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AP014887.1__BAV81066.1__X__00022

Bact-Vir

AP014887.1__BAV81066.1__X__00022

Identity

Accession:
AP014887 ↗
Kingdom:
phage

Quality

93.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_CKB-S1

TaxID: 1903259

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 2-46
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4gi3C00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.68 52.0 4.92e-01 91.1% 68.4%
3fsyA02 3.30.60.70 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › Trimeric LpxA-like enzymes 0.61 44.0 4.54e-01 84.4% 90.0%
6jzaA00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.59 42.0 3.57e-01 93.3% 44.4%
7ct1A01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.54 41.0 3.56e-01 91.1% 90.6%
2hvfA00 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.53 39.0 3.77e-01 80.0% 84.6%
1wh2A01 3.30.1490.40 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › GYF domain 0.53 37.0 3.56e-01 82.2% 67.2%
3b34A04 2.60.40.1840 Mainly Beta › Sandwich › Immunoglobulin-like › Aminopeptidase N, middle-beta domain 0.52 38.0 3.01e-01 82.2% 52.0%
6icmD00 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.51 36.0 3.14e-01 82.2% 94.3%
5g5tA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.50 33.0 2.39e-01 73.3% 18.6%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3430198 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.72 56.0 5.70e-01 95.6% 88.9%
3949142 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.62 43.0 4.74e-01 73.3% 100.0%
3783859 221.1.1.51 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › USP7_C2 0.61 52.0 3.90e-01 100.0% 39.8%
3245312 375.1.1.51 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zinc_ribbon_9 0.59 40.0 4.31e-01 73.3% 97.1%
3461223 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.58 41.0 3.83e-01 84.4% 56.7%
3958264 4076.1.1.0 ↗ a+b two layers › L9 N-domain-like › L9 N-domain-like › L9 N-domain-like 0.57 45.0 4.34e-01 95.6% 94.5%
3764556 906.1.1.46 ↗ few secondary structure elements › CCCH zinc finger › CCCH zinc finger › CCCH zinc finger › zf-CCCH_4, zf-CCCH_10 0.57 38.0 3.14e-01 88.9% 36.5%
3570514 192.4.1.54 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › zf-CCCH_4, zf-CCCH_10 0.57 38.0 3.02e-01 88.9% 32.6%
4068274 4076.1.1.1 ↗ a+b two layers › L9 N-domain-like › L9 N-domain-like › L9 N-domain-like › Ribosomal_L9_N 0.53 41.0 3.98e-01 95.6% 92.7%
4220222 4076.1.1.1 ↗ a+b two layers › L9 N-domain-like › L9 N-domain-like › L9 N-domain-like › Ribosomal_L9_N 0.52 41.0 3.88e-01 88.9% 85.5%
4031664 375.1.1.75 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF2197 0.52 33.0 3.47e-01 95.6% 70.0%
4318792 4076.1.1.1 ↗ a+b two layers › L9 N-domain-like › L9 N-domain-like › L9 N-domain-like › Ribosomal_L9_N 0.52 42.0 3.67e-01 95.6% 69.3%
4439291 4281.1.1.1 ↗ a+b two layers › Ribosomal protein L35p › Ribosomal protein L35p › Ribosomal protein L35p › Ribosomal_L35p 0.52 29.0 2.71e-01 84.4% 36.7%
D2 high residues 58-169
PDB
Domain cluster: rep: BML_08042016_6_5m_scaffold_3_prodigal-single.1__X__X__00175__D95-204
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.72 51.0 5.24e-01 95.5% 76.1%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 53.0 5.45e-01 95.5% 85.8%
3vp7A00 1.10.418.40 Mainly Alpha › Orthogonal Bundle › Actin-binding Protein, T-fimbrin; domain 1 › Autophagy protein 6/Beclin 1 0.66 35.0 3.07e-01 83.0% 34.9%
3aeiA00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 47.0 5.07e-01 95.5% 90.4%
1fxkC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 54.0 5.08e-01 95.5% 79.7%
2p92A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.59 35.0 3.81e-01 91.1% 69.5%
3jysA01 1.25.40.390 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.59 43.0 3.47e-01 95.5% 39.1%
2zdiC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 51.0 4.64e-01 94.6% 77.7%
7wu7501 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 49.0 4.76e-01 95.5% 85.7%
3zqmA00 6.10.140.2160 Special › Helix non-globular › Helix Hairpins › 0.56 27.0 3.39e-01 92.9% 79.7%
3aonA00 1.10.287.3240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 50.0 4.16e-01 97.3% 95.7%
3qthB00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.56 46.0 4.04e-01 89.3% 67.7%
3qcpA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 41.0 3.63e-01 78.6% 98.8%
4qjvB00 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.55 36.0 3.90e-01 87.5% 77.7%
4n4nB00 3.90.640.100 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › 0.55 29.0 3.77e-01 74.1% 100.0%
2qmaA02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.54 30.0 2.94e-01 76.8% 48.8%
3n5fA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 38.0 3.81e-01 85.7% 71.1%
3dxpA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.53 28.0 3.05e-01 70.5% 58.1%
2cteA01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.53 32.0 3.72e-01 80.4% 86.1%
3p9aF00 1.10.132.80 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.52 34.0 3.17e-01 90.2% 54.5%
7z67A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 42.0 3.41e-01 88.4% 59.2%
1j4wA01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.51 30.0 3.60e-01 75.0% 87.8%
4oycB00 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.51 33.0 3.68e-01 79.5% 84.3%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3985490 192.2.1.5 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › DUF4376 0.77 70.0 6.75e-01 100.0% 87.9%
