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NC_051639.1__YP_009955186.1__I5H19_gp074__00074

Bact-Vir

NC_051639.1__YP_009955186.1__I5H19_gp074__00074

Identity

Accession:
NC_051639 ↗
Kingdom:
phage

Quality

68.6 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

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

D1 high residues 68-118
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1he1A00 1.20.120.260 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Virulence factor YopE uncharacterised domain 0.59 45.0 3.42e-01 86.3% 79.3%
4dsfA04 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.58 49.0 3.92e-01 100.0% 46.4%
4ikbA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.57 46.0 3.58e-01 98.0% 74.4%
7dwqL01 1.20.1240.10 Mainly Alpha › Up-down Bundle › Photosystem 1 Reaction Centre Subunit Xi; Chain: L; › Photosystem I PsaL, reaction centre subunit XI 0.56 47.0 3.68e-01 100.0% 42.4%
2iqcA00 1.25.40.490 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.54 38.0 2.63e-01 98.0% 22.0%
1e3mB03 6.10.140.80 Special › Helix non-globular › Helix Hairpins › 0.53 41.0 4.05e-01 98.0% 82.1%
1e8cA02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.53 39.0 2.66e-01 88.2% 28.2%
1lvlA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 43.0 2.98e-01 98.0% 93.5%
1g4uS01 1.20.120.260 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Virulence factor YopE uncharacterised domain 0.52 37.0 2.98e-01 82.4% 98.4%
4c12A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.51 39.0 2.65e-01 94.1% 29.0%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4383552 2004.1.1.159 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.62 52.0 3.39e-01 100.0% 26.5%
54515 601.9.1.0 alpha bundles › Four-helical up-and-down bundle › Bacterial GAP domain › Bacterial GAP domain 0.59 46.0 3.44e-01 86.3% 79.3%
3782485 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.59 35.0 2.76e-01 100.0% 24.3%
3738 601.9.1.1 alpha bundles › Four-helical up-and-down bundle › Bacterial GAP domain › Bacterial GAP domain › YopE 0.59 45.0 3.42e-01 86.3% 79.3%
4433009 2004.1.1.159 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.58 44.0 2.87e-01 84.3% 18.3%
3838408 2004.1.1.159 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.56 47.0 3.12e-01 100.0% 28.3%
3504309 386.1.1.133 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2+zf-C2H2_4 0.55 43.0 3.91e-01 100.0% 62.5%
4031091 2004.1.1.159 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.54 43.0 2.85e-01 96.1% 23.6%
D2 high residues 132-186
PDB
Domain cluster: representative
CATH (46)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4cbvA02 2.40.50.1020 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › LytTr DNA-binding domain 0.70 46.0 3.64e-01 76.4% 32.2%
3pg7A02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.70 51.0 4.06e-01 78.2% 43.6%
4nswA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.67 52.0 4.19e-01 85.5% 77.1%
3buuB00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.65 48.0 3.20e-01 80.0% 89.5%
4bndA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.65 46.0 3.32e-01 74.5% 97.4%
1nrkA01 3.30.70.1630 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 44.0 3.64e-01 72.7% 75.3%
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 46.0 3.70e-01 78.2% 41.3%
1httA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.62 47.0 4.03e-01 87.3% 91.8%
1vw4F02 3.90.930.12 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › Ribosomal protein L6 0.61 44.0 3.81e-01 80.0% 84.8%
2c9oB02 2.40.50.360 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RuvBL1 DNA/RNA binding domain 0.61 44.0 3.56e-01 78.2% 63.7%
4oxwA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.60 43.0 3.58e-01 78.2% 86.8%
3p0cA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.60 43.0 3.54e-01 80.0% 43.2%
4m7xA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.60 41.0 3.54e-01 72.7% 45.1%
2wdtC02 3.30.1490.420 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Ubiquitin carboxyl-terminal hydrolase, domain 2 0.60 50.0 4.23e-01 100.0% 88.1%
3k6qA02 3.30.160.620 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.59 44.0 3.68e-01 83.6% 48.3%
4osnA00 2.30.29.100 Mainly Beta › Roll › PH-domain like › 0.59 48.0 3.90e-01 92.7% 67.3%
