←Back to structures
RepA
Euk-VirTomato_associated_geminivirus_1
RepA__YP_009417308__Tomato_associated_geminivirus_1__2027645
Identity
- Accession:
- YP_009417308 ↗
- Protein ID:
- RepA
- Kingdom:
- euk
Quality
77.2
mean pLDDT
Taxonomy
Shotokuvirae›
Cressdnaviricota›
Repensiviricetes›
Geplafuvirales›
Geminiviridae›
Topilevirus›
Tomato_associated_geminivirus_1
TaxID: 2027645
Cluster
View cluster (48 members)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 12-115
Domain cluster:
rep: replication-associated_protein__YP_009553348__Odonata-associated_circular_virus-7_Viruses.__X__D5-106
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00799.27 best | Gemini_AL1 | 101.0 | 5.50e-29 | 100.0% | 91.1% |
D2
high
residues 128-171
Domain cluster:
rep: replication_associated_protein__YP_006331073__Maize_streak_Reunion_virus__1182518__D173-216
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF08283.17 best | Gemini_AL1_M | 25.6 | 1.50e-05 | 100.0% | 38.3% |
CATH (28)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1cg5B00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.72 | 62.0 | 4.37e-01 | 100.0% | 84.4% |
| 5x68A00 | 3.50.50.60 | Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain | 0.70 | 59.0 | 3.51e-01 | 100.0% | 16.7% |
| 4z4qA04 | 1.10.268.10 | Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 | 0.70 | 55.0 | 4.45e-01 | 97.7% | 44.9% |
| 3iu0A00 | 3.90.1360.10 | Alpha Beta › Alpha-Beta Complex › Microbial transglutaminase. Chain: a › Protein-glutamine gamma-glutamyltransferase | 0.69 | 55.0 | 3.35e-01 | 100.0% | 15.0% |
| 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 | 0.68 | 56.0 | 4.43e-01 | 100.0% | 50.0% |
| 3g2eB00 | 3.40.920.10 | Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | 0.66 | 53.0 | 3.64e-01 | 100.0% | 90.8% |
| 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 | 0.64 | 53.0 | 4.45e-01 | 100.0% | 63.1% |
| 3bf7A00 | 3.40.50.1820 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain | 0.63 | 49.0 | 3.17e-01 | 100.0% | 18.0% |
| 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 | 0.62 | 52.0 | 4.30e-01 | 100.0% | 95.3% |
| 2mbfA01 | 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 | 4.06e-01 | 100.0% | 58.8% |
| 2c2jA00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.60 | 42.0 | 2.88e-01 | 75.0% | 67.9% |
| 1eg7A02 | 3.30.1510.10 | Alpha Beta › 2-Layer Sandwich › Domain 2, N(10)-formyltetrahydrofolate synthetase › Domain 2, N(10)-formyltetrahydrofolate synthetase | 0.60 | 48.0 | 3.69e-01 | 97.7% | 71.4% |
| 2oxlA00 | 1.20.5.5260 | Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › | 0.58 | 48.0 | 4.34e-01 | 95.5% | 90.3% |
| 4wzsB00 | 1.10.20.10 | Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A | 0.58 | 46.0 | 3.60e-01 | 97.7% | 50.4% |
| 1x4qA01 | 1.20.1390.10 | Mainly Alpha › Up-down Bundle › PWI domain › PWI domain | 0.57 | 45.0 | 4.06e-01 | 100.0% | 60.6% |
| 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 | 0.57 | 46.0 | 3.94e-01 | 100.0% | 75.6% |
| 4ixjA02 | 3.30.1690.20 | Alpha Beta › 2-Layer Sandwich › TcpA-like pilin › | 0.57 | 48.0 | 3.37e-01 | 97.7% | 44.9% |
| 2yjgA01 | 3.90.226.30 | Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › LarA, C-terminal domain | 0.57 | 46.0 | 3.15e-01 | 100.0% | 35.1% |
| 3dfgA01 | 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 | 47.0 | 4.60e-01 | 100.0% | 100.0% |
| 4k90A02 | 1.10.390.10 | Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 | 0.55 | 46.0 | 3.14e-01 | 100.0% | 26.6% |
| 1tzzB01 | 3.30.390.10 | Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain | 0.55 | 43.0 | 3.37e-01 | 100.0% | 45.4% |
| 1v9mA02 | 1.20.1690.10 | Mainly Alpha › Up-down Bundle › V-type ATP synthase subunit C fold › V-type ATP synthase subunit C domain | 0.54 | 45.0 | 3.57e-01 | 100.0% | 45.5% |
| 3fdiB00 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.52 | 43.0 | 2.93e-01 | 95.5% | 64.2% |
| 7e9uA01 | 1.50.10.10 | Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › | 0.52 | 44.0 | 2.58e-01 | 100.0% | 13.5% |
