←Back to structures

NC_027981.1__YP_009167710.1__APL38_gp03__00003

Bact-Vir

NC_027981.1__YP_009167710.1__APL38_gp03__00003

Identity

Accession:
NC_027981 ↗
Kingdom:
phage

Quality

73.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vhmlvirus› Vibrio_phage_VP585

TaxID: 631719

Cluster

View cluster (8 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 13-73
PDB
Domain cluster: rep: MK291445.1__AZV00452.1__pyei1_p35__00035__D6-61
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1r8gA00 3.30.590.20 Alpha Beta › 2-Layer Sandwich › Creatine Kinase; Chain A, domain 2 › 0.81 45.0 2.72e-01 91.8% 9.7%
2oarB00 1.10.1200.120 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Large-conductance mechanosensitive channel, MscL; domain 1 0.72 36.0 2.82e-01 72.1% 24.0%
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.69 59.0 4.59e-01 98.4% 64.3%
2w9jA00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.65 49.0 4.67e-01 95.1% 70.4%
7wu7501 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 55.0 4.42e-01 100.0% 62.7%
1ewqB01 3.40.1170.10 Alpha Beta › 3-Layer(aba) Sandwich › MutS, DNA mismatch repair protein, domain I › DNA repair protein MutS, domain I 0.62 44.0 3.67e-01 77.0% 69.5%
1gutA00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.62 42.0 4.10e-01 88.5% 62.7%
1b9mA03 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.62 40.0 3.87e-01 88.5% 56.3%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.62 45.0 4.41e-01 78.7% 75.8%
1kyzA01 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 0.61 36.0 3.01e-01 98.4% 34.0%
1z47A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.61 39.0 4.15e-01 88.5% 81.6%
2h7fX02 3.90.15.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase I; Chain A, domain 3 › Topoisomerase I; Chain A, domain 3 0.60 47.0 3.15e-01 85.2% 33.2%
3uoxB01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.60 52.0 3.39e-01 100.0% 71.2%
5i47B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.60 37.0 3.20e-01 98.4% 40.0%
3tcaA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.59 40.0 3.55e-01 70.5% 98.9%
6tepC02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.59 44.0 3.17e-01 80.3% 64.1%
2k4qA00 4.10.410.40 Few Secondary Structures › Irregular › Factor Xa Inhibitor › 0.59 42.0 3.23e-01 78.7% 82.1%
4dmzA02 3.30.70.2880 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 46.0 3.69e-01 91.8% 96.4%
2zdiC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 49.0 3.80e-01 100.0% 52.7%
4g6tA00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.58 45.0 3.57e-01 85.2% 93.0%
1ukfA00 3.90.70.20 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.58 46.0 3.45e-01 96.7% 42.6%
1sfxB00 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 50.0 4.20e-01 100.0% 87.5%
3mr0A01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 38.0 3.27e-01 73.8% 46.4%
2d42A02 3.10.450.380 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.56 41.0 4.02e-01 77.0% 84.6%
2wweA01 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.56 44.0 3.76e-01 88.5% 82.7%
4gs5A01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.55 46.0 3.17e-01 98.4% 46.3%
2v79A00 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 0.55 44.0 3.62e-01 88.5% 67.8%
2p92A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.54 46.0 4.06e-01 100.0% 87.4%
3ezjA02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.54 42.0 4.03e-01 100.0% 73.5%
1a41A01 3.90.15.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase I; Chain A, domain 3 › Topoisomerase I; Chain A, domain 3 0.54 44.0 3.59e-01 95.1% 48.0%
4lniJ01 3.10.20.70 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Glutamine synthetase, N-terminal domain 0.53 42.0 3.64e-01 90.2% 98.1%
1va0B02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.53 40.0 3.31e-01 90.2% 42.7%
2v8qA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.52 40.0 3.54e-01 83.6% 76.4%
4f3nA00 3.40.50.12710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 37.0 2.27e-01 75.4% 22.5%
4k15A00 2.60.40.3860 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 38.0 3.04e-01 83.6% 73.2%
2fhqA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 37.0 2.97e-01 78.7% 74.1%
1yz7A02 3.30.70.1130 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › EIF_2_alpha 0.51 44.0 3.87e-01 100.0% 64.4%
2qbyA03 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 38.0 3.47e-01 85.2% 100.0%
1uzxA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.51 40.0 3.18e-01 90.2% 91.4%
3m4aA03 3.90.15.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase I; Chain A, domain 3 › Topoisomerase I; Chain A, domain 3 0.51 40.0 3.33e-01 90.2% 58.5%
4esbA00 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 0.50 43.0 3.71e-01 98.4% 89.3%
1y96A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.50 38.0 3.52e-01 86.9% 65.1%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4677683 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.79 54.0 3.64e-01 72.1% 20.9%
3595207 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.78 54.0 3.65e-01 72.1% 22.4%
3370453 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.77 54.0 3.69e-01 75.4% 21.4%
4067342 5069.1.1.15 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cytochrom_C_asm 0.76 66.0 4.09e-01 98.4% 32.1%
4651132 109.4.1.1297 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TIMELESS, PF27570 0.75 53.0 2.96e-01 100.0% 6.9%
3303720 3336.1.1.1 ↗ alpha complex topology › plant-specific ROP nucleotide exchanger (PRONE) domain › plant-specific ROP nucleotide exchanger (PRONE) domain › plant-specific ROP nucleotide exchanger (PRONE) domain › PRONE 0.75 51.0 3.06e-01 100.0% 11.0%
3239066 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.74 52.0 3.14e-01 75.4% 10.8%
