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NC_020866.1__YP_007676385.1__RHVG_00006__00006

Bact-Vir

NC_020866.1__YP_007676385.1__RHVG_00006__00006

Identity

Accession:
NC_020866 ↗
Kingdom:
phage

Quality

83.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhodovulum_phage_RS1

TaxID: 754056

Cluster

Singleton — not in a non-trivial cluster

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 medium residues 10-48
PDB
Domain cluster: representative
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1wxcB01 3.30.1880.10 Alpha Beta › 2-Layer Sandwich › protein ne1242 fold › protein ne1242 domain like 0.78 61.0 5.33e-01 94.9% 56.5%
4r2qA00 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.75 53.0 4.10e-01 79.5% 34.1%
1g2dC03 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.74 49.0 5.29e-01 79.5% 100.0%
1wv8A00 3.30.2390.10 Alpha Beta › 2-Layer Sandwich › TTHA1013/TTHA0281-like › TTHA1013-like 0.74 61.0 5.18e-01 100.0% 62.0%
1ncsA00 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.72 57.0 5.56e-01 97.4% 80.9%
2el8A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.71 55.0 4.34e-01 97.4% 39.6%
2ffgA00 3.30.720.20 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Protein of unknown function DUF1797 0.70 59.0 4.82e-01 100.0% 66.3%
5yrzA01 3.30.160.250 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.70 58.0 4.37e-01 100.0% 44.8%
2dsyD00 3.30.160.250 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.70 58.0 4.72e-01 100.0% 54.3%
2l6mA00 3.30.160.400 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.69 56.0 4.34e-01 100.0% 58.4%
4hqeA00 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 0.69 47.0 3.39e-01 100.0% 26.7%
2r1fA03 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.67 50.0 5.09e-01 84.6% 84.6%
3hh8A01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.67 46.0 3.10e-01 74.4% 77.2%
3mpxA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.66 55.0 4.22e-01 97.4% 42.3%
1d4tA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.65 53.0 4.01e-01 97.4% 40.4%
4fk1A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.65 45.0 2.95e-01 84.6% 15.5%
7wrgB01 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.64 54.0 3.22e-01 100.0% 26.9%
2codA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.64 52.0 4.04e-01 100.0% 39.6%
3laaA00 2.150.10.10 Mainly Beta › 2 Solenoid › Alkaline Protease, subunit P, domain 1 › Serralysin-like metalloprotease, C-terminal 0.63 50.0 3.38e-01 92.3% 29.6%
7pi0S01 1.10.3460.10 Mainly Alpha › Orthogonal Bundle › Chlorophyll a-b binding protein › Chlorophyll a/b binding protein domain 0.63 42.0 2.72e-01 71.8% 16.0%
1vx7000 2.30.170.20 Mainly Beta › Roll › Ribosomal Protein L24e; Chain: T; › Ribosomal protein L24 0.62 44.0 3.86e-01 76.9% 48.4%
2eo6A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.61 52.0 3.85e-01 100.0% 47.2%
5b7hB01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.61 43.0 3.24e-01 76.9% 32.4%
2cs0A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.60 51.0 3.91e-01 100.0% 41.1%
2kinA00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.60 49.0 3.12e-01 100.0% 34.9%
2uz8A01 3.40.30.90 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.58 43.0 4.07e-01 92.3% 100.0%
2h84A02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.58 47.0 3.26e-01 100.0% 34.5%
3au4A04 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 45.0 3.47e-01 100.0% 37.6%
4ap5A01 3.40.50.11340 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 44.0 2.86e-01 94.9% 28.0%
3d6wB02 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.54 37.0 3.76e-01 76.9% 87.2%
1ha6A00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 36.0 3.21e-01 74.4% 54.3%
4rt5A00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.53 36.0 2.67e-01 94.9% 19.8%
4fdyA02 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.52 37.0 2.65e-01 97.4% 23.1%
2qtlA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.52 34.0 2.49e-01 84.6% 24.3%
3jyyA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.52 39.0 2.92e-01 94.9% 91.8%
5uc6A00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.51 39.0 2.83e-01 100.0% 37.1%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3178127 386.1.1.1 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2 0.86 70.0 6.49e-01 94.9% 72.0%
