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RNA-dependent_RNA_polymerase
Euk-VirUstilaginoidea_virens_RNA_virus_3
RNA-dependent_RNA_polymerase__YP_009004156__Ustilaginoidea_virens_RNA_virus_3__1460374
Identity
- Accession:
- YP_009004156 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
92.8
mean pLDDT
Cluster
View cluster (56 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 1-91_190-225
Domain cluster:
representative
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2qyuA02 | 1.25.40.300 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Putative secreted effector protein | 0.54 | 41.0 | 3.63e-01 | 81.9% | 90.3% |
ECOD (3)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4489668 | 109.2.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid | 0.51 | 45.0 | 3.27e-01 | 100.0% | 66.3% |
| 4013683 | 109.2.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid | 0.51 | 44.0 | 3.19e-01 | 96.9% | 95.1% |
| 3711255 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.50 | 44.0 | 4.16e-01 | 100.0% | 85.0% |
D2
medium
residues 92-189
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009254736__Nigrospora_oryzae_victorivirus_1__1765736__D113-183_214-225
CATH (10)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2ffjA01 | 1.10.8.380 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 | 0.68 | 38.0 | 4.90e-01 | 74.5% | 96.4% |
| 2jmlA00 | 1.10.1660.10 | Mainly Alpha › Orthogonal Bundle › Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 › | 0.61 | 43.0 | 4.64e-01 | 72.4% | 91.4% |
| 3qybA02 | 1.10.8.270 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › putative rabgap domain of human tbc1 domain family member 14 like domains | 0.59 | 47.0 | 4.87e-01 | 100.0% | 91.4% |
| 5grqA00 | 1.10.8.810 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Daxx helical bundle domain | 0.58 | 44.0 | 4.58e-01 | 84.7% | 91.1% |
| 2aplA01 | 1.10.8.330 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › PG0816-like | 0.57 | 38.0 | 4.41e-01 | 78.6% | 100.0% |
| 4s1hA00 | 3.40.1190.20 | Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase | 0.56 | 49.0 | 3.56e-01 | 99.0% | 88.2% |
| 2q7rB00 | 1.20.120.550 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Membrane associated eicosanoid/glutathione metabolism-like domain | 0.54 | 42.0 | 3.75e-01 | 84.7% | 84.4% |
| 4axzA00 | 1.10.3160.10 | Mainly Alpha › Orthogonal Bundle › Bbcrasp-1 › Bbcrasp-1 | 0.54 | 46.0 | 3.64e-01 | 96.9% | 71.6% |
| 4i8qA01 | 3.40.605.10 | Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 | 0.51 | 42.0 | 3.05e-01 | 90.8% | 78.1% |
| 3dtoA01 | 1.10.472.50 | Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › HD-domain/PDEase-like | 0.51 | 40.0 | 4.25e-01 | 84.7% | 100.0% |
ECOD (18)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4871035 | 3833.1.1.0 ↗ | alpha complex topology › TcA alpha-helical shell domain › TcA alpha-helical shell domain › TcA alpha-helical shell domain | 0.63 | 42.0 | 4.50e-01 | 89.8% | 79.5% |
| 3742359 | 3361.1.1.1 ↗ | alpha bundles › C-terminal Pdr1-activating domain of J-protein Zuo1 › C-terminal Pdr1-activating domain of J-protein Zuo1 › C-terminal Pdr1-activating domain of J-protein Zuo1 › RAC_head | 0.61 | 47.0 | 4.79e-01 | 82.7% | 86.3% |
| 2133274 | 611.10.1.1 ↗ | alpha bundles › N-cbl like › DAXX helical bundle domain › DAXX helical bundle domain › Daxx | 0.59 | 45.0 | 4.71e-01 | 82.7% | 95.3% |
| 5074875 | 181.1.1.1 ↗ | alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N | 0.57 | 41.0 | 4.25e-01 | 100.0% | 80.0% |
| 5053895 | 181.1.1.1 ↗ | alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N | 0.57 | 43.0 | 4.65e-01 | 100.0% | 91.8% |
| 4928130 | 181.1.1.1 ↗ | alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N | 0.57 | 42.0 | 4.42e-01 | 100.0% | 84.4% |
| 5043220 | 181.1.1.1 ↗ | alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N | 0.57 | 43.0 | 4.59e-01 | 100.0% | 90.6% |
| 5044994 | 181.1.1.1 ↗ | alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N | 0.57 | 41.0 | 4.41e-01 | 100.0% | 88.2% |
| 3754986 | 181.1.1.0 ↗ | alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins | 0.56 | 41.0 | 3.99e-01 | 100.0% | 68.8% |
| 3549720 | 2498.1.1.69 ↗ | mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › PIG-S | 0.55 | 39.0 | 3.46e-01 | 73.5% | 88.3% |
| 4130802 | 181.1.1.1 ↗ | alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N | 0.55 | 40.0 | 4.32e-01 | 100.0% | 89.4% |
| 4943201 | 181.1.1.32 ↗ | alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54 | 0.54 | 40.0 | 4.24e-01 | 100.0% | 89.4% |
| 3471776 | 524.1.1.1 ↗ | alpha arrays › Ypt/Rab-GAP domain of gyp1p-like › Ypt/Rab-GAP domain of gyp1p › Ypt/Rab-GAP domain of gyp1p › RabGAP-TBC | 0.53 | 45.0 | 3.74e-01 | 100.0% | 51.4% |
| 3744738 | 1016.1.1.3 ↗ | alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › PF26434 | 0.52 | 35.0 | 3.69e-01 | 93.9% | 76.7% |
