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RNA-dependent_RNA_polymerase

Euk-Vir

Eimeria_stiedai_RNA_virus_1

RNA-dependent_RNA_polymerase__YP_009551684__Eimeria_stiedai_RNA_virus_1__1898175

Identity

Accession:
YP_009551684 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

78.9 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 medium residues 8-120_438-464
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2cdqA02 1.20.120.1320 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Aspartokinase, catalytic domain 0.51 29.0 3.32e-01 89.3% 77.3%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4021066 2007.1.19.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › FabD/lysophospholipase-like › SAT 0.54 46.0 3.62e-01 94.3% 89.0%
4984545 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.50 30.0 3.66e-01 90.7% 91.1%
D2 medium residues 242-288_344-375
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zbtA01 6.10.140.1950 Special › Helix non-globular › Helix Hairpins › 0.76 34.0 3.36e-01 70.9% 41.0%
4dbgB02 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.68 48.0 5.23e-01 94.9% 96.7%
2e1vA02 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.66 60.0 4.40e-01 100.0% 55.1%
3b89A01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.66 44.0 4.99e-01 88.6% 100.0%
1a5tA02 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.66 35.0 4.43e-01 79.7% 100.0%
153lA00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.63 55.0 4.28e-01 100.0% 50.8%
1xb2B01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.62 43.0 4.70e-01 98.7% 95.0%
2w0gA00 1.20.58.610 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Cdc37, Hsp90 binding domain 0.61 56.0 4.72e-01 100.0% 86.8%
1x42A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.61 46.0 4.60e-01 84.8% 78.3%
4dvyP01 1.10.357.130 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.60 49.0 3.62e-01 87.3% 71.6%
4nooB00 1.10.8.1160 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.60 47.0 4.45e-01 84.8% 87.4%
4dtdA02 1.10.3680.20 Mainly Alpha › Orthogonal Bundle › TerB-like › Actin cross-linking domain 0.59 40.0 3.38e-01 70.9% 46.7%
1wz9A01 3.30.497.10 Alpha Beta › 2-Layer Sandwich › Antithrombin; Chain I, domain 2 › Antithrombin, subunit I, domain 2 0.58 48.0 3.47e-01 89.9% 98.2%
4f7nB01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.57 39.0 3.37e-01 84.8% 41.9%
1owlA02 1.25.40.80 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.57 39.0 3.37e-01 70.9% 85.4%
2no4A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.56 40.0 4.12e-01 75.9% 80.0%
2ch5B02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 39.0 2.88e-01 74.7% 48.0%
3ih6E00 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.55 49.0 3.73e-01 100.0% 60.4%
4akgA06 1.10.8.710 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Dynein motor, AAA1 domain, small subdomain 0.55 44.0 4.02e-01 89.9% 96.3%
3f2kB00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 45.0 3.55e-01 98.7% 74.9%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.53 43.0 3.56e-01 87.3% 85.8%
2bzlA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.51 36.0 2.52e-01 74.7% 87.7%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4050561 323.1.1.7 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Transferase 0.72 66.0 4.50e-01 100.0% 51.5%
3693574 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.67 53.0 5.34e-01 100.0% 87.5%
1873138 323.1.1.7 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Transferase 0.67 59.0 4.15e-01 100.0% 44.5%
5043726 2006.1.1.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.64 49.0 3.50e-01 82.3% 28.1%
3901204 101.1.10.18 ↗ alpha arrays › HTH › HTH › Cyclin-like › BRF2-like_C_cyclin_rpt 0.64 51.0 4.04e-01 86.1% 80.6%
3982976 235.1.1.0 ↗ a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like 0.60 46.0 4.00e-01 86.1% 94.6%
3187211 592.1.1.2 ↗ alpha arrays › PWI domain-like › PWI domain › PWI domain › Helicase_PWI 0.59 39.0 3.40e-01 75.9% 44.2%
5082378 2006.1.1.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.58 43.0 3.12e-01 81.0% 26.5%
4198250 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.57 46.0 4.83e-01 93.7% 100.0%
4017306 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.56 47.0 4.78e-01 96.2% 100.0%
3505644 101.1.1.3 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-binding 0.56 35.0 3.74e-01 79.7% 73.8%
4367778 601.14.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin 0.54 44.0 3.94e-01 89.9% 84.3%
5000613 7014.1.1.1 ↗ alpha bundles › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › BacA 0.53 41.0 3.89e-01 98.7% 68.4%
4156739 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.53 44.0 3.20e-01 89.9% 48.0%
5061320 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.53 43.0 4.30e-01 86.1% 86.3%
4082034 3317.1.1.2 ↗ alpha arrays › KorB C-terminal domain-like › KorB C-terminal domain › KorB C-terminal domain › HTH_ParB 0.53 40.0 4.17e-01 96.2% 92.9%
3835056 1128.1.1.0 ↗ alpha bundles › LYR protein › LYR protein › LYR protein 0.53 45.0 4.02e-01 100.0% 75.4%
3525714 101.1.1.286 ↗ alpha arrays › HTH › HTH › Three-helical HTH › PF27813 0.53 39.0 3.61e-01 98.7% 62.0%
5044025 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.52 38.0 3.72e-01 75.9% 76.5%
4959131 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.51 42.0 4.32e-01 87.3% 94.7%
4959129 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.51 42.0 4.25e-01 88.6% 93.8%
3892515 632.22.1.173 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › DUF2678 0.51 43.0 4.00e-01 93.7% 93.0%
4942761 4009.1.1.0 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.50 39.0 3.90e-01 88.6% 95.3%
1503807 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.50 41.0 3.58e-01 87.3% 80.9%
D3 medium residues 376-437_465-494_866-883
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009254736__Nigrospora_oryzae_victorivirus_1__1765736__D113-183_214-225
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3v39A01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.53 33.0 2.65e-01 91.8% 28.0%
4giwB00 1.20.58.900 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › RUN domain 0.53 38.0 3.36e-01 90.0% 49.4%
1zboA02 1.10.4060.10 Mainly Alpha › Orthogonal Bundle › LON domain-like fold › BPP1347 like domain 0.53 37.0 4.13e-01 91.8% 96.4%
6vynC01 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.52 26.0 3.00e-01 77.3% 63.5%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4029649 516.1.1.1 ↗ alpha arrays › YgfY-like (DUP399, Pfam03937) › YgfY-like (DUP399, Pfam03937) › YgfY-like (DUP399, Pfam03937) › Sdh5 0.53 34.0 3.81e-01 71.8% 85.5%
3361550 5081.1.1.1 ↗ alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.51 40.0 3.59e-01 83.6% 59.4%
D4 medium residues 495-653_697-744
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009336713__Beihai_toti-like_virus_4__1922734__D167-187_213-323_360-427
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 93.7 1.70e-26 81.6% 32.9%