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NC_016567.1__YP_004957507.1__VPEG_00014__00014

Bact-Vir

NC_016567.1__YP_004957507.1__VPEG_00014__00014

Identity

Accession:
NC_016567 ↗
Kingdom:
phage

Quality

95.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_SIO-2

TaxID: 700512

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 medium residues 1-65
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04447.18 best dATP-dGTP_PPHyd 43.0 6.20e-11 87.7% 50.5%
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.88 60.0 6.35e-01 70.8% 86.2%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.87 60.0 6.14e-01 70.8% 79.0%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.87 78.0 6.35e-01 96.9% 64.6%
7odyC01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.87 78.0 6.86e-01 96.9% 68.5%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.85 80.0 7.30e-01 100.0% 82.9%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.85 62.0 6.06e-01 76.9% 73.2%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.83 56.0 5.60e-01 70.8% 94.0%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.82 56.0 5.66e-01 70.8% 78.1%
1w99A01 1.20.190.10 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › Pesticidal crystal protein, N-terminal domain 0.79 54.0 3.88e-01 70.8% 28.3%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 54.0 4.97e-01 72.3% 59.3%
2hjmA01 1.20.120.460 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › protein pf1176 like 0.76 58.0 5.22e-01 80.0% 98.8%
2qr4A01 1.20.140.70 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Oligopeptidase f, N-terminal domain 0.74 55.0 4.14e-01 80.0% 80.8%
2mmbA00 4.10.640.20 Few Secondary Structures › Irregular › 30s Ribosomal Protein S18 › 0.74 57.0 4.86e-01 87.7% 51.4%
1iwpG02 1.10.1510.20 Mainly Alpha › Orthogonal Bundle › Hypothetical Protein Yqey; Chain: A; domain1 › Propanediol/glycerol dehydratase, small subunit 0.73 48.0 4.25e-01 80.0% 47.3%
4x5mA00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.73 60.0 5.46e-01 89.2% 75.6%
2pziB03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.73 52.0 3.89e-01 75.4% 89.3%
1bgfA00 1.10.532.10 Mainly Alpha › Orthogonal Bundle › Transcription Factor, Stat-4 › STAT transcription factor, N-terminal domain 0.70 54.0 4.29e-01 81.5% 61.3%
1quuA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 55.0 4.41e-01 86.2% 71.4%
1u89A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.69 55.0 4.37e-01 89.2% 77.7%
3nbxX03 1.20.58.1510 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 53.0 4.61e-01 84.6% 82.2%
3k3uA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.67 56.0 4.42e-01 93.8% 46.7%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.66 45.0 3.65e-01 70.8% 75.4%
6xz3A01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.66 49.0 4.05e-01 80.0% 64.1%
3oxfA05 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.65 47.0 4.55e-01 80.0% 68.0%
3ezuA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.64 54.0 4.01e-01 98.5% 85.7%
3v5uA02 1.20.1420.30 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › NCX, central ion-binding region 0.63 52.0 3.71e-01 96.9% 74.2%
3lmfA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.62 51.0 4.37e-01 93.8% 98.2%
3kfwX03 1.20.58.1460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 44.0 4.19e-01 73.8% 75.0%
1evsA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.59 45.0 3.53e-01 89.2% 68.1%
1cg5B00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.58 49.0 3.92e-01 98.5% 48.2%
1rvkA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.57 49.0 4.11e-01 98.5% 90.5%
2og9A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.57 45.0 3.71e-01 90.8% 66.9%
2da3A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.57 37.0 4.08e-01 95.4% 91.5%
2pkeA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.55 37.0 3.53e-01 78.5% 59.0%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.53 42.0 4.31e-01 98.5% 100.0%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3947647 159.1.2.3 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › dATP-dGTP_PPHyd 0.91 86.0 7.36e-01 100.0% 68.4%
4674 192.7.1.1 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › FemAB 0.87 60.0 6.01e-01 70.8% 75.4%
2772442 159.1.2.3 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › dATP-dGTP_PPHyd 0.87 80.0 6.80e-01 100.0% 64.6%
5007466 159.1.2.2 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › MazG 0.85 79.0 6.99e-01 100.0% 73.3%
3574609 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.84 58.0 4.02e-01 70.8% 33.7%
