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NC_019518.1__YP_007006405.1__F397_gp16__00016

Bact-Vir

NC_019518.1__YP_007006405.1__F397_gp16__00016

Identity

Accession:
NC_019518 ↗
Kingdom:
phage

Quality

73.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_vB_VchM-138

TaxID: 1127518

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 high residues 7-74
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3k3oA02 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 55.0 5.17e-01 82.4% 94.0%
1yo7A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.70 59.0 4.99e-01 98.5% 95.0%
4hwhE00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.69 51.0 4.69e-01 79.4% 88.6%
6t0bf00 1.25.40.40 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Cytochrome c oxidase, subunit Va/VI 0.69 50.0 4.41e-01 77.9% 52.9%
3wd6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.68 53.0 4.36e-01 82.4% 66.9%
3lxzB02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.68 49.0 3.95e-01 77.9% 60.1%
3ay8A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.68 51.0 4.13e-01 82.4% 86.8%
2b0hA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.67 50.0 4.09e-01 80.9% 64.1%
1pn9B02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.67 52.0 4.17e-01 83.8% 86.2%
4g26A01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.66 49.0 3.25e-01 80.9% 19.3%
1r5aA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.66 51.0 4.12e-01 85.3% 85.3%
3cbuA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 47.0 3.84e-01 79.4% 62.7%
4k0dA00 1.20.120.1730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.64 45.0 3.62e-01 75.0% 51.7%
2dsjA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.64 45.0 4.60e-01 75.0% 76.1%
2qyuA04 1.10.4140.10 Mainly Alpha › Orthogonal Bundle › effector protein (NleL) fold › effector protein (NleL) 0.63 48.0 3.51e-01 82.4% 40.4%
1yz5B00 1.20.190.20 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › 14-3-3 domain 0.61 47.0 3.36e-01 88.2% 63.3%
4l9pA00 1.25.40.120 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Protein prenylyltransferase 0.60 48.0 3.17e-01 94.1% 20.3%
2cr7A01 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.60 47.0 4.88e-01 88.2% 95.2%
4od8D00 6.10.140.1880 Special › Helix non-globular › Helix Hairpins › 0.59 40.0 4.36e-01 79.4% 98.0%
4me2A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.58 50.0 3.69e-01 100.0% 43.8%
2janA02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.58 45.0 4.03e-01 88.2% 86.1%
2d2sA02 1.20.58.1220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Exo84p, C-terminal helical domain 0.57 46.0 4.06e-01 88.2% 84.2%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.57 40.0 3.55e-01 76.5% 93.4%
1vpwA01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.55 37.0 3.94e-01 72.1% 82.5%
2wyhB04 1.20.1270.50 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Glycoside hydrolase family 38, central domain 0.54 38.0 3.45e-01 76.5% 71.3%
2z6vA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 46.0 2.95e-01 100.0% 49.5%
2yhsA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.53 40.0 3.63e-01 91.2% 58.8%
2zs0A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.53 43.0 3.56e-01 97.1% 86.4%
3b4qA00 1.10.1200.100 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › conserved protein domain from corynebacterium diphtheriae 0.51 42.0 3.89e-01 89.7% 80.5%
1yhuB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 43.0 3.54e-01 100.0% 87.5%
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.51 36.0 3.53e-01 79.4% 100.0%
ECOD (62)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4992790 601.2.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Cytochromes › Cytochromes 0.78 60.0 5.38e-01 82.4% 74.7%
None — 0.77 57.0 3.74e-01 82.4% 19.6%
3457281 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.76 56.0 4.11e-01 77.9% 30.9%
3318819 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.76 53.0 3.85e-01 72.1% 28.6%
3336147 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.76 54.0 3.50e-01 76.5% 17.3%
3363711 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.75 55.0 4.27e-01 77.9% 37.1%
3641056 109.4.1.1256 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3 0.75 54.0 4.82e-01 77.9% 53.7%
3764093 6171.1.1.1 ↗ alpha bundles › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › JHD 0.75 55.0 4.92e-01 77.9% 83.2%
3680233 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.75 55.0 4.21e-01 79.4% 35.3%
3398541 109.4.1.1492 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_SCC3-SA, PF31007 0.75 57.0 3.42e-01 80.9% 16.8%
3811200 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.74 55.0 4.16e-01 77.9% 34.8%
3821378 109.4.1.1262 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_long 0.74 55.0 3.50e-01 77.9% 17.4%
3516432 604.29.1.1 ↗ alpha bundles › Spectrin repeat-like › Trehalose-6-phosphate phosphatase N-terminal helical bundle › Trehalose-6-phosphate phosphatase N-terminal helical bundle › T6PP_N 0.74 56.0 4.81e-01 80.9% 79.0%
3364559 109.4.1.1261 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1, PPR_2, PPR_long 0.73 53.0 4.31e-01 76.5% 42.4%
