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Rep

Euk-Vir

Rice_latent_virus_2

Rep__YP_009551800__Rice_latent_virus_2__2012857

Identity

Accession:
YP_009551800 ↗
Protein ID:
Rep
Kingdom:
euk

Quality

76.8 mean pLDDT

Taxonomy

Shotokuvirae› Cressdnaviricota› Repensiviricetes› Geplafuvirales› Geminiviridae› Mastrevirus› Rice_latent_virus_2

TaxID: 2012857

Cluster

View cluster (21 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 16-113
PDB
Domain cluster: rep: replication-associated_protein__YP_009553348__Odonata-associated_circular_virus-7_Viruses.__X__D5-106
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00799.27 best Gemini_AL1 75.0 6.80e-21 99.0% 88.5%
D2 high residues 223-362
PDB
Domain cluster: rep: IMGVR_UViG_638276918_000001-638276918-638305645__D148-283
D3 medium residues 164-220
PDB
Domain cluster: rep: replication_associated_protein__YP_006331073__Maize_streak_Reunion_virus__1182518__D173-216
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08283.17 best Gemini_AL1_M 35.3 1.40e-08 100.0% 50.5%
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4z4qA04 1.10.268.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 0.68 45.0 3.98e-01 78.9% 44.9%
3iu0A00 3.90.1360.10 Alpha Beta › Alpha-Beta Complex › Microbial transglutaminase. Chain: a › Protein-glutamine gamma-glutamyltransferase 0.65 50.0 3.13e-01 86.0% 17.5%
1x4qA01 1.20.1390.10 Mainly Alpha › Up-down Bundle › PWI domain › PWI domain 0.64 44.0 4.15e-01 80.7% 59.2%
1vtnC00 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 49.0 4.09e-01 86.0% 70.6%
3g2eB00 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.62 46.0 3.31e-01 82.5% 91.4%
2qbyB03 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 0.61 50.0 4.37e-01 94.7% 69.2%
2l7kA00 1.10.10.1850 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Sporulation protein-like 0.61 41.0 3.74e-01 80.7% 52.6%
3p01A01 6.10.140.590 Special › Helix non-globular › Helix Hairpins › 0.60 47.0 4.21e-01 87.7% 72.3%
4wzsB00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.60 40.0 3.34e-01 71.9% 46.9%
2wgmA01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.59 40.0 3.61e-01 70.2% 52.4%
5nl9A01 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 46.0 4.20e-01 91.2% 94.0%
2ph7A01 1.10.3400.10 Mainly Alpha › Orthogonal Bundle › af_2093 domain like fold › af_2093 domain like 0.59 46.0 3.79e-01 94.7% 55.6%
4rayA01 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 46.0 4.17e-01 91.2% 89.4%
2zj2A03 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 46.0 4.14e-01 89.5% 79.8%
4f92B10 1.10.3380.10 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › Sec63 N-terminal domain-like domain 0.58 43.0 3.38e-01 84.2% 81.8%
1gkrA02 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.58 44.0 2.75e-01 84.2% 15.9%
2a8eA00 3.30.930.20 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Protein of unknown function DUF1054 0.57 41.0 2.82e-01 78.9% 39.5%
3eyyA01 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 44.0 3.99e-01 89.5% 70.7%
1bccB02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.56 38.0 2.72e-01 71.9% 77.3%
2lhrA00 1.20.58.1270 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 44.0 4.15e-01 96.5% 84.6%
2vixA02 1.10.150.630 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.56 42.0 3.64e-01 82.5% 73.0%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.55 40.0 3.95e-01 80.7% 82.3%
4wbyA02 1.10.3090.10 Mainly Alpha › Orthogonal Bundle › cca-adding enzyme, domain 2 › cca-adding enzyme, domain 2 0.54 45.0 3.02e-01 94.7% 43.6%
3nwoA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 42.0 2.77e-01 91.2% 74.9%
3ol4A02 1.10.10.2390 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.53 39.0 3.90e-01 82.5% 93.3%
7e9uA01 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.53 42.0 2.60e-01 98.2% 31.4%
3elkA00 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 40.0 3.47e-01 91.2% 56.2%
5mv9A01 1.25.40.530 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › MyTH4 domain 0.52 39.0 2.94e-01 91.2% 34.7%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 35.0 3.32e-01 75.4% 83.6%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3719708 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.70 53.0 4.26e-01 82.5% 45.2%
3690022 592.1.1.2 ↗ alpha arrays › PWI domain-like › PWI domain › PWI domain › Helicase_PWI 0.70 50.0 4.50e-01 82.5% 55.0%
3783806 592.1.1.2 ↗ alpha arrays › PWI domain-like › PWI domain › PWI domain › Helicase_PWI 0.69 52.0 4.22e-01 80.7% 44.8%
3608495 109.4.1.31 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MA3 0.66 50.0 3.23e-01 80.7% 23.6%
4972840 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.66 49.0 3.41e-01 82.5% 82.0%
4411140 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.66 48.0 4.17e-01 80.7% 53.7%
3631439 592.7.1.0 ↗ alpha arrays › PWI domain-like › GIPC1 GH2 domain › GIPC1 GH2 domain 0.64 45.0 3.89e-01 80.7% 45.3%
4939370 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.63 47.0 3.97e-01 82.5% 72.0%
3407793 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 49.0 4.38e-01 87.7% 75.0%
4314672 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.61 49.0 4.13e-01 93.0% 60.0%
5061536 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.61 48.0 4.00e-01 87.7% 54.4%
5000777 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.60 45.0 3.83e-01 80.7% 48.9%
3016249 532.2.1.0 ↗ alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains 0.59 45.0 3.84e-01 86.0% 70.7%
3964425 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.58 43.0 4.50e-01 84.2% 100.0%
4543408 101.35.1.5 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH1 0.57 44.0 4.34e-01 87.7% 88.3%
4173843 532.2.1.1 ↗ alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains › HrpJ 0.57 43.0 3.54e-01 84.2% 63.6%
5002258 109.7.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Cytochrome c oxidase subunit E › Cytochrome c oxidase subunit E 0.55 42.0 3.93e-01 91.2% 72.5%
158755 592.1.1.1 ↗ alpha arrays › PWI domain-like › PWI domain › PWI domain › PWI 0.55 39.0 3.47e-01 82.5% 48.9%
5048562 2500.1.1.4 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › DUF711 0.54 40.0 2.49e-01 89.5% 11.5%
4996068 109.4.1.210 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_19 0.54 42.0 2.81e-01 93.0% 59.6%
4947212 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.53 36.0 3.09e-01 73.7% 42.0%
3953723 7579.1.1.6 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.52 35.0 2.32e-01 71.9% 54.7%