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RNA-dependent_RNA_polymerase
Euk-VirWhite_clover_mottle_virus
RNA-dependent_RNA_polymerase__YP_009315896__White_clover_mottle_virus__1913024
Identity
- Accession:
- YP_009315896 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
72.4
mean pLDDT
Cluster
View cluster (38 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 91-194
Domain cluster:
rep: P1_protein__YP_667839__Chickpea_chlorotic_stunt_virus__328430__D113-193
D2
medium
residues 212-230_317-442
Domain cluster:
rep: hypothetical_protein_1__YP_009337259__Shuangao_sobemo-like_virus_2__1923475__D83-106_193-282
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02122.22 best | Peptidase_S39 | 111.0 | 8.50e-32 | 74.5% | 50.7% |
D3
medium
residues 231-316
Domain cluster:
rep: hypothetical_protein__YP_009825042__Birds-foot_trefoil_enamovirus_1__2283314__D329-413
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02122.22 best | Peptidase_S39 | 108.1 | 6.30e-31 | 100.0% | 42.4% |
D4
medium
residues 675-719_740-771
Domain cluster:
representative
D5
medium
residues 772-804_935-1026_1044-1097
Domain cluster:
rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 96.1 | 3.50e-27 | 98.3% | 43.7% |
D6
medium
residues 805-934_1027-1043
Domain cluster:
rep: hypothetical_protein_2__YP_009337098__Changjiang_polero-like_virus_1__1922799__D1-82_112-138
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 94.1 | 1.30e-26 | 98.0% | 30.3% |
D7
medium
residues 1098-1178
Domain cluster:
representative
CATH (22)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2pqrA01 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.78 | 51.0 | 4.89e-01 | 70.4% | 58.1% |
| 3n2oA03 | 1.20.58.930 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.70 | 50.0 | 4.78e-01 | 75.3% | 84.4% |
| 4iluA02 | 1.20.58.1290 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › CarD-like, C-terminal domain | 0.66 | 46.0 | 4.18e-01 | 74.1% | 87.4% |
| 1yz5B00 | 1.20.190.20 | Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › 14-3-3 domain | 0.65 | 55.0 | 4.06e-01 | 96.3% | 58.5% |
| 3llwD00 | 1.10.600.10 | Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase | 0.65 | 54.0 | 3.62e-01 | 88.9% | 29.8% |
| 3cbuA02 | 1.20.1050.10 | Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › | 0.64 | 51.0 | 4.41e-01 | 88.9% | 63.4% |
| 2qr4A01 | 1.20.140.70 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Oligopeptidase f, N-terminal domain | 0.64 | 55.0 | 4.43e-01 | 95.1% | 63.5% |
| 2yfaA02 | 1.20.1440.210 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › | 0.64 | 55.0 | 4.89e-01 | 96.3% | 71.6% |
| 3pjaJ01 | 1.20.58.190 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 | 0.63 | 50.0 | 4.30e-01 | 86.4% | 70.2% |
| 5mlc900 | 1.10.132.20 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor | 0.62 | 49.0 | 4.44e-01 | 85.2% | 92.5% |
| 1wrdA00 | 1.20.58.160 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.61 | 53.0 | 5.00e-01 | 96.3% | 91.8% |
| 4s2rQ03 | 3.90.230.10 | Alpha Beta › Alpha-Beta Complex › Creatine Amidinohydrolase › Creatinase/methionine aminopeptidase superfamily | 0.61 | 48.0 | 3.28e-01 | 86.4% | 97.3% |
| 5jqkA03 | 3.90.230.10 | Alpha Beta › Alpha-Beta Complex › Creatine Amidinohydrolase › Creatinase/methionine aminopeptidase superfamily | 0.60 | 46.0 | 3.16e-01 | 82.7% | 98.3% |
| 2wauA02 | 1.20.58.830 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.60 | 51.0 | 4.52e-01 | 96.3% | 99.2% |
| 6jkvA00 | 3.60.40.10 | Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain | 0.59 | 42.0 | 3.02e-01 | 72.8% | 52.6% |
| 8alzB08 | 1.10.3380.10 | Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › Sec63 N-terminal domain-like domain | 0.58 | 44.0 | 3.81e-01 | 82.7% | 94.7% |
| 4oydB00 | 1.10.132.20 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor | 0.58 | 49.0 | 4.36e-01 | 93.8% | 94.9% |
| 4mk3A02 | 1.20.1050.10 | Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › | 0.57 | 46.0 | 4.14e-01 | 90.1% | 80.0% |
| 3dadA00 | 1.25.10.10 | Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant | 0.57 | 49.0 | 3.34e-01 | 100.0% | 44.8% |
| 4yxtA02 | 3.40.47.10 | Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase | 0.55 | 36.0 | 2.92e-01 | 70.4% | 35.5% |
| 4h0pB02 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.53 | 45.0 | 3.38e-01 | 97.5% | 52.2% |
| 3ccyA02 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.53 | 44.0 | 3.71e-01 | 95.1% | 58.5% |
ECOD (12)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3861871 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.68 | 49.0 | 4.74e-01 | 90.1% | 66.3% |
| 3173503 | 109.4.1.235 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SRP68 | 0.68 | 60.0 | 4.12e-01 | 100.0% | 53.3% |
| 4639996 | 150.7.1.1 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PE › PE › PE | 0.64 | 44.0 | 4.30e-01 | 71.6% | 78.9% |
| 3306390 | 604.9.1.1 ↗ | alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p | 0.64 | 55.0 | 5.06e-01 | 96.3% | 83.8% |
| 3440537 | 109.4.1.91 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec10_HB | 0.64 | 55.0 | 3.91e-01 | 100.0% | 78.9% |
| 3739447 | 109.46.1.1 ↗ | alpha superhelices › Repetitive alpha hairpins › Helical domain in TOPLESS related protein 2 (TPR2) › Helical domain in TOPLESS related protein 2 (TPR2) › CTLH | 0.62 | 54.0 | 4.56e-01 | 97.5% | 71.4% |
| 3890229 | 603.1.1.64 ↗ | alpha bundles › STAT-like › t-snare proteins › t-snare proteins › CUPID | 0.62 | 54.0 | 5.11e-01 | 96.3% | 89.5% |
| 3923718 | 109.4.1.163 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SYMPK_PTA1_N | 0.59 | 51.0 | 3.02e-01 | 100.0% | 22.7% |
| 185553 | 109.4.1.80 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RRN3 | 0.58 | 50.0 | 3.77e-01 | 98.8% | 45.9% |
| 3691039 | 605.1.1.1 ↗ | alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA | 0.56 | 40.0 | 4.06e-01 | 75.3% | 80.0% |
| 4393207 | 5049.1.3.1 ↗ | alpha complex topology › Ammonium transporter-related › Ammonium transporter-related › Na(+)-translocating NADH-quinone reductase subunit B › NQR2_RnfD_RnfE | 0.54 | 43.0 | 2.94e-01 | 91.4% | 76.7% |
| 3309675 | 226.1.1.0 ↗ | a+b two layers › POZ domain › POZ domain › POZ domain | 0.53 | 40.0 | 2.92e-01 | 82.7% | 96.3% |