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RNA-dependent_polymerase

Euk-Vir

Penaeid_shrimp_infectious_myonecrosis_virus

RNA-dependent_polymerase__YP_529549__Penaeid_shrimp_infectious_myonecrosis_virus__282786

Identity

Accession:
YP_529549 ↗
Protein ID:
RNA-dependent_polymerase
Kingdom:
euk

Quality

87.2 mean pLDDT

Cluster

View cluster (10 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 11-80
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009256209__Golden_shiner_totivirus__1856030__D1-63
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1xl3C00 1.20.1280.80 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.61 45.0 4.25e-01 81.4% 71.4%
4efcA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.53 39.0 4.04e-01 100.0% 93.4%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3347263 109.4.1.509 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RRP12_HEAT 0.59 44.0 3.13e-01 80.0% 25.9%
3695417 6155.1.1.2 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.58 44.0 4.26e-01 81.4% 91.3%
3534511 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.58 43.0 3.37e-01 81.4% 49.4%
4221151 150.3.1.8 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › EPO_TPO 0.57 50.0 3.82e-01 100.0% 60.4%
3632684 101.1.21.0 ↗ alpha arrays › HTH › HTH › HTH in T7 RNA polymerase 0.56 41.0 2.52e-01 78.6% 28.6%
3181110 5086.1.1.110 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HisKA 0.55 39.0 3.58e-01 100.0% 55.8%
3394861 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.53 43.0 3.20e-01 91.4% 90.3%
D2 medium residues 81-103_144-216_316-332
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5anvA00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.53 39.0 3.55e-01 77.0% 97.4%
1ib8A01 3.30.300.70 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › RimP-like superfamily, N-terminal 0.52 25.0 2.86e-01 81.4% 57.8%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3038102 1.1.3.0 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB 0.55 22.0 3.10e-01 72.6% 75.0%
D3 medium residues 104-143_217-244_264-315_333-359
PDB
Domain cluster: representative
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r7rA05 1.10.357.80 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.65 52.0 4.92e-01 84.4% 94.9%
1n5uA05 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.61 28.0 3.26e-01 74.1% 58.9%
2imsA00 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.59 37.0 3.66e-01 80.3% 56.4%
4kp3C00 1.20.58.1770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 27.0 3.43e-01 74.8% 72.8%
5xtck00 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.55 29.0 3.51e-01 70.1% 75.3%
4iluA02 1.20.58.1290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › CarD-like, C-terminal domain 0.51 29.0 3.32e-01 78.2% 72.1%
2hytA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.51 37.0 3.41e-01 91.8% 57.5%
5bqnA02 1.20.1120.10 Mainly Alpha › Up-down Bundle › "Clostridium botulinum neurotoxin B, ""coiled-coil"" domain" › "Clostridium botulinum neurotoxin b, ""coiled-coil"" domain" 0.50 40.0 3.02e-01 85.0% 76.5%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3471234 3832.1.1.1 ↗ alpha bundles › Tumor necrosis factor alpha-induced protein 8-like protein 2 › Tumor necrosis factor alpha-induced protein 8-like protein 2 › Tumor necrosis factor alpha-induced protein 8-like protein 2 › DUF758 0.54 39.0 3.68e-01 74.8% 94.1%
5039282 1075.1.1.12 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › CcmB 0.53 42.0 3.74e-01 83.7% 77.6%
3599901 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 43.0 3.34e-01 89.8% 91.4%
1407186 3832.1.1.1 ↗ alpha bundles › Tumor necrosis factor alpha-induced protein 8-like protein 2 › Tumor necrosis factor alpha-induced protein 8-like protein 2 › Tumor necrosis factor alpha-induced protein 8-like protein 2 › DUF758 0.51 35.0 3.31e-01 70.7% 86.6%
3415309 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.50 42.0 3.95e-01 90.5% 72.8%
4020741 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.50 36.0 3.12e-01 75.5% 58.8%
