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DNA-directed_RNA_polymerase_RPB1
Euk-VirPithovirus_sibericum
DNA-directed_RNA_polymerase_RPB1__YP_009001052__Pithovirus_sibericum__1450746
Identity
- Accession:
- YP_009001052 ↗
- Protein ID:
- DNA-directed_RNA_polymerase_RPB1
- Kingdom:
- euk
Quality
51.9
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 167-300
Domain cluster:
rep: NP1450L__YP_009703155__African_swine_fever_virus__10497__D1120-1260
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF04990.18 best | RNA_pol_Rpb1_7 | 26.7 | 6.70e-06 | 73.9% | 63.2% |
CATH (32)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3hozA02 | 3.30.1360.140 | Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › | 0.83 | 62.0 | 7.07e-01 | 87.3% | 100.0% |
| 5flmA02 | 3.30.1360.140 | Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › | 0.77 | 72.0 | 7.19e-01 | 98.5% | 96.3% |
| 2if1A00 | 3.30.780.10 | Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain | 0.69 | 39.0 | 4.05e-01 | 91.8% | 58.7% |
| 3va7A05 | 3.30.1360.40 | Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › | 0.68 | 43.0 | 4.95e-01 | 95.5% | 86.0% |
| 4v1al00 | 3.30.780.10 | Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain | 0.66 | 43.0 | 4.35e-01 | 97.8% | 66.2% |
| 4wovA01 | 3.30.200.20 | Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 | 0.64 | 33.0 | 4.07e-01 | 83.6% | 78.6% |
| 4ks7A01 | 3.30.200.20 | Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 | 0.64 | 34.0 | 3.93e-01 | 83.6% | 69.4% |
| 4r78A01 | 3.30.200.20 | Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 | 0.64 | 33.0 | 3.81e-01 | 79.9% | 67.7% |
| 2vz6B01 | 3.30.200.20 | Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 | 0.63 | 35.0 | 4.21e-01 | 83.6% | 84.3% |
| 1d5aA03 | 3.90.1600.10 | Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain | 0.62 | 45.0 | 4.17e-01 | 74.6% | 81.1% |
| 3im8A02 | 3.30.70.250 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding | 0.62 | 31.0 | 3.93e-01 | 85.1% | 84.9% |
| 3hvaA00 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.61 | 44.0 | 4.17e-01 | 77.6% | 61.7% |
| 1zodA01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.61 | 40.0 | 3.98e-01 | 94.0% | 61.7% |
| 2d9oA00 | 3.30.70.330 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain | 0.61 | 36.0 | 4.05e-01 | 85.1% | 76.0% |
| 6eibD00 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.61 | 44.0 | 4.22e-01 | 77.6% | 64.1% |
| 3kxyJ00 | 3.30.1460.10 | Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › | 0.61 | 41.0 | 4.23e-01 | 89.6% | 72.1% |
| 1k3sA00 | 3.30.1460.10 | Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › | 0.61 | 39.0 | 4.28e-01 | 89.6% | 79.6% |
| 2anrA02 | 3.30.1370.10 | Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 | 0.60 | 34.0 | 4.28e-01 | 85.8% | 97.3% |
| 4ritA01 | 3.90.1150.170 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › | 0.60 | 38.0 | 3.26e-01 | 91.8% | 38.2% |
| 3havA01 | 3.30.200.20 | Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 | 0.59 | 30.0 | 3.55e-01 | 82.1% | 70.8% |
| 3jr1A01 | 3.30.200.20 | Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 | 0.59 | 31.0 | 3.55e-01 | 83.6% | 67.7% |
| 1dq3A04 | 3.10.28.10 | Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases | 0.57 | 39.0 | 4.14e-01 | 97.0% | 80.7% |
| 1b24A01 | 3.10.28.10 | Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases | 0.57 | 38.0 | 4.33e-01 | 96.3% | 94.7% |