86702 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.83 68.0 6.28e-01 94.9% 84.6%
3675633 902.1.1.0 ↗ few secondary structure elements › Amb V allergen › Amb V allergen › Amb V allergen 0.79 62.0 6.24e-01 84.6% 92.3%
4944829 4100.1.1.0 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.77 63.0 6.17e-01 100.0% 91.1%
5029920 4100.1.1.3 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › HicB_lk_antitox 0.76 64.0 5.52e-01 100.0% 66.2%
4826872 2010.1.1.4 ↗ a/b three-layered sandwiches › EDD domain › EDD domain › EDD domain › FakA-like_C 0.76 63.0 4.74e-01 100.0% 50.5%
3518078 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.75 62.0 6.00e-01 100.0% 95.6%
4380861 386.1.1.127 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › WT1 0.74 60.0 5.33e-01 94.9% 68.3%
4950216 4100.1.1.3 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › HicB_lk_antitox 0.74 60.0 5.76e-01 97.4% 85.4%
7730 4100.1.1.1 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › DUF1902 0.74 61.0 5.18e-01 100.0% 62.0%
4432021 386.1.1.70 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-SCNM1 0.74 59.0 4.84e-01 100.0% 47.5%
5075488 4100.1.1.0 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.73 62.0 5.26e-01 100.0% 61.8%
4967687 4100.1.1.3 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › HicB_lk_antitox 0.73 62.0 5.18e-01 100.0% 57.1%
8321 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.72 57.0 5.56e-01 97.4% 80.9%
5028523 4100.1.1.3 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › HicB_lk_antitox 0.72 61.0 5.23e-01 100.0% 66.2%
3988603 101.1.2.92 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_11 0.72 49.0 3.76e-01 100.0% 32.9%
3857959 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.72 58.0 5.44e-01 94.9% 84.0%
4946414 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.70 57.0 4.15e-01 100.0% 50.4%
4431929 4100.1.1.4 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › UPF0150 0.70 57.0 5.00e-01 100.0% 66.2%
3247329 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.69 57.0 4.22e-01 100.0% 34.5%
3801400 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.67 56.0 3.43e-01 100.0% 15.2%
None — 0.66 47.0 2.74e-01 84.6% 8.1%
3486284 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.66 48.0 4.54e-01 87.2% 64.0%
3578128 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.65 55.0 5.00e-01 100.0% 96.4%
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 0.64 51.0 3.18e-01 89.7% 36.4%
3839435 330.9.1.0 ↗ a+b two layers › dsRBD-like › C-terminal domain in LINE-1 ORF1p › C-terminal domain in LINE-1 ORF1p 0.64 48.0 4.18e-01 97.4% 50.7%
3236787 2484.1.1.200 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FTH 0.64 54.0 3.81e-01 100.0% 46.2%
3479095 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 53.0 3.85e-01 100.0% 33.0%
4440203 2.1.1.9 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_S4e 0.62 49.0 4.40e-01 94.9% 76.7%
4065466 220.1.1.150 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF986 0.62 54.0 4.23e-01 100.0% 47.5%
167520 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.61 52.0 3.68e-01 100.0% 39.8%
3068467 5077.1.1.1 ↗ extended segments › Chlorophyll a-b binding protein › Chlorophyll a-b binding protein › Chlorophyll a-b binding protein › Chloroa_b-bind 0.61 47.0 2.87e-01 87.2% 16.0%
3235525 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.61 50.0 3.28e-01 100.0% 28.5%
4927970 2003.1.2.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.59 46.0 3.31e-01 92.3% 97.0%
4679015 220.1.1.150 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF986 0.59 49.0 4.02e-01 100.0% 48.8%
3706176 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.58 50.0 3.01e-01 100.0% 63.2%
3990001 4.8.1.5 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.58 40.0 3.74e-01 74.4% 64.2%
151365 2002.1.1.195 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › SPL 0.58 46.0 2.68e-01 87.2% 39.4%
3263180 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 46.0 3.44e-01 100.0% 34.5%
5070218 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.56 49.0 3.49e-01 100.0% 54.2%
3715334 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.54 40.0 2.46e-01 84.6% 11.3%
4034336 4.8.1.13 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › ComK 0.52 44.0 3.08e-01 100.0% 27.6%
D2 medium residues 55-87
PDB
Domain cluster: rep: KX077179.1__ANT39877.1__Rhks_6__00006__D50-79