D4 medium residues 245-263_360-440
PDB
Domain cluster: rep: KR816341.1__AKQ06880.1__X__00021__D162-195_238-325
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 24.0 2.60e-05 82.0% 14.0%
D5 medium residues 441-520
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009333270__Wenzhou_toti-like_virus_1__1923680__D689-754
D6 medium residues 521-614
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_003934934__Armigeres_subalbatus_virus_SaX06-AK20__556524__D523-603
D7 medium residues 615-691
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_003934934__Armigeres_subalbatus_virus_SaX06-AK20__556524__D636-699
D8 medium residues 692-749
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3pm6A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.72 61.0 3.87e-01 93.1% 87.1%
3vm9A02 6.10.140.2110 Special › Helix non-globular › Helix Hairpins › 0.71 54.0 5.49e-01 81.0% 93.0%
2g8lB01 1.10.8.380 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 0.70 53.0 5.09e-01 82.8% 79.1%
1icrA00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.69 47.0 3.16e-01 70.7% 21.3%
4o1jA00 3.40.1050.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-carbonic Anhydrase; Chain A › Carbonic anhydrase 0.67 55.0 3.84e-01 93.1% 50.3%
1b10A00 1.10.790.10 Mainly Alpha › Orthogonal Bundle › Major Prion Protein › Prion/Doppel protein, beta-ribbon domain 0.67 52.0 4.31e-01 86.2% 49.0%
3l4aA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.66 50.0 3.95e-01 82.8% 46.3%
1dqeA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.65 48.0 3.69e-01 79.3% 90.5%
3fhnA04 1.20.58.670 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain D 0.65 50.0 3.85e-01 82.8% 47.3%
2zj2A04 1.10.3380.20 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › 0.64 52.0 3.79e-01 91.4% 67.7%
1aisB01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.64 50.0 4.22e-01 86.2% 88.9%
3dteA01 1.10.10.2910 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.62 48.0 3.96e-01 89.7% 81.2%
5k29A00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.58 50.0 4.27e-01 100.0% 58.8%
2w02B01 1.10.150.640 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle 0.57 44.0 4.10e-01 84.5% 94.6%
1pujA02 1.10.1580.10 Mainly Alpha › Orthogonal Bundle › Conserved Hypothetical Protein Ylqf; Chain: A; domain 2 › 0.56 46.0 3.96e-01 91.4% 72.0%
2og9A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.55 43.0 3.38e-01 87.9% 86.2%
3cz1A00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.54 39.0 3.24e-01 81.0% 68.4%
3keyA01 1.10.10.1080 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Stn1, N-terminal wHTH domain 0.54 45.0 4.01e-01 96.6% 75.9%
2r7hB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 42.0 3.10e-01 86.2% 52.8%
2looA02 1.10.10.1740 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Transmembrane protein 14-like 0.51 40.0 3.78e-01 91.4% 69.3%
3etuA01 1.10.287.3290 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 39.0 3.76e-01 87.9% 73.8%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3807618 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.73 50.0 5.18e-01 72.4% 80.0%
3193842 145.1.1.0 ↗ alpha arrays › F-box domain › F-box domain › F-box domain 0.67 55.0 4.33e-01 91.4% 69.6%
3562783 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.67 46.0 3.57e-01 70.7% 42.0%
3989928 148.1.3.197 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › Transgly_assoc 0.66 53.0 4.93e-01 91.4% 82.7%
3508753 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.66 45.0 3.84e-01 72.4% 58.9%
4964442 2003.1.1.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Shikimate_DH 0.64 50.0 3.29e-01 87.9% 21.5%
4028506 2004.1.1.73 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.64 51.0 3.17e-01 89.7% 69.3%
3837790 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.62 48.0 3.92e-01 84.5% 71.8%
3486313 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.62 43.0 3.80e-01 72.4% 70.6%
3947190 10.12.1.104 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding, Cupin_2 0.59 52.0 3.75e-01 100.0% 91.4%