| 3gb5A00 | 3.40.109.10 | Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase | 0.57 | 40.0 | 3.60e-01 | 71.6% | 58.9% |
| 1zhvA00 | 3.30.2130.10 | Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like | 0.56 | 48.0 | 4.87e-01 | 96.3% | 91.8% |
| 4gt8A00 | 3.30.565.10 | Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain | 0.55 | 35.0 | 3.52e-01 | 80.6% | 63.2% |
| 3c1mA02 | 3.30.2130.10 | Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like | 0.53 | 47.0 | 4.43e-01 | 97.0% | 98.8% |
| 3aawA02 | 3.30.2130.10 | Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like | 0.53 | 45.0 | 4.27e-01 | 92.5% | 92.7% |
| 3tviA02 | 3.30.2130.10 | Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like | 0.52 | 46.0 | 4.39e-01 | 97.8% | 96.2% |
| 1p4xA01 | 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 | 33.0 | 3.37e-01 | 99.3% | 66.1% |
| 1jgsA00 | 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 | 29.0 | 2.96e-01 | 96.3% | 53.6% |
| 3d3yA02 | 3.30.830.10 | Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like | 0.50 | 42.0 | 3.73e-01 | 90.3% | 86.8% |
ECOD (48)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5047025 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.89 | 55.0 | 6.94e-01 | 96.3% | 98.8% |
| 5065987 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.85 | 53.0 | 6.54e-01 | 94.8% | 97.6% |
| 4649672 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.85 | 51.0 | 6.52e-01 | 93.3% | 100.0% |
| 4943247 | 4955.1.1.12 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5 | 0.85 | 55.0 | 6.66e-01 | 97.0% | 97.8% |
| 3479522 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.84 | 53.0 | 6.62e-01 | 94.8% | 100.0% |
| 5070513 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.82 | 49.0 | 6.22e-01 | 95.5% | 100.0% |
| 3486997 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.81 | 73.0 | 7.29e-01 | 94.0% | 98.5% |
| 3734348 | 4955.1.1.1 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_7 | 0.81 | 74.0 | 7.44e-01 | 96.3% | 99.3% |
| 4942837 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.79 | 47.0 | 5.97e-01 | 94.0% | 98.8% |
| 4519566 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.79 | 48.0 | 5.97e-01 | 93.3% | 100.0% |
| 4100594 | 4955.1.1.1 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_7 | 0.79 | 68.0 | 7.14e-01 | 93.3% | 100.0% |
| 3599154 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.79 | 73.0 | 7.40e-01 | 96.3% | 99.2% |
| 3711502 | 4955.1.1.1 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_7 | 0.78 | 71.0 | 7.20e-01 | 94.0% | 99.2% |
| 2754605 | 4955.1.1.1 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_7 | 0.78 | 72.0 | 7.00e-01 | 100.0% | 90.3% |
| 5028902 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.78 | 44.0 | 5.70e-01 | 91.8% | 100.0% |
| 4038458 | 101.1.2.28 ↗ | alpha arrays › HTH › HTH › winged helix domain › eIF-5_eIF-2B | 0.75 | 40.0 | 4.72e-01 | 93.3% | 73.7% |
| 3642268 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.71 | 62.0 | 6.52e-01 | 95.5% | 100.0% |
| 3641694 | 306.3.1.1 ↗ | a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › SUI1 | 0.71 | 39.0 | 4.43e-01 | 91.8% | 69.5% |
| 3307802 | 306.3.1.1 ↗ | a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › SUI1 | 0.71 | 40.0 | 4.82e-01 | 91.8% | 84.1% |
| 4136209 | 304.28.1.0 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain | 0.68 | 39.0 | 4.68e-01 | 86.6% | 87.1% |
| 3593859 | 306.3.1.0 ↗ | a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like | 0.67 | 39.0 | 4.38e-01 | 92.5% | 73.3% |
