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NC_020866.1__YP_007676391.1__RHVG_00012__00012

Bact-Vir

NC_020866.1__YP_007676391.1__RHVG_00012__00012

Identity

Accession:
NC_020866 ↗
Kingdom:
phage

Quality

80.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhodovulum_phage_RS1

TaxID: 754056

Cluster

View cluster (2 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 7-102
PDB
Domain cluster: rep: MW273922.1__QPZ53454.1__HTVC034P_gp20__00020__D68-159
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08299.18 best Bac_DnaA_C 39.2 8.30e-10 71.9% 95.7%
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1j1vA00 1.10.1750.10 Mainly Alpha › Orthogonal Bundle › Chromosomal Replication Initiator Protein Dnaa; Chain: A; › DnaA protein, C-terminal DNA-binding domain 0.94 86.0 8.70e-01 96.9% 97.9%
1l8qA03 1.10.1750.10 Mainly Alpha › Orthogonal Bundle › Chromosomal Replication Initiator Protein Dnaa; Chain: A; › DnaA protein, C-terminal DNA-binding domain 0.91 84.0 8.02e-01 100.0% 86.9%
2dbbB01 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 0.79 40.0 5.22e-01 72.9% 87.3%
1jkwA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.58 47.0 3.88e-01 93.8% 48.9%
1c9bA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.58 42.0 4.28e-01 84.4% 77.3%
4ioeA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.57 30.0 3.12e-01 100.0% 55.2%
3gi8C00 1.20.1740.10 Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I 0.57 50.0 3.30e-01 100.0% 75.6%
7ml0M01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.56 40.0 4.24e-01 75.0% 86.6%
3m03B00 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.55 42.0 4.25e-01 99.0% 82.1%
4fm3A00 1.20.1270.390 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.55 32.0 3.26e-01 94.8% 57.9%
3d3mA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.55 45.0 3.81e-01 88.5% 65.8%
1ywfA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.54 46.0 3.62e-01 100.0% 95.4%
2f07B00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.54 37.0 3.01e-01 71.9% 49.0%
1vs5O00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.53 42.0 4.41e-01 88.5% 94.3%
1aisB02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.53 41.0 4.23e-01 84.4% 86.2%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.52 35.0 3.86e-01 71.9% 88.0%
4rflA02 1.20.1090.10 Mainly Alpha › Up-down Bundle › Dehydroquinate synthase-like, alpha domain › Dehydroquinate synthase-like - alpha domain 0.52 45.0 3.62e-01 97.9% 82.9%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.52 36.0 3.22e-01 70.8% 58.2%
3bj6B00 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 0.52 43.0 3.73e-01 90.6% 62.9%
3lcnB00 1.10.340.40 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain 0.52 39.0 3.94e-01 97.9% 80.4%
2genA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.52 41.0 3.31e-01 86.5% 67.0%
8sbeA02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.51 37.0 3.04e-01 75.0% 81.3%
5m0nA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.51 45.0 2.96e-01 99.0% 37.1%
4rocA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.51 40.0 3.93e-01 84.4% 81.6%
1zk8B02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.51 39.0 3.60e-01 84.4% 78.0%
1fc3B00 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 0.51 43.0 4.32e-01 96.9% 100.0%
2ibdA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.51 39.0 3.47e-01 84.4% 81.0%
4jgiA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.51 35.0 3.77e-01 70.8% 96.2%
1he8A03 1.25.40.70 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Phosphatidylinositol 3-kinase, accessory domain (PIK) 0.50 39.0 3.72e-01 82.3% 71.2%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4604979 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.96 88.0 8.53e-01 96.9% 87.5%
4601417 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.96 88.0 8.93e-01 96.9% 96.8%
4102935 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.95 88.0 8.54e-01 97.9% 88.6%
4346134 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.94 91.0 8.80e-01 100.0% 92.3%
4174198 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.94 89.0 8.74e-01 100.0% 94.0%
4606105 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.94 86.0 8.48e-01 94.8% 91.0%
4270831 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.94 87.0 8.38e-01 97.9% 88.6%
4051624 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.94 87.0 8.46e-01 100.0% 89.5%
4524648 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.93 86.0 8.28e-01 96.9% 87.6%
4125972 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.93 84.0 8.27e-01 94.8% 90.0%
4165809 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.93 79.0 8.36e-01 90.6% 100.0%
4281674 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.93 87.0 8.46e-01 100.0% 90.5%
4559046 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.92 88.0 8.46e-01 100.0% 91.4%
4106860 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.91 83.0 8.42e-01 96.9% 96.8%
4529157 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.91 81.0 8.43e-01 94.8% 100.0%
4266587 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.91 83.0 8.38e-01 96.9% 96.8%
3385990 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.91 87.0 8.38e-01 100.0% 91.4%
4197050 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.91 87.0 8.38e-01 100.0% 91.4%
4067934 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.91 80.0 8.31e-01 92.7% 98.9%
4533441 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.90 82.0 8.25e-01 96.9% 96.8%
4347676 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.90 80.0 8.30e-01 94.8% 100.0%
4146099 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.90 83.0 8.38e-01 96.9% 98.9%
