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VP1_RNA-dependent_RNA_polymerase
Euk-VirInfectious_bursal_disease_virus
VP1_RNA-dependent_RNA_polymerase__NP_690839__Infectious_bursal_disease_virus__10995
Identity
- Accession:
- NP_690839 ↗
- Protein ID:
- VP1_RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
71.9
mean pLDDT
Cluster
View cluster (6 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
medium
residues 189-259_308-337_421-491
Domain cluster:
representative
Pfam (3)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF04197.18 best | Birna_RdRp_palm | 152.0 | 4.10e-44 | 42.4% | 13.6% |
| PF04197.18 | Birna_RdRp_palm | 91.3 | 9.60e-26 | 41.9% | 12.6% |
| PF04197.18 | Birna_RdRp_palm | 50.4 | 2.40e-13 | 18.0% | 5.7% |
CATH (2)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2pggA01 | 3.90.1730.10 | Alpha Beta › Alpha-Beta Complex › Infectious bursal virus vp1 polymerase fold › Infectious bursal virus vp1 polymerase domain | 0.90 | 84.0 | 6.45e-01 | 96.5% | 70.0% |
| 2r7rA05 | 1.10.357.80 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › | 0.53 | 47.0 | 4.68e-01 | 95.3% | 94.9% |
ECOD (4)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| None | — | 0.90 | 87.0 | 5.95e-01 | 100.0% | 58.9% | |
| 1145898 | 304.48.2.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › 'palm' domain in birnaviruse RNA-dependent RNA polymerase › Birna_RdRp_palm | 0.89 | 87.0 | 5.91e-01 | 100.0% | 57.5% |
| 2541763 | 304.48.1.8 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 | 0.64 | 59.0 | 4.54e-01 | 100.0% | 65.1% |
| 4524063 | 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 | 52.0 | 3.51e-01 | 100.0% | 39.4% |
D2
medium
residues 365-420_492-602
Domain cluster:
representative
Pfam (3)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF20488.4 best | Birna_VP1_thumb | 108.4 | 4.70e-31 | 40.1% | 41.9% |
| PF04197.18 | Birna_RdRp_palm | 98.1 | 8.70e-28 | 34.7% | 10.9% |
| PF04197.18 | Birna_RdRp_palm | 63.8 | 2.20e-17 | 26.4% | 8.3% |
CATH (4)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 6j9eJ00 | 3.30.160.560 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › | 0.60 | 22.0 | 3.40e-01 | 79.0% | 81.8% |
| 2nvnA00 | 2.30.31.10 | Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A | 0.56 | 28.0 | 3.34e-01 | 89.2% | 66.7% |
| 3k44B00 | 3.30.2450.30 | Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › | 0.52 | 30.0 | 3.27e-01 | 89.8% | 67.1% |
| 4py5A01 | 3.30.310.10 | Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein | 0.50 | 19.0 | 2.84e-01 | 82.0% | 79.2% |
ECOD (5)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4171382 | 295.1.1.12 ↗ | a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › UPF0231 | 0.60 | 33.0 | 3.84e-01 | 86.2% | 73.3% |
| 4963443 | 5.1.10.0 ↗ | beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed | 0.57 | 29.0 | 3.69e-01 | 77.2% | 83.2% |
| 4315725 | 295.1.1.12 ↗ | a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › UPF0231 | 0.57 | 32.0 | 3.69e-01 | 85.6% | 75.8% |
| 3590950 | 79.1.1.0 ↗ | beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain | 0.53 | 26.0 | 2.73e-01 | 98.2% | 49.7% |
| 4029635 | 241.6.1.0 ↗ | a+b two layers › Type III secretory system chaperone-like › Arp2/3 complex subunits › Arp2/3 complex subunits | 0.50 | 36.0 | 3.98e-01 | 87.4% | 89.9% |
D3
medium
residues 603-698
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF20488.4 best | Birna_VP1_thumb | 160.9 | 3.50e-47 | 99.0% | 58.1% |
CATH (13)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2pusA04 | 6.10.140.300 | Special › Helix non-globular › Helix Hairpins › | 0.92 | 88.0 | 8.35e-01 | 99.0% | 88.9% |
| 4nn1A00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.63 | 51.0 | 4.07e-01 | 90.6% | 67.8% |
| 1q6aA00 | 1.10.1240.30 | Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain | 0.61 | 46.0 | 4.53e-01 | 81.2% | 82.2% |
| 3bqoA00 | 1.25.40.210 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Telomere repeat-binding factor, dimerisation domain | 0.59 | 50.0 | 3.85e-01 | 89.6% | 84.2% |
| 8gr7A01 | 1.10.600.10 | Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase | 0.59 | 53.0 | 3.66e-01 | 99.0% | 43.6% |
| 7w5gA01 | 1.10.600.10 | Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase | 0.59 | 53.0 | 3.54e-01 | 97.9% | 39.8% |
| 1vctA01 | 1.20.58.220 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 | 0.58 | 48.0 | 4.63e-01 | 88.5% | 94.5% |
| 7kypB01 | 1.10.3470.10 | Mainly Alpha › Orthogonal Bundle › ABC transporter involved in vitamin B12 uptake, BtuC › ABC transporter involved in vitamin B12 uptake, BtuC | 0.56 | 42.0 | 3.14e-01 | 83.3% | 70.4% |
| 1n81A00 | 1.10.3030.10 | Mainly Alpha › Orthogonal Bundle › Gametocyte protein Pfg27 › Gametocyte protein Pfg27 | 0.54 | 39.0 | 3.19e-01 | 76.0% | 85.5% |
| 3mnlB00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.54 | 45.0 | 3.72e-01 | 92.7% | 74.7% |
| 5ayvA02 | 1.10.1040.10 | Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 | 0.54 | 37.0 | 3.44e-01 | 71.9% | 57.6% |
| 7powA01 | 1.20.120.1760 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain | 0.53 | 45.0 | 3.58e-01 | 94.8% | 48.5% |
| 1vpdA02 | 1.10.1040.10 | Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 | 0.52 | 42.0 | 3.84e-01 | 89.6% | 93.9% |
ECOD (9)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1578946 | 4967.1.1.15 ↗ | 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 › Birna_VP1_thumb | 0.92 | 88.0 | 6.97e-01 | 100.0% | 55.5% |
| 3287061 | 138.1.1.0 ↗ | alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain | 0.73 | 61.0 | 5.63e-01 | 89.6% | 98.3% |
| 1712471 | 4967.1.1.17 ↗ | 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 › Permu_RdRp_thumb | 0.69 | 62.0 | 5.46e-01 | 99.0% | 68.8% |
| 3215141 | 5086.1.1.0 ↗ | alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins | 0.60 | 42.0 | 3.49e-01 | 72.9% | 66.1% |
| 3694638 | 5059.1.1.10 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › Sulf_transp | 0.55 | 47.0 | 3.36e-01 | 94.8% | 98.7% |
| 4128138 | 604.12.1.4 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › ATG1-like_MIT1 | 0.55 | 45.0 | 3.81e-01 | 89.6% | 65.5% |
| 3560925 | 604.1.1.20 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › AKNA | 0.55 | 43.0 | 4.15e-01 | 85.4% | 89.1% |
| 3663289 | 3755.3.1.0 ↗ | alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin | 0.54 | 43.0 | 3.36e-01 | 84.4% | 77.3% |
| 3230413 | 5001.1.1.0 ↗ | alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like | 0.51 | 40.0 | 3.07e-01 | 84.4% | 38.3% |