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NC_009813.1__YP_001468782.1__LiPB054_gp78__00078

Bact-Vir

NC_009813.1__YP_001468782.1__LiPB054_gp78__00078

Identity

Accession:
NC_009813 ↗
Kingdom:
phage

Quality

91.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Listeria_phage_B054

TaxID: 330397

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 3-64
PDB
Domain cluster: representative
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2zttA00 6.10.140.720 Special › Helix non-globular › Helix Hairpins › 0.77 51.0 4.86e-01 71.0% 58.9%
3kd3A02 1.10.150.210 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Phosphoserine phosphatase; domain 2 0.73 49.0 5.04e-01 90.3% 71.7%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.73 59.0 4.78e-01 88.7% 67.5%
1t7lB01 3.20.20.210 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › 0.70 54.0 3.35e-01 96.8% 14.0%
3behB01 1.20.120.540 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels 0.70 62.0 5.05e-01 100.0% 