4437729 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.89 78.0 7.77e-01 100.0% 90.0%
4379676 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.88 83.0 8.02e-01 100.0% 92.4%
4606821 101.1.6.4 ↗ alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.86 80.0 7.91e-01 100.0% 95.0%
3793393 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.65 44.0 4.73e-01 100.0% 82.5%
4989143 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.61 52.0 4.97e-01 92.7% 100.0%
3837515 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 46.0 4.72e-01 82.3% 100.0%
4965872 101.1.10.3 ↗ alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.60 43.0 4.26e-01 74.0% 92.0%
5060820 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.58 51.0 3.34e-01 100.0% 91.5%
4612523 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.58 40.0 3.26e-01 70.8% 89.2%
3328279 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.56 34.0 3.37e-01 71.9% 56.0%
4961655 101.1.10.3 ↗ alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.56 44.0 4.44e-01 84.4% 89.5%
3273891 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.55 43.0 3.98e-01 84.4% 66.7%
4947863 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.55 42.0 4.39e-01 84.4% 88.9%
5001331 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.54 44.0 4.21e-01 89.6% 91.3%
3729506 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 0.54 38.0 2.97e-01 74.0% 62.2%
5025139 101.1.10.3 ↗ alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.54 42.0 4.28e-01 84.4% 84.2%
4994316 101.1.10.3 ↗ alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.54 42.0 3.75e-01 87.5% 57.9%
3374895 101.1.10.3 ↗ alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.53 44.0 3.96e-01 92.7% 67.4%
5000679 101.1.10.3 ↗ alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.53 45.0 4.35e-01 96.9% 87.3%
5049072 5050.1.1.10 ↗ 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_2 0.52 38.0 2.97e-01 78.1% 92.0%
3387475 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.51 44.0 3.25e-01 100.0% 74.7%
3269341 101.1.10.22 ↗ alpha arrays › HTH › HTH › Cyclin-like › ORC6 0.51 38.0 3.91e-01 84.4% 85.6%
4215393 4067.1.1.1 ↗ alpha bundles › FdhE-like › FdhE-like › FdhE-like › FdhE 0.51 45.0 3.83e-01 100.0% 86.5%
3291667 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.51 36.0 3.18e-01 75.0% 52.0%
3308044 109.4.1.189 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_2 0.50 37.0 3.34e-01 88.5% 54.8%
D2 high residues 112-163
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.75 56.0 4.41e-01 76.9% 42.2%
3wd6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.73 51.0 3.90e-01 73.1% 33.1%
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.72 59.0 5.22e-01 100.0% 62.0%
8ctsB01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 44.0 3.80e-01 71.2% 73.6%
3ousA00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 45.0 3.83e-01 73.1% 47.6%
2w02B01 1.10.150.640 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle 0.64 45.0 4.03e-01 75.0% 82.4%
1t9xA05 1.20.1640.10 Mainly Alpha › Up-down Bundle › Multidrug efflux transporter AcrB transmembrane fold › Multidrug efflux transporter AcrB transmembrane domain 0.63 43.0 2.84e-01 71.2% 70.3%
3d3oA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.62 43.0 3.00e-01 73.1% 86.4%
3kavA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.62 54.0 4.38e-01 100.0% 54.9%
2lpeA01 6.10.140.1120 Special › Helix non-globular › Helix Hairpins › 0.61 43.0 3.90e-01 76.9% 56.4%
3vm9A02 6.10.140.2110 Special › Helix non-globular › Helix Hairpins › 0.61 42.0 4.13e-01 71.2% 68.4%
1cjaA02 1.10.1070.11 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › Phosphatidylinositol 3-/4-kinase, catalytic domain 0.60 45.0 3.12e-01 80.8% 94.9%
1w36C06 1.10.10.990 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.60 41.0 3.68e-01 71.2% 76.4%
8e9gE01 1.10.10.1590 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › NADH-quinone oxidoreductase subunit E 0.60 35.0 3.34e-01 71.2% 46.0%
2wzvA01 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.59 46.0 3.03e-01 84.6% 60.6%
2hroA02 1.10.274.10 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › PtsI, HPr-binding domain 0.58 48.0 3.76e-01 100.0% 67.2%
2e9xB02 1.20.58.1020 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 44.0 3.56e-01 92.3% 52.3%
2ppxA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.53 41.0 3.90e-01 100.0% 72.1%
3h4cA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.52 46.0 3.78e-01 100.0% 85.4%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4303437 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.76 52.0 3.20e-01 71.2% 65.8%
3783029 633.31.1.0 ↗ alpha bundles › Bromodomain-like › Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase › Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase 0.70 48.0 4.12e-01 71.2% 100.0%
4324499 3755.1.1.3 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › SPAM 0.69 48.0 3.48e-01 73.1% 66.9%
4441101 2007.2.1.2 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Flavoproteins › Flavodoxin_2 0.68 58.0 3.88e-01 98.1% 29.9%
3593009 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.66 54.0 4.76e-01 94.2% 63.7%
3508812 7525.1.1.2 ↗ a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_2 0.62 47.0 2.81e-01 80.8% 12.7%
4936993 601.7.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.62 52.0 3.96e-01 100.0% 48.9%
4406266 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.59 48.0 4.19e-01 100.0% 60.0%
2623599 192.4.1.2 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › MRP-L47 0.58 40.0 3.52e-01 73.1% 55.4%
3589876 186.1.1.3 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_5 0.56 48.0 3.94e-01 98.1% 62.0%
3958903 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.54 46.0 3.73e-01 100.0% 77.1%