3530149 6171.1.1.1 ↗ alpha bundles › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › JHD 0.73 55.0 4.60e-01 80.9% 71.3%
2992201 6171.1.1.1 ↗ alpha bundles › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › JHD 0.72 53.0 4.56e-01 79.4% 70.9%
3421022 109.4.1.1279 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_long, TPR_24 0.72 50.0 3.35e-01 77.9% 18.9%
3324200 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.72 53.0 3.57e-01 79.4% 21.2%
3802117 109.4.1.1356 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_2, PPR_3, PPR_long 0.72 49.0 3.39e-01 75.0% 20.4%
3381334 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.72 53.0 4.12e-01 80.9% 36.6%
3784566 604.1.1.191 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF29057 0.71 52.0 4.61e-01 77.9% 86.0%
3678347 109.4.1.1440 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_long, TPR_24 0.71 52.0 2.86e-01 79.4% 5.2%
3828970 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.71 54.0 4.84e-01 82.4% 84.2%
3718035 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.71 50.0 5.13e-01 73.5% 76.9%
3708186 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.71 51.0 3.33e-01 79.4% 17.1%
3361779 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.71 51.0 3.67e-01 79.4% 25.9%
3443556 109.4.1.1271 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, TPR_24 0.71 51.0 3.72e-01 76.5% 28.6%
3808321 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.71 52.0 3.66e-01 79.4% 25.2%
3647548 109.4.1.1280 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_long 0.70 51.0 3.45e-01 77.9% 21.2%
3356444 109.4.1.1271 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, TPR_24 0.69 49.0 4.20e-01 77.9% 46.4%
3233740 604.29.1.1 ↗ alpha bundles › Spectrin repeat-like › Trehalose-6-phosphate phosphatase N-terminal helical bundle › Trehalose-6-phosphate phosphatase N-terminal helical bundle › T6PP_N 0.69 53.0 4.60e-01 82.4% 82.9%
3452003 109.4.1.1273 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3 0.68 48.0 3.45e-01 79.4% 24.9%
3187013 109.4.1.1228 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_24 0.68 49.0 3.56e-01 77.9% 27.7%
3356189 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.67 49.0 3.71e-01 77.9% 31.2%
3804606 109.4.1.1256 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3 0.67 49.0 4.22e-01 77.9% 49.5%
4605138 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.67 47.0 4.01e-01 75.0% 58.3%
3300436 109.4.1.1336 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1, PPR_2, PPR_3 0.66 48.0 3.39e-01 77.9% 24.1%
3802524 109.4.1.1382 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3, TPR_24 0.66 48.0 3.66e-01 77.9% 32.1%
3600071 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.66 48.0 4.91e-01 77.9% 89.2%
4066056 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.66 48.0 4.08e-01 77.9% 60.9%
3372011 109.4.1.621 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_3 0.65 48.0 3.36e-01 79.4% 24.0%
3518412 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.64 44.0 3.04e-01 70.6% 74.2%
3296396 109.59.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Intraflagellar transport protein 80 (IFT80) C-terminal domain › Intraflagellar transport protein 80 (IFT80) C-terminal domain 0.64 46.0 4.48e-01 80.9% 69.3%
3653175 109.4.1.1156 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › E_motif 0.64 46.0 3.71e-01 77.9% 37.9%
3648886 109.4.1.94 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ANTH 0.64 46.0 3.52e-01 76.5% 74.2%
3837289 509.1.1.0 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain 0.63 50.0 5.10e-01 89.7% 95.4%
3739546 109.4.1.18 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPTA 0.63 52.0 3.28e-01 89.7% 28.2%
3818805 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.62 52.0 5.30e-01 100.0% 100.0%
3176273 109.4.1.332 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Mtf2 0.62 47.0 3.56e-01 80.9% 34.1%
3737310 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.61 51.0 5.09e-01 98.5% 94.3%
3832531 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.61 48.0 4.54e-01 94.1% 72.2%
3437288 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.59 48.0 4.76e-01 98.5% 88.0%
3809254 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.58 47.0 4.76e-01 100.0% 100.0%
3808658 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.58 48.0 4.45e-01 100.0% 70.5%
3992501 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.58 47.0 4.44e-01 98.5% 88.9%
3226328 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.58 47.0 4.40e-01 97.1% 88.9%
3617789 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 44.0 3.30e-01 89.7% 47.1%
3426927 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.57 40.0 3.52e-01 76.5% 48.6%
3737309 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.56 44.0 4.51e-01 94.1% 98.5%
3818442 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.55 46.0 4.44e-01 100.0% 93.8%
3252433 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 43.0 2.88e-01 91.2% 48.3%
3598468 5051.1.1.6 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Aa_trans 0.54 47.0 2.96e-01 100.0% 81.7%