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NC_023502.1__YP_009003232.1__CC53_gp075__00075

Bact-Vir

NC_023502.1__YP_009003232.1__CC53_gp075__00075

Identity

Accession:
NC_023502 ↗
Kingdom:
phage

Quality

92.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_vB_RleS_L338C

TaxID: 1414737

Cluster

Singleton — not in a non-trivial cluster

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 5-50
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5hayA02 1.25.40.440 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Nucleoporin, helical domain, central subdomain 0.78 52.0 4.32e-01 73.9% 40.5%
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.77 54.0 4.91e-01 73.9% 68.9%
3f1xA01 1.10.3130.10 Mainly Alpha › Orthogonal Bundle › serine acetyltransferase, domain 1 › serine acetyltransferase, domain 1 0.71 48.0 3.32e-01 71.7% 40.9%
1irxA04 1.10.10.770 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.70 49.0 3.73e-01 73.9% 84.3%
1zylA03 1.20.1270.170 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.70 61.0 4.70e-01 100.0% 73.8%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.69 48.0 4.00e-01 73.9% 42.4%
2oznB01 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.68 55.0 4.81e-01 100.0% 83.7%
3bvoB01 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.67 50.0 3.88e-01 80.4% 40.8%
2zxqA06 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.66 53.0 4.90e-01 100.0% 84.8%
3r2qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 43.0 3.35e-01 73.9% 29.2%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.63 52.0 3.62e-01 93.5% 82.2%
4wz9A04 1.25.50.20 Mainly Alpha › Alpha Horseshoe › Zincin-like fold › 0.63 43.0 2.62e-01 73.9% 11.7%
3nhiA01 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.62 49.0 3.66e-01 100.0% 51.7%
1iqcA01 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.62 46.0 3.22e-01 80.4% 85.7%
3nc3B00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.62 54.0 3.16e-01 100.0% 27.8%
2gsvA00 6.10.140.40 Special › Helix non-globular › Helix Hairpins › 0.61 43.0 3.81e-01 80.4% 52.2%
4gltA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.60 41.0 3.14e-01 76.1% 28.9%
3behB01 1.20.120.540 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels 0.58 40.0 3.12e-01 76.1% 29.9%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.58 39.0 3.49e-01 73.9% 48.7%
3ay5A01 1.20.1420.10 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain 0.58 47.0 3.47e-01 93.5% 69.9%
1zvwA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.58 40.0 3.66e-01 73.9% 56.1%
3ez0C00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.57 45.0 2.99e-01 93.5% 64.4%
3e3vA03 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 0.57 41.0 3.83e-01 100.0% 62.5%
1tzvA00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.56 42.0 3.11e-01 87.0% 65.2%
3ld9A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 45.0 3.12e-01 100.0% 37.4%
4dolA02 1.10.890.20 Mainly Alpha › Orthogonal Bundle › 10k-s Protein, Hypothetical Protein A; Chain A › 0.54 43.0 4.19e-01 100.0% 78.4%
3lvyE01 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.54 43.0 2.96e-01 89.1% 57.0%
2elcA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.53 43.0 3.78e-01 89.1% 62.7%
1yozA00 1.10.3200.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af0941 › AF0941-like 0.53 38.0 2.96e-01 78.3% 45.1%
1eyvB00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.52 44.0 3.29e-01 100.0% 97.0%
1hqoA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.51 38.0 2.78e-01 82.6% 29.0%
2vqxA02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.51 40.0 2.92e-01 100.0% 92.2%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5050487 141.1.1.1 ↗ alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases › polyprenyl_synt 0.86 77.0 4.49e-01 100.0% 14.6%
4986840 141.1.1.1 ↗ alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases › polyprenyl_synt 0.79 68.0 4.39e-01 100.0% 23.6%
4455505 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 0.77 66.0 4.96e-01 100.0% 75.7%
5059791 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.76 63.0 4.99e-01 100.0% 71.4%
3989722 632.24.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › GBS CAMP factor C-terminal domain › GBS CAMP factor C-terminal domain 0.73 60.0 5.53e-01 100.0% 89.2%
4158788 632.2.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.72 62.0 5.31e-01 100.0% 87.0%
4567993 632.21.1.2 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › FIVAR 0.72 59.0 5.41e-01 100.0% 90.8%
4041623 632.2.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › FIVAR 0.71 60.0 5.18e-01 97.8% 80.0%
3392823 101.1.2.79 ↗ alpha arrays › HTH › HTH › winged helix domain › RNA_pol_I_A49 0.71 61.0 4.47e-01 100.0% 52.3%
5001961 632.2.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › FIVAR 0.70 57.0 4.92e-01 100.0% 83.7%
2764889 4944.1.1.1 ↗ alpha bundles › Helical bundle in flu nucleocapsid protein › Helical bundle in flu nucleocapsid protein › Helical bundle in flu nucleocapsid protein › Flu_NP 0.70 58.0 4.36e-01 100.0% 62.2%
2507424 6091.1.1.1 ↗ alpha bundles › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › FIVAR 0.69 55.0 4.75e-01 100.0% 83.5%
4648665 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 0.68 54.0 4.66e-01 100.0% 75.3%
4136265 632.2.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.68 55.0 4.78e-01 100.0% 83.7%
4968057 632.2.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.68 57.0 4.98e-01 100.0% 61.3%
5003008 632.2.1.35 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF4972 0.68 56.0 4.82e-01 100.0% 83.7%
5001960 632.2.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › FIVAR 0.67 54.0 4.79e-01 100.0% 89.3%
