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2a_protein
Euk-VirOlive_latent_virus_2
2a_protein__NP_620043__Olive_latent_virus_2__33773
Identity
- Accession:
- NP_620043 ↗
- Protein ID:
- 2a_protein
- Kingdom:
- euk
Quality
56.9
mean pLDDT
Taxonomy
Orthornavirae›
Kitrinoviricota›
Alsuviricetes›
Martellivirales›
Bromoviridae›
Oleavirus›
Olive_latent_virus_2
TaxID: 33773
Cluster
View cluster (23 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 659-736
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00978.27 best | RdRP_2 | 42.9 | 4.40e-11 | 94.9% | 17.5% |
CATH (30)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1uhsA01 | 1.10.10.60 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like | 0.64 | 39.0 | 4.50e-01 | 87.2% | 88.9% |
| 7ymiZ01 | 1.10.287.740 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre | 0.63 | 41.0 | 4.54e-01 | 78.2% | 87.9% |
| 3g2bA00 | 1.10.10.1150 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Coenzyme PQQ synthesis protein D (PqqD) | 0.63 | 43.0 | 4.15e-01 | 70.5% | 82.2% |
| 1rykA00 | 1.10.1470.10 | Mainly Alpha › Orthogonal Bundle › Protein Yjbj; Chain: A; › YjbJ | 0.62 | 39.0 | 4.16e-01 | 84.6% | 72.5% |
| 4d7rA01 | 1.10.220.20 | Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › | 0.62 | 39.0 | 3.93e-01 | 85.9% | 61.0% |
| 2da4A01 | 1.10.10.60 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like | 0.61 | 40.0 | 4.33e-01 | 91.0% | 80.3% |
| 2ptfB02 | 1.20.58.290 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. | 0.61 | 39.0 | 4.36e-01 | 93.6% | 89.5% |
| 3sfvB02 | 6.10.140.2010 | Special › Helix non-globular › Helix Hairpins › | 0.59 | 44.0 | 3.30e-01 | 79.5% | 90.0% |
| 2nr4A02 | 1.20.58.290 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. | 0.58 | 36.0 | 4.02e-01 | 92.3% | 84.5% |
| 4nb5B02 | 1.10.287.160 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat | 0.57 | 39.0 | 4.18e-01 | 74.4% | 85.9% |
| 5i1uA00 | 1.10.600.10 | Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase | 0.57 | 44.0 | 3.00e-01 | 84.6% | 54.0% |
| 6iumA01 | 3.90.226.10 | Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 | 0.57 | 45.0 | 3.15e-01 | 88.5% | 55.0% |
| 3ctwB00 | 1.10.8.930 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Protein of unknown function DUF1465 | 0.57 | 44.0 | 3.85e-01 | 84.6% | 98.3% |
| 5t3wA00 | 1.20.120.1160 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › | 0.57 | 46.0 | 3.98e-01 | 94.9% | 54.0% |
| 3ee4A00 | 1.10.620.20 | Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A | 0.56 | 42.0 | 2.92e-01 | 80.8% | 49.8% |
| 5zw7A03 | 1.20.140.10 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 | 0.55 | 42.0 | 3.45e-01 | 83.3% | 96.1% |
| 1cxzB00 | 1.10.287.160 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat | 0.55 | 42.0 | 4.14e-01 | 84.6% | 100.0% |
| 3jcuZ00 | 1.10.287.740 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre | 0.55 | 38.0 | 4.06e-01 | 75.6% | 91.8% |
| 1rfyB00 | 1.10.287.160 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat | 0.55 | 40.0 | 3.92e-01 | 78.2% | 83.0% |
| 1tuoA03 | 3.40.120.10 | Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 | 0.55 | 38.0 | 3.32e-01 | 71.8% | 80.3% |
| 3iqtA01 | 1.20.120.160 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain | 0.55 | 41.0 | 3.67e-01 | 97.4% | 56.1% |
| 2go7A02 | 1.10.150.240 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 | 0.55 | 37.0 | 3.94e-01 | 87.2% | 82.1% |
| 1mw9X02 | 1.10.460.10 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; domain 2 › Topoisomerase I, domain 2 | 0.54 | 40.0 | 3.20e-01 | 79.5% | 47.2% |
| 2jifA03 | 1.20.140.10 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 | 0.53 | 42.0 | 3.45e-01 | 88.5% | 74.0% |
| 2oi8A00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.53 | 43.0 | 3.24e-01 | 89.7% | 62.6% |
| 2js5A00 | 1.10.287.660 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin | 0.53 | 38.0 | 3.94e-01 | 75.6% | 84.5% |
| 2yhsA01 | 1.20.120.140 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain | 0.52 | 40.0 | 3.73e-01 | 94.9% | 66.0% |
| 4bf9A02 | 1.20.225.30 | Mainly Alpha › Up-down Bundle › Bacteriocin As-48; Chain A › Dihydrouridine synthase, C-terminal recognition domain | 0.51 | 35.0 | 3.57e-01 | 70.5% | 97.3% |
| 4gxbA02 | 1.20.80.60 | Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › | 0.51 | 34.0 | 3.70e-01 | 88.5% | 85.5% |
| 4ioeA00 | 1.10.287.850 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain | 0.50 | 35.0 | 3.46e-01 | 74.4% | 71.3% |
ECOD (22)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3944885 | 101.1.1.355 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › DUF2857 | 0.70 | 40.0 | 4.34e-01 | 79.5% | 67.7% |
| 3806413 | 4133.1.1.0 ↗ | alpha arrays › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like | 0.67 | 44.0 | 3.48e-01 | 91.0% | 33.5% |