| 2vk9A03 | 1.10.3730.30 | Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › | 0.51 | 40.0 | 3.28e-01 | 95.5% | 86.7% |
| 1bqbA02 | 1.10.390.10 | Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 | 0.51 | 40.0 | 2.98e-01 | 100.0% | 34.0% |
| 5czlA00 | 1.50.10.10 | Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › | 0.51 | 38.0 | 2.45e-01 | 100.0% | 21.0% |
| 2ff4A01 | 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 | 0.50 | 38.0 | 3.19e-01 | 100.0% | 62.6% |
ECOD (27)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3345589 | 4016.1.1.1 ↗ | alpha bundles › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase › DNA_topoisoIV | 0.73 | 55.0 | 3.66e-01 | 90.9% | 20.0% |
| 3719708 | 378.1.1.2 ↗ | few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH | 0.71 | 60.0 | 4.52e-01 | 100.0% | 37.4% |
| 4994323 | 2004.1.3.1 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR | 0.69 | 58.0 | 3.96e-01 | 100.0% | 92.4% |
| 4945578 | 2004.1.3.1 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR | 0.68 | 55.0 | 3.75e-01 | 97.7% | 93.3% |
| 4991219 | 2004.1.3.1 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR | 0.67 | 56.0 | 3.61e-01 | 100.0% | 73.8% |
| 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 | 54.0 | 4.40e-01 | 100.0% | 51.6% |
| 5000777 | 601.7.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain | 0.64 | 51.0 | 4.08e-01 | 93.2% | 44.7% |
| 3605601 | 108.1.1.0 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand | 0.63 | 53.0 | 4.32e-01 | 100.0% | 55.6% |
| 3806070 | 101.1.17.0 ↗ | alpha arrays › HTH › HTH › FF domain | 0.63 | 49.0 | 4.81e-01 | 100.0% | 94.0% |
| 3810002 | 101.1.2.111 ↗ | alpha arrays › HTH › HTH › winged helix domain › RQC | 0.62 | 50.0 | 3.93e-01 | 100.0% | 48.2% |
| 3480146 | 101.1.2.178 ↗ | alpha arrays › HTH › HTH › winged helix domain › HTH_61 | 0.62 | 51.0 | 3.96e-01 | 100.0% | 83.6% |
| 5073598 | 101.1.2.392 ↗ | alpha arrays › HTH › HTH › winged helix domain › SNRNP200_wHTH | 0.62 | 50.0 | 4.17e-01 | 100.0% | 64.4% |
| 4033427 | 639.2.1.0 ↗ | alpha arrays › HHA-like › Regulator of acid resistance influenced by indole (AriR) › Regulator of acid resistance influenced by indole (AriR) | 0.62 | 51.0 | 4.50e-01 | 97.7% | 78.6% |
| 4258338 | 101.35.1.5 ↗ | alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH1 | 0.61 | 52.0 | 3.98e-01 | 100.0% | 88.2% |
| 3799518 | 101.1.2.392 ↗ | alpha arrays › HTH › HTH › winged helix domain › SNRNP200_wHTH | 0.61 | 48.0 | 4.06e-01 | 100.0% | 75.6% |
| 4173843 | 532.2.1.1 ↗ | alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains › HrpJ | 0.61 | 51.0 | 3.92e-01 | 97.7% | 61.8% |
| 5049790 | 2004.1.3.1 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR | 0.61 | 49.0 | 3.43e-01 | 100.0% | 92.4% |
| 4232234 | 101.1.2.309 ↗ | alpha arrays › HTH › HTH › winged helix domain › GPAT_C | 0.61 | 50.0 | 3.42e-01 | 100.0% | 36.3% |
| 3554755 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.60 | 47.0 | 4.18e-01 | 100.0% | 73.3% |
| 3981539 | 532.2.1.1 ↗ | alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains › HrpJ | 0.59 | 49.0 | 4.15e-01 | 100.0% | 70.0% |
| 4544981 | 101.35.1.0 ↗ | alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX | 0.59 | 49.0 | 4.77e-01 | 100.0% | 94.0% |
| 4543408 | 101.35.1.5 ↗ | alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH1 | 0.59 | 49.0 | 4.56e-01 | 100.0% | 80.0% |
| 3334378 | 101.35.1.32 ↗ | alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › PF25874 | 0.58 | 47.0 | 4.51e-01 | 100.0% | 81.8% |
| 3740038 | 101.1.1.256 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › Clr5 | 0.58 | 46.0 | 4.57e-01 | 100.0% | 94.0% |
| 3964425 | 101.35.1.0 ↗ | alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX | 0.58 | 47.0 | 4.60e-01 | 100.0% | 94.0% |
| 3651728 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.55 | 45.0 | 3.73e-01 | 100.0% | 63.3% |
| 3933561 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.55 | 45.0 | 3.54e-01 | 97.7% | 75.2% |
D3
high
residues 191-249