54e-01 71.4% 32.2%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.67 52.0 4.65e-01 84.4% 70.0%
1dlwA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.67 54.0 4.78e-01 89.6% 100.0%
2vebA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.67 58.0 4.43e-01 100.0% 83.2%
1or4B00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.67 59.0 4.65e-01 98.7% 100.0%
1ldjA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.66 53.0 4.63e-01 87.0% 66.1%
1zcdA00 1.20.1530.10 Mainly Alpha › Up-down Bundle › Na+/H+ antiporter like fold › Na+/H+ antiporter like domain 0.65 58.0 3.65e-01 97.4% 22.6%
3kkbA00 1.20.120.880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain 0.65 51.0 4.34e-01 84.4% 61.9%
1aj3A00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 49.0 4.60e-01 83.1% 98.0%
2c0kB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.65 55.0 4.51e-01 97.4% 100.0%
3e3vA03 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 43.0 4.84e-01 80.5% 96.4%
6bmeA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.63 53.0 4.53e-01 93.5% 96.9%
3tl4X02 1.10.10.2420 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.63 49.0 5.08e-01 90.9% 91.7%
3hn2A02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.63 47.0 4.00e-01 79.2% 59.4%
3pmcA00 1.10.490.70 Mainly Alpha › Orthogonal Bundle › Globin-like › Histidine kinase N-terminal domain 0.63 50.0 4.28e-01 89.6% 97.7%
2ys8A00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.62 48.0 4.62e-01 84.4% 85.6%
3u4qA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.61 49.0 3.53e-01 87.0% 38.2%
1x8zB00 1.20.140.40 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Invertase/pectin methylesterase inhibitor family protein 0.61 51.0 4.16e-01 93.5% 73.5%
2gkmA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.61 51.0 4.43e-01 96.1% 92.9%
1gzsB00 1.10.4120.10 Mainly Alpha › Orthogonal Bundle › SopE-like GEF fold › SopE-like, GEF domain 0.61 50.0 3.95e-01 92.2% 83.6%
3axjB01 1.20.58.190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 0.61 46.0 3.70e-01 81.8% 53.5%
3aq5A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.60 52.0 4.62e-01 100.0% 100.0%
3pe0A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 45.0 4.20e-01 83.1% 96.0%
2c2uA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.59 46.0 3.55e-01 84.4% 84.8%
3ghyA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.59 45.0 3.88e-01 81.8% 56.8%
3b9qA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.59 41.0 3.98e-01 74.0% 66.3%
4xxiA00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.58 49.0 4.05e-01 96.1% 82.3%
3u61D03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.58 41.0 3.92e-01 75.3% 71.4%
3mggA02 6.10.140.1580 Special › Helix non-globular › Helix Hairpins › 0.57 46.0 4.44e-01 90.9% 86.5%
2klqA00 1.20.58.870 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 49.0 4.37e-01 97.4% 72.8%
1v07A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.57 43.0 3.85e-01 80.5% 100.0%
1bbnA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.56 47.0 4.03e-01 97.4% 83.5%
2ii2A03 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.55 41.0 3.81e-01 79.2% 96.9%
1f68A00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.55 45.0 4.15e-01 92.2% 85.4%
4f92B10 1.10.3380.10 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › Sec63 N-terminal domain-like domain 0.55 46.0 3.77e-01 92.2% 85.3%
1u84A00 1.10.340.20 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Apc36109-like domain 0.54 42.0 4.15e-01 89.6% 82.7%
7qocA01 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.53 44.0 3.40e-01 93.5% 82.4%
8einA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.53 44.0 3.06e-01 94.8% 47.5%
4z7xB00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 40.0 3.05e-01 84.4% 67.3%
3nb0B02 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.52 42.0 2.97e-01 87.0% 39.8%
1xv5A02 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.52 35.0 2.64e-01 71.4% 68.1%
4yyfA00 3.20.20.300 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycoside hydrolase, family 3, N-terminal domain 0.51 42.0 2.92e-01 100.0% 54.7%
3deeA01 1.10.150.690 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DUF2063 0.51 39.0 3.85e-01 90.9% 77.9%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3530124 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.74 55.0 5.45e-01 83.1% 75.0%
