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RNA_polymerase

Euk-Vir

NY_014_poxvirus

RNA_polymerase__YP_009408524__NY_014_poxvirus__2025360

Identity

Accession:
YP_009408524 ↗
Protein ID:
RNA_polymerase
Kingdom:
euk

Quality

80.7 mean pLDDT

Cluster

View cluster (58 members)

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 173-354
PDB
Domain cluster: rep: DNA-directed_RNA_polymerase_subunit_beta__YP_009162498__Salmon_gill_poxvirus__1680908__D173-349
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF12415.15 best rpo132 63.8 9.70e-18 17.6% 100.0%
D2 medium residues 33-50_153-170_355-419
PDB
Domain cluster: representative
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.64 36.0 4.45e-01 88.1% 89.1%
1tf5A04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.62 54.0 4.39e-01 94.1% 87.9%
5yixA00 1.10.601.10 Mainly Alpha › Orthogonal Bundle › RNA Polymerase Primary Sigma Factor › RNA Polymerase Primary Sigma Factor 0.58 42.0 2.88e-01 74.3% 46.9%
4dvyP01 1.10.357.130 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.57 40.0 3.15e-01 82.2% 36.5%
4oh3A00 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.56 46.0 3.03e-01 94.1% 70.5%
1jfiB00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.55 37.0 3.36e-01 83.2% 51.9%
1xwjA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.53 38.0 3.51e-01 74.3% 66.2%
2l09A01 1.10.8.550 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Proto-chlorophyllide reductase 57 kD subunit B 0.53 25.0 3.32e-01 81.2% 86.5%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3492370 4010.1.1.2 ↗ a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_1,RNA_pol_Rpb2_3 0.78 73.0 5.09e-01 100.0% 69.8%
3509883 4010.1.1.1 ↗ a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_1 0.74 68.0 4.76e-01 100.0% 68.5%
4513137 4010.1.1.2 ↗ a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_1,RNA_pol_Rpb2_3 0.70 63.0 4.37e-01 100.0% 75.5%
5009207 4010.1.1.1 ↗ a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_1 0.70 63.0 4.36e-01 100.0% 74.4%
5000297 4010.1.1.0 ↗ a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase 0.69 62.0 4.37e-01 100.0% 69.4%
3372215 3226.1.1.3 ↗ alpha complex topology › Uracil Transporter UraA › Uracil Transporter UraA › Uracil Transporter UraA › HCO3_cotransp 0.60 54.0 3.39e-01 100.0% 22.9%
3841130 3226.1.1.3 ↗ alpha complex topology › Uracil Transporter UraA › Uracil Transporter UraA › Uracil Transporter UraA › HCO3_cotransp 0.57 45.0 2.84e-01 86.1% 43.1%
4030263 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.55 50.0 4.33e-01 98.0% 80.0%
3588302 1076.1.1.1 ↗ alpha bundles › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Rce1-like 0.55 45.0 3.47e-01 87.1% 78.6%
3331106 174.1.1.57 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › ABCC10_N 0.54 42.0 3.31e-01 82.2% 69.5%
None — 0.53 44.0 3.14e-01 89.1% 50.0%
4458494 3684.1.1.23 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › CA109-like 0.53 45.0 3.81e-01 96.0% 92.0%
3336422 3226.1.1.3 ↗ alpha complex topology › Uracil Transporter UraA › Uracil Transporter UraA › Uracil Transporter UraA › HCO3_cotransp 0.53 48.0 3.00e-01 100.0% 19.6%
3894027 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.52 40.0 3.21e-01 82.2% 67.5%
4352176 5050.1.1.1 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.51 45.0 3.32e-01 98.0% 68.5%
3980578 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.50 44.0 3.54e-01 99.0% 69.3%
D3 medium residues 51-133
PDB
Domain cluster: rep: RNA_polymerase_RPO132__YP_008004199__Choristoneura_biennis_entomopoxvirus__10288__D47-126
D4 medium residues 420-441_458-489_671-725
PDB
D5 medium residues 490-589
PDB
Domain cluster: rep: DNA-directed_RNA_polymerase_subunit_beta__YP_003406778__Marseillevirus_marseillevirus__694581__D519-604
D6 medium residues 590-670
PDB
Domain cluster: rep: DNA-directed_RNA_polymerase_subunit_2__YP_004346997__Lausannevirus__999883__D585-653
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04567.23 best RNA_pol_Rpb2_5 31.9 2.70e-07 60.5% 57.6%
D7 medium residues 726-777_877-927_987-1027
PDB
Domain cluster: rep: PHAGE-A8--js4906-27-3_S30_scaffold_1_curated_closed_complete_prodigal-single.1__X__X__00064__D205-229_383-459
Pfam (3)
AccessionNameScoreE-valueQ covHMM cov
PF00562.34 best RNA_pol_Rpb2_6 57.6 1.80e-15 44.4% 14.8%
PF00562.34 RNA_pol_Rpb2_6 27.0 3.40e-06 36.1% 10.2%
PF00562.34 RNA_pol_Rpb2_6 29.0 8.50e-07 29.2% 9.4%
D8 medium residues 778-800_817-875
PDB
Domain cluster: rep: putative_RNA_polymerase_beta_subunit__YP_009052296__Aureococcus_anophagefferens_virus__1474867__D765-873
D9 medium residues 928-986
