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RNA-dependent_RNA_polymerase

Euk-Vir

Hubei_noda-like_virus_9

RNA-dependent_RNA_polymerase__YP_009337879__Hubei_noda-like_virus_9__1922989

Identity

Accession:
YP_009337879 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

77.6 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 high residues 136-259_287-345
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF19222.6 best Noda_Vmethyltr 133.8 5.50e-39 66.7% 77.0%
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2h85A02 3.40.50.11580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › nsp15 middle domain 0.59 39.0 4.57e-01 79.2% 96.8%
3luqB00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 33.0 4.04e-01 90.2% 90.4%
4mt1A06 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.56 22.0 2.89e-01 91.8% 60.4%
3daaA01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.55 25.0 3.09e-01 91.3% 63.6%
4dqnA01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.53 27.0 2.94e-01 91.3% 55.1%
1zhhB01 3.30.450.220 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › LuxQ periplasmic domain, N-terminal subdomain 0.53 36.0 3.88e-01 91.3% 80.9%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4971928 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.63 51.0 4.40e-01 85.2% 88.9%
5069527 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.52 32.0 3.90e-01 92.3% 100.0%
4958534 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.51 27.0 3.61e-01 91.3% 100.0%
3237375 101.1.2.571 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF3557 0.51 33.0 3.82e-01 71.0% 89.6%
3735309 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.50 25.0 3.52e-01 71.0% 96.7%
1875469 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.50 38.0 2.75e-01 77.0% 98.7%
D2 medium residues 2-128
PDB
D3 medium residues 260-286_346-439
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 35.0 1.60e-08 28.9% 18.9%
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4usaA02 1.10.150.120 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › [2Fe-2S]-binding domain 0.61 39.0 3.99e-01 90.9% 65.5%
1t3qA02 1.10.150.120 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › [2Fe-2S]-binding domain 0.60 38.0 4.42e-01 76.0% 93.8%
1df0A02 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.56 27.0 3.07e-01 78.5% 57.6%
5kdiA00 1.10.3520.10 Mainly Alpha › Orthogonal Bundle › Glycolipid transfer protein, GLTP › Glycolipid transfer protein 0.56 41.0 3.46e-01 76.9% 78.2%
2yf0A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 33.0 3.80e-01 75.2% 86.2%
4hdoA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 34.0 3.73e-01 76.0% 84.8%
2digA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.51 24.0 3.15e-01 75.2% 79.4%
5hdiA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.51 44.0 3.09e-01 95.9% 63.7%
2ra1A03 1.20.58.770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 22.0 2.86e-01 72.7% 71.4%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3331569 375.1.1.31 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Elf1 0.66 25.0 3.61e-01 70.2% 74.5%
3907738 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.64 35.0 4.36e-01 96.7% 90.0%
3964745 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.61 33.0 3.93e-01 71.1% 78.8%
3519665 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 38.0 4.29e-01 90.1% 87.8%
3284535 295.1.1.13 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › DUF3090 0.58 41.0 4.13e-01 71.9% 87.5%
4032084 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.55 32.0 3.54e-01 94.2% 71.6%
5053839 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.55 34.0 4.04e-01 95.9% 98.7%
4024456 101.1.2.663 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF7602 0.54 31.0 3.52e-01 73.6% 74.4%
5039029 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.54 30.0 3.44e-01 71.1% 73.3%
3771647 189.1.1.2 ↗ alpha bundles › GTPase activation domain, GAP › GTPase activation domain, GAP › GTPase activation domain, GAP › RhoGAP 0.53 38.0 2.66e-01 95.0% 22.6%
4641867 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.53 38.0 3.42e-01 72.7% 85.6%
4192693 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.53 30.0 3.47e-01 93.4% 77.6%
4451022 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 40.0 4.05e-01 95.0% 80.8%
4527507 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.52 36.0 3.59e-01 71.9% 90.8%
4034140 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.52 30.0 3.44e-01 72.7% 78.8%
4027723 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.51 27.0 3.30e-01 73.6% 82.9%
4032882 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.50 30.0 3.35e-01 94.2% 75.3%
D4 medium residues 460-486_792-939
PDB
Domain cluster: rep: hypothetical_protein__YP_009329984__Beihai_noda-like_virus_29__1922483__D408-447_732-867
D5 medium residues 487-509_529-617_664-696
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337881__Hubei_noda-like_virus_8__1922988__D582-599_632-711_764-802
D6 medium residues 510-528_618-663_697-791
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181