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DNA-directed_RNA_polymerase_subunit_2
Euk-VirBrazilian_marseillevirus
DNA-directed_RNA_polymerase_subunit_2__YP_009238550__Brazilian_marseillevirus__1813599
Identity
- Accession:
- YP_009238550 ↗
- Protein ID:
- DNA-directed_RNA_polymerase_subunit_2
- Kingdom:
- euk
Quality
76.8
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Megaviricetes›
Pimascovirales›
Marseilleviridae›
Marseillevirus›
Brazilian_marseillevirus
TaxID: 1813599
Cluster
View cluster (58 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 189-348
Domain cluster:
rep: DNA-directed_RNA_polymerase_subunit_B__YP_009021104__Anopheles_minimus_iridovirus__1465751__D170-274
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF04561.20 best | RNA_pol_Rpb2_2 | 22.0 | 1.60e-04 | 90.6% | 60.5% |
D2
medium
residues 24-47_171-188_365-427
Domain cluster:
representative
CATH (5)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2i7uA00 | 6.10.250.1010 | Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › | 0.57 | 33.0 | 4.09e-01 | 89.5% | 95.2% |
| 2jswA00 | 1.20.1410.10 | Mainly Alpha › Up-down Bundle › I/LWEQ domain › I/LWEQ domain | 0.55 | 45.0 | 3.73e-01 | 88.6% | 76.7% |
| 6lumD01 | 1.20.1300.10 | Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit | 0.54 | 40.0 | 3.80e-01 | 77.1% | 82.4% |
| 2wdqD00 | 1.20.1300.10 | Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit | 0.54 | 40.0 | 4.00e-01 | 77.1% | 94.3% |
| 3jvoA00 | 1.10.3230.30 | Mainly Alpha › Orthogonal Bundle › Hypothetical protein yqbg › Phage gp6-like head-tail connector protein | 0.51 | 35.0 | 3.68e-01 | 88.6% | 77.1% |
ECOD (14)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3601611 | 4010.1.1.2 ↗ | a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_1,RNA_pol_Rpb2_3 | 0.90 | 86.0 | 5.80e-01 | 100.0% | 70.5% |
| 5026625 | 4010.1.1.0 ↗ | a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase | 0.89 | 83.0 | 5.68e-01 | 97.1% | 71.9% |
| 4416308 | 4010.1.1.2 ↗ | a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_1,RNA_pol_Rpb2_3 | 0.84 | 76.0 | 5.38e-01 | 95.2% | 77.5% |
| 4402835 | 4010.1.1.2 ↗ | a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_1,RNA_pol_Rpb2_3 | 0.83 | 75.0 | 5.42e-01 | 95.2% | 73.6% |
| 3515716 | 4010.1.1.2 ↗ | a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_1,RNA_pol_Rpb2_3 | 0.82 | 78.0 | 5.50e-01 | 100.0% | 70.5% |
| 3870572 | 148.1.3.0 ↗ | alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain | 0.63 | 57.0 | 5.14e-01 | 100.0% | 96.6% |
| 3248839 | 605.1.1.0 ↗ | alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase | 0.59 | 43.0 | 4.14e-01 | 84.8% | 66.7% |
| 3243162 | 5001.1.1.7 ↗ | alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Frizzled | 0.56 | 46.0 | 3.28e-01 | 90.5% | 47.7% |
| 5007869 | 601.33.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain | 0.55 | 32.0 | 3.31e-01 | 86.7% | 60.0% |
| 398972 | 5069.1.3.0 ↗ | alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits | 0.54 | 40.0 | 4.00e-01 | 77.1% | 94.3% |
| 3198437 | 150.1.1.0 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin | 0.53 | 37.0 | 3.30e-01 | 71.4% | 52.9% |
| 3574826 | 605.1.1.236 ↗ | alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Strabismus | 0.53 | 37.0 | 3.94e-01 | 73.3% | 83.2% |
| 3618159 | 601.1.1.95 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › F_actin_bind | 0.51 | 36.0 | 3.47e-01 | 72.4% | 90.8% |
| 4119318 | 108.2.1.1 ↗ | alpha arrays › EF-hand › Insect pheromone/odorant-binding proteins › Insect pheromone/odorant-binding proteins › PBP_GOBP | 0.51 | 36.0 | 3.44e-01 | 84.8% | 62.4% |
D3
medium
residues 72-170
Domain cluster:
rep: RNA_polymerase_beta_subunit__YP_009342128__Lymphocystis_disease_virus_Sa__1898060__D32-96_108-123
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF04563.21 best | RNA_pol_Rpb2_1 | 38.6 | 1.20e-09 | 89.9% | 37.0% |
D4
medium
residues 353-364_428-500_658-725
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF04565.22 best | RNA_pol_Rpb2_3 | 48.5 | 1.10e-12 | 43.1% | 100.0% |
ECOD (8)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4818392 | 1.1.2.1 ↗ | beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb2_6 | 0.61 | 40.0 | 4.22e-01 | 96.7% | 72.3% |
| 1108095 | 4042.1.1.0 ↗ | a+b complex topology › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase | 0.60 | 37.0 | 4.33e-01 | 92.8% | 83.5% |
| 2700180 | 4042.1.1.1 ↗ | a+b complex topology › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_6 | 0.59 | 37.0 | 4.27e-01 | 92.8% | 83.5% |
| 3450033 | 4042.1.1.1 ↗ | a+b complex topology › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_6 | 0.59 | 40.0 | 4.32e-01 | 96.7% | 79.1% |
| 5062682 | 4042.1.1.3 ↗ | a+b complex topology › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_5 | 0.58 | 38.0 | 3.93e-01 | 93.5% | 70.3% |
| 3608067 | 4042.1.1.1 ↗ | a+b complex topology › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_6 | 0.57 | 38.0 | 4.10e-01 | 93.5% | 79.2% |
| 4902577 | 4042.1.1.2 ↗ | a+b complex topology › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › barrel domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_6,RNA_pol_Rpb2_5 | 0.54 | 40.0 | 3.98e-01 | 96.1% | 71.3% |
| 3720517 | 244.1.1.0 ↗ | a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C | 0.51 | 26.0 | 3.11e-01 | 72.5% | 72.6% |
D5
medium
residues 501-582
Domain cluster:
rep: DNA-directed_RNA_polymerase_subunit_beta__YP_003406778__Marseillevirus_marseillevirus__694581__D519-604
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF04566.19 best | RNA_pol_Rpb2_4 | 42.5 | 7.60e-11 | 65.8% | 87.1% |
D6
medium
residues 583-657
Domain cluster:
rep: DNA-directed_RNA_polymerase_subunit_2__YP_004346997__Lausannevirus__999883__D585-653
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF04567.23 best | RNA_pol_Rpb2_5 | 36.0 | 1.50e-08 | 57.3% | 100.0% |
D7
medium
residues 726-772_945-1035_1064-1126
Domain cluster:
rep: KU935715.1__AND75470.1__ME3_309__00309__D264-326_420-534
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00562.34 best | RNA_pol_Rpb2_6 | 136.7 | 1.60e-39 | 78.6% | 35.9% |
| PF00562.34 | RNA_pol_Rpb2_6 | 24.0 | 2.80e-05 | 22.9% | 10.7% |
D8
medium
residues 787-839