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DNA-directed_RNA_polymerase_subunit_RPB1
Euk-VirPithovirus_sibericum
DNA-directed_RNA_polymerase_subunit_RPB1__YP_009001268__Pithovirus_sibericum__1450746
Identity
- Accession:
- YP_009001268 ↗
- Protein ID:
- DNA-directed_RNA_polymerase_subunit_RPB1
- Kingdom:
- euk
Quality
74.1
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Megaviricetes›
Pimascovirales›
Pithoviridae›
Alphapithovirus›
Pithovirus_sibericum
TaxID: 1450746
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 151-275
Domain cluster:
rep: DNA-directed_RNA_polymerase_II_largest_subunit__YP_010084808__Shrimp_hemocyte_iridescent_virus__2039780__D81-188
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3e0zA00 | 1.20.58.1400 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Domain of unknown function DUF3837 | 0.56 | 27.0 | 2.92e-01 | 100.0% | 49.5% |
ECOD (23)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4877330 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.86 | 71.0 | 5.33e-01 | 100.0% | 38.5% |
| 3596097 | 4246.1.1.0 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit | 0.84 | 79.0 | 5.66e-01 | 100.0% | 38.7% |
| 3610049 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.80 | 76.0 | 5.33e-01 | 100.0% | 42.6% |
| 4871979 | 4246.1.1.4 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_2, RNA_pol_Rpb1_1 | 0.79 | 71.0 | 5.83e-01 | 100.0% | 56.2% |
| 4380798 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.77 | 73.0 | 5.24e-01 | 100.0% | 39.7% |
| 4648965 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.77 | 73.0 | 5.18e-01 | 100.0% | 37.6% |
| 3393665 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.77 | 72.0 | 5.08e-01 | 100.0% | 44.0% |
| 3487002 | 4246.1.1.0 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit | 0.77 | 73.0 | 5.11e-01 | 100.0% | 41.4% |
| 4023558 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.76 | 72.0 | 5.10e-01 | 100.0% | 43.2% |
| 3166784 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.76 | 72.0 | 4.99e-01 | 100.0% | 43.5% |
| 3348138 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.76 | 71.0 | 5.04e-01 | 100.0% | 41.7% |
| 5026630 | 4246.1.1.0 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit | 0.75 | 69.0 | 5.00e-01 | 100.0% | 37.8% |
| 3596876 | 4246.1.1.0 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit | 0.75 | 70.0 | 5.01e-01 | 100.0% | 45.9% |
| 4079870 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.75 | 70.0 | 4.94e-01 | 100.0% | 42.0% |
| 3717545 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.75 | 70.0 | 5.01e-01 | 100.0% | 46.6% |
| 3185006 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.74 | 70.0 | 4.95e-01 | 100.0% | 40.9% |
| 4027469 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.73 | 69.0 | 4.93e-01 | 100.0% | 39.4% |
| 4801458 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.72 | 61.0 | 4.63e-01 | 100.0% | 40.5% |
| 3205937 | 4246.1.1.2 ↗ | a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 | 0.68 | 63.0 | 4.24e-01 | 100.0% | 54.8% |
| 3773038 | 4.1.1.31 ↗ | beta barrels › SH3 › SH3 › SH3 › Spin-Ssty | 0.54 | 22.0 | 3.27e-01 | 88.8% | 93.3% |
| 4966836 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.53 | 26.0 | 3.53e-01 | 84.0% | 100.0% |
| 3642329 | 206.1.1.1 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase | 0.53 | 38.0 | 3.16e-01 | 74.4% | 74.7% |