| 3337628 | 4955.1.1.0 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | 0.66 | 59.0 | 6.07e-01 | 94.8% | 100.0% |
| 3346945 | 4955.1.1.1 ↗ | a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_7 | 0.66 | 59.0 | 6.06e-01 | 94.8% | 100.0% |
| 3316720 | 304.9.1.47 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › DUF4283 | 0.65 | 36.0 | 4.36e-01 | 85.8% | 83.5% |
| 3739575 | 327.11.2.1 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 | 0.64 | 37.0 | 4.38e-01 | 91.0% | 84.4% |
| 3512920 | 327.11.2.1 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 | 0.63 | 37.0 | 4.40e-01 | 88.8% | 86.7% |
| 3300216 | 306.3.1.1 ↗ | a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › SUI1 | 0.63 | 41.0 | 4.58e-01 | 97.0% | 83.8% |
| 3843541 | 306.3.1.1 ↗ | a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › SUI1 | 0.62 | 41.0 | 4.47e-01 | 97.0% | 80.0% |
| 2465371 | 3016.1.1.2 ↗ | a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_3 | 0.62 | 40.0 | 4.24e-01 | 94.8% | 72.1% |
| 3999969 | 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 | 0.61 | 39.0 | 4.53e-01 | 85.8% | 90.5% |
| 3483786 | 327.11.2.1 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 | 0.60 | 37.0 | 4.48e-01 | 89.6% | 96.5% |
| 3177030 | 306.3.1.1 ↗ | a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › SUI1 | 0.60 | 39.0 | 4.34e-01 | 97.0% | 81.8% |
| 3612606 | 304.20.1.0 ↗ | a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain | 0.59 | 44.0 | 4.81e-01 | 86.6% | 93.6% |
| 3489258 | 306.8.1.0 ↗ | a+b two layers › Glucose permease domain IIB-like › TM1457-like › TM1457-like | 0.58 | 36.0 | 3.93e-01 | 91.8% | 75.2% |
| 134075 | 304.9.1.15 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RNA_bind | 0.58 | 35.0 | 3.90e-01 | 76.1% | 77.5% |
| 3505380 | 327.11.2.0 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) | 0.57 | 38.0 | 4.35e-01 | 87.3% | 93.7% |
| 4026919 | 306.3.1.1 ↗ | a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › SUI1 | 0.56 | 39.0 | 4.29e-01 | 97.8% | 87.3% |
| 1211839 | 242.1.1.7 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 | 0.56 | 37.0 | 4.23e-01 | 95.5% | 93.8% |
| 3486660 | 327.11.2.1 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 | 0.56 | 34.0 | 3.93e-01 | 85.8% | 85.3% |
| 4993130 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.56 | 31.0 | 3.98e-01 | 73.9% | 97.3% |
| 3171981 | 327.11.2.1 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 | 0.55 | 38.0 | 4.09e-01 | 93.3% | 84.1% |
| 3792269 | 304.9.1.1 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 | 0.55 | 37.0 | 3.92e-01 | 92.5% | 77.5% |
| 4945934 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.54 | 35.0 | 3.70e-01 | 92.5% | 74.8% |
| 4025573 | 327.11.2.1 ↗ | a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 | 0.53 | 33.0 | 3.94e-01 | 85.8% | 93.3% |
| 3495591 | 304.20.1.0 ↗ | a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain | 0.52 | 43.0 | 4.17e-01 | 86.6% | 95.9% |
| 3739321 | 216.1.1.2 ↗ | a+b two layers › UBC-like › UBC-like › UBC-like › Autophagy_act_C | 0.51 | 43.0 | 3.91e-01 | 97.0% | 68.7% |
| 4933638 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.51 | 34.0 | 3.40e-01 | 82.8% | 64.3% |
| 5081044 | 101.1.2.26 ↗ | alpha arrays › HTH › HTH › winged helix domain › HxlR | 0.50 | 29.0 | 3.31e-01 | 91.8% | 79.8% |
D2
high
residues 324-410
D3
medium
residues 15-28_48-93
D4
medium
residues 488-539_553-565