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NC_054460.1__YP_010052620.1__KEM13_gp62__00062

Bact-Vir

NC_054460.1__YP_010052620.1__KEM13_gp62__00062

Identity

Accession:
NC_054460 ↗
Kingdom:
phage

Quality

93.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Beograduvirus› Xanthomonas_phage_KPhi1

TaxID: 1927017

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 high residues 1-63
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1w53A00 1.10.1240.30 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain 0.72 60.0 5.51e-01 95.2% 84.5%
1fioA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 60.0 4.23e-01 95.2% 75.8%
2ii2A04 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.69 55.0 5.11e-01 100.0% 69.6%
1vw4L01 3.90.1030.10 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › Ribosomal protein L17 0.65 51.0 3.96e-01 82.5% 40.0%
3ea5D00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.64 54.0 3.05e-01 98.4% 7.5%
3i9yA00 1.20.58.920 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 56.0 3.76e-01 98.4% 92.1%
4epzA00 1.25.40.810 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › UpxZ 0.63 50.0 3.85e-01 90.5% 90.3%
4htpB00 1.10.3260.10 Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain 0.62 52.0 3.68e-01 98.4% 81.5%
3ppuB02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.61 56.0 4.54e-01 100.0% 67.3%
1xdpA01 1.20.58.310 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Polyphosphate kinase N-terminal domain 0.59 52.0 4.44e-01 100.0% 75.2%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.58 51.0 4.00e-01 98.4% 73.1%
1cg5B00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.58 49.0 3.88e-01 100.0% 53.2%
2mbgA01 1.10.555.10 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase; Chain A › Rho GTPase activation protein 0.56 47.0 3.40e-01 98.4% 42.2%
2g47A03 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.55 40.0 2.78e-01 77.8% 67.4%
1s2xA00 1.20.190.30 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › CAG pathogenicity island protein, CagZ 0.54 49.0 3.52e-01 100.0% 62.2%
3ripA02 1.20.120.1900 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Gamma-tubulin complex, C-terminal domain 0.54 40.0 2.79e-01 88.9% 72.8%
2fu2A00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.53 42.0 3.99e-01 100.0% 73.1%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3603633 3997.1.1.1 ↗ alpha arrays › Helical insertion domain in magnesium chelatase catalytic subunit › Helical insertion domain in magnesium chelatase catalytic subunit › Helical insertion domain in magnesium chelatase catalytic subunit › CobN-Mg_chel 0.79 61.0 4.28e-01 82.5% 67.9%
3520011 109.4.1.835 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › INT10 0.75 47.0 3.49e-01 96.8% 26.7%
3423827 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 0.71 58.0 5.65e-01 93.7% 91.4%
3639947 603.1.1.1 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Syntaxin 0.69 60.0 4.24e-01 95.2% 81.6%
3597604 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.69 60.0 4.17e-01 95.2% 81.5%
3744376 109.4.1.309 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Med12 0.69 59.0 3.29e-01 96.8% 8.8%
3700107 206.1.2.5 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › SAICAR synthase › CLU 0.67 60.0 3.74e-01 100.0% 84.1%
3709363 109.4.1.17 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cullin 0.66 55.0 4.73e-01 96.8% 79.0%
3464353 109.4.1.418 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Condensin2nSMC 0.66 56.0 3.25e-01 95.2% 13.0%
3964363 1051.1.1.0 ↗ alpha superhelices › Putative 3-oxoacyl-(acyl-carrier-protein) synthase N-terminal domain › Putative 3-oxoacyl-(acyl-carrier-protein) synthase N-terminal domain › Putative 3-oxoacyl-(acyl-carrier-protein) synthase N-terminal domain 0.65 56.0 4.91e-01 98.4% 65.3%
3861871 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 46.0 4.03e-01 98.4% 54.7%
3511868 309.1.1.4 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16_C 0.57 49.0 3.47e-01 98.4% 65.0%
3579629 309.1.1.0 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase 0.55 47.0 3.46e-01 96.8% 77.7%
4946403 3646.1.1.1 ↗ alpha complex topology › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › CbiQ 0.54 46.0 3.17e-01 98.4% 41.2%
3786602 1128.1.1.1 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.53 39.0 3.48e-01 79.4% 60.0%