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RNA-dependent_RNA_polymerase,_partial

Euk-Vir

Persimmon_latent_virus

RNA-dependent_RNA_polymerase,_partial__YP_009025166__Persimmon_latent_virus__1211481

Identity

Accession:
YP_009025166 ↗
Protein ID:
RNA-dependent_RNA_polymerase,_partial
Kingdom:
euk

Quality

68.3 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 16-137
PDB
D2 medium residues 170-246_266-341
PDB
D3 medium residues 342-380_426-437
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1t6aA02 3.30.310.120 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Rbstp2229 like protein 0.63 52.0 4.51e-01 92.2% 89.7%
2hc5A01 3.30.160.170 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › FlaG-like 0.63 45.0 3.66e-01 100.0% 39.8%
4wxaA00 3.30.310.50 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Alpha-D-phosphohexomutase, C-terminal domain 0.62 39.0 3.43e-01 76.5% 39.3%
2azeB00 6.10.250.540 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.60 38.0 3.12e-01 74.5% 31.7%
5b55A01 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.60 47.0 3.24e-01 90.2% 84.2%
6bhdA03 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.59 34.0 3.22e-01 88.2% 41.3%
2v4jB03 3.30.70.20 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 41.0 3.91e-01 76.5% 72.3%
1b35B00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.59 33.0 2.09e-01 86.3% 10.2%
1l1dA00 2.170.150.20 Mainly Beta › Beta Complex › Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A › Peptide methionine sulfoxide reductase. 0.57 38.0 2.83e-01 100.0% 23.6%
3o6qA02 3.30.70.2720 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 39.0 3.11e-01 76.5% 90.4%
2k3iA01 3.30.70.860 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 38.0 3.39e-01 76.5% 52.9%
2d8iA01 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.55 44.0 3.78e-01 100.0% 53.4%
1yu9A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 42.0 3.04e-01 90.2% 73.7%
4fidA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 43.0 2.96e-01 90.2% 80.8%
3p9aF00 1.10.132.80 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.54 36.0 2.83e-01 70.6% 55.2%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.54 38.0 3.39e-01 74.5% 88.2%
2ookA00 3.40.50.10600 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SpoIIaa-like domains 0.54 40.0 3.21e-01 88.2% 82.4%
2ztbA03 2.60.40.3040 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 36.0 3.67e-01 86.3% 75.0%
3dmgA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 41.0 2.85e-01 90.2% 47.4%
3f6gA01 3.30.160.740 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 38.0 3.74e-01 90.2% 70.7%
2pgeA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 43.0 3.32e-01 98.0% 84.3%
3bt7A02 2.40.50.1070 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 40.0 3.16e-01 100.0% 64.1%
6l4qB01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 43.0 3.17e-01 92.2% 47.4%
1t3yA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.52 40.0 3.24e-01 100.0% 92.4%
3ke6B01 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.52 43.0 2.90e-01 100.0% 38.5%
2l72A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.51 39.0 3.22e-01 96.1% 92.4%
2jqjA01 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.51 41.0 3.25e-01 100.0% 56.2%
2joiA00 3.30.310.190 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.51 35.0 3.00e-01 76.5% 54.2%
2hj1A00 3.10.20.280 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RnfH-like 0.50 33.0 3.04e-01 88.2% 46.8%
4lgvD02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.50 37.0 2.49e-01 88.2% 61.1%
5h7kA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 39.0 2.59e-01 90.2% 77.7%
1d1rA00 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.50 39.0 3.47e-01 92.2% 66.3%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4364399 318.1.1.1 ↗ a+b two layers › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal_L6 0.65 46.0 3.85e-01 76.5% 45.6%
3838561 3454.1.1.0 ↗ beta barrels › GspC HR domain/PilP-like › GspC HR domain/PilP-like › GspC HR domain/PilP-like 0.65 40.0 3.68e-01 96.1% 47.7%
4589697 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.61 43.0 3.76e-01 76.5% 48.8%
3653236 3347.1.1.0 ↗ beta meanders › Uncharacterized protein BF3112 › Uncharacterized protein BF3112 › Uncharacterized protein BF3112 0.60 42.0 3.01e-01 76.5% 57.0%
4463014 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.59 41.0 3.66e-01 76.5% 50.7%
3605370 221.1.1.2 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › ubiquitin 0.58 38.0 3.64e-01 90.2% 56.7%
4940657 101.1.2.269 ↗ alpha arrays › HTH › HTH › winged helix domain › SocA_Panacea 0.57 40.0 2.89e-01 76.5% 28.0%