5070758 109.4.1.5 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1 0.84 58.0 4.72e-01 70.8% 41.8%
3714621 109.4.1.210 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_19 0.84 61.0 3.93e-01 83.1% 18.8%
3973900 192.8.1.331 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › DUF4824 0.84 57.0 5.17e-01 70.8% 54.1%
5010954 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.84 57.0 4.69e-01 70.8% 44.5%
5047397 159.1.1.1 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 › MazG 0.83 77.0 6.63e-01 100.0% 70.4%
3329315 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.80 57.0 3.73e-01 76.9% 19.6%
3740779 604.12.1.2 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 0.80 60.0 5.66e-01 80.0% 68.0%
4977808 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.79 59.0 5.74e-01 78.5% 88.6%
3936950 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.78 64.0 5.48e-01 87.7% 67.0%
3856019 604.1.1.92 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › SR_desmoplakin_3 0.77 58.0 4.34e-01 80.0% 76.1%
5001620 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 0.76 56.0 4.78e-01 78.5% 52.4%
4030521 604.12.1.2 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 0.75 55.0 5.24e-01 76.9% 74.7%
3904779 3922.1.1.0 ↗ 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 0.74 67.0 5.57e-01 98.5% 79.1%
3944339 3939.1.1.0 ↗ alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain 0.74 50.0 4.50e-01 70.8% 52.2%
3664940 192.4.1.22 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › PF26575 0.72 61.0 5.71e-01 92.3% 83.7%
2628027 101.1.11.90 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix › DotY 0.71 52.0 5.03e-01 78.5% 75.3%
3580914 604.12.1.2 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 0.69 56.0 5.11e-01 87.7% 90.6%
4959129 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.68 46.0 4.35e-01 70.8% 60.0%
3389599 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.68 52.0 4.19e-01 81.5% 71.7%
1902251 612.1.1.4 ↗ alpha arrays › Retroviral matrix proteins › Retroviral matrix proteins › Retroviral matrix proteins › Gag_p10 0.67 58.0 4.81e-01 96.9% 63.2%
5047148 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.66 45.0 2.91e-01 72.3% 15.2%
3262410 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.65 53.0 5.11e-01 92.3% 81.3%
4929285 632.18.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › hypothetical protein PA2901 › hypothetical protein PA2901 0.64 44.0 4.44e-01 72.3% 73.8%
3946272 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.64 55.0 4.15e-01 98.5% 47.3%
5062562 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.63 53.0 4.34e-01 92.3% 70.4%
4933577 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.61 50.0 4.19e-01 92.3% 74.8%
4055608 3826.1.1.21 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › DUF986 0.61 49.0 4.71e-01 90.8% 85.3%
3990247 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 51.0 3.30e-01 92.3% 40.0%
4505178 106.1.1.1 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › Globin 0.59 51.0 4.54e-01 98.5% 71.6%
3977558 639.2.1.3 ↗ alpha arrays › HHA-like › Regulator of acid resistance influenced by indole (AriR) › Regulator of acid resistance influenced by indole (AriR) › BDM 0.57 42.0 4.41e-01 81.5% 100.0%
3679148 108.1.1.26 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5 0.56 40.0 3.50e-01 76.9% 67.6%
4660186 2008.1.1.159 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Csa1 0.54 47.0 3.07e-01 96.9% 54.4%
D2 medium residues 66-148
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6wk3A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.56 40.0 3.42e-01 75.9% 95.2%
6pnjL00 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 41.0 3.37e-01 78.3% 67.9%
3wctD00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.54 38.0 3.20e-01 73.5% 45.6%
4rm7A01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.51 37.0 3.32e-01 77.1% 57.4%
1fntc01 1.20.120.180 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Proteasome activator pa28, C-terminal domain 0.50 34.0 2.63e-01 71.1% 60.1%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3788539 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.62 36.0 2.30e-01 100.0% 12.0%
3281755 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.62 32.0 3.74e-01 98.8% 68.3%
3380671 5050.1.1.8 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › FPN1 0.57 49.0 4.08e-01 100.0% 61.9%
1406103 3694.1.1.3 ↗ alpha bundles › Tail specific protease helical domain › Tail specific protease helical domain › Tail specific protease helical domain › TSP_NTD 0.53 45.0 3.49e-01 100.0% 68.2%