| 3265819 | 4.1.1.224 ↗ | beta barrels › SH3 › SH3 › SH3 › Integrase_p58_C | 0.50 | 27.0 | 2.91e-01 | 92.0% | 58.2% |
D2
high
residues 699-843
Domain cluster:
rep: IMGVR_UViG_3300026526_001751-3300026526-Ga0256869_10341511__D627-809
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05000.23 best | RNA_pol_Rpb1_4 | 61.4 | 9.80e-17 | 85.5% | 82.2% |
CATH (32)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5fj8A06 | 1.10.132.30 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain | 0.90 | 82.0 | 8.16e-01 | 93.8% | 95.9% |
| 3h0gA05 | 1.10.132.30 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain | 0.90 | 82.0 | 8.20e-01 | 94.5% | 97.3% |
| 4aybA07 | 1.10.132.30 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain | 0.87 | 67.0 | 7.35e-01 | 78.6% | 99.2% |
| 4c2mA06 | 1.10.132.30 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain | 0.86 | 78.0 | 7.47e-01 | 94.5% | 97.6% |
| 5uh5D02 | 1.10.132.30 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain | 0.86 | 65.0 | 6.71e-01 | 92.4% | 81.9% |
| 2b1eA04 | 1.20.1280.170 | Mainly Alpha › Up-down Bundle › Monooxygenase › Exocyst complex component Exo70 | 0.64 | 38.0 | 4.01e-01 | 84.1% | 66.1% |
| 3q5dA02 | 1.20.58.420 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP | 0.61 | 37.0 | 4.33e-01 | 85.5% | 87.6% |
| 5mlc900 | 1.10.132.20 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor | 0.60 | 43.0 | 4.99e-01 | 80.0% | 100.0% |
| 6xz3A01 | 1.20.120.230 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like | 0.60 | 45.0 | 4.90e-01 | 88.3% | 95.7% |
| 2wzkA01 | 1.20.1310.10 | Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats | 0.60 | 37.0 | 3.92e-01 | 86.2% | 69.3% |
| 4xpwA00 | 1.20.120.50 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like | 0.60 | 44.0 | 4.66e-01 | 86.2% | 85.5% |
| 4oydB00 | 1.10.132.20 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor | 0.57 | 43.0 | 4.79e-01 | 80.0% | 98.3% |
| 3behB01 | 1.20.120.540 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels | 0.57 | 39.0 | 4.26e-01 | 87.6% | 85.5% |
| 4iggB02 | 1.20.120.230 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like | 0.56 | 41.0 | 4.48e-01 | 86.9% | 92.6% |
| 4nx9A01 | 1.20.1330.10 | Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain | 0.56 | 45.0 | 4.46e-01 | 90.3% | 79.4% |
| 3pjaJ01 | 1.20.58.190 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 | 0.56 | 42.0 | 4.46e-01 | 93.8% | 87.0% |
| 2nrjA01 | 1.20.1170.10 | Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › | 0.56 | 46.0 | 3.55e-01 | 89.0% | 90.0% |
| 1io1A01 | 1.20.1330.10 | Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain | 0.56 | 46.0 | 4.40e-01 | 90.3% | 75.1% |
| 4w8pA02 | 1.20.120.230 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like | 0.55 | 43.0 | 4.51e-01 | 89.0% | 90.8% |
| 3kkbA00 | 1.20.120.880 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain | 0.55 | 38.0 | 4.04e-01 | 80.7% | 79.4% |
| 6xkyA01 | 1.20.1330.10 | Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain | 0.55 | 46.0 | 4.26e-01 | 90.3% | 69.5% |
| 5h5mA02 | 1.20.120.230 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like | 0.55 | 45.0 | 4.72e-01 | 88.3% | 96.9% |
| 5z7qA00 | 1.20.1330.10 | Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain | 0.54 | 46.0 | 4.30e-01 | 90.3% | 75.6% |
| 2x64A02 | 1.20.1050.10 | Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › | 0.53 | 38.0 | 4.25e-01 | 89.7% | 92.9% |
