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IMGVR_UViG_3300030398_000005-3300030398-Ga0188181_106758

Arc-Vir

IMGVR_UViG_3300030398_000005-3300030398-Ga0188181_106758

Quality

82.6 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 248-333
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3juiA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.71 52.0 4.16e-01 77.9% 44.3%
3r2cA00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.69 52.0 4.43e-01 80.2% 94.9%
2jbyA00 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.66 48.0 4.29e-01 77.9% 56.7%
2ew2A02 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 0.65 49.0 4.31e-01 82.6% 75.4%
1yozA00 1.10.3200.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af0941 › AF0941-like 0.64 47.0 4.31e-01 77.9% 95.6%
1v07A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.64 46.0 4.24e-01 75.6% 80.9%
1vb5A01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.63 48.0 4.75e-01 83.7% 90.4%
1q6aA00 1.10.1240.30 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain 0.63 47.0 4.46e-01 81.4% 86.9%
1t98A01 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 0.62 43.0 4.33e-01 73.3% 96.6%
1ks9A02 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 0.61 47.0 4.26e-01 83.7% 77.2%
7dl9A01 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.59 43.0 3.37e-01 77.9% 90.7%
2elcA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.59 39.0 4.35e-01 74.4% 88.1%
4ga6A02 1.20.970.50 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › 0.59 43.0 3.69e-01 80.2% 73.0%
2oi8A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.59 45.0 3.50e-01 83.7% 62.6%
1vquA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.58 40.0 4.48e-01 75.6% 94.0%
4gtnA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.57 40.0 4.29e-01 73.3% 85.1%
5f64A02 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 38.0 4.01e-01 97.7% 78.7%
1tt5C01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 49.0 3.37e-01 100.0% 83.7%
3qhaB02 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 0.56 43.0 3.87e-01 82.6% 84.0%
3h5qA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.56 38.0 4.13e-01 72.1% 88.6%
1p4wA00 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 39.0 3.95e-01 96.5% 72.4%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 39.0 3.59e-01 74.4% 77.8%
2gmyD00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.55 47.0 4.00e-01 95.3% 82.1%
3w6zA02 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 0.54 41.0 3.71e-01 81.4% 68.6%
2qytA02 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 0.54 48.0 4.59e-01 100.0% 93.1%
4muoA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.53 38.0 4.11e-01 75.6% 93.1%
5u1aL00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.53 38.0 3.07e-01 75.6% 91.6%
3nfqB02 1.20.930.10 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.52 36.0 3.44e-01 73.3% 63.0%
1jgcA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.51 39.0 3.34e-01 87.2% 60.0%
2b0hA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.50 41.0 3.67e-01 91.9% 84.4%
2i5tA00 3.10.490.10 Alpha Beta › Roll › Hypothetical upf0131 protein ytfp › Gamma-glutamyl cyclotransferase-like 0.50 36.0 2.96e-01 74.4% 84.6%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5064030 182.1.3.0 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX 0.76 68.0 6.56e-01 97.7% 95.8%
5081313 182.1.3.0 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX 0.72 61.0 6.09e-01 93.0% 87.8%
4942022 182.1.3.3 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.71 64.0 5.71e-01 100.0% 76.7%
3255571 109.4.1.27 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › W2 0.70 52.0 4.04e-01 77.9% 43.9%
3720036 108.1.1.0 alpha arrays › EF-hand › EF-hand-related › EF-hand 0.70 62.0 5.15e-01 100.0% 91.0%
3502846 109.4.1.27 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › W2 0.70 52.0 4.18e-01 80.2% 43.7%