| 4345084 | 4973.1.1.0 ↗ | alpha bundles › helical domain in DNA primase DnaG catalytic core › helical domain in DNA primase DnaG catalytic core › helical domain in DNA primase DnaG catalytic core | 0.66 | 44.0 | 4.47e-01 | 91.0% | 69.3% |
| 3259221 | 101.1.1.1 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain | 0.65 | 41.0 | 4.62e-01 | 85.9% | 85.0% |
| 4948785 | 7524.1.1.3 ↗ | a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › LuxC | 0.63 | 49.0 | 3.49e-01 | 85.9% | 27.1% |
| 3653791 | 3826.1.1.0 ↗ | alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) | 0.62 | 45.0 | 4.58e-01 | 75.6% | 81.3% |
| 3243227 | 198.1.1.0 ↗ | alpha arrays › Saposin-like › Saposin-like › Saposin-like | 0.61 | 46.0 | 4.80e-01 | 82.1% | 98.6% |
| 3880919 | 633.23.1.0 ↗ | alpha bundles › Bromodomain-like › Claudin › Claudin | 0.60 | 49.0 | 4.01e-01 | 91.0% | 73.0% |
| 4945888 | 5041.1.1.0 ↗ | extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C | 0.60 | 41.0 | 4.16e-01 | 84.6% | 71.2% |
| 3934928 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.60 | 49.0 | 4.67e-01 | 92.3% | 87.4% |
| 3473557 | 198.1.1.0 ↗ | alpha arrays › Saposin-like › Saposin-like › Saposin-like | 0.56 | 44.0 | 4.37e-01 | 85.9% | 98.8% |
| 3685817 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.56 | 38.0 | 4.05e-01 | 98.7% | 83.1% |
| 3215052 | 198.1.1.0 ↗ | alpha arrays › Saposin-like › Saposin-like › Saposin-like | 0.56 | 41.0 | 4.04e-01 | 80.8% | 98.8% |
| 4614244 | 589.1.2.1 ↗ | alpha arrays › Triger factor/SurA peptide-binding domain-like › Triger factor/SurA peptide-binding domain-like › TF C-terminus (Pfam 05698) › Trigger_C | 0.55 | 39.0 | 3.16e-01 | 75.6% | 60.6% |
| 3932692 | 604.6.1.0 ↗ | alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain | 0.54 | 45.0 | 4.38e-01 | 96.2% | 88.9% |
| 3923696 | 198.1.1.0 ↗ | alpha arrays › Saposin-like › Saposin-like › Saposin-like | 0.54 | 40.0 | 3.93e-01 | 83.3% | 85.6% |
| 3473554 | 198.1.1.0 ↗ | alpha arrays › Saposin-like › Saposin-like › Saposin-like | 0.52 | 39.0 | 3.91e-01 | 83.3% | 91.3% |
| 4017461 | 3860.1.1.0 ↗ | alpha bundles › Myosin VI lever arm › Myosin VI lever arm › Myosin VI lever arm | 0.52 | 43.0 | 3.98e-01 | 93.6% | 80.0% |
| 4010267 | 192.8.1.131 ↗ | alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › GNVR | 0.52 | 37.0 | 3.12e-01 | 74.4% | 44.6% |
| 3718408 | 3922.1.1.0 ↗ | alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 | 0.51 | 41.0 | 3.66e-01 | 87.2% | 74.5% |
| 3357244 | 4106.1.1.1 ↗ | few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC | 0.51 | 40.0 | 3.68e-01 | 88.5% | 80.0% |
| 3494616 | 4106.1.1.1 ↗ | few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC | 0.51 | 39.0 | 3.88e-01 | 88.5% | 94.1% |
D2
medium
residues 282-377
D3
medium
residues 378-441_457-482_515-591
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00978.27 best | RdRP_2 | 116.3 | 2.30e-33 | 47.3% | 17.7% |
CATH (2)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2r7rA05 | 1.10.357.80 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › | 0.65 | 55.0 | 5.42e-01 | 89.8% | 94.9% |
| 5jbrA01 | 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 | 0.51 | 26.0 | 3.29e-01 | 82.6% | 88.4% |
ECOD (11)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 217141 | 304.48.1.15 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_3 | 0.77 | 72.0 | 5.52e-01 | 100.0% | 67.2% |
| 3983816 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.76 | 58.0 | 5.04e-01 | 79.6% | 68.8% |
| 3877925 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.74 | 69.0 | 5.19e-01 | 100.0% | 76.1% |
| 3772920 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.74 | 69.0 | 5.58e-01 | 100.0% | 85.3% |
| 3766919 | 304.48.1.0 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like | 0.74 | 68.0 | 4.44e-01 | 100.0% | 36.6% |
| 3878013 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.73 | 68.0 | 5.04e-01 | 100.0% | 63.2% |
| 4188583 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.72 | 68.0 | 4.98e-01 | 100.0% | 66.5% |
| 3939319 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.72 | 66.0 | 4.99e-01 | 100.0% | 78.5% |
| 3691350 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.70 | 65.0 | 5.52e-01 | 100.0% | 91.9% |
| 3923013 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.69 | 65.0 | 5.04e-01 | 100.0% | 68.4% |
| 4361688 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.64 | 59.0 | 4.50e-01 | 98.8% | 64.3% |
D4
medium
residues 483-514_592-643
Domain cluster:
rep: RdRp__YP_009329875__Hubei_partiti-like_virus_11__1923017__D203-236_315-377
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00978.27 best | RdRP_2 | 53.3 | 3.10e-14 | 61.9% | 10.4% |