| 3ls1A00 | 1.20.120.290 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle | 0.53 | 41.0 | 4.26e-01 | 93.1% | 88.0% |
| 6yz2A01 | 1.20.120.350 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C | 0.53 | 40.0 | 4.28e-01 | 93.1% | 94.2% |
| 4oe8C00 | 1.10.8.1170 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › | 0.53 | 30.0 | 3.81e-01 | 72.4% | 93.1% |
| 4hkuB00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.52 | 35.0 | 3.34e-01 | 91.7% | 56.1% |
| 2gsqA02 | 1.20.1050.10 | Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › | 0.52 | 36.0 | 4.10e-01 | 91.0% | 95.4% |
| 5u56A02 | 1.20.1050.10 | Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › | 0.52 | 38.0 | 4.29e-01 | 98.6% | 100.0% |
| 1st6A03 | 1.20.120.810 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vinculin, Vh2 four-helix bundle | 0.51 | 43.0 | 3.74e-01 | 93.1% | 95.6% |
| 3vurA02 | 1.20.1050.10 | Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › | 0.50 | 35.0 | 3.83e-01 | 90.3% | 90.3% |
ECOD (55)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3583849 | 4958.1.1.1 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 | 0.95 | 71.0 | 5.82e-01 | 77.2% | 46.8% |
| 5063898 | 4958.1.1.2 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_4 | 0.93 | 90.0 | 7.45e-01 | 100.0% | 65.2% |
| 3784119 | 4958.1.1.1 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 | 0.92 | 90.0 | 6.45e-01 | 100.0% | 42.9% |
| 3938779 | 4958.1.1.1 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 | 0.92 | 89.0 | 7.66e-01 | 100.0% | 71.4% |
| 5081035 | 4958.1.1.0 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit | 0.92 | 89.0 | 7.33e-01 | 100.0% | 63.8% |
| None | — | 0.92 | 87.0 | 7.50e-01 | 97.9% | 70.3% | |
| 3907707 | 4958.1.1.2 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_4 | 0.92 | 89.0 | 6.22e-01 | 100.0% | 38.5% |
| 3596868 | 4958.1.1.0 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit | 0.92 | 89.0 | 5.99e-01 | 100.0% | 33.6% |
| 4932735 | 4958.1.1.2 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_4 | 0.92 | 82.0 | 7.34e-01 | 100.0% | 70.5% |
| 4943462 | 4958.1.1.4 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5 | 0.92 | 89.0 | 7.36e-01 | 100.0% | 65.2% |
| 5031555 | 4958.1.1.2 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_4 | 0.91 | 88.0 | 6.75e-01 | 100.0% | 51.7% |
| 5049548 | 4958.1.1.4 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5 | 0.91 | 88.0 | 7.33e-01 | 100.0% | 66.5% |
| 4966695 | 4958.1.1.0 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit | 0.91 | 88.0 | 7.51e-01 | 100.0% | 69.8% |
| 5023529 | 4958.1.1.4 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5 | 0.91 | 87.0 | 7.14e-01 | 100.0% | 74.2% |
| 2629809 | 4958.1.1.1 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 | 0.90 | 87.0 | 7.14e-01 | 100.0% | 63.0% |
| 3711496 | 4958.1.1.1 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 | 0.90 | 87.0 | 7.39e-01 | 100.0% | 69.8% |
| 5028612 | 4958.1.1.4 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5 | 0.89 | 86.0 | 7.27e-01 | 100.0% | 71.4% |
| 4877205 | 4958.1.1.1 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 | 0.89 | 86.0 | 7.43e-01 | 100.0% | 72.2% |
| 4015744 | 4958.1.1.0 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit | 0.88 | 84.0 | 6.99e-01 | 100.0% | 73.5% |
