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RNA-dependent_RNA_polymerase

Euk-Vir

Hubei_orthoptera_virus_4

RNA-dependent_RNA_polymerase__YP_009337883__Hubei_orthoptera_virus_4__1923012

Identity

Accession:
YP_009337883 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

81.8 mean pLDDT

Cluster

View cluster (17 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 66-184_221-268
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337879__Hubei_noda-like_virus_9__1922989__D136-259_287-345
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF19222.6 best Noda_Vmethyltr 132.9 1.10e-38 74.2% 70.3%
D2 medium residues 185-220_269-385
PDB
Domain cluster: rep: hypothetical_protein__YP_009329958__Beihai_noda-like_virus_18__1922471__D201-230_309-395
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF19222.6 best Noda_Vmethyltr 39.6 6.10e-10 27.5% 24.3%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5058484 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.58 24.0 3.32e-01 70.6% 77.1%
D3 medium residues 386-402_711-848
PDB
Domain cluster: rep: hypothetical_protein__YP_009329984__Beihai_noda-like_virus_29__1922483__D408-447_732-867
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2i5hA02 1.10.150.280 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AF1531-like domain 0.51 24.0 2.95e-01 81.3% 68.8%
D4 medium residues 403-423_445-527_584-621
PDB
Domain cluster: rep: hypothetical_protein__YP_009336491__Shuangao_insect_virus_10__1923466__D348-411_426-443_486-529
D5 medium residues 424-444_528-583_622-710
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h5xA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.80 55.0 6.53e-01 75.9% 100.0%
1gx5A03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.79 57.0 6.63e-01 80.7% 100.0%
1ra6A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.76 48.0 5.95e-01 71.7% 100.0%
5jxsA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.75 60.0 6.47e-01 87.3% 96.5%
6qwtA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.74 58.0 6.32e-01 87.3% 96.5%
1khvA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.72 55.0 6.24e-01 80.1% 100.0%
7uinD01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.72 63.0 6.31e-01 91.0% 100.0%
4ol8A01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.68 47.0 5.22e-01 100.0% 87.4%
1u8sA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.66 35.0 4.83e-01 74.1% 100.0%
1s7hA02 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 32.0 4.37e-01 72.3% 98.8%
1hi8A03 3.30.70.1600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 53.0 5.25e-01 89.8% 88.6%
2rilA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 33.0 4.27e-01 72.3% 96.8%
3hvwA00 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.56 44.0 4.53e-01 81.3% 84.9%
2oi2A02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.55 34.0 3.71e-01 72.9% 75.4%
4fzlA01 1.10.150.790 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.53 29.0 3.75e-01 78.9% 97.7%
2x7iA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.53 33.0 3.74e-01 74.1% 81.2%
1lwbA00 1.20.90.10 Mainly Alpha › Up-down Bundle › Phospholipase A2 › Phospholipase A2 domain 0.53 26.0 2.98e-01 84.9% 60.7%
4uskA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.52 33.0 3.42e-01 75.3% 66.9%
2y8nA00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.51 46.0 2.97e-01 100.0% 92.5%
3k17A02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.51 32.0 3.46e-01 70.5% 73.6%
1kvkA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.51 33.0 3.50e-01 79.5% 73.0%
4i8qA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.50 36.0 3.02e-01 72.3% 67.9%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4875416 304.48.1.13 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flavi_NS5 0.86 82.0 6.04e-01 100.0% 85.7%
3983816 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.75 63.0 5.38e-01 87.3% 74.8%
3173834 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.73 61.0 4.47e-01 87.3% 80.7%
3483524 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 0.72 62.0 5.02e-01 91.0% 62.3%
None — 0.72 63.0 4.98e-01 91.6% 80.6%
3679386 4967.1.1.0 ↗ 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 0.72 63.0 4.82e-01 91.6% 56.6%
4152428 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.72 63.0 4.79e-01 91.6% 54.9%
3068775 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.72 61.0 5.64e-01 88.6% 82.3%
3495499 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 0.72 62.0 5.00e-01 91.6% 61.3%
3353681 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.70 54.0 5.27e-01 79.5% 93.3%
4934655 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.69 34.0 4.68e-01 72.3% 96.2%
5048300 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.69 36.0 4.45e-01 71.1% 80.0%
3284562 304.8.1.9 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_6 0.66 35.0 4.81e-01 72.3% 100.0%
3590710 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.65 36.0 4.59e-01 72.9% 93.7%
3743450 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.63 34.0 4.42e-01 70.5% 95.6%
5047189 304.56.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like 0.60 32.0 4.34e-01 71.7% 100.0%
5056225 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.60 32.0 4.23e-01 72.9% 92.6%
4116290 304.8.1.5 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › NIL 0.59 36.0 4.46e-01 81.9% 99.0%
3953369 304.4.1.2 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › MIase 0.59 38.0 4.54e-01 86.7% 98.2%
4056966 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.58 39.0 4.20e-01 74.1% 80.0%
4511949 304.48.1.74 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Phage_GPA 0.57 45.0 3.97e-01 81.3% 83.3%
4173939 304.8.1.5 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › NIL 0.57 32.0 4.10e-01 72.3% 97.8%
4987385 304.4.1.2 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › MIase 0.56 32.0 4.12e-01 71.1% 100.0%
4132144 304.9.1.14 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › DUF1743 0.56 33.0 4.11e-01 72.9% 98.9%
4946980 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.55 34.0 3.73e-01 75.3% 72.9%
4951235 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.55 34.0 3.66e-01 74.7% 71.4%
4933627 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.54 34.0 3.50e-01 75.3% 65.8%
4926825 304.4.1.2 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › MIase 0.53 34.0 4.11e-01 71.1% 100.0%
5009733 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 0.52 40.0 4.06e-01 89.8% 79.4%
4963628 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.52 37.0 3.80e-01 71.7% 98.1%
4062740 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.52 36.0 3.85e-01 71.1% 94.5%
4118156 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.51 37.0 3.92e-01 74.1% 94.5%
4984310 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.51 38.0 4.10e-01 77.1% 100.0%
3987392 304.4.1.4 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.51 32.0 3.82e-01 74.1% 95.5%