3233262 706.1.1.0 ↗ beta complex topology › Head domain of nucleotide exchange factor GrpE › Head domain of nucleotide exchange factor GrpE › Head domain of nucleotide exchange factor GrpE 0.57 38.0 4.00e-01 88.2% 100.0%
3798236 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.57 48.0 3.17e-01 94.1% 30.5%
5000798 3926.1.1.1 ↗ alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.57 45.0 3.07e-01 88.2% 28.1%
3271024 2003.1.5.73 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.57 48.0 3.17e-01 92.2% 33.2%
3334359 221.4.1.1 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX 0.57 41.0 2.85e-01 98.0% 21.7%
3325991 10.32.1.198 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › PP2 0.55 47.0 3.22e-01 98.0% 79.5%
5067865 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.55 38.0 3.47e-01 72.5% 94.3%
4982249 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.55 38.0 3.28e-01 76.5% 66.3%
3596282 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.55 36.0 3.10e-01 76.5% 36.8%
3712782 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 36.0 3.21e-01 70.6% 75.0%
3549652 109.26.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Nuclear pore complex component Nup133/Nup170/Nup157 C-terminal domains › Nuclear pore complex component Nup133/Nup170/Nup157 C-terminal domains › Nucleoporin_C 0.54 44.0 2.43e-01 92.2% 13.1%
3996281 110.3.1.1 ↗ alpha arrays › DEATH domain › SLED domain › SLED domain › SLED 0.54 41.0 3.33e-01 96.1% 39.1%
3277889 327.5.1.6 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-dom_DIP2-like 0.54 41.0 3.28e-01 88.2% 88.7%
4183868 878.1.1.1 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.54 37.0 3.34e-01 76.5% 53.2%
3905302 284.1.3.8 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › Fy-3 0.53 39.0 3.41e-01 94.1% 49.4%
4987228 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.53 37.0 2.69e-01 76.5% 54.4%
4679312 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.53 44.0 3.89e-01 98.0% 72.5%
5080543 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.53 43.0 2.88e-01 96.1% 33.2%
4932060 3054.1.1.0 ↗ alpha arrays › Insert all-alpha domain in prim-pol › Insert all-alpha domain in prim-pol › Insert all-alpha domain in prim-pol 0.52 43.0 3.39e-01 92.2% 83.6%
4923381 304.51.1.6 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › Cas_Cmr3 0.52 45.0 3.05e-01 94.1% 45.8%
5059752 206.1.1.17 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Kdo 0.52 40.0 2.71e-01 88.2% 33.8%
4937853 3501.1.1.0 ↗ a+b two layers › protein PCC1 › protein PCC1 › protein PCC1 0.52 37.0 3.41e-01 76.5% 55.7%
3989293 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.52 42.0 3.43e-01 100.0% 64.3%
4411246 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.51 43.0 3.78e-01 98.0% 71.2%
1665018 298.1.1.6 ↗ a+b two layers › FwdE/GAPDH domain-like › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › G6PD_C 0.51 38.0 2.52e-01 90.2% 64.0%
3466238 206.1.1.14 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › ABC1 0.51 42.0 2.53e-01 100.0% 33.6%
3805766 4.1.1.28 ↗ beta barrels › SH3 › SH3 › SH3 › BPL_C 0.51 37.0 3.69e-01 86.3% 74.5%
3740385 4156.1.1.4 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › HA2_C 0.51 36.0 2.59e-01 86.3% 23.5%
4976317 206.1.1.14 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › ABC1 0.50 40.0 2.77e-01 96.1% 34.8%
4034138 7520.1.1.0 ↗ a/b three-layered sandwiches › CinA-like › CinA-like › CinA-like 0.50 35.0 2.80e-01 90.2% 30.8%
3242105 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.50 35.0 2.47e-01 90.2% 20.0%
3236725 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 0.50 43.0 2.79e-01 100.0% 57.7%
5035978 206.1.1.9 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › RIO1 0.50 42.0 2.85e-01 96.1% 35.5%
D4 medium residues 381-425_438-529
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009667008__Macrophomina_phaseolina_chrysovirus_1__1708483__D328-448
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1udyA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.56 30.0 3.17e-01 70.8% 56.7%
8hdlA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.54 45.0 3.78e-01 91.2% 86.3%
2j1oA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.53 43.0 3.60e-01 89.1% 85.5%
1v4aA01 1.10.4050.10 Mainly Alpha › Orthogonal Bundle › Nucleotidyltransferase substrate binding subunit/domain fold › Glutamine synthase adenylyltransferase GlnE 0.50 37.0 4.09e-01 97.1% 100.0%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4010438 616.1.1.40 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › DUF1315 0.60 27.0 3.91e-01 86.1% 100.0%
4012420 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.57 35.0 3.64e-01 87.6% 66.4%