5039859 6035.1.1.0 alpha bundles › Primase helical domain › Primase helical domain › Primase helical domain 0.68 54.0 5.33e-01 83.7% 92.2%
3530124 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.66 49.0 5.06e-01 79.1% 91.3%
3743133 7064.1.1.1 alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › VIT1 0.64 45.0 3.77e-01 74.4% 84.5%
3926112 601.1.1.60 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Death_MADD 0.63 55.0 4.94e-01 100.0% 94.4%
4427282 101.8.1.2 alpha arrays › HTH › An anticodon-binding domain of class I aminoacyl-tRNA synthetases › An anticodon-binding domain of class I aminoacyl-tRNA synthetases › Anticodon_2 0.62 44.0 3.67e-01 74.4% 51.3%
4556778 3919.1.1.2 alpha duplicates or obligate multimers › N-terminal domain of COMMD9 › N-terminal domain of COMMD9 › N-terminal domain of COMMD9 › COMM_HN 0.62 45.0 4.13e-01 77.9% 99.1%
3251818 4133.1.1.0 alpha arrays › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like 0.61 39.0 4.31e-01 73.3% 86.2%
3638575 109.3.1.170 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank, Ank_4 0.61 50.0 3.63e-01 91.9% 65.6%
4122483 4018.1.1.1 a+b two layers › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › FBPase 0.59 46.0 3.86e-01 84.9% 92.9%
5058156 314.1.1.9 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.59 52.0 3.60e-01 100.0% 53.4%
4008038 5050.1.1.20 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_4 0.59 46.0 3.66e-01 87.2% 94.2%
3272819 3919.1.1.2 alpha duplicates or obligate multimers › N-terminal domain of COMMD9 › N-terminal domain of COMMD9 › N-terminal domain of COMMD9 › COMM_HN 0.58 44.0 4.14e-01 82.6% 100.0%
4018207 310.2.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.58 40.0 3.33e-01 72.1% 72.1%
None 0.58 50.0 3.22e-01 100.0% 60.0%
3278439 191.1.1.8 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_33 0.58 46.0 3.65e-01 88.4% 77.2%
3784891 3755.4.1.0 alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.56 39.0 3.39e-01 73.3% 95.7%
3435792 2003.1.9.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.56 49.0 3.32e-01 100.0% 75.9%
4996913 604.5.1.1 alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU_div 0.56 45.0 3.52e-01 91.9% 63.9%
4471463 3455.1.1.0 alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors 0.55 41.0 3.86e-01 80.2% 67.6%
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 0.55 40.0 2.69e-01 76.7% 55.2%
3865201 150.3.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › Hormone_1 0.54 45.0 3.52e-01 95.3% 90.0%
3590283 5051.1.1.17 alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Branch_AA_trans 0.54 46.0 2.89e-01 93.0% 88.1%
3773546 810.1.1.3 a+b two layers › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) › AIG2_2 0.54 38.0 3.10e-01 74.4% 83.2%
3504034 190.1.1.1 alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.54 38.0 3.90e-01 73.3% 91.3%
4348094 181.1.1.1 alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.50 36.0 3.59e-01 83.7% 72.2%
D2 medium residues 42-103
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF09250.17 best Prim-Pol 28.0 3.70e-06 90.3% 29.8%
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1rniA01 3.30.720.160 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Bifunctional DNA primase/polymerase, N-terminal 0.64 55.0 5.37e-01 100.0% 88.6%
4e6zA01 3.40.1350.100 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.62 46.0 3.86e-01 80.6% 52.3%
5mz2I00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.61 53.0 4.16e-01 100.0% 48.9%
3oa8A02 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.56 38.0 3.27e-01 90.3% 44.0%
3r4cA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.54 47.0 4.04e-01 100.0% 68.3%
2pq0A02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.54 47.0 4.04e-01 100.0% 65.0%
1sg5A01 2.30.30.400 Mainly Beta › Roll › SH3 type barrels. › Rof-like 0.54 45.0 4.26e-01 98.4% 87.0%
