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RNA-dependent_RNA_polymerase
Euk-VirGigaspora_margarita_mitovirus_4
RNA-dependent_RNA_polymerase__YP_009551961__Gigaspora_margarita_mitovirus_4__2082668
Identity
- Accession:
- YP_009551961 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
49.9
mean pLDDT
Taxonomy
Orthornavirae›
Lenarviricota›
Howeltoviricetes›
Cryppavirales›
Mitoviridae›
Duamitovirus›
Gigaspora_margarita_mitovirus_4
TaxID: 2082668
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
medium
residues 26-100_148-172
D2
medium
residues 173-296
Domain cluster:
rep: RNA_dependent_RNA_polymerase__YP_005352912__Clitocybe_odora_virus__1162083__D59-187_563-580
CATH (10)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2jbwA01 | 1.20.1440.110 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › acylaminoacyl peptidase | 0.63 | 41.0 | 4.41e-01 | 99.2% | 77.7% |
| 2x1dA02 | 1.10.10.2120 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › | 0.60 | 32.0 | 3.94e-01 | 71.0% | 83.8% |
| 3pivA00 | 1.20.1250.10 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › | 0.55 | 44.0 | 4.13e-01 | 86.3% | 84.6% |
| 4k84A00 | 1.10.3520.10 | Mainly Alpha › Orthogonal Bundle › Glycolipid transfer protein, GLTP › Glycolipid transfer protein | 0.55 | 49.0 | 4.18e-01 | 99.2% | 90.8% |
| 1tdpA00 | 1.20.1440.50 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like | 0.54 | 39.0 | 4.09e-01 | 100.0% | 83.8% |
| 1f5qB02 | 1.10.472.10 | Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like | 0.54 | 38.0 | 3.69e-01 | 91.9% | 64.5% |
| 4nt1A00 | 1.10.3520.10 | Mainly Alpha › Orthogonal Bundle › Glycolipid transfer protein, GLTP › Glycolipid transfer protein | 0.54 | 47.0 | 4.01e-01 | 95.2% | 95.5% |
| 2nq2A00 | 1.10.3470.10 | Mainly Alpha › Orthogonal Bundle › ABC transporter involved in vitamin B12 uptake, BtuC › ABC transporter involved in vitamin B12 uptake, BtuC | 0.53 | 42.0 | 3.14e-01 | 83.1% | 90.9% |
| 2vcnA01 | 1.10.520.10 | Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › | 0.53 | 42.0 | 4.02e-01 | 84.7% | 75.4% |
| 3wvoC02 | 1.10.132.100 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › | 0.50 | 43.0 | 4.30e-01 | 98.4% | 90.0% |
ECOD (6)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3809284 | 2004.1.1.30 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C | 0.65 | 54.0 | 4.02e-01 | 100.0% | 36.4% |
| 3835030 | 604.5.1.7 ↗ | alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › ALMT | 0.60 | 54.0 | 4.92e-01 | 100.0% | 95.2% |
| 4472717 | 3930.1.1.0 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase | 0.59 | 48.0 | 5.12e-01 | 100.0% | 99.1% |
| 4110399 | 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 | 0.58 | 46.0 | 3.67e-01 | 83.9% | 89.2% |
| 3250971 | 616.1.1.0 ↗ | alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain | 0.58 | 43.0 | 4.74e-01 | 86.3% | 98.0% |
| 1487362 | 3930.2.1.1 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in endoribonuclease Dicer › Helical bundle in endoribonuclease Dicer › Dicer_PBD | 0.54 | 46.0 | 4.75e-01 | 100.0% | 96.6% |
D3
medium
residues 505-534_557-654
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009336518__Wenzhou_narna-like_virus_2__1923577__D318-359_395-457
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05919.17 best | Mitovir_RNA_pol | 65.7 | 5.80e-18 | 76.6% | 15.7% |
D4
medium
residues 535-556_655-711
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05919.17 best | Mitovir_RNA_pol | 60.4 | 2.30e-16 | 81.0% | 10.3% |
CATH (22)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 7uinD01 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.81 | 73.0 | 5.67e-01 | 100.0% | 90.4% |
| 1ayeA01 | 3.30.70.340 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like | 0.66 | 54.0 | 5.04e-01 | 88.6% | 85.9% |
