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RNA-dependent_RNA_polymerase
Euk-VirTuber_aestivum_mitovirus
RNA-dependent_RNA_polymerase__YP_004564622__Tuber_aestivum_mitovirus__1037523
Identity
- Accession:
- YP_004564622 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
56.4
mean pLDDT
Taxonomy
Orthornavirae›
Lenarviricota›
Howeltoviricetes›
Cryppavirales›
Mitoviridae›
Duamitovirus›
Tuber_aestivum_mitovirus
TaxID: 1037523
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 4-115
Domain cluster:
rep: RNA_dependent_RNA_polymerase__YP_005352912__Clitocybe_odora_virus__1162083__D59-187_563-580
CATH (19)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1vkeB00 | 1.20.1290.10 | Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like | 0.69 | 35.0 | 3.68e-01 | 89.3% | 53.5% |
| 2np3A00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.59 | 43.0 | 3.94e-01 | 89.3% | 59.2% |
| 5tgtA02 | 1.10.10.350 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › | 0.58 | 49.0 | 4.78e-01 | 93.8% | 86.2% |
| 2ja2A05 | 1.10.10.350 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › | 0.57 | 45.0 | 4.80e-01 | 86.6% | 100.0% |
| 7p2yd01 | 1.10.520.20 | Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase | 0.57 | 44.0 | 4.65e-01 | 84.8% | 98.0% |
| 1abvA00 | 1.10.520.20 | Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase | 0.56 | 46.0 | 4.79e-01 | 99.1% | 98.1% |
| 3o7qA02 | 1.20.1250.20 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains | 0.56 | 44.0 | 3.74e-01 | 84.8% | 95.3% |
| 3o7pA01 | 1.20.1250.20 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains | 0.56 | 42.0 | 3.44e-01 | 80.4% | 90.8% |
| 3f4mA00 | 1.20.1440.160 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tumor necrosis factor alpha-induced protein 8-like | 0.56 | 47.0 | 4.28e-01 | 93.8% | 91.6% |
| 3pjxA01 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.55 | 43.0 | 3.66e-01 | 83.0% | 80.7% |
| 7d5qA01 | 1.20.1250.20 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains | 0.55 | 41.0 | 3.54e-01 | 80.4% | 98.4% |
| 5dikA00 | 1.20.1290.10 | Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like | 0.54 | 36.0 | 3.64e-01 | 75.9% | 67.9% |
| 8ex5A01 | 1.20.1250.20 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains | 0.53 | 41.0 | 3.53e-01 | 100.0% | 49.2% |
| 2id6A02 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.53 | 42.0 | 3.81e-01 | 87.5% | 61.7% |
| 2xq0A03 | 1.10.390.10 | Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 | 0.53 | 38.0 | 3.48e-01 | 75.9% | 89.8% |
| 2jifA01 | 1.10.540.10 | Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain | 0.52 | 37.0 | 3.71e-01 | 95.5% | 69.5% |
| 3hd5B01 | 3.40.30.10 | Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin | 0.52 | 32.0 | 2.83e-01 | 75.0% | 41.7% |
| 7dl9A01 | 1.20.1250.20 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains | 0.51 | 40.0 | 3.41e-01 | 100.0% | 49.0% |
| 7ri3A02 | 1.10.490.40 | Mainly Alpha › Orthogonal Bundle › Globin-like › Diphtheria toxin, translocation domain | 0.50 | 39.0 | 3.47e-01 | 98.2% | 57.4% |
ECOD (32)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3468690 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.65 | 34.0 | 3.02e-01 | 78.6% | 33.9% |
| 4039114 | 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 | 0.64 | 57.0 | 4.89e-01 | 98.2% | 77.7% |
| 4007921 | 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 | 0.59 | 46.0 | 3.77e-01 | 83.0% | 90.2% |
| 4386395 | 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 | 0.58 | 46.0 | 4.81e-01 | 85.7% | 100.0% |
| 3970773 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.58 | 45.0 | 3.70e-01 | 83.0% | 88.9% |
| 4978388 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.58 | 44.0 | 3.54e-01 | 82.1% | 87.2% |
| 3282784 | 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 | 0.56 | 45.0 | 3.71e-01 | 84.8% | 92.5% |
| 3537334 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.56 | 44.0 | 3.49e-01 | 83.9% | 79.9% |
| 5049594 | 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 | 0.56 | 42.0 | 3.58e-01 | 78.6% | 91.6% |
| 3387265 | 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 | 0.56 | 39.0 | 3.27e-01 | 70.5% | 96.3% |
| 3941981 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.55 | 43.0 | 3.62e-01 | 83.9% | 92.0% |
| 3385722 | 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 | 0.55 | 41.0 | 3.48e-01 | 100.0% | 45.8% |
| 4080077 | 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 | 0.55 | 47.0 | 4.80e-01 | 99.1% | 100.0% |
| 4934758 | 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 | 0.55 | 43.0 | 3.67e-01 | 100.0% | 51.7% |
