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KY653124.1__ARM68218.1__X__00026

Bact-Vir

KY653124.1__ARM68218.1__X__00026

Identity

Accession:
KY653124 ↗
Kingdom:
phage

Quality

84.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Staphylococcus_phage_IME1367_01

TaxID: 1965491

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 8-62
PDB
Domain cluster: representative
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4oxwA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.65 50.0 4.11e-01 87.3% 93.4%
1u3eM01 3.90.75.20 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › 0.64 44.0 3.59e-01 96.4% 37.7%
2lbcA02 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.63 41.0 4.21e-01 81.8% 69.8%
1xb2B01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.61 39.0 3.90e-01 100.0% 61.7%
4dg8A02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.60 47.0 4.03e-01 89.1% 82.6%
5b55A01 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 45.0 3.15e-01 85.5% 39.5%
4jpbW02 2.40.50.180 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › CheA-289, Domain 4 0.58 44.0 3.96e-01 83.6% 93.7%
7ob9B01 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.58 51.0 3.51e-01 98.2% 51.0%
1zcdA00 1.20.1530.10 Mainly Alpha › Up-down Bundle › Na+/H+ antiporter like fold › Na+/H+ antiporter like domain 0.58 46.0 2.83e-01 92.7% 50.0%
3nybA01 1.10.1410.10 Mainly Alpha › Orthogonal Bundle › Poly(a)-polymerase, middle domain › 0.57 47.0 3.26e-01 98.2% 82.2%
2kvkA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.57 44.0 3.35e-01 89.1% 83.3%
2bzlA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.55 41.0 2.65e-01 83.6% 39.1%
4ljiB00 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.54 43.0 3.31e-01 89.1% 75.6%
1yx3A01 3.30.1420.10 Alpha Beta › 2-Layer Sandwich › Dissimilatory Siroheme-sulfite Reductase; Chain: A; domain 1 › DsrC protein, N-terminal domain 0.53 29.0 3.28e-01 70.9% 68.3%
3bzwF00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.53 41.0 2.72e-01 87.3% 70.4%
4p1mB01 3.30.160.880 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Cell division protein ZapA protomer, N-terminal domain 0.53 34.0 3.59e-01 72.7% 77.8%
1qlmA02 3.30.1030.10 Alpha Beta › 2-Layer Sandwich › Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2 › Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2 0.52 38.0 2.72e-01 85.5% 98.0%
3wgtA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 38.0 2.69e-01 83.6% 96.0%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3213123 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.79 41.0 5.23e-01 92.7% 93.3%
3260588 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.69 50.0 5.23e-01 85.5% 86.0%
3482807 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.68 49.0 3.94e-01 76.4% 93.5%
4219081 7056.1.1.3 ↗ few secondary structure elements › Zinc binding domain of metalloprotease Spartan › Zinc binding domain of metalloprotease Spartan › Zinc binding domain of metalloprotease Spartan › Zn_ribbon_SprT 0.66 44.0 4.73e-01 74.5% 84.4%
3893624 2496.1.1.7 ↗ a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like › BNIP2+CRAL_TRIO_2 0.64 48.0 3.37e-01 83.6% 60.5%
4025401 243.6.1.5 ↗ a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain › UPF0113_N 0.61 42.0 3.68e-01 90.9% 44.4%
3525928 226.1.1.1 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › BTB 0.61 55.0 4.08e-01 100.0% 63.6%
3807989 109.4.1.2070 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_2, E_motif 0.61 35.0 2.05e-01 92.7% 6.7%
4113514 304.51.1.6 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › Cas_Cmr3 0.61 49.0 3.38e-01 92.7% 25.4%
5081162 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 42.0 3.65e-01 90.9% 47.1%
3343945 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.60 46.0 3.70e-01 87.3% 80.0%
3224052 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.59 53.0 3.63e-01 100.0% 53.2%
3220364 6166.1.1.1 ↗ alpha bundles › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › ERG4_ERG24 0.58 42.0 2.98e-01 98.2% 22.5%
3790364 226.1.1.0 ↗ a+b two layers › POZ domain › POZ domain › POZ domain 0.58 48.0 3.90e-01 90.9% 83.8%
4003733 5054.1.1.8 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 0.55 37.0 2.33e-01 70.9% 13.9%
3603679 183.1.1.0 ↗ alpha duplicates or obligate multimers › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain 0.55 39.0 3.12e-01 76.4% 94.2%
5062758 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.55 40.0 2.90e-01 81.8% 80.0%
3951875 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.55 33.0 3.67e-01 83.6% 91.4%
3341056 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 47.0 4.15e-01 100.0% 100.0%
4412641 148.1.3.203 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › PF28760 0.55 40.0 3.04e-01 83.6% 72.9%
4028791 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.54 37.0 3.79e-01 74.5% 90.9%
4211951 2.1.1.14 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RuvA_N 0.54 43.0 3.99e-01 98.2% 72.5%
4559532 4232.1.1.0 ↗ few secondary structure elements › Ribosomal protein bL28-related › Ribosomal protein bL28-related › Ribosomal protein L28 0.53 39.0 3.83e-01 81.8% 76.7%
3027028 101.1.1.31 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4 0.53 40.0 3.29e-01 85.5% 87.2%
3307718 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.53 45.0 3.52e-01 96.4% 60.8%
4959094 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.53 39.0 3.97e-01 85.5% 94.5%
4986319 1.1.3.2 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB › MazE_antitoxin 0.53 35.0 3.65e-01 96.4% 74.0%
3622943 101.1.2.28 ↗ alpha arrays › HTH › HTH › winged helix domain › eIF-5_eIF-2B 0.52 41.0 3.76e-01 89.1% 97.3%
3786529 2004.1.1.186 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_12 0.52 42.0 2.86e-01 92.7% 64.9%
3302133 109.4.1.202 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_16 0.51 36.0 2.35e-01 76.4% 14.0%
3266079 2003.1.5.73 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.51 42.0 2.80e-01 94.5% 83.6%
4505972 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.50 43.0 2.70e-01 98.2% 35.9%
D2 medium residues 67-131
PDB
Domain cluster: rep: AY954951.1__AAX90802.1__X__00064__D13-69
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF07768.16 best PVL_ORF50 31.8 2.10e-07 89.2% 37.1%
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3chtA00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.62 50.0 3.20e-01 86.2% 81.1%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3530014 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.65 52.0 2.99e-01 89.2% 49.9%
3881493 109.3.1.96 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank+Ank_2+Ank_4 0.62 55.0 3.69e-01 100.0% 29.2%
4971428 2498.1.1.10 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M48 0.59 47.0 3.15e-01 84.6% 24.4%