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1uw4B00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.65 45.0 3.00e-01 74.6% 58.5%
1ujoA00 1.10.418.10 Mainly Alpha › Orthogonal Bundle › Actin-binding Protein, T-fimbrin; domain 1 › Calponin-like domain 0.64 55.0 4.19e-01 100.0% 61.8%
1lp1A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.62 47.0 4.87e-01 86.4% 89.1%
2ettA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.60 52.0 4.08e-01 100.0% 72.7%
1oxjA02 1.25.40.170 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Smaug, PHAT domain 0.59 52.0 4.26e-01 100.0% 78.9%
4o2zA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.57 45.0 3.38e-01 88.1% 54.2%
7prrB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.57 43.0 3.10e-01 81.4% 54.4%
3venA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 47.0 3.21e-01 98.3% 60.5%
2yayA02 1.20.1670.10 Mainly Alpha › Up-down Bundle › all-alpha NTP pyrophosphatase › Type II deoxyuridine triphosphatase 0.55 44.0 3.43e-01 89.8% 94.1%
4bujE03 1.10.3380.30 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › 0.55 43.0 2.94e-01 88.1% 55.2%
3kh1A00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.54 38.0 2.74e-01 76.3% 82.6%
1jetA03 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.53 43.0 3.08e-01 100.0% 30.1%
3s3lA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.52 38.0 2.89e-01 81.4% 59.1%
4hfvA02 6.10.280.170 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Substrate of the Dot/Icm secretion system 0.52 35.0 3.32e-01 71.2% 93.0%
3f4mA00 1.20.1440.160 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tumor necrosis factor alpha-induced protein 8-like 0.52 43.0 3.30e-01 100.0% 91.6%
8hbfB01 3.90.1520.10 Alpha Beta › Alpha-Beta Complex › H-NOX domain › H-NOX domain 0.51 41.0 3.11e-01 100.0% 35.9%
1u7kA00 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.50 38.0 3.15e-01 89.8% 89.3%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3381639 109.4.1.349 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RIX1 0.65 45.0 2.56e-01 72.9% 19.4%
3618722 101.31.1.2 ↗ alpha arrays › HTH › Bacteriophage Sf6 terminase small subunit › Bacteriophage Sf6 terminase small subunit › Swi3 0.63 47.0 4.25e-01 83.1% 58.7%
4244535 5104.1.1.0 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases 0.63 49.0 3.60e-01 88.1% 32.9%
4458167 5104.1.1.1 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.60 46.0 3.36e-01 84.7% 30.9%
4640120 621.1.1.3 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Sey1_3HB 0.58 42.0 2.57e-01 76.3% 33.8%
3276479 621.1.1.3 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Sey1_3HB 0.58 42.0 2.98e-01 79.7% 77.6%
3601980 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 52.0 3.17e-01 100.0% 19.7%
3286182 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.56 39.0 3.46e-01 88.1% 48.9%
3934652 7579.1.1.0 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.55 46.0 2.85e-01 98.3% 23.9%
3740986 621.1.1.3 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Sey1_3HB 0.55 41.0 2.53e-01 79.7% 39.5%
4572672 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.55 43.0 2.67e-01 88.1% 29.7%
4608699 621.1.1.3 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Sey1_3HB 0.55 41.0 2.55e-01 83.1% 39.0%
4530958 621.1.1.3 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Sey1_3HB 0.54 40.0 2.52e-01 81.4% 40.5%
3184221 109.4.1.681 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans_2 0.54 43.0 2.72e-01 100.0% 20.2%
4029612 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 41.0 2.67e-01 84.7% 50.7%
None — 0.54 39.0 2.52e-01 83.1% 88.2%
5053707 208.1.1.1 ↗ beta duplicates or obligate multimers › Single-stranded left-handed beta-helix › Trimeric LpxA-like enzymes › Trimeric LpxA-like enzymes › Hexapep 0.52 43.0 2.89e-01 91.5% 40.4%
4550154 621.1.1.3 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Sey1_3HB 0.52 40.0 3.03e-01 88.1% 40.0%
4426094 621.1.1.3 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Sey1_3HB 0.52 39.0 3.54e-01 86.4% 72.2%
4072766 109.4.1.889 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_M 0.52 43.0 2.95e-01 100.0% 34.7%
3200960 5069.1.3.5 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › DUF2418 0.51 38.0 2.69e-01 83.1% 65.1%
4530180 621.1.1.0 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain 0.50 37.0 2.91e-01 78.0% 67.7%
4391132 7510.1.1.1 ↗ a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Iso_dh 0.50 40.0 2.89e-01 96.6% 69.3%
D10 medium residues 1080-1166
PDB
Domain cluster: rep: IMGVR_UViG_3300025836_000142-3300025836-Ga0209748_10097103__D124-188