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RNA-dependent_RNA_polymerase

Euk-Vir

Carrot_mottle_virus

RNA-dependent_RNA_polymerase__YP_002302259__Carrot_mottle_virus__68033

Identity

Accession:
YP_002302259 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

72.5 mean pLDDT

Cluster

View cluster (58 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 686-838
PDB
Domain cluster: rep: P95_replicase__YP_009259667__Pelargonium_leaf_curl_virus__35280__D527-559_693-852
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 97.2 1.40e-27 83.0% 27.4%
D2 medium residues 1-67
PDB
Domain cluster: rep: hypothetical_protein_1__YP_009337296__Changjiang_tombus-like_virus_3__1922817__D1-56
D3 medium residues 254-317
PDB
Domain cluster: representative
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1tfeA02 1.10.286.20 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.80 52.0 5.99e-01 71.9% 95.6%
3t38A01 1.10.8.1060 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Corynebacterium glutamicum thioredoxin-dependent arsenate reductase, N-terminal domain 0.74 53.0 5.15e-01 79.7% 67.6%
6m36O01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.73 57.0 4.96e-01 84.4% 92.7%
3s64A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.70 61.0 5.64e-01 98.4% 79.0%
1l0oA00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.69 56.0 4.39e-01 90.6% 88.7%
2hlzA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.68 55.0 3.47e-01 85.9% 84.1%
3bm1A00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.68 53.0 3.84e-01 84.4% 42.9%
5ts9B00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.67 52.0 3.85e-01 84.4% 93.8%
2ew2A02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.66 56.0 4.51e-01 98.4% 53.7%
5l3wA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.65 46.0 4.26e-01 75.0% 59.5%
4e69A00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.65 51.0 3.25e-01 85.9% 84.2%
3o60A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.64 54.0 3.96e-01 96.9% 42.9%
1ynbA00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.64 49.0 3.60e-01 82.8% 39.5%
7vtgA01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.64 53.0 3.39e-01 90.6% 83.0%
3hwrA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.63 53.0 4.30e-01 96.9% 57.4%
1t98A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.63 53.0 4.85e-01 96.9% 88.5%
1rr7A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.62 41.0 4.75e-01 71.9% 95.7%
4o1gA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.62 51.0 3.24e-01 90.6% 74.3%
5c0yA02 1.10.150.80 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › HRDC domain 0.62 43.0 3.80e-01 71.9% 51.6%
3dd7C00 1.20.120.1870 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Fic/DOC protein, Fido domain 0.62 46.0 3.73e-01 79.7% 66.4%
3kzhB00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.62 51.0 3.25e-01 90.6% 77.7%
2nn4A00 1.10.287.760 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YqgQ-like 0.61 42.0 4.33e-01 76.6% 75.8%
3c7jA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.60 44.0 3.94e-01 92.2% 54.9%
3ilkA02 1.10.8.590 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.60 42.0 4.15e-01 73.4% 73.5%
1f5qB02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.59 44.0 3.48e-01 81.2% 76.8%
2f33A01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.58 42.0 4.15e-01 78.1% 85.9%
2yi9A02 1.10.287.540 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.58 37.0 3.97e-01 87.5% 78.8%
2r1iA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 44.0 3.51e-01 82.8% 80.8%
4k7cA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.57 43.0 2.63e-01 79.7% 86.5%
4dooA02 1.10.890.20 Mainly Alpha › Orthogonal Bundle › 10k-s Protein, Hypothetical Protein A; Chain A › 0.57 44.0 4.65e-01 85.9% 100.0%
2gbbB00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.56 47.0 3.65e-01 100.0% 48.4%
3fgrA02 1.10.439.20 Mainly Alpha › Orthogonal Bundle › Penicillin Amidohydrolase; domain 1 › Phospholipase B-like, domain 2 0.55 40.0 3.20e-01 76.6% 43.8%
3rmiA00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.55 46.0 4.03e-01 100.0% 68.6%
2vm6A00 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.55 41.0 3.33e-01 85.9% 38.2%
1euvA01 1.10.418.20 Mainly Alpha › Orthogonal Bundle › Actin-binding Protein, T-fimbrin; domain 1 › 0.54 43.0 3.70e-01 87.5% 92.4%
1ailA00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.53 37.0 3.62e-01 73.4% 77.1%
1vw4T01 6.10.330.20 Special › Helix non-globular › Monooxygenase › 0.53 39.0 3.21e-01 78.1% 58.0%
2e9fB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.52 38.0 3.38e-01 76.6% 63.5%
1v63A00 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.52 45.0 3.85e-01 96.9% 77.2%
ECOD (57)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3227634 101.38.1.1 ↗ alpha arrays › HTH › DNA-binding domain of the replication initiator protein ColE2-Rep › DNA-binding domain of the replication initiator protein ColE2-Rep › C_tripleX 0.81 65.0 6.51e-01 85.9% 92.3%
4318142 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.79 60.0 4.53e-01 79.7% 46.4%
4426344 101.35.1.4 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3 0.76 62.0 6.16e-01 93.8% 85.3%
4060628 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.76 60.0 4.69e-01 84.4% 50.8%
4337032 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.76 59.0 4.58e-01 82.8% 66.2%
4630575 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.75 58.0 4.61e-01 82.8% 67.2%
3984466 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.74 50.0 3.45e-01 71.9% 21.4%
4328219 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.74 58.0 4.45e-01 82.8% 60.0%