| 4971617 | 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 | 0.55 | 41.0 | 3.40e-01 | 80.4% | 85.1% |
| 3971251 | 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 | 0.55 | 42.0 | 3.49e-01 | 81.2% | 89.0% |
| 3560434 | 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 | 0.55 | 42.0 | 3.51e-01 | 83.0% | 95.7% |
| 5048958 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.54 | 43.0 | 3.67e-01 | 100.0% | 51.4% |
| 3943533 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.54 | 41.0 | 3.49e-01 | 82.1% | 92.4% |
| 3973571 | 601.3.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain | 0.54 | 43.0 | 4.33e-01 | 87.5% | 100.0% |
| 5010019 | 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 | 0.54 | 42.0 | 3.67e-01 | 83.9% | 97.1% |
| 3998127 | 5050.1.1.5 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Folate_carrier | 0.54 | 40.0 | 3.22e-01 | 77.7% | 73.0% |
| 2649515 | 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 | 0.53 | 42.0 | 3.54e-01 | 83.9% | 94.2% |
| 5013468 | 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 | 0.53 | 41.0 | 3.50e-01 | 100.0% | 49.2% |
| 3986321 | 5050.1.1.1 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr | 0.53 | 40.0 | 3.25e-01 | 100.0% | 40.0% |
| 3607259 | 5050.1.1.4 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Nucleoside_tran | 0.53 | 40.0 | 3.14e-01 | 79.5% | 89.8% |
| 4936746 | 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 | 0.53 | 40.0 | 3.38e-01 | 100.0% | 46.7% |
| 4999485 | 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 | 0.52 | 41.0 | 3.47e-01 | 100.0% | 50.3% |
| 3286869 | 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 | 0.51 | 40.0 | 3.41e-01 | 100.0% | 49.7% |
| 3981551 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.51 | 46.0 | 3.89e-01 | 100.0% | 85.9% |
| 3863240 | 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 | 0.50 | 42.0 | 3.40e-01 | 100.0% | 46.8% |
| 3969784 | 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 | 0.50 | 45.0 | 3.70e-01 | 100.0% | 75.6% |
D2
medium
residues 118-129_153-163_186-270_309-375
Domain cluster:
rep: RNA_dependent_RNA_polymerase__YP_005352912__Clitocybe_odora_virus__1162083__D188-234_322-366_403-448
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05919.17 best | Mitovir_RNA_pol | 42.3 | 7.50e-11 | 53.1% | 9.3% |
| PF05919.17 | Mitovir_RNA_pol | 26.0 | 6.30e-06 | 30.9% | 6.6% |
CATH (3)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5cqgA02 | 3.10.10.20 | Alpha Beta › Roll › HIV Type 1 Reverse Transcriptase; Chain A, domain 1 › | 0.64 | 25.0 | 3.86e-01 | 100.0% | 87.5% |
| 1mhxA00 | 3.10.20.10 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › | 0.56 | 17.0 | 2.81e-01 | 77.7% | 70.8% |
| 1t6aA02 | 3.30.310.120 | Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Rbstp2229 like protein | 0.51 | 19.0 | 2.82e-01 | 82.9% | 73.1% |
ECOD (10)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2636124 | 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 | 0.56 | 46.0 | 4.12e-01 | 100.0% | 64.1% |
| 2033701 | 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 | 0.56 | 46.0 | 4.11e-01 | 100.0% | 64.1% |
| 4478414 | 103.15.1.2 ↗ | alpha arrays › RuvA-C › Mitoribosomal protein mS23 › Mitoribosomal protein mS23 › MRP-S25 | 0.55 | 21.0 | 2.37e-01 | 88.0% | 43.8% |
| 3960648 | 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 | 0.55 | 48.0 | 3.98e-01 | 93.1% | 64.6% |
| 3792091 | 304.48.1.25 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 | 0.54 | 47.0 | 3.72e-01 | 93.1% | 55.1% |
| 3615272 | 304.48.1.25 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 | 0.54 | 47.0 | 3.59e-01 | 93.1% | 55.3% |
| 3598902 | 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 | 0.54 | 47.0 | 3.60e-01 | 93.1% | 56.1% |
| 3419370 | 6063.1.1.0 ↗ | alpha duplicates or obligate multimers › BNIP3 transmembrane domain › BNIP3 transmembrane domain › BNIP3 transmembrane domain | 0.53 | 17.0 | 3.13e-01 | 97.7% | 98.0% |
| 4936001 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.53 | 25.0 | 3.05e-01 | 93.1% | 66.1% |
| 3590189 | 4967.1.1.0 ↗ | alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases | 0.52 | 27.0 | 2.81e-01 | 93.1% | 51.2% |
D3
medium
residues 130-152_271-308_376-463
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009272901__Fusarium_poae_mitovirus_4__1848153__D300-342_409-485
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05919.17 best | Mitovir_RNA_pol | 121.6 | 6.90e-35 | 57.0% | 16.1% |
| PF05919.17 | Mitovir_RNA_pol | 29.1 | 7.30e-07 | 38.3% | 7.6% |