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RNA-dependent_RNA_polymerase

Euk-Vir

Botryosphaeria_dothidea_victorivirus_1

RNA-dependent_RNA_polymerase__YP_009072433__Botryosphaeria_dothidea_victorivirus_1__1547580

Identity

Accession:
YP_009072433 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

91.8 mean pLDDT

Cluster

View cluster (56 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 high residues 1-88
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3lszA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.58 40.0 3.62e-01 72.7% 88.8%
1s2xA00 1.20.190.30 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › CAG pathogenicity island protein, CagZ 0.55 39.0 3.18e-01 75.0% 77.8%
4wjg400 1.20.1260.80 Mainly Alpha › Up-down Bundle › Ferritin › 0.53 39.0 2.88e-01 80.7% 72.4%
2n0sA01 3.40.50.1780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 38.0 3.15e-01 80.7% 66.1%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3058754 3819.1.1.0 ↗ alpha complex topology › CRISPR-associated endonuclease Cas9 alpha-helical lobe › CRISPR-associated endonuclease Cas9 alpha-helical lobe › CRISPR-associated endonuclease Cas9 alpha-helical lobe 0.66 45.0 2.97e-01 79.5% 16.8%
3928041 219.1.1.22 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Rad4 0.61 43.0 3.17e-01 73.9% 51.6%
3960025 605.1.1.13 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Transposase_mut 0.59 43.0 4.11e-01 77.3% 87.6%
3961709 633.16.1.7 ↗ alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like › Transposase_mut 0.59 43.0 4.09e-01 77.3% 87.6%
4073449 3949.1.1.0 ↗ alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain 0.53 43.0 3.19e-01 90.9% 96.2%
5050809 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 46.0 3.06e-01 100.0% 32.3%
4934796 6049.1.1.0 ↗ alpha bundles › PH0832-like › PH0832-like › PH0832-like 0.51 40.0 3.99e-01 85.2% 100.0%
D2 medium residues 99-248
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__NP_624323__Trichomonas_vaginalis_virus_2__674954__D796-923
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 23.0 5.10e-05 83.3% 25.2%
D3 medium residues 253-399_440-492
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009336713__Beihai_toti-like_virus_4__1922734__D167-187_213-323_360-427
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 116.2 2.70e-33 74.5% 31.4%
PF02123.22 RdRP_4 42.4 6.50e-11 28.0% 12.5%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ztbA03 2.60.40.3040 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 14.0 2.91e-01 70.0% 87.5%
1jwnA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.54 32.0 3.64e-01 88.5% 77.9%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4516798 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 0.66 52.0 3.96e-01 82.5% 45.1%
4071235 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 0.66 52.0 3.84e-01 82.5% 40.6%
3938749 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 0.65 60.0 4.91e-01 100.0% 69.5%
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 0.65 53.0 4.43e-01 86.0% 59.4%
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 0.65 54.0 4.30e-01 87.0% 59.7%
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 0.64 53.0 4.23e-01 86.0% 60.0%
D4 medium residues 400-439_493-565
PDB
Domain cluster: rep: KR816341.1__AKQ06880.1__X__00021__D162-195_238-325
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 73.8 2.00e-20 64.6% 15.5%
PF02123.22 RdRP_4 25.0 1.20e-05 37.2% 8.6%
D5 medium residues 566-618
PDB
Domain cluster: rep: RNA_dependent_RNA_polymerase__YP_009508249__Aspergillus_foetidus_slow_virus_1__1087070__D571-625
D6 medium residues 619-745_764-775
PDB
Domain cluster: representative
D7 medium residues 746-763_807-840
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7wm5A01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 37.0 2.56e-01 80.8% 42.0%
3mweB01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.50 39.0 2.91e-01 86.5% 96.4%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4370162 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 39.0 3.07e-01 88.5% 100.0%
3401292 7568.1.1.1 ↗ a/b three-layered sandwiches › BRCT domain › BRCT domain › BRCT domain › BRCT 0.51 40.0 3.25e-01 88.5% 60.0%