| 3821041 | 4958.1.1.1 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 | 0.87 | 83.0 | 6.90e-01 | 100.0% | 72.8% |
| 3360995 | 4958.1.1.1 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 | 0.87 | 83.0 | 6.53e-01 | 100.0% | 61.8% |
| None | — | 0.84 | 69.0 | 7.06e-01 | 100.0% | 87.9% | |
| 4298800 | 4958.1.1.1 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 | 0.83 | 68.0 | 5.57e-01 | 100.0% | 50.2% |
| 3959563 | 4958.1.1.0 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit | 0.83 | 68.0 | 5.62e-01 | 100.0% | 52.3% |
| 4886353 | 4958.1.1.2 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_4 | 0.82 | 68.0 | 6.53e-01 | 100.0% | 76.9% |
| 4642508 | 4958.1.1.1 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 | 0.77 | 65.0 | 5.23e-01 | 100.0% | 49.4% |
| 4647018 | 4958.1.1.2 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_4 | 0.77 | 64.0 | 5.89e-01 | 100.0% | 68.9% |
| 4887310 | 4958.1.1.2 ↗ | a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_4 | 0.77 | 72.0 | 6.38e-01 | 100.0% | 71.4% |
| 4578841 | 603.1.1.0 ↗ | alpha bundles › STAT-like › t-snare proteins › t-snare proteins | 0.68 | 41.0 | 5.16e-01 | 74.5% | 96.7% |
| 3939708 | 601.24.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) › FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) | 0.64 | 44.0 | 4.96e-01 | 89.0% | 91.8% |
| 3980912 | 601.4.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains | 0.61 | 44.0 | 4.84e-01 | 90.3% | 93.9% |
| 3510163 | 604.5.1.0 ↗ | alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) | 0.59 | 37.0 | 4.21e-01 | 70.3% | 82.7% |
| 5029140 | 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 | 34.0 | 4.24e-01 | 96.6% | 92.2% |
| 4263647 | 192.13.1.1 ↗ | alpha bundles › Long alpha-hairpin › ISY1 N-terminal domain-like › ISY1 N-terminal domain-like › Isy1 | 0.58 | 36.0 | 3.67e-01 | 71.7% | 61.4% |
| 3780254 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.58 | 38.0 | 3.32e-01 | 81.4% | 41.8% |
| 4999868 | 604.1.1.264 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Oxidored_q2 | 0.58 | 35.0 | 4.24e-01 | 70.3% | 94.4% |
| 4796713 | 4031.1.1.1 ↗ | a+b three layers › Nigritoxin middle domain › Nigritoxin middle domain › Nigritoxin middle domain › Flagellin_N,Flagellin_C | 0.58 | 41.0 | 4.45e-01 | 71.7% | 89.2% |
| 4980095 | 310.2.1.0 ↗ | a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF | 0.57 | 39.0 | 4.42e-01 | 75.9% | 95.2% |
| 3892002 | 603.1.1.0 ↗ | alpha bundles › STAT-like › t-snare proteins › t-snare proteins | 0.57 | 38.0 | 3.78e-01 | 71.7% | 63.2% |
| 3386714 | 601.51.1.1 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-helical domain in phase 1 flagellin › alpha-helical domain in phase 1 flagellin › Flagellin_N | 0.57 | 44.0 | 3.64e-01 | 91.0% | 47.0% |
| 4409950 | 601.51.1.2 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-helical domain in phase 1 flagellin › alpha-helical domain in phase 1 flagellin › Flagellin_N,Flagellin_C | 0.56 | 45.0 | 3.66e-01 | 90.3% | 46.9% |
| 3236795 | 601.16.1.2 ↗ | alpha bundles › Four-helical up-and-down bundle › FAT domain of focal adhesion kinase › FAT domain of focal adhesion kinase › Focal_AT | 0.55 | 43.0 | 4.37e-01 | 89.0% | 83.6% |
| 3943720 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.55 | 38.0 | 3.88e-01 | 95.2% | 72.1% |
| 3998998 | 601.16.1.2 ↗ | alpha bundles › Four-helical up-and-down bundle › FAT domain of focal adhesion kinase › FAT domain of focal adhesion kinase › Focal_AT | 0.55 | 44.0 | 4.45e-01 | 89.0% | 83.1% |
