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AY147036.1__AAN74014.1__X__00005

Bact-Vir

AY147036.1__AAN74014.1__X__00005

Identity

Accession:
AY147036 ↗
Kingdom:
phage

Quality

88.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Peduoviridae› Peduovirus› Vibrio_phage_O395

TaxID: 213780

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 medium residues 1-66
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3k6tB00 1.20.5.4010 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.66 43.0 4.73e-01 71.2% 89.8%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.64 45.0 4.38e-01 72.7% 64.9%
1vb3A01 3.90.1380.10 Alpha Beta › Alpha-Beta Complex › threonine synthase, domain 1, chain A › Threonine synthase, N-terminal domain 0.64 37.0 3.49e-01 84.8% 44.4%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 47.0 4.71e-01 80.3% 91.3%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.63 44.0 4.47e-01 74.2% 84.6%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.63 43.0 4.22e-01 77.3% 66.2%
1kf6D00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.62 44.0 3.68e-01 75.8% 73.1%
7myqB02 1.10.1270.20 Mainly Alpha › Orthogonal Bundle › Trp Operon Repressor; Chain A › tRNA(m1g37)methyltransferase, domain 2 0.61 33.0 3.63e-01 98.5% 63.6%
3qavA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.61 44.0 3.53e-01 78.8% 37.1%
2wgmA01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.59 44.0 4.17e-01 83.3% 84.1%
2nr5A00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.57 42.0 4.41e-01 80.3% 91.4%
4nv0A02 1.10.150.340 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain 0.55 45.0 4.27e-01 100.0% 76.8%
2oap101 3.30.450.380 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.54 40.0 2.82e-01 80.3% 36.4%
5u1xA01 1.10.287.940 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › atp-gated p2x4 ion channel 0.53 35.0 3.98e-01 80.3% 100.0%
3lf2A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 42.0 2.87e-01 89.4% 32.4%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4363733 4312.1.1.13 ↗ a+b two layers › RelE-like › RelE-like › RelE-like › Toxin_YhaV 0.96 82.0 6.09e-01 89.4% 40.7%
3245748 316.1.1.25 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Nrap_D4 0.77 57.0 3.92e-01 78.8% 49.8%
4011834 109.4.1.777 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.69 49.0 3.36e-01 74.2% 37.6%
4334669 3456.1.1.1 ↗ extended segments › NADH-quinone oxidoreductase subunit A › NADH-quinone oxidoreductase subunit A › NADH-quinone oxidoreductase subunit A › Oxidored_q4 0.67 46.0 3.71e-01 72.7% 43.1%
4948948 177.1.1.0 ↗ alpha bundles › Phospholipase C/P1 nuclease › Phospholipase C/P1 nuclease › Phospholipase C/P1 nuclease 0.66 58.0 4.14e-01 100.0% 76.0%
3285148 3730.1.1.5 ↗ alpha arrays › CCM3/GCKIII dimerization domain › CCM3/GCKIII dimerization domain › CCM3/GCKIII dimerization domain › DUF6247 0.65 47.0 5.07e-01 90.9% 90.9%
4930198 605.1.1.2 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › H-kinase_dim 0.62 44.0 4.56e-01 78.8% 81.7%
1176726 4325.1.1.2 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › P53_C 0.62 42.0 4.14e-01 77.3% 66.2%
3976988 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.61 53.0 4.09e-01 100.0% 76.1%
3401966 2.1.1.350 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF30298 0.61 47.0 3.48e-01 84.8% 44.4%
3474564 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.60 43.0 3.76e-01 77.3% 76.2%
D2 medium residues 67-161
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF11663.15 best Toxin_YhaV 102.2 3.50e-29 93.7% 59.4%
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ro6C01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.55 40.0 3.94e-01 78.9% 94.3%
4jn7A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.55 41.0 3.83e-01 80.0% 80.7%
2f96A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.54 37.0 2.99e-01 71.6% 47.8%
3uh0A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.53 40.0 2.91e-01 82.1% 44.9%
4ewfA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.53 41.0 3.04e-01 88.4% 30.2%
2db2A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.53 41.0 4.20e-01 84.2% 98.9%
4dkkA02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 36.0 3.93e-01 81.1% 90.5%
6nydC00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.51 42.0 3.56e-01 90.5% 62.7%
2xrnA02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.51 42.0 3.50e-01 91.6% 55.9%
3cawA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 36.0 3.68e-01 81.1% 76.9%
2xp1A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.50 38.0 3.84e-01 87.4% 82.1%
2iwtB00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.50 37.0 3.04e-01 78.9% 82.9%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5056462 4312.1.1.0 ↗ a+b two layers › RelE-like › RelE-like › RelE-like 0.68 40.0 4.16e-01 74.7% 62.2%
3933051 2003.1.1.51 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › DFP 0.61 45.0 3.29e-01 80.0% 90.5%
3592741 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.57 40.0 4.23e-01 74.7% 82.4%
3614613 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.56 45.0 3.76e-01 87.4% 60.6%
5052185 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.56 42.0 3.80e-01 96.8% 58.5%
3605340 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.56 50.0 3.00e-01 100.0% 39.9%
3742002 5.1.5.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40 0.55 39.0 2.69e-01 73.7% 41.2%
3508680 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.54 31.0 3.05e-01 70.5% 47.6%
3446029 859.1.1.1 ↗ a+b two layers › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › HORMA 0.54 39.0 3.37e-01 76.8% 83.9%
3492441 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 38.0 4.17e-01 74.7% 92.0%
3586471 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.54 45.0 2.96e-01 92.6% 39.0%
3936025 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.53 37.0 3.65e-01 83.2% 67.0%
3603733 4121.1.1.19 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › PF27230 0.53 42.0 3.02e-01 89.5% 53.8%
3805475 5.1.3.67 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_1 0.52 40.0 2.81e-01 82.1% 24.3%
3601509 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 46.0 2.99e-01 96.8% 49.2%
3237754 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 38.0 3.92e-01 75.8% 81.1%
3709987 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.52 42.0 3.86e-01 90.5% 86.2%
1169854 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.52 39.0 3.91e-01 81.1% 94.9%
3440964 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.52 40.0 2.79e-01 82.1% 33.0%
3172425 5.1.4.172 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_CAF1B_HIR1 0.52 40.0 2.68e-01 85.3% 62.2%
3783610 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.52 43.0 2.91e-01 93.7% 40.5%
4489443 218.1.1.8 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.51 38.0 3.71e-01 82.1% 86.4%
3572755 330.1.1.6 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Staufen_C 0.51 36.0 3.44e-01 84.2% 61.7%
3994368 5.1.8.5 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › putative conserved lipoprotein NT01CX_1156 › APEH_N 0.51 41.0 3.25e-01 93.7% 62.7%
4243468 5.1.4.262 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, Beta-prop_CAF1B_HIR1 0.51 39.0 2.61e-01 85.3% 57.0%
5034706 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.50 35.0 3.83e-01 76.8% 93.3%
3538687 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.50 39.0 3.79e-01 84.2% 77.1%