3290062 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.73 45.0 2.85e-01 100.0% 13.0%
3716174 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.72 66.0 5.38e-01 100.0% 56.4%
3985490 192.2.1.5 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › DUF4376 0.70 57.0 4.57e-01 100.0% 45.2%
2325417 3012.1.1.0 ↗ a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.69 36.0 3.18e-01 75.4% 35.6%
5010819 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.69 47.0 3.57e-01 100.0% 29.3%
3589473 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.69 52.0 4.84e-01 98.4% 63.7%
3508714 295.1.1.29 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › YjeJ 0.68 54.0 4.00e-01 88.5% 67.5%
3469215 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.67 59.0 3.51e-01 100.0% 40.6%
3598920 7573.1.1.0 ↗ a/b three-layered sandwiches › PRTase-like › PRTase-like › PRTase-like 0.67 44.0 2.97e-01 100.0% 18.2%
3471111 7573.1.1.4 ↗ a/b three-layered sandwiches › PRTase-like › PRTase-like › PRTase-like › UPRTase 0.67 45.0 3.03e-01 100.0% 18.8%
3515855 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.67 43.0 3.68e-01 85.2% 40.0%
4523828 101.26.1.2 ↗ alpha arrays › HTH › Tex N-terminal domain › Tex N-terminal domain › HTH_44 0.66 41.0 3.10e-01 100.0% 27.1%
3841567 7573.1.1.4 ↗ a/b three-layered sandwiches › PRTase-like › PRTase-like › PRTase-like › UPRTase 0.66 44.0 3.04e-01 100.0% 20.0%
4934732 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.66 61.0 4.76e-01 100.0% 69.2%
3742561 7573.1.1.4 ↗ a/b three-layered sandwiches › PRTase-like › PRTase-like › PRTase-like › UPRTase 0.65 44.0 3.02e-01 100.0% 20.0%
3923219 5001.1.1.44 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srv 0.65 55.0 3.53e-01 100.0% 77.1%
3942738 295.1.1.29 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › YjeJ 0.64 52.0 3.96e-01 93.4% 71.0%
5032335 7581.1.1.1 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Thiolase_N 0.64 43.0 2.71e-01 95.1% 14.1%
3220699 282.1.1.1 ↗ a+b duplicates or obligate multimers › CBS-domain › CBS-domain › CBS-domain › CBS 0.63 48.0 3.68e-01 83.6% 41.3%
3514906 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.62 37.0 2.62e-01 70.5% 19.5%
3582308 220.1.1.16 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF1681 0.62 50.0 4.36e-01 100.0% 57.9%
3789900 220.1.1.5 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PID 0.62 50.0 3.95e-01 98.4% 41.5%
3238035 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.61 43.0 4.59e-01 86.9% 90.0%
3516854 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 47.0 3.91e-01 98.4% 47.0%
4076240 4002.1.1.4 ↗ alpha bundles › alpha-helical domain in dehydroquinate synthase-like enzymes › alpha-helical domain in dehydroquinate synthase-like enzymes › alpha-helical domain in dehydroquinate synthase-like enzymes › DHQS_C 0.60 44.0 3.22e-01 82.0% 93.5%
5077402 2007.15.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › N-deoxyribosyltransferase › N-deoxyribosyltransferase 0.59 50.0 3.66e-01 100.0% 51.9%
4426276 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 40.0 3.91e-01 73.8% 82.9%
3508428 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.57 41.0 3.02e-01 77.0% 26.1%
4028484 7.1.1.7 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ_3 0.57 45.0 3.42e-01 86.9% 61.4%
3212968 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.57 47.0 3.70e-01 100.0% 42.2%
2687 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.56 50.0 4.13e-01 100.0% 81.7%
3960610 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.56 40.0 2.84e-01 78.7% 22.3%
3945142 252.2.1.7 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › PF30395 0.56 42.0 4.62e-01 90.2% 98.0%
5060792 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.56 48.0 3.90e-01 100.0% 80.6%
3189419 267.1.1.0 ↗ a+b complex topology › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain 0.56 44.0 2.91e-01 90.2% 37.1%
1203379 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.55 46.0 3.16e-01 98.4% 46.1%
3998938 6110.1.1.1 ↗ alpha superhelices › Linker domain of cytoplasmic dynein heavy chain › Linker domain of cytoplasmic dynein heavy chain › Linker domain of cytoplasmic dynein heavy chain › DHC_N2 0.55 44.0 2.71e-01 98.4% 20.6%
3255946 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 41.0 3.77e-01 93.4% 62.5%
4023956 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.54 44.0 3.44e-01 88.5% 89.2%
4968695 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.54 43.0 3.17e-01 86.9% 76.9%
3727253 3922.1.1.250 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › ATG14 0.53 46.0 2.87e-01 100.0% 35.7%
4498099 207.11.1.1 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Urease accessory protein ureH › Urease accessory protein ureH › UreD 0.53 42.0 2.94e-01 96.7% 61.2%
5040104 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.53 43.0 2.59e-01 95.1% 22.2%
5044892 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.52 45.0 3.72e-01 100.0% 90.4%
3627409 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 0.52 48.0 3.25e-01 100.0% 70.0%
3416523 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.52 36.0 2.66e-01 90.2% 26.5%
3934420 5001.1.1.44 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srv 0.51 42.0 3.06e-01 100.0% 59.5%
3924318 6166.1.1.0 ↗ 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 0.51 45.0 3.15e-01 100.0% 69.7%
5077287 304.139.1.2 ↗ a+b two layers › Alpha-beta plaits › Cas7-related › CRISPR-associated protein Cas7/Csa2-related › RAMPs 0.50 45.0 2.95e-01 100.0% 67.6%
4026519 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.50 42.0 3.33e-01 95.1% 85.2%
154263 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.50 43.0 3.71e-01 98.4% 89.3%