| 4142061 | 601.51.1.2 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-helical domain in phase 1 flagellin › alpha-helical domain in phase 1 flagellin › Flagellin_N,Flagellin_C | 0.55 | 46.0 | 3.74e-01 | 90.3% | 47.6% |
| 4054678 | 601.51.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-helical domain in phase 1 flagellin › alpha-helical domain in phase 1 flagellin | 0.55 | 46.0 | 3.35e-01 | 90.3% | 64.5% |
| 3714806 | 4121.1.1.1 ↗ | a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA | 0.55 | 38.0 | 3.08e-01 | 71.7% | 42.1% |
| 3309392 | 5054.1.1.99 ↗ | alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › TMEM33_Pom33 | 0.53 | 46.0 | 4.06e-01 | 93.1% | 85.7% |
| 3208136 | 7022.1.1.1 ↗ | alpha bundles › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › MBOAT | 0.53 | 43.0 | 3.90e-01 | 86.2% | 76.4% |
| 3233670 | 601.1.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin | 0.53 | 44.0 | 4.43e-01 | 89.7% | 92.4% |
| 5029293 | 192.29.1.0 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) | 0.52 | 43.0 | 4.37e-01 | 89.0% | 90.3% |
| 3459730 | 601.3.1.13 ↗ | alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain › TMEM33_Pom33 | 0.52 | 45.0 | 3.91e-01 | 93.1% | 84.4% |
| 3769542 | 109.4.1.595 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › COG7 | 0.51 | 46.0 | 3.38e-01 | 96.6% | 63.9% |
| 3642593 | 109.10.1.1 ↗ | alpha superhelices › Repetitive alpha hairpins › Translin › Translin › Translin | 0.51 | 44.0 | 3.76e-01 | 93.1% | 81.7% |
| 3718789 | 4121.1.1.0 ↗ | a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like | 0.50 | 36.0 | 2.93e-01 | 71.7% | 41.9% |
D3
medium
residues 382-554
Domain cluster:
rep: LC680885.1__BDE75759.1__X__00221__D247-427
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00623.26 best | RNA_pol_Rpb1_2 | 108.1 | 7.90e-31 | 96.5% | 96.4% |
D4
medium
residues 564-609_628-652
Domain cluster:
representative
D5
medium
residues 610-627_653-698
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF04983.24 best | RNA_pol_Rpb1_3 | 33.5 | 5.30e-08 | 73.4% | 25.9% |
CATH (4)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1twfA05 | 1.10.274.100 | Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › RNA polymerase Rpb1, domain 3 | 0.93 | 81.0 | 5.89e-01 | 92.2% | 66.7% |
| 4c3iA04 | 1.10.274.100 | Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › RNA polymerase Rpb1, domain 3 | 0.87 | 74.0 | 5.36e-01 | 90.6% | 68.3% |
| 1xvxA02 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.59 | 47.0 | 3.54e-01 | 87.5% | 47.4% |
| 2rinA01 | 3.40.190.10 | Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II | 0.50 | 39.0 | 2.77e-01 | 81.2% | 92.1% |
ECOD (4)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5061902 | 4959.1.1.1 ↗ | a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_3 | 0.91 | 77.0 | 5.96e-01 | 89.1% | 82.4% |
| 4445936 | 4959.1.1.1 ↗ | a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_3 | 0.83 | 70.0 | 5.19e-01 | 90.6% | 80.0% |
| 4394123 | 4959.1.1.1 ↗ | a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_3 | 0.82 | 72.0 | 5.36e-01 | 93.8% | 78.6% |
| 4955710 | 1075.3.1.1 ↗ | alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC importer transmembrane domain fold › Type I ABC importer transmembrane domain fold › BPD_transp_1 | 0.53 | 45.0 | 3.06e-01 | 96.9% | 52.7% |