3595902 310.2.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.74 61.0 4.45e-01 88.3% 90.5%
5048577 621.1.1.0 alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain 0.71 53.0 5.27e-01 79.2% 93.8%
None 0.71 55.0 5.56e-01 81.8% 100.0%
3746214 170.1.1.5 alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C 0.70 51.0 5.17e-01 76.6% 97.3%
5022215 195.1.1.1 alpha complex topology › NusB-like › NusB-like › NusB-like › NusB 0.69 53.0 4.55e-01 90.9% 51.2%
2568911 170.1.1.5 alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C 0.68 50.0 4.72e-01 77.9% 94.6%
5044192 2004.1.1.42 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.68 61.0 3.74e-01 98.7% 33.6%
3407641 106.1.1.8 alpha arrays › Globin-like › Globin-like › Globin-like › HisK-N-like 0.68 60.0 4.81e-01 100.0% 86.5%
5019219 7516.1.1.2 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.67 49.0 3.27e-01 77.9% 55.0%
3596608 1134.1.1.0 alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.66 55.0 5.37e-01 93.5% 90.6%
3953005 195.1.1.1 alpha complex topology › NusB-like › NusB-like › NusB-like › NusB 0.66 54.0 4.34e-01 92.2% 46.0%
4288099 106.1.1.3 alpha arrays › Globin-like › Globin-like › Globin-like › Bac_globin 0.66 56.0 4.73e-01 94.8% 93.8%
4402843 604.1.1.20 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › AKNA 0.66 50.0 4.47e-01 84.4% 89.6%
4083216 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.64 56.0 5.36e-01 98.7% 96.7%
3542152 397.7.1.7 few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 › BSMAP 0.64 54.0 5.19e-01 93.5% 86.7%
3506491 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.64 57.0 5.27e-01 100.0% 92.0%
5077999 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.63 50.0 3.79e-01 87.0% 56.3%
4433075 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.63 55.0 5.30e-01 98.7% 97.8%
4396592 7064.1.1.3 alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › FUSC_2 0.63 51.0 4.19e-01 92.2% 72.0%
4071397 5050.1.1.9 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.62 52.0 3.89e-01 93.5% 79.0%
4093848 3584.1.1.1 alpha arrays › DNA polymerase III finger domain › DNA polymerase III finger domain › DNA polymerase III finger domain › DNA_pol3_finger 0.62 51.0 3.75e-01 90.9% 41.9%
3597946 650.1.1.0 alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.62 47.0 4.24e-01 83.1% 67.3%
5073264 7577.1.1.4 a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Pyridoxal_deC 0.61 51.0 3.18e-01 90.9% 18.8%
2583874 106.1.1.3 alpha arrays › Globin-like › Globin-like › Globin-like › Bac_globin 0.61 53.0 4.54e-01 100.0% 97.6%
3911689 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.61 47.0 4.65e-01 87.0% 89.4%
4681455 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 50.0 4.08e-01 93.5% 75.2%
3234488 2004.1.1.104 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Sulfotransfer_2 0.59 46.0 3.30e-01 87.0% 83.1%
4991188 2004.1.1.76 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87 0.59 45.0 3.00e-01 89.6% 19.4%
5043878 102.3.1.1 alpha arrays › HhH/H2TH › eIF2alpha middle domain › eIF2alpha middle domain › EIF_2_alpha 0.58 45.0 4.39e-01 87.0% 76.5%
3728950 650.1.1.0 alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.58 43.0 4.35e-01 79.2% 90.7%
3213313 611.3.1.0 alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.57 41.0 4.07e-01 83.1% 73.8%
3530949 3291.1.1.231 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › PF27745 0.57 45.0 3.69e-01 88.3% 86.7%
3931889 633.1.1.1 alpha bundles › Bromodomain-like › Bromodomain › Bromodomain › Bromodomain 0.56 45.0 4.04e-01 92.2% 80.9%
3229646 2004.1.1.104 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Sulfotransfer_2 0.56 45.0 3.25e-01 92.2% 67.7%
3733881 106.1.1.0 alpha arrays › Globin-like › Globin-like › Globin-like 0.56 49.0 3.78e-01 100.0% 100.0%
3703318 650.1.1.0 alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.54 44.0 4.14e-01 93.5% 73.0%
5009824 2006.1.4.2 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN 0.54 38.0 3.30e-01 76.6% 48.5%
3291508 131.1.1.0 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like 0.53 46.0 3.41e-01 100.0% 53.0%
3937049 2004.1.1.104 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Sulfotransfer_2 0.51 41.0 2.94e-01 93.5% 65.2%