5076674 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.73 50.0 3.18e-01 71.9% 16.7%
4120017 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.72 57.0 4.39e-01 84.4% 63.6%
4682225 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.72 56.0 4.27e-01 82.8% 61.5%
5073149 2488.1.1.1 ↗ a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › SpoU_methylase 0.71 47.0 3.19e-01 73.4% 18.7%
4378189 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.70 59.0 4.16e-01 90.6% 31.9%
4992350 2488.1.1.1 ↗ a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › SpoU_methylase 0.70 46.0 3.14e-01 73.4% 18.3%
3535295 101.1.10.1 ↗ alpha arrays › HTH › HTH › Cyclin-like › Cyclin_N 0.70 47.0 3.67e-01 70.3% 63.7%
5058202 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.69 47.0 3.16e-01 70.3% 37.8%
5025050 2488.1.1.1 ↗ a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › SpoU_methylase 0.69 46.0 3.18e-01 75.0% 19.6%
5036736 181.1.1.1 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.69 56.0 5.19e-01 92.2% 76.5%
4351255 191.1.1.91 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › PF29842 0.69 59.0 5.31e-01 96.9% 81.1%
3648217 101.1.10.1 ↗ alpha arrays › HTH › HTH › Cyclin-like › Cyclin_N 0.69 47.0 4.06e-01 71.9% 48.0%
4969123 2488.1.1.1 ↗ a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › SpoU_methylase 0.69 46.0 3.07e-01 73.4% 18.0%
3387056 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.69 57.0 4.02e-01 90.6% 31.1%
4980959 2488.1.1.1 ↗ a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › SpoU_methylase 0.69 46.0 3.14e-01 73.4% 20.0%
4939151 2488.1.1.1 ↗ a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › SpoU_methylase 0.68 45.0 3.66e-01 75.0% 35.8%
4946945 2488.1.1.1 ↗ a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › SpoU_methylase 0.67 47.0 3.17e-01 73.4% 20.9%
4028839 181.1.1.1 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.66 45.0 4.22e-01 79.7% 57.5%
4931308 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.65 44.0 3.52e-01 71.9% 38.5%
4948728 181.1.1.1 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.64 53.0 4.71e-01 93.8% 68.4%
3991789 101.1.10.1 ↗ alpha arrays › HTH › HTH › Cyclin-like › Cyclin_N 0.62 42.0 3.15e-01 71.9% 57.2%
3600922 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.62 46.0 4.76e-01 87.5% 88.3%
5079416 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.61 48.0 3.28e-01 85.9% 85.6%
3356191 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.60 38.0 2.69e-01 78.1% 19.5%
5082058 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.59 49.0 4.66e-01 92.2% 85.3%
4934951 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.59 48.0 4.35e-01 92.2% 71.1%
5011971 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.58 46.0 4.39e-01 92.2% 80.0%
4957352 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.57 45.0 4.31e-01 93.8% 86.3%
3643487 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.57 44.0 4.07e-01 90.6% 68.9%
5039471 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.57 48.0 4.38e-01 100.0% 77.8%
5075474 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.56 48.0 4.53e-01 98.4% 85.0%
4927512 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.56 46.0 4.16e-01 92.2% 71.1%
4960526 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.56 45.0 4.30e-01 93.8% 87.5%
1146718 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.56 47.0 3.65e-01 100.0% 44.2%
5074758 164.1.1.0 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II 0.56 45.0 4.26e-01 92.2% 80.0%
4296658 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.56 47.0 4.21e-01 100.0% 75.5%
3603891 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.56 47.0 4.28e-01 100.0% 76.6%
3666476 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.56 39.0 3.08e-01 76.6% 33.1%
4948274 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.56 47.0 4.50e-01 98.4% 90.7%
4992636 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.55 46.0 4.04e-01 100.0% 71.4%
4948961 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.55 47.0 4.35e-01 100.0% 81.2%
3579624 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.55 39.0 3.71e-01 76.6% 90.0%
4932440 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.55 48.0 4.41e-01 100.0% 83.5%
4055 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.55 46.0 3.55e-01 100.0% 43.0%
3607406 6026.1.1.0 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain 0.54 40.0 3.80e-01 81.2% 70.0%
4422226 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.53 46.0 3.00e-01 100.0% 45.0%
3818643 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.53 39.0 3.22e-01 82.8% 41.6%
3817217 109.4.1.1271 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, TPR_24 0.52 35.0 2.58e-01 76.6% 23.1%
3681153 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.51 38.0 2.99e-01 87.5% 44.8%
D4 medium residues 318-399_466-482
PDB
Domain cluster: rep: replicase__NP_620846__Pea_enation_mosaic_virus_2__193120__D300-380
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 29.5 4.80e-07 54.5% 10.1%
D5 medium residues 400-465_483-511_552-611
PDB
Domain cluster: rep: hypothetical_protein_1__YP_009342279__Wenzhou_tombus-like_virus_1__1923662__D230-295_314-343_386-449
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 41.8 8.80e-11 56.8% 18.7%
PF00998.29 RdRP_3 73.9 1.60e-20 38.7% 12.6%
D6 medium residues 512-551_612-685
PDB
Domain cluster: rep: hypothetical_protein_1__YP_009337274__Changjiang_tombus-like_virus_14__1922807__D158-196_253-344
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 93.8 1.40e-26 64.9% 15.2%
PF00998.29 RdRP_3 48.3 9.50e-13 36.0% 8.0%