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NC_027982.1__YP_009167767.1__APL49_gp02__00002

Bact-Vir

NC_027982.1__YP_009167767.1__APL49_gp02__00002

Identity

Accession:
NC_027982 ↗
Kingdom:
phage

Quality

91.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Lactobacillus_phage_phiPYB5

TaxID: 438780

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 1-51
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1j30A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.75 59.0 4.23e-01 84.3% 32.6%
1bm9A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.74 50.0 3.70e-01 70.6% 93.3%
4gzrC00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.71 62.0 5.88e-01 98.0% 95.1%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.70 55.0 4.78e-01 86.3% 57.1%
1zu4A01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.70 54.0 4.62e-01 92.2% 51.7%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.70 54.0 5.02e-01 86.3% 67.2%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 55.0 5.13e-01 86.3% 74.2%
1lwbA00 1.20.90.10 Mainly Alpha › Up-down Bundle › Phospholipase A2 › Phospholipase A2 domain 0.69 62.0 4.61e-01 100.0% 95.9%
2ewfA02 1.20.1270.310 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.68 56.0 4.85e-01 92.2% 59.3%
1x0tA01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.67 54.0 5.12e-01 90.2% 83.6%
5j1hA01 1.20.58.1060 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 56.0 3.88e-01 98.0% 27.5%
8a0rA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.66 52.0 3.92e-01 90.2% 33.8%
2lrmA00 1.10.890.30 Mainly Alpha › Orthogonal Bundle › 10k-s Protein, Hypothetical Protein A; Chain A › YmgD protein 0.66 43.0 3.71e-01 78.4% 40.5%
1hr5A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.66 52.0 5.39e-01 86.3% 93.8%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 53.0 4.72e-01 88.2% 93.2%
6ygiB01 1.10.4090.10 Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus 0.66 57.0 4.07e-01 96.1% 57.5%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.65 53.0 3.68e-01 90.2% 27.4%
1grjA01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.65 52.0 4.66e-01 90.2% 71.6%
1y71A00 2.30.30.430 Mainly Beta › Roll › SH3 type barrels. › Kinase associated protein B domain 0.64 46.0 3.69e-01 78.4% 36.7%
3kztA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.64 52.0 4.03e-01 100.0% 87.1%
1n69B00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.64 44.0 3.96e-01 82.4% 48.8%
1eo0A00 1.20.930.10 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.63 45.0 4.02e-01 82.4% 51.9%
3ehfD01 1.20.5.1930 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.63 52.0 4.96e-01 100.0% 98.4%
4ui9P01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.62 52.0 3.30e-01 100.0% 40.7%
1khbA03 3.90.228.20 Alpha Beta › Alpha-Beta Complex › Phosphoenolpyruvate Carboxykinase; domain 3 › 0.53 46.0 2.95e-01 100.0% 92.1%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3673670 639.2.1.4 ↗ alpha arrays › HHA-like › Regulator of acid resistance influenced by indole (AriR) › Regulator of acid resistance influenced by indole (AriR) › Ovate 0.80 60.0 5.51e-01 86.3% 63.1%
4436335 3390.1.1.0 ↗ extended segments › Photosystem II reaction center protein T, PsbT › Photosystem II reaction center protein T, PsbT › Photosystem II reaction center protein T, PsbT 0.69 55.0 5.73e-01 90.2% 100.0%
4466193 397.7.1.1 ↗ few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 › Vicilin_N 0.68 47.0 5.15e-01 86.3% 100.0%
5048408 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.68 56.0 5.50e-01 92.2% 100.0%
4398992 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.68 59.0 3.55e-01 98.0% 19.0%
3883588 604.1.1.125 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › SYNRG_C 0.68 58.0 4.03e-01 100.0% 82.2%
3888160 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.67 49.0 5.16e-01 84.3% 91.1%
1108845 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.66 53.0 5.44e-01 86.3% 93.8%
4685 192.16.1.1 ↗ alpha bundles › Long alpha-hairpin › SPy1572-like › SPy1572-like › DUF1912 0.66 53.0 4.72e-01 88.2% 93.2%
3568856 198.1.1.1 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2 0.65 47.0 3.99e-01 84.3% 44.4%
3876450 198.1.1.1 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2 0.65 51.0 4.29e-01 88.2% 53.3%
4984288 2004.1.1.85 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ArsA_ATPase 0.64 52.0 3.17e-01 90.2% 14.9%
3331938 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.64 54.0 4.70e-01 96.1% 77.5%
3276052 198.1.1.2 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2,SapB_1 0.63 46.0 2.95e-01 76.5% 20.9%
182184 109.4.1.1288 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_11 0.63 45.0 3.25e-01 76.5% 45.2%
3846955 198.1.1.10 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2, SapB_1, Saposin 0.63 49.0 4.33e-01 90.2% 57.5%
3775067 198.1.1.21 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapA, SapB_2 0.62 46.0 3.58e-01 80.4% 34.2%
4947248 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 51.0 3.96e-01 96.1% 94.8%
3568854 198.1.1.2 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2,SapB_1 0.59 45.0 4.11e-01 88.2% 69.3%