4364347 632.21.1.2 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › FIVAR 0.67 53.0 5.09e-01 100.0% 100.0%
3237461 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.66 59.0 3.54e-01 100.0% 29.3%
4374012 6091.1.1.1 ↗ alpha bundles › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › FIVAR 0.66 53.0 5.03e-01 100.0% 100.0%
3634546 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.65 51.0 4.63e-01 100.0% 80.0%
5069402 632.23.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical linker domain in nicking endonuclease N.BspD6I › Helical linker domain in nicking endonuclease N.BspD6I 0.65 53.0 4.77e-01 97.8% 65.7%
4937823 3558.1.1.0 ↗ alpha arrays › HSDR subunit helical domain › HSDR subunit helical domain › HSDR subunit helical domain 0.63 45.0 3.59e-01 78.3% 36.0%
3838012 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.63 51.0 3.89e-01 97.8% 75.2%
3266110 592.7.1.0 ↗ alpha arrays › PWI domain-like › GIPC1 GH2 domain › GIPC1 GH2 domain 0.61 45.0 3.76e-01 80.4% 95.0%
4945538 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 0.60 42.0 3.78e-01 78.3% 98.6%
3346146 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.60 51.0 3.43e-01 100.0% 44.3%
3971226 10.12.1.126 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › PF28724 0.59 48.0 3.31e-01 95.7% 88.6%
3964536 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.58 49.0 3.99e-01 100.0% 93.7%
4492000 4120.1.1.0 ↗ few secondary structure elements › Tim10/DDP › Tim10/DDP › Tim10/DDP 0.57 45.0 4.13e-01 100.0% 94.3%
5004484 1134.1.1.0 ↗ alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.53 37.0 3.20e-01 78.3% 69.4%
4378877 3711.1.1.20 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein › DUF444 0.52 37.0 3.25e-01 76.1% 50.7%
3721415 608.1.1.0 ↗ alpha arrays › AhpD-like › AhpD-like › AhpD-like 0.52 45.0 3.02e-01 95.7% 55.6%
4116460 246.2.1.14 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › FBPase_2 0.52 40.0 2.40e-01 100.0% 43.9%
5026634 4957.1.1.0 ↗ a+b complex topology › helical domain in yeast RNA-polymerases › third helical domain in yeast RNA-polymerase II beta-prime subunit › third helical domain in yeast RNA-polymerase II beta-prime subunit 0.52 39.0 3.42e-01 97.8% 55.6%
4542550 2007.2.3.12 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Tc-R-P 0.50 42.0 2.74e-01 100.0% 48.8%
D2 medium residues 60-194
PDB
Domain cluster: rep: gwf2_scaffold_96_prodigal-single.1__X__X__00137__D4-158
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF19474.5 best DUF6011 52.8 3.00e-14 27.4% 97.3%
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6epkA02 3.30.67.10 Alpha Beta › 2-Layer Sandwich › Viral Envelope Glycoprotein; domain 2 › Viral Envelope Glycoprotein, domain 2 0.65 30.0 4.04e-01 77.0% 81.7%
2wqlA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.61 43.0 4.19e-01 71.9% 94.1%
6j5cA02 3.30.67.10 Alpha Beta › 2-Layer Sandwich › Viral Envelope Glycoprotein; domain 2 › Viral Envelope Glycoprotein, domain 2 0.60 31.0 3.89e-01 76.3% 80.7%
2ra2B00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.60 25.0 3.67e-01 77.0% 87.9%
1fm4A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.59 42.0 3.98e-01 72.6% 89.9%
2flhB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.57 41.0 3.95e-01 72.6% 94.8%
2gfaB01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.56 28.0 3.77e-01 71.1% 100.0%
2qpvA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.55 38.0 3.93e-01 71.9% 95.5%
5ay6A01 2.60.98.20 Mainly Beta › Sandwich › Tick-borne Encephalitis virus Glycoprotein; domain 1 › Flagellar hook protein FlgE 0.54 38.0 3.58e-01 73.3% 98.2%
2ehbD00 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.54 36.0 3.73e-01 71.9% 72.2%
6c6sD02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.51 24.0 3.23e-01 74.1% 91.7%
4cvbA00 2.140.10.10 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Quinoprotein alcohol dehydrogenase-like superfamily 0.51 41.0 2.78e-01 88.9% 84.9%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3931993 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 28.0 3.87e-01 71.1% 100.0%
3267345 4.1.1.33 ↗ beta barrels › SH3 › SH3 › SH3 › Myosin_N 0.57 26.0 3.73e-01 77.0% 100.0%
3471771 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 25.0 3.61e-01 74.8% 100.0%
6331 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.55 38.0 3.92e-01 71.9% 94.7%
3389161 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 29.0 3.32e-01 77.8% 69.5%
3936430 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 27.0 3.34e-01 80.0% 76.2%
4178970 4026.1.1.2 ↗ a+b three layers › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) › Bud3_N 0.54 38.0 3.57e-01 74.1% 93.7%
3926207 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.53 23.0 3.39e-01 73.3% 100.0%
3926430 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.53 26.0 3.53e-01 72.6% 100.0%
3725498 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 29.0 3.68e-01 70.4% 100.0%
3512143 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 27.0 3.57e-01 77.0% 100.0%
3547093 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.52 29.0 3.35e-01 81.5% 76.7%
4992282 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.52 37.0 3.71e-01 71.9% 95.6%
3701195 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.52 41.0 3.04e-01 85.2% 89.2%
3628131 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.51 28.0 3.14e-01 77.0% 67.0%
3449268 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.51 31.0 3.68e-01 93.3% 95.3%
4870495 304.169.1.1 ↗ a+b two layers › Alpha-beta plaits › RspWYL1 C-terminal domain › RspWYL1 C-terminal domain › WYL 0.51 31.0 3.37e-01 83.7% 73.1%
3342793 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.50 33.0 2.96e-01 96.3% 46.3%