| 3227761 | 5001.1.1.66 ↗ | alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Srg | 0.51 | 40.0 | 2.86e-01 | 84.7% | 55.3% |
| 4982708 | 3896.1.2.0 ↗ | alpha duplicates or obligate multimers › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-archaeol synthase | 0.51 | 40.0 | 3.40e-01 | 86.7% | 86.8% |
| 5030521 | 5060.2.1.1 ↗ | alpha bundles › V-type ATP synthase subunit C › Toxin coregulated pilus biosynthesis protein E cytoplasmic domain › Toxin coregulated pilus biosynthesis protein E cytoplasmic domain › T2SSF | 0.50 | 35.0 | 3.25e-01 | 71.4% | 75.2% |
| 4960619 | 5060.2.1.1 ↗ | alpha bundles › V-type ATP synthase subunit C › Toxin coregulated pilus biosynthesis protein E cytoplasmic domain › Toxin coregulated pilus biosynthesis protein E cytoplasmic domain › T2SSF | 0.50 | 34.0 | 3.22e-01 | 71.4% | 76.0% |
D3
medium
residues 226-252_280-381_426-477
Domain cluster:
rep: hypothetical_protein_2__YP_009336713__Beihai_toti-like_virus_4__1922734__D167-187_213-323_360-427
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 87.7 | 1.20e-24 | 71.8% | 23.0% |
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2ztbA03 | 2.60.40.3040 | Mainly Beta › Sandwich › Immunoglobulin-like › | 0.55 | 14.0 | 2.81e-01 | 74.6% | 83.3% |
ECOD (4)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3615272 | 304.48.1.25 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 | 0.64 | 51.0 | 4.00e-01 | 85.1% | 55.6% |
| 3792091 | 304.48.1.25 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 | 0.63 | 51.0 | 4.11e-01 | 85.1% | 54.8% |
| 3598902 | 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 | 0.63 | 51.0 | 4.00e-01 | 85.1% | 55.8% |
| 3960648 | 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 | 0.62 | 50.0 | 4.20e-01 | 85.1% | 64.9% |
D4
medium
residues 253-279_382-425_478-548
Domain cluster:
rep: KR816341.1__AKQ06880.1__X__00021__D162-195_238-325
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 63.6 | 2.40e-17 | 50.7% | 14.8% |
| PF02123.22 | RdRP_4 | 37.8 | 1.60e-09 | 47.2% | 9.0% |
D5
medium
residues 549-610
Domain cluster:
rep: RNA_dependent_RNA_polymerase__YP_009508249__Aspergillus_foetidus_slow_virus_1__1087070__D571-625
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 29.7 | 4.80e-07 | 46.8% | 6.2% |
CATH (12)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1xb4B01 | 1.10.10.570 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › """Winged helix"" DNA-binding domain. Chain C. Domain 1" | 0.62 | 45.0 | 3.79e-01 | 77.4% | 96.2% |
| 1h65B00 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.60 | 52.0 | 3.43e-01 | 96.8% | 40.6% |
| 2qrjA02 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.59 | 42.0 | 2.96e-01 | 75.8% | 34.0% |
| 6bfnB02 | 1.10.510.10 | Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 | 0.58 | 47.0 | 3.41e-01 | 93.5% | 54.5% |
| 2e9yB00 | 3.40.1160.10 | Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like | 0.58 | 41.0 | 2.61e-01 | 74.2% | 59.0% |
| 3ismC01 | 1.25.40.240 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ku, C-terminal domain | 0.58 | 48.0 | 3.60e-01 | 91.9% | 53.2% |
| 1fvpA00 | 3.20.20.30 | Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain | 0.56 | 40.0 | 2.74e-01 | 77.4% | 47.2% |
| 3nkyA03 | 1.20.960.20 | Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › | 0.56 | 35.0 | 3.35e-01 | 75.8% | 50.7% |
| 1exzB00 | 1.20.1250.10 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › | 0.56 | 44.0 | 3.48e-01 | 90.3% | 40.0% |
| 8dqaA01 | 3.30.429.10 | Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor | 0.55 | 49.0 | 4.16e-01 | 96.8% | 80.6% |
| 4g4sO01 | 3.40.50.12120 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › POC1 chaperone | 0.53 | 43.0 | 3.14e-01 | 96.8% | 71.0% |
| 7b00A01 | 1.20.1740.10 | Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I | 0.52 | 43.0 | 2.58e-01 | 91.9% | 69.3% |
ECOD (8)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3536798 | 633.24.1.4 ↗ | alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain › RIN1 | 0.69 | 48.0 | 4.12e-01 | 74.2% | 66.0% |
| 4012747 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.67 | 54.0 | 4.95e-01 | 87.1% | 97.5% |
| 4971971 | 5059.1.1.1 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA | 0.65 | 46.0 | 3.59e-01 | 74.2% | 35.7% |
| 1560743 | 4967.1.1.8 ↗ | 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 | 0.65 | 53.0 | 3.86e-01 | 100.0% | 31.9% |
| 3926897 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.61 | 48.0 | 4.10e-01 | 91.9% | 51.4% |
| 3376945 | 109.4.1.1258 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2 | 0.59 | 51.0 | 3.55e-01 | 100.0% | 52.1% |
| 3462836 | 604.6.1.0 ↗ | alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain | 0.54 | 44.0 | 3.41e-01 | 91.9% | 76.6% |
| 3950725 | 301.2.1.1 ↗ | a+b three layers › Bacillus chorismate mutase-like › PurM N-terminal domain-like › PurM N-terminal domain-like › AIRS | 0.52 | 43.0 | 3.07e-01 | 91.9% | 45.3% |