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KC131130.1__AGB07153.1__X__00039

Bact-Vir

KC131130.1__AGB07153.1__X__00039

Identity

Accession:
KC131130 ↗
Kingdom:
phage

Quality

80.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Tidunavirus› Vibrio_phage_VP4B

TaxID: 1262540

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 2-88
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4gnxC03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.64 56.0 4.48e-01 100.0% 72.7%
2k4nA00 3.30.720.70 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.64 46.0 4.32e-01 77.0% 91.9%
4dduA07 2.60.510.20 Mainly Beta › Sandwich › EV matrix protein fold › 0.62 51.0 4.77e-01 88.5% 75.7%
8c5yA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.61 54.0 4.36e-01 100.0% 80.0%
3k8aB00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.59 53.0 5.06e-01 100.0% 85.4%
1wjjA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.59 53.0 4.90e-01 100.0% 80.9%
1vpbA01 3.30.2290.10 Alpha Beta › 2-Layer Sandwich › PmbA/TldD fold › PmbA/TldD superfamily 0.58 45.0 3.32e-01 83.9% 31.6%
1v1qA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.58 52.0 4.80e-01 100.0% 82.7%
3fhwA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 51.0 4.92e-01 100.0% 87.9%
1vl4A01 3.30.2290.10 Alpha Beta › 2-Layer Sandwich › PmbA/TldD fold › PmbA/TldD superfamily 0.56 42.0 3.27e-01 83.9% 34.1%
3cyjA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.56 46.0 4.14e-01 89.7% 92.6%
2chrA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.56 47.0 4.18e-01 93.1% 94.5%
1gkuB07 2.60.510.20 Mainly Beta › Sandwich › EV matrix protein fold › 0.55 44.0 4.21e-01 87.4% 78.4%
3bjsA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 44.0 4.04e-01 89.7% 100.0%
3n4fA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 47.0 4.17e-01 95.4% 78.7%
1l3aA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.54 44.0 3.60e-01 89.7% 68.7%
3f6gA01 3.30.160.740 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.54 35.0 4.13e-01 97.7% 98.3%
4p2iA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.54 45.0 4.16e-01 95.4% 100.0%
2r5rA00 3.10.270.10 Alpha Beta › Roll › Urate Oxidase › Urate Oxidase; 0.54 47.0 3.39e-01 96.6% 66.3%
3qtdA01 3.30.2290.10 Alpha Beta › 2-Layer Sandwich › PmbA/TldD fold › PmbA/TldD superfamily 0.54 41.0 3.10e-01 83.9% 32.0%
5nj5A01 3.30.2290.10 Alpha Beta › 2-Layer Sandwich › PmbA/TldD fold › PmbA/TldD superfamily 0.53 40.0 3.00e-01 81.6% 37.7%
3aj3A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.53 39.0 2.80e-01 79.3% 97.8%
4jhmA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.53 44.0 4.05e-01 94.3% 99.1%
4mt4A00 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.52 40.0 2.53e-01 83.9% 55.1%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3215090 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.65 44.0 4.90e-01 98.9% 92.3%
3932155 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.65 46.0 3.27e-01 74.7% 26.2%
3628355 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.63 46.0 3.10e-01 75.9% 27.0%
5078764 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.63 56.0 5.08e-01 100.0% 78.3%
3738561 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.60 54.0 5.10e-01 100.0% 100.0%
3578613 9.2.1.3 ↗ beta barrels › Lipocalins/Streptavidin › Avidin/Streptavidin › Avidin/Streptavidin › FBO_C 0.59 48.0 3.88e-01 89.7% 67.4%
5068131 2.1.1.17 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › OB_aCoA_assoc 0.59 48.0 4.68e-01 100.0% 80.0%
4955607 3435.1.1.0 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC 0.59 48.0 3.57e-01 88.5% 80.9%
3394321 9.1.1.45 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › FBO_C 0.58 51.0 4.08e-01 97.7% 96.6%
3734589 3080.1.1.2 ↗ a+b complex topology › Necrosis and ethylene-inducing peptide 1-like proteins › Necrosis and ethylene-inducing peptide 1-like proteins › Necrosis and ethylene-inducing peptide 1-like proteins › Vps62 0.58 49.0 3.34e-01 93.1% 86.4%
3282895 912.1.1.0 ↗ few secondary structure elements › HIV-1 VPU cytoplasmic domain › HIV-1 VPU cytoplasmic domain › HIV-1 VPU cytoplasmic domain 0.58 47.0 3.69e-01 89.7% 74.9%
5011023 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.57 40.0 4.21e-01 80.5% 80.0%
3509180 9.2.1.3 ↗ beta barrels › Lipocalins/Streptavidin › Avidin/Streptavidin › Avidin/Streptavidin › FBO_C 0.57 49.0 3.93e-01 97.7% 96.0%
5055109 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.56 44.0 4.41e-01 90.8% 82.2%
3617894 9.1.1.45 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › FBO_C 0.56 44.0 3.73e-01 87.4% 61.3%
5071965 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.56 44.0 4.35e-01 89.7% 80.0%
4946616 512.1.1.2 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_2nd 0.55 42.0 4.22e-01 90.8% 80.0%
4023312 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.55 48.0 4.26e-01 95.4% 97.6%
1582440 218.1.1.0 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like 0.55 48.0 4.41e-01 95.4% 92.0%
5072529 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.55 40.0 4.00e-01 80.5% 74.4%
5073695 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.55 43.0 4.18e-01 90.8% 75.0%
3972938 5085.1.1.1 ↗ a+b duplicates or obligate multimers › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › OEP 0.55 42.0 2.71e-01 83.9% 60.0%
3592295 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 46.0 3.84e-01 96.6% 80.6%
5077563 2004.1.1.293 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_15 0.54 38.0 2.53e-01 95.4% 17.6%
3193145 2003.1.2.29 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › NAD_binding_8 0.54 37.0 2.42e-01 74.7% 15.4%
3967497 5085.1.1.1 ↗ a+b duplicates or obligate multimers › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › OEP 0.53 41.0 2.72e-01 86.2% 61.9%
5075588 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.52 42.0 4.23e-01 89.7% 86.7%
4034521 220.1.1.87 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_3 0.52 35.0 3.37e-01 77.0% 60.0%
3739406 330.1.1.9 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dcr1-like_dsRNA-bd_dom 0.52 44.0 4.16e-01 92.0% 80.0%
3242737 5.1.5.47 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › BCAS3_WD40 0.52 43.0 2.72e-01 96.6% 26.5%
3943722 5085.1.1.1 ↗ a+b duplicates or obligate multimers › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › OEP 0.52 40.0 2.61e-01 86.2% 58.6%
4965185 7099.1.1.1 ↗ a+b complex topology › VP5 N-terminal domain › VP5 N-terminal domain › VP5 N-terminal domain › Viral_env_HRPV 0.52 36.0 2.48e-01 100.0% 19.7%
3635380 511.1.1.2 ↗ beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › PF27034 0.51 43.0 3.41e-01 89.7% 65.9%
3208374 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.51 43.0 3.79e-01 97.7% 80.7%
4451157 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.51 41.0 3.08e-01 89.7% 83.5%
4948537 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.51 34.0 2.26e-01 71.3% 17.2%
3509891 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.50 45.0 2.96e-01 97.7% 34.7%
3596522 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.50 38.0 3.52e-01 80.5% 63.6%
3896925 5089.1.1.3 ↗ beta complex topology › Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains › Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains › Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains › Gasdermin 0.50 40.0 3.02e-01 90.8% 82.9%