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NC_049430.1__YP_009879935.1__HYP57_gp056__00056

Bact-Vir

NC_049430.1__YP_009879935.1__HYP57_gp056__00056

Identity

Accession:
NC_049430 ↗
Kingdom:
phage

Quality

89.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Nahantvirus› Vibrio_phage_1.026.O._10N.222.49.C7

TaxID: 1881421

Cluster

View cluster (6 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 medium residues 1-56
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.81 54.0 4.34e-01 82.1% 36.8%
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 51.0 4.08e-01 82.1% 34.9%
1fxkC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 51.0 3.85e-01 80.4% 45.9%
2jynA01 1.10.3560.10 Mainly Alpha › Orthogonal Bundle › yst0336 like fold › yst0336 like domain 0.68 56.0 4.18e-01 89.3% 89.7%
3kreA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.63 40.0 3.25e-01 80.4% 38.1%
1nj4A01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.58 45.0 3.02e-01 89.3% 60.4%
6ko5A02 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.56 42.0 2.67e-01 82.1% 31.2%
4mgrA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.55 40.0 2.45e-01 76.8% 58.5%
3iq2A00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.54 43.0 3.42e-01 98.2% 40.7%
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 0.54 41.0 3.13e-01 100.0% 36.8%
3zqmA00 6.10.140.2160 Special › Helix non-globular › Helix Hairpins › 0.53 29.0 2.94e-01 94.6% 50.8%
6z3tA01 1.10.3370.10 Mainly Alpha › Orthogonal Bundle › Preprotein translocase SecY subunit › SecY subunit domain 0.53 45.0 2.73e-01 96.4% 32.1%
2qiyA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 35.0 2.79e-01 73.2% 29.9%
3ogzA01 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.52 43.0 2.59e-01 100.0% 57.7%
4e1pA00 3.30.60.230 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › Lsr2, dimerisation domain 0.51 39.0 3.94e-01 98.2% 83.6%
4n4nB00 3.90.640.100 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › 0.51 34.0 3.44e-01 80.4% 67.9%
2e5vA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 36.0 2.27e-01 75.0% 34.1%
2wshA00 3.40.1440.40 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › 0.51 34.0 2.66e-01 71.4% 29.1%
1ciiA02 3.30.305.10 Alpha Beta › 2-Layer Sandwich › Colicin Ia; domain 2 › Colicin Ia; domain 2 0.50 41.0 3.35e-01 89.3% 76.2%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3244537 6060.1.1.1 ↗ alpha arrays › Yst0336-like › Yst0336-like › Yst0336-like › PBDC1 0.77 56.0 4.13e-01 78.6% 31.0%
3260626 10.12.1.52 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_8 0.73 55.0 3.35e-01 82.1% 13.5%
4979945 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.72 57.0 4.36e-01 85.7% 50.4%
3691694 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.68 50.0 3.83e-01 80.4% 35.2%
3927718 304.7.1.1 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Propep_M14 0.65 41.0 3.43e-01 100.0% 37.9%
3997600 5001.1.1.41 ↗ 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_Srw 0.64 44.0 2.75e-01 73.2% 36.4%
1828185 2003.1.2.18 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.60 41.0 2.71e-01 80.4% 14.8%
3714160 3501.1.1.1 ↗ a+b two layers › protein PCC1 › protein PCC1 › protein PCC1 › Pcc1 0.60 41.0 3.54e-01 71.4% 86.7%
3945340 235.1.1.9 ↗ a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.59 45.0 3.27e-01 80.4% 76.7%
4418047 7523.1.1.46 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Lipoprotein_10+Lipoprotein_X 0.59 43.0 2.57e-01 78.6% 83.4%
3597121 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 41.0 2.51e-01 75.0% 30.8%
3218209 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 0.56 44.0 2.78e-01 85.7% 19.3%
3963083 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.55 38.0 2.82e-01 71.4% 34.1%
3578140 3937.1.1.2 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Innexin 0.55 47.0 2.88e-01 100.0% 64.4%
3284357 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.54 41.0 3.17e-01 100.0% 35.4%
2757968 304.48.1.12 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mononeg_RNA_pol 0.54 46.0 3.16e-01 100.0% 48.4%
3519677 101.1.2.4 ↗ alpha arrays › HTH › HTH › winged helix domain › Forkhead 0.54 34.0 2.56e-01 71.4% 24.3%
3578502 2006.1.6.39 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › Mat89Bb 0.54 38.0 2.51e-01 76.8% 85.5%
4948253 2006.1.3.30 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › Topoisom_bac 0.53 44.0 2.66e-01 98.2% 58.8%
4958102 1.1.3.2 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB › MazE_antitoxin 0.53 43.0 4.12e-01 92.9% 76.9%
3754192 5051.1.1.1 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › SNF 0.52 44.0 2.61e-01 100.0% 83.9%
3259076 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.52 43.0 2.98e-01 100.0% 93.0%
2035461 3380.1.1.1 ↗ a+b duplicates or obligate multimers › Dimerization domain of Lsr2 › Dimerization domain of Lsr2 › Dimerization domain of Lsr2 › Lsr2 0.51 39.0 3.91e-01 98.2% 82.1%
4990897 2007.15.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › N-deoxyribosyltransferase › N-deoxyribosyltransferase 0.51 36.0 2.63e-01 76.8% 45.4%
3610665 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 40.0 2.66e-01 92.9% 18.9%
3550392 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 43.0 2.88e-01 89.3% 42.2%
4013535 3896.1.1.0 ↗ alpha duplicates or obligate multimers › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase 0.50 39.0 2.41e-01 85.7% 14.2%
D2 medium residues 60-103
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM02 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 0.82 74.0 6.34e-01 100.0% 70.6%
5i41B00 1.10.1660.10 Mainly Alpha › Orthogonal Bundle › Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 › 0.67 48.0 4.20e-01 77.3% 97.0%
5tjjA01 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 0.62 52.0 4.40e-01 95.5% 58.9%
3h5tA01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.61 53.0 5.22e-01 100.0% 100.0%
2mkxA00 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.58 47.0 4.56e-01 93.2% 82.4%
3eetA01 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 0.52 43.0 3.88e-01 97.7% 72.3%
1e0gA00 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.52 39.0 3.91e-01 90.9% 87.5%
2ae0X02 2.40.240.50 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Barwin-like endoglucanases 0.51 39.0 2.97e-01 97.7% 82.6%
3czbA02 2.40.240.50 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Barwin-like endoglucanases 0.50 38.0 2.83e-01 95.5% 84.5%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4414927 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.82 74.0 6.27e-01 100.0% 71.0%
3171408 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.78 68.0 6.52e-01 97.7% 96.0%
4196673 101.1.9.8 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain › IF2_N 0.70 51.0 4.73e-01 77.3% 94.5%
3788382 101.1.15.0 ↗ alpha arrays › HTH › HTH › HAT1, C-terminal domain 0.62 54.0 4.42e-01 97.7% 60.0%
3306283 101.15.1.8 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM3_NFP 0.61 51.0 4.50e-01 93.2% 66.2%
3703451 101.1.15.0 ↗ alpha arrays › HTH › HTH › HAT1, C-terminal domain 0.60 50.0 4.00e-01 95.5% 57.8%
3838194 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.60 50.0 4.99e-01 93.2% 95.6%