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NC_021073.1__YP_007878004.1__VPDG_00032__00031

Bact-Vir

NC_021073.1__YP_007878004.1__VPDG_00032__00031

Identity

Accession:
NC_021073 ↗
Kingdom:
phage

Quality

94.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_henriette_12B8

TaxID: 573174

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 7-79
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1c1kA01 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.85 79.0 6.92e-01 100.0% 76.5%
3tjmA02 1.10.1470.20 Mainly Alpha › Orthogonal Bundle › Protein Yjbj; Chain: A; › Fatty acid synthase; domain 2 0.60 37.0 3.49e-01 93.2% 48.9%
2h09A02 1.10.60.10 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Iron dependent repressor, metal binding and dimerisation domain 0.54 34.0 3.77e-01 95.9% 82.1%
3d0wA00 1.10.760.20 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Protein of unknown function DUF3243 0.53 39.0 3.80e-01 82.2% 83.7%
2x64A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.51 29.0 2.57e-01 72.6% 35.4%
2lklA01 1.10.1900.40 Mainly Alpha › Orthogonal Bundle › c-terminal domain of poly(a) binding protein › Acidic terminal segments, variant surface antigen of PfEMP1 0.51 43.0 4.33e-01 93.2% 95.8%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4954669 102.1.1.0 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.60 36.0 3.57e-01 94.5% 56.0%
3622067 611.3.1.1 ↗ alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Med26 0.56 35.0 3.39e-01 84.9% 56.2%
4176786 2002.1.1.102 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PHP 0.53 37.0 2.51e-01 75.3% 98.7%
4011043 109.4.1.496 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec5 0.52 45.0 3.42e-01 93.2% 49.4%
D2 high residues 94-197
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1c1kA02 1.10.220.50 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Bacteriophage T4, Gp59, helicase assembly protein, C-terminal domain 0.88 83.0 7.99e-01 100.0% 89.6%
1x3kA01 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.59 41.0 3.68e-01 71.2% 85.7%
4ezbA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.58 40.0 3.87e-01 70.2% 88.9%
1u6zA03 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.57 43.0 3.90e-01 100.0% 58.2%
3w6zA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.55 39.0 3.76e-01 73.1% 91.7%
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.55 28.0 3.33e-01 90.4% 74.2%
4gf0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 43.0 4.27e-01 87.5% 98.2%
1by1A00 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.54 40.0 3.18e-01 76.9% 65.1%
1gcvB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.54 38.0 3.54e-01 74.0% 85.3%
1l8qA03 1.10.1750.10 Mainly Alpha › Orthogonal Bundle › Chromosomal Replication Initiator Protein Dnaa; Chain: A; › DnaA protein, C-terminal DNA-binding domain 0.53 41.0 4.09e-01 95.2% 80.4%
1ed1A00 1.10.150.90 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Immunodeficiency lentiviruses, gag gene matrix protein p17 0.53 38.0 3.69e-01 74.0% 88.6%
4nqwA02 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 28.0 3.36e-01 88.5% 82.8%
5xsoA02 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 34.0 3.72e-01 99.0% 90.8%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4841 546.1.1.1 ↗ alpha complex topology › gene 59 helicase assembly protein › gene 59 helicase assembly protein › gene 59 helicase assembly protein 0.88 83.0 6.31e-01 100.0% 47.5%
4990287 4323.1.1.0 ↗ alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C 0.61 31.0 3.02e-01 93.3% 44.3%
137999 106.1.1.1 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › Globin 0.57 41.0 3.65e-01 75.0% 81.6%
3718740 109.46.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Helical domain in TOPLESS related protein 2 (TPR2) › Helical domain in TOPLESS related protein 2 (TPR2) 0.57 40.0 3.87e-01 79.8% 65.2%
3723452 109.4.1.1129 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_TRAPPC9-Trs120 0.56 47.0 4.00e-01 94.2% 79.4%
4992090 5060.2.1.0 ↗ alpha bundles › V-type ATP synthase subunit C › Toxin coregulated pilus biosynthesis protein E cytoplasmic domain › Toxin coregulated pilus biosynthesis protein E cytoplasmic domain 0.55 38.0 3.76e-01 100.0% 66.1%
3967650 101.1.2.378 ↗ alpha arrays › HTH › HTH › winged helix domain › MksE 0.54 43.0 4.18e-01 100.0% 77.4%
4942097 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.52 42.0 3.38e-01 90.4% 68.6%
4381446 3896.1.1.0 ↗ alpha duplicates or obligate multimers › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase 0.51 37.0 2.91e-01 76.0% 73.3%