2wyhB06 2.70.98.30 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Golgi alpha-mannosidase II; domain 4 0.59 49.0 3.22e-01 100.0% 97.9%
3cxbB00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.59 42.0 3.50e-01 76.4% 44.7%
3ib5A00 3.10.570.10 Alpha Beta › Roll › sex pheromone staph- cam373 precursor fold › sex pheromone staph- cam373 precursor domain 0.58 46.0 2.80e-01 85.5% 39.8%
3k1rA02 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.58 43.0 3.45e-01 80.0% 81.1%
3sfvB02 6.10.140.2010 Special › Helix non-globular › Helix Hairpins › 0.58 44.0 2.89e-01 80.0% 24.0%
4wi1A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.57 47.0 3.81e-01 100.0% 86.2%
2lt1A00 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.57 39.0 3.65e-01 74.5% 82.7%
2qx2A00 3.10.570.10 Alpha Beta › Roll › sex pheromone staph- cam373 precursor fold › sex pheromone staph- cam373 precursor domain 0.57 44.0 2.74e-01 83.6% 49.7%
4upkA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.57 41.0 2.45e-01 78.2% 89.8%
1maiA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 44.0 3.58e-01 90.9% 58.8%
4zyaB00 3.30.1910.20 Alpha Beta › 2-Layer Sandwich › so0334 like fold › asparaginyl-tRNA synthetase, N-terminal domain 0.57 41.0 3.67e-01 76.4% 98.7%
2vc8A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.57 39.0 3.63e-01 72.7% 81.9%
1d4tA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.56 46.0 3.83e-01 94.5% 61.5%
2z15A00 3.90.640.90 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › Anti-proliferative protein, N-terminal domain 0.56 37.0 2.90e-01 78.2% 31.9%
2do3A01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.55 38.0 3.97e-01 74.5% 98.0%
2dixA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 43.0 3.83e-01 85.5% 62.8%
7cr6D01 3.100.10.20 Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › CRISPR-associated endonuclease Cas1, N-terminal domain 0.55 40.0 3.60e-01 80.0% 76.8%
1w5rA01 3.30.2140.10 Alpha Beta › 2-Layer Sandwich › Arylamine N-acetyltransferase fold › Arylamine N-acetyltransferase 0.55 43.0 3.10e-01 89.1% 31.2%
1tuoA04 3.30.310.50 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Alpha-D-phosphohexomutase, C-terminal domain 0.54 37.0 3.56e-01 80.0% 61.5%
2gwcA00 3.30.590.20 Alpha Beta › 2-Layer Sandwich › Creatine Kinase; Chain A, domain 2 › 0.53 45.0 2.71e-01 100.0% 59.1%
5vmzA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.52 35.0 3.87e-01 78.2% 100.0%
3d6wB01 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 34.0 3.23e-01 70.9% 51.4%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.52 41.0 4.08e-01 89.1% 94.7%
2wfpA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 40.0 3.41e-01 87.3% 67.3%
3s24A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 43.0 3.66e-01 94.5% 87.2%
2bn8A00 3.30.730.20 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › Cell division activator CedA 0.52 43.0 4.06e-01 96.4% 88.1%
4l80D00 3.20.20.60 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphoenolpyruvate-binding domains 0.51 40.0 2.46e-01 85.5% 25.0%
2fgeA01 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.51 40.0 2.80e-01 100.0% 93.6%
2e50B02 3.30.1120.90 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › Nucleosome assembly protein 0.51 35.0 2.99e-01 78.2% 70.3%
4hn3A00 3.10.570.10 Alpha Beta › Roll › sex pheromone staph- cam373 precursor fold › sex pheromone staph- cam373 precursor domain 0.50 45.0 2.76e-01 100.0% 40.4%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3714703 1021.1.1.0 a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases 0.81 59.0 4.81e-01 78.2% 49.0%
3177024 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.77 63.0 5.04e-01 94.5% 45.5%
3904747 101.1.8.0 alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.76 58.0 4.27e-01 81.8% 32.9%
3930986 4292.2.1.0 a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain 0.74 60.0 4.80e-01 89.1% 83.8%
3400449 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.73 54.0 3.78e-01 80.0% 25.7%
4971601 241.14.1.0 a+b two layers › Type III secretory system chaperone-like › SARS-unique domain-C › SARS-unique domain-C 0.72 58.0 5.44e-01 90.9% 81.4%
3685784 511.1.1.0 beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain 0.71 53.0 3.73e-01 80.0% 94.7%
5014250 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.71 51.0 4.55e-01 78.2% 81.2%