| 2bvfA03 | 3.40.462.20 | Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › | 0.64 | 47.0 | 3.52e-01 | 79.7% | 74.3% |
| 3d68A01 | 3.30.70.340 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like | 0.63 | 51.0 | 4.84e-01 | 87.3% | 92.4% |
| 1vdhA01 | 3.30.70.1030 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Apc35880; domain 1 | 0.62 | 49.0 | 4.29e-01 | 86.1% | 85.1% |
| 1kwmA01 | 3.30.70.340 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like | 0.61 | 50.0 | 4.84e-01 | 88.6% | 97.7% |
| 1vk8A00 | 3.30.70.930 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.59 | 46.0 | 4.40e-01 | 84.8% | 97.8% |
| 2hg4D03 | 3.40.366.10 | Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 | 0.58 | 48.0 | 3.24e-01 | 91.1% | 51.0% |
| 1zpwX00 | 3.30.70.240 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.57 | 44.0 | 4.38e-01 | 83.5% | 98.8% |
| 2aj2A02 | 3.30.70.1300 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › VC0467-like domains | 0.57 | 37.0 | 3.57e-01 | 72.2% | 57.8% |
| 6u9hF02 | 3.30.70.1150 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT-like. Chain A, domain 2 | 0.56 | 44.0 | 4.46e-01 | 83.5% | 97.4% |
| 1earA02 | 3.30.70.790 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain | 0.55 | 40.0 | 4.18e-01 | 75.9% | 92.8% |
| 1lfpA03 | 3.30.70.980 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain | 0.55 | 44.0 | 4.59e-01 | 88.6% | 100.0% |
| 1gmuA01 | 3.30.70.790 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain | 0.54 | 38.0 | 4.02e-01 | 73.4% | 92.5% |
| 1zd0A01 | 3.30.2380.10 | Alpha Beta › 2-Layer Sandwich › PF0523-like › CGI121/TPRKB | 0.53 | 42.0 | 3.61e-01 | 86.1% | 100.0% |
| 5ijgA01 | 3.40.640.10 | Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) | 0.53 | 42.0 | 3.07e-01 | 84.8% | 90.6% |
| 3hx9B00 | 3.30.70.100 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.52 | 40.0 | 3.77e-01 | 83.5% | 98.0% |
| 1ycyA00 | 2.30.30.100 | Mainly Beta › Roll › SH3 type barrels. › | 0.52 | 27.0 | 2.95e-01 | 96.2% | 58.1% |
| 1hc7A01 | 3.30.930.10 | Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 | 0.51 | 45.0 | 3.16e-01 | 100.0% | 62.5% |
| 2kviA00 | 3.30.70.330 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain | 0.51 | 39.0 | 4.00e-01 | 83.5% | 100.0% |
| 1wr2A02 | 3.30.1490.20 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain | 0.50 | 35.0 | 3.60e-01 | 73.4% | 76.9% |
| 1vbkA01 | 3.30.70.1510 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › THUMP domain-like | 0.50 | 37.0 | 3.73e-01 | 81.0% | 98.8% |
ECOD (38)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3810170 | 304.48.1.43 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mitovir_RNA_pol | 0.93 | 89.0 | 6.53e-01 | 100.0% | 93.3% |
| 3306901 | 304.48.1.43 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mitovir_RNA_pol | 0.93 | 89.0 | 6.70e-01 | 100.0% | 91.5% |
| 3336938 | 304.48.1.43 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mitovir_RNA_pol | 0.92 | 87.0 | 5.87e-01 | 100.0% | 65.6% |
| 3068775 | 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 | 0.82 | 75.0 | 5.48e-01 | 100.0% | 74.9% |
| 3934202 | 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 | 0.80 | 72.0 | 5.84e-01 | 100.0% | 97.9% |
| 3257066 | 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 | 68.0 | 4.81e-01 | 100.0% | 56.7% |
| 3315278 | 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 | 57.0 | 4.94e-01 | 86.1% | 83.2% |
| 4988159 | 304.37.1.1 ↗ | a+b two layers › Alpha-beta plaits › Sulfite reductase, domains 1 and 3 › Sulfite reductase, domains 1 and 3 › NIR_SIR_ferr | 0.71 | 49.0 | 4.36e-01 | 72.2% | 87.8% |
| 2038566 | 304.8.1.22 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › AHAS-like_ACT | 0.66 | 46.0 | 4.58e-01 | 72.2% | 100.0% |