3939311 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.73 53.0 5.35e-01 95.5% 76.4%
3790375 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.72 54.0 5.22e-01 95.5% 70.4%
3506058 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.67 52.0 5.48e-01 98.2% 92.0%
5050732 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.67 45.0 4.42e-01 91.1% 64.2%
4047429 3281.1.1.3 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M,Proton_antipo_N,Proton_antipo_C 0.66 48.0 2.90e-01 89.3% 12.8%
4954729 3281.1.1.1 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M 0.65 46.0 2.78e-01 89.3% 11.8%
3350168 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.65 51.0 5.03e-01 83.0% 85.0%
4457710 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.64 50.0 4.89e-01 95.5% 76.7%
3550392 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 43.0 3.70e-01 95.5% 42.2%
5038015 3281.1.1.1 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M 0.63 46.0 3.02e-01 89.3% 18.9%
3519635 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.62 53.0 5.35e-01 94.6% 93.6%
3489283 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.61 54.0 5.06e-01 95.5% 80.0%
5077393 3281.1.1.1 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M 0.61 45.0 2.94e-01 100.0% 17.7%
3917315 3937.1.1.1 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Connexin 0.61 46.0 3.66e-01 98.2% 40.9%
4564040 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.61 53.0 5.02e-01 95.5% 84.4%
3843693 3937.1.1.1 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Connexin 0.60 46.0 3.71e-01 92.0% 44.5%
3594109 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.60 52.0 4.75e-01 95.5% 81.3%
4458171 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.59 51.0 4.88e-01 95.5% 80.8%
3241305 295.1.1.3 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PurA 0.59 43.0 4.02e-01 75.9% 85.7%
4557416 3937.1.1.1 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Connexin 0.58 44.0 3.37e-01 93.8% 35.7%
4927222 4961.1.1.1 ↗ a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4 0.57 30.0 3.27e-01 75.9% 56.8%
3487129 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.57 35.0 3.85e-01 82.1% 75.6%
4023956 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.57 42.0 4.00e-01 100.0% 66.2%
3198044 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.57 38.0 4.05e-01 85.7% 80.0%
4272772 3281.1.1.3 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M,Proton_antipo_N,Proton_antipo_C 0.56 49.0 2.98e-01 94.6% 65.9%
4965888 304.39.1.0 ↗ a+b two layers › Alpha-beta plaits › Mechanosensitive channel protein MscS (YggB), C-terminal domain › Mechanosensitive channel protein MscS (YggB), C-terminal domain 0.56 32.0 3.71e-01 81.2% 78.8%
4315272 3281.1.1.3 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M,Proton_antipo_N,Proton_antipo_C 0.55 50.0 3.01e-01 97.3% 68.0%
3789630 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.55 38.0 3.03e-01 94.6% 34.8%
3619691 109.4.1.1148 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_NUP160_120_M 0.55 43.0 3.79e-01 83.0% 58.8%
4836806 1063.1.1.1 ↗ alpha complex topology › Tegument protein U14 › Tegument protein U14 › Tegument protein U14 › Herpes_pp85 0.55 49.0 3.33e-01 98.2% 72.2%
4951717 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.55 25.0 2.93e-01 100.0% 60.0%
4546878 5061.1.1.2 ↗ alpha complex topology › Preprotein translocase SecY subunit › Preprotein translocase SecY subunit › Preprotein translocase SecY subunit › SecY,Plug_translocon 0.54 47.0 3.07e-01 93.8% 46.1%
5005923 5061.1.1.1 ↗ alpha complex topology › Preprotein translocase SecY subunit › Preprotein translocase SecY subunit › Preprotein translocase SecY subunit › SecY 0.54 47.0 3.07e-01 93.8% 46.1%
5077402 2007.15.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › N-deoxyribosyltransferase › N-deoxyribosyltransferase 0.54 47.0 4.03e-01 98.2% 98.4%
3877940 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.53 29.0 3.67e-01 75.0% 87.1%
4041226 2484.1.1.263 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › SHS2_FTSA, EutA, FtsA 0.52 44.0 3.03e-01 92.0% 58.5%
4959193 304.39.1.0 ↗ a+b two layers › Alpha-beta plaits › Mechanosensitive channel protein MscS (YggB), C-terminal domain › Mechanosensitive channel protein MscS (YggB), C-terminal domain 0.52 33.0 3.64e-01 82.1% 83.5%
3177126 2003.1.5.95 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › TRM13 0.51 43.0 3.00e-01 91.1% 90.1%
3923143 633.23.1.17 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › DuoxA 0.51 43.0 3.41e-01 92.9% 82.1%
3799917 633.23.1.17 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › DuoxA 0.51 43.0 3.37e-01 93.8% 84.7%
3664519 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 0.51 43.0 2.87e-01 93.8% 75.5%
4298643 3281.1.1.2 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M,Proton_antipo_N 0.51 46.0 2.95e-01 100.0% 45.3%
3936932 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 44.0 2.66e-01 94.6% 15.1%
4028841 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.50 35.0 3.32e-01 77.7% 59.3%
3627409 6166.1.1.1 ↗ alpha bundles › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › ERG4_ERG24 0.50 40.0 3.34e-01 86.6% 75.0%
3604612 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.50 30.0 3.56e-01 79.5% 89.3%