←Back to structures

NC_048875.1__YP_009859353.1__HWD31_gp40__00040

Bact-Vir

NC_048875.1__YP_009859353.1__HWD31_gp40__00040

Identity

Accession:
NC_048875 ↗
Kingdom:
phage

Quality

66.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chaseviridae› Loessnervirus› Pantoea_phage_vB_PagM_SSEM1

TaxID: 2721760

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 21-86
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1f05A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.76 60.0 3.78e-01 84.8% 23.6%
3l8kA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.72 51.0 3.51e-01 74.2% 30.0%
1eyvB00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.69 61.0 4.83e-01 97.0% 56.4%
4nooB00 1.10.8.1160 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.68 52.0 4.57e-01 81.8% 69.5%
1h3lB00 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.67 48.0 4.57e-01 75.8% 65.4%
4ex8A00 3.40.1790.10 Alpha Beta › 3-Layer(aba) Sandwich › Indigoidine synthase fold › Indigoidine synthase domain 0.63 50.0 3.25e-01 87.9% 28.6%
1iuqA01 1.10.1200.50 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Glycerol-3-phosphate acyltransferase, alpha helical bundle, N-terminal 0.59 44.0 4.30e-01 83.3% 100.0%
2x3fA02 3.30.1300.10 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › Pantoate-beta-alanine ligase, C-terminal domain 0.57 39.0 3.52e-01 86.4% 48.0%
3w3sA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.57 47.0 3.04e-01 97.0% 80.7%
2gk6A03 6.10.140.1240 Special › Helix non-globular › Helix Hairpins › 0.56 40.0 4.50e-01 84.8% 100.0%
1v9mA03 1.20.1690.10 Mainly Alpha › Up-down Bundle › V-type ATP synthase subunit C fold › V-type ATP synthase subunit C domain 0.56 40.0 3.60e-01 77.3% 97.9%
4k7cA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.56 46.0 2.94e-01 97.0% 58.1%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.55 38.0 3.56e-01 74.2% 60.9%
4d6wB02 6.10.140.740 Special › Helix non-globular › Helix Hairpins › 0.54 36.0 3.25e-01 77.3% 50.0%
4didB01 1.20.58.450 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Cell division control protein 42 homolog 0.53 47.0 3.93e-01 98.5% 87.7%
3mxtA02 3.30.1300.10 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › Pantoate-beta-alanine ligase, C-terminal domain 0.53 35.0 3.17e-01 84.8% 45.0%
3id7A00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.53 45.0 2.79e-01 95.5% 63.7%
1b3qA01 1.10.287.560 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Histidine kinase CheA-like, homodimeric domain 0.52 37.0 3.79e-01 74.2% 98.4%
3rx6A00 1.20.58.1090 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phage polarity suppression protein monomer 0.51 42.0 3.20e-01 98.5% 73.3%
2p67A01 1.20.5.170 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.50 26.0 2.94e-01 98.5% 63.5%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3607753 3291.1.1.123 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › DUF4110 0.79 59.0 4.83e-01 78.8% 45.2%
3885862 524.1.1.0 ↗ alpha arrays › Ypt/Rab-GAP domain of gyp1p-like › Ypt/Rab-GAP domain of gyp1p › Ypt/Rab-GAP domain of gyp1p 0.75 56.0 4.21e-01 80.3% 33.5%
3588332 5069.1.1.23 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › DUF2798 0.67 54.0 4.30e-01 90.9% 63.6%
2832675 2006.1.4.8 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN_5 0.67 47.0 3.25e-01 72.7% 23.9%
3999314 5058.1.1.35 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › EMC6 0.63 47.0 4.57e-01 95.5% 72.0%
3181588 2004.1.1.366 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NPHP3_N 0.60 42.0 2.89e-01 77.3% 18.5%
3343753 101.1.10.7 ↗ alpha arrays › HTH › HTH › Cyclin-like › Cyclin_C 0.60 43.0 3.88e-01 84.8% 53.7%
3173246 143.1.1.0 ↗ alpha arrays › PABP domain-like › PABC(PABP) domain › PABC(PABP) domain 0.58 40.0 3.76e-01 72.7% 60.7%
3377889 632.1.1.31 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › TB2_DP1_HVA22 0.56 44.0 3.95e-01 93.9% 70.5%
3965294 3558.1.1.0 ↗ alpha arrays › HSDR subunit helical domain › HSDR subunit helical domain › HSDR subunit helical domain 0.53 37.0 3.23e-01 71.2% 61.1%
3956710 5000.4.1.0 ↗ alpha arrays › Toxins' membrane translocation domains › delta-Endotoxin (insectocide), N-terminal domain › delta-Endotoxin (insectocide), N-terminal domain 0.51 42.0 2.95e-01 95.5% 40.4%