3453949 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.69 54.0 3.36e-01 87.3% 85.3%
4072685 7502.1.1.1 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.68 58.0 5.28e-01 98.2% 96.0%
4992470 896.1.1.0 a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.66 47.0 4.59e-01 80.0% 70.0%
4478971 4.1.1.174 beta barrels › SH3 › SH3 › SH3 › DUF951 0.66 46.0 4.39e-01 74.5% 80.0%
3689915 109.4.1.1227 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › NPHP3_N 0.65 51.0 2.92e-01 87.3% 9.7%
4021531 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.65 43.0 3.60e-01 72.7% 37.8%
3439202 220.1.1.30 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_BEACH 0.64 46.0 4.10e-01 78.2% 65.9%
3394097 7502.1.1.0 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.64 50.0 4.25e-01 90.9% 88.0%
5017214 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.63 46.0 4.61e-01 78.2% 87.3%
1921564 101.1.2.237 alpha arrays › HTH › HTH › winged helix domain › ThcOx 0.63 44.0 3.57e-01 80.0% 36.5%
4980247 7515.1.1.2 a/b three-layered sandwiches › Alkaline phosphatase-like › Alkaline phosphatase-like › Alkaline phosphatase-like › Sulfatase 0.61 45.0 2.73e-01 81.8% 12.3%
3562938 220.1.1.1 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 45.0 3.55e-01 81.8% 68.0%
3806421 247.1.1.38 a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › CPSF73-100_C 0.60 42.0 4.00e-01 72.7% 81.5%
4964910 300.1.1.25 a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › TbsP_N 0.60 47.0 3.50e-01 85.5% 85.7%
4248887 7502.1.1.1 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.60 48.0 3.87e-01 100.0% 76.2%
3928803 4967.1.1.0 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases 0.60 51.0 3.53e-01 100.0% 64.0%
4027440 277.1.1.1 a+b two layers › PX domain › PX domain › PX domain › PX 0.58 43.0 3.48e-01 80.0% 43.6%
None 0.58 43.0 2.54e-01 83.6% 8.6%
227631 3282.1.1.1 a+b complex topology › LidA › LidA › LidA › LidA_Long_CC 0.58 44.0 2.63e-01 80.0% 14.3%
3908555 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.57 45.0 2.88e-01 83.6% 19.2%
3658251 63.1.1.4 beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › PRKCSH_1 0.57 41.0 3.44e-01 80.0% 76.2%
5066347 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.57 39.0 2.84e-01 80.0% 26.7%
3740923 4.1.1.107 beta barrels › SH3 › SH3 › SH3 › XRN1_D1 0.57 45.0 3.23e-01 90.9% 69.4%
3958991 231.1.1.0 a+b two layers › MocoBD/DmpA-related › MocoBD/DmpA-related › Molybdenum cofactor-binding domain 0.56 43.0 2.79e-01 81.8% 24.4%
None 0.56 45.0 3.10e-01 98.2% 97.1%
3716928 2008.1.1.107 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NERD 0.56 49.0 3.40e-01 100.0% 70.4%
3695142 12.3.1.2 beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Cu_amine_oxid 0.55 46.0 2.79e-01 100.0% 75.1%
3524696 633.23.1.1 alpha bundles › Bromodomain-like › Claudin › Claudin › PMP22_Claudin 0.55 41.0 2.88e-01 80.0% 60.6%
3927286 4099.1.1.0 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.55 44.0 4.02e-01 89.1% 90.7%
2701125 3146.1.1.1 a+b complex topology › gH main domain › gH main domain › gH main domain › Herpes_glycop_H 0.54 48.0 2.77e-01 100.0% 11.5%
3289616 2002.1.1.73 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TGT 0.54 39.0 2.42e-01 80.0% 13.0%
3959495 219.1.1.8 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › NLPC_P60 0.54 38.0 3.51e-01 78.2% 84.6%
4307219 4.8.1.5 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.54 35.0 3.50e-01 70.9% 65.5%
5061231 4100.1.1.0 a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.53 40.0 3.87e-01 83.6% 71.7%
4959480 4100.1.1.0 a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.53 37.0 3.65e-01 72.7% 81.7%
5043213 71.1.1.0 beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.53 40.0 2.84e-01 89.1% 48.5%
3222321 207.1.1.81 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.52 42.0 2.87e-01 100.0% 24.3%
3619889 331.23.1.7 a+b two layers › TBP-like › Integrator IntS9/IntS11 C-terminal domain › Integrator IntS9/IntS11 C-terminal domain › CPSF73-100_C 0.52 36.0 3.40e-01 74.5% 80.0%
4820773 2484.1.1.70 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FtsA 0.50 37.0 2.84e-01 81.8% 39.6%
3634974 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.50 45.0 2.81e-01 100.0% 69.7%