| 3859590 | 386.1.1.248 ↗ | few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_ZNF592 | 0.66 | 41.0 | 4.81e-01 | 83.5% | 98.0% |
| 3405197 | 304.7.1.1 ↗ | a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Propep_M14 | 0.64 | 51.0 | 5.11e-01 | 84.8% | 100.0% |
| 4060507 | 304.117.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg | 0.64 | 44.0 | 4.60e-01 | 70.9% | 100.0% |
| 5054705 | 304.7.1.0 ↗ | a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors | 0.63 | 48.0 | 4.80e-01 | 81.0% | 90.0% |
| 3946828 | 304.11.1.0 ↗ | a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase | 0.63 | 44.0 | 4.76e-01 | 73.4% | 100.0% |
| 5047263 | 304.24.1.3 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_III | 0.62 | 43.0 | 4.39e-01 | 72.2% | 100.0% |
| 4965210 | 304.163.1.0 ↗ | a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain | 0.61 | 44.0 | 4.96e-01 | 84.8% | 100.0% |
| 3593586 | 304.3.1.0 ↗ | a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain | 0.61 | 47.0 | 4.74e-01 | 83.5% | 93.8% |
| 4263279 | 304.11.1.0 ↗ | a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase | 0.60 | 48.0 | 4.71e-01 | 86.1% | 92.9% |
| 4565839 | 304.120.1.0 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI | 0.60 | 43.0 | 4.79e-01 | 79.7% | 100.0% |
| 3961146 | 304.11.1.1 ↗ | a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Acyl_transf_1 | 0.60 | 49.0 | 4.18e-01 | 89.9% | 63.6% |
| 5022748 | 304.56.1.2 ↗ | a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like › CRISPR_Cas2 | 0.59 | 45.0 | 4.32e-01 | 81.0% | 100.0% |
| 4943089 | 304.126.1.0 ↗ | a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C | 0.59 | 41.0 | 4.17e-01 | 74.7% | 100.0% |
| 4614439 | 304.117.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg | 0.58 | 46.0 | 4.60e-01 | 86.1% | 100.0% |
| 4944520 | 304.8.1.0 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like | 0.57 | 47.0 | 3.42e-01 | 91.1% | 61.7% |
| 4329557 | 304.24.1.0 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like | 0.56 | 45.0 | 4.31e-01 | 86.1% | 93.3% |
| 4520709 | 304.117.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg | 0.56 | 44.0 | 4.43e-01 | 86.1% | 100.0% |
| 3723383 | 304.3.1.1 ↗ | a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA | 0.56 | 43.0 | 4.33e-01 | 84.8% | 96.2% |
| 4070496 | 304.117.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg | 0.56 | 43.0 | 4.47e-01 | 86.1% | 97.3% |
| 1145775 | 3268.1.1.1 ↗ | a+b two layers › N-terminal domain in xanthine dehydrogenase › N-terminal domain in xanthine dehydrogenase › N-terminal domain in xanthine dehydrogenase › XdhC_CoxI | 0.54 | 41.0 | 4.05e-01 | 81.0% | 100.0% |
| 3502962 | 4.1.1.89 ↗ | beta barrels › SH3 › SH3 › SH3 › SM-ATX | 0.54 | 31.0 | 3.10e-01 | 98.7% | 52.5% |
| 4990783 | 2004.1.1.73 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 | 0.54 | 38.0 | 2.83e-01 | 78.5% | 26.9% |
| 4030243 | 304.24.1.0 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like | 0.54 | 42.0 | 3.85e-01 | 84.8% | 79.0% |
| 5293 | 304.22.1.1 ↗ | a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C | 0.53 | 39.0 | 4.16e-01 | 79.7% | 92.6% |
| 3945340 | 235.1.1.9 ↗ | a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT | 0.53 | 38.0 | 3.08e-01 | 75.9% | 76.7% |
| None | — | 0.52 | 39.0 | 3.52e-01 | 82.3% | 95.7% | |
| 4156338 | 304.117.1.1 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg | 0.52 | 41.0 | 4.24e-01 | 88.6% | 97.3% |
| 4215974 | 304.22.1.1 ↗ | a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C | 0.51 | 40.0 | 4.16e-01 | 87.3% | 97.1% |
| 4598958 | 4113.1.1.0 ↗ | beta barrels › VC0467-like › VC0467-like › VC0467-like | 0.51 | 43.0 | 3.35e-01 | 94.9% | 82.8% |
D5
medium
residues 712-751_779-796