2gnrA01 6.10.30.10 Special › Helix non-globular › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › 0.54 38.0 3.76e-01 100.0% 69.6%
1v6eA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.53 45.0 4.20e-01 100.0% 97.5%
2yqrA01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.52 35.0 3.13e-01 72.6% 84.5%
1qruA04 3.90.800.10 Alpha Beta › Alpha-Beta Complex › Glutamyl-tRNA Synthetase; domain 3 › Glutamyl-tRNA Synthetase; Domain 3 0.51 43.0 3.71e-01 100.0% 66.1%
2qv8A00 3.55.40.10 Alpha Beta › 3-Layer(bab) Sandwich › minor pseudopilin epsh fold › minor pseudopilin epsh domain 0.50 39.0 3.13e-01 90.3% 74.3%
2o36A02 1.10.1370.10 Mainly Alpha › Orthogonal Bundle › Neurolysin; domain 3 › Neurolysin, domain 3 0.50 43.0 2.71e-01 100.0% 54.9%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3280020 862.1.1.3 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › Prim-Pol 0.86 73.0 5.16e-01 98.4% 32.6%
5073504 206.1.3.8 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATP-grasp_3 0.68 56.0 3.40e-01 100.0% 14.4%
4458862 4261.1.1.0 a+b two layers › TrkA C-terminal domain-like › TrkA C-terminal domain-like › TrkA C-terminal domain-like 0.68 44.0 4.38e-01 100.0% 63.1%
4170959 320.1.1.0 a+b two layers › R3H domain-like › R3H domain › R3H domain 0.66 34.0 3.47e-01 100.0% 45.0%
7174 862.1.1.3 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › Prim-Pol 0.64 54.0 3.82e-01 100.0% 29.0%
5050543 375.1.1.48 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF35_N 0.60 42.0 4.44e-01 100.0% 85.5%
4470741 4.1.1.400 beta barrels › SH3 › SH3 › SH3 › Spore-coat_CotZ 0.59 50.0 4.20e-01 100.0% 93.0%
3184602 373.1.1.1 few secondary structure elements › Zn2/Cys6 DNA-binding domain › Zn2/Cys6 DNA-binding domain › Zn2/Cys6 DNA-binding domain › Zn_clus 0.57 36.0 3.34e-01 90.3% 48.8%
3167568 101.46.1.0 alpha arrays › HTH › Parafibromin N-terminal domain › Parafibromin N-terminal domain 0.55 36.0 2.99e-01 100.0% 35.0%
2544590 2.1.1.58 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF35_N 0.52 38.0 3.15e-01 100.0% 41.5%
3437270 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.51 44.0 4.29e-01 100.0% 92.9%
3942526 4.1.1.257 beta barrels › SH3 › SH3 › SH3 › Flag1_repress 0.51 42.0 3.86e-01 95.2% 76.5%
3924113 221.7.1.1 a+b two layers › beta-Grasp › E2-binding domain of E1 › E2-binding domain of E1 › E2_bind 0.51 39.0 3.58e-01 90.3% 93.3%
D3 medium residues 105-234
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF09250.17 best Prim-Pol 53.4 5.70e-14 90.0% 63.9%
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1g71A01 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.65 52.0 4.23e-01 83.8% 54.2%
2m6pA00 2.20.28.270 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › RNA polymerase-binding protein A 0.55 22.0 3.32e-01 98.5% 97.8%
3otdA00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.53 42.0 3.56e-01 86.9% 93.8%
2gwcA00 3.30.590.20 Alpha Beta › 2-Layer Sandwich › Creatine Kinase; Chain A, domain 2 › 0.50 39.0 2.76e-01 83.8% 63.9%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3280020 862.1.1.3 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › Prim-Pol 0.80 69.0 6.18e-01 100.0% 67.4%
4959587 862.1.1.3 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › Prim-Pol 0.78 65.0 5.90e-01 99.2% 67.1%
4940784 862.1.1.3 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › Prim-Pol 0.77 59.0 5.56e-01 95.4% 66.5%
4960053 862.1.1.3 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › Prim-Pol 0.74 62.0 5.43e-01 87.7% 69.7%
5019731 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.65 51.0 3.85e-01 83.1% 72.5%
4667955 304.150.1.0 a+b two layers › Alpha-beta plaits › Adapter protein mecA 2 C-terminal domain › Adapter protein mecA 2 C-terminal domain 0.59 39.0 4.45e-01 86.2% 91.6%
3370992 304.48.1.21 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Thg1,Thg1C 0.53 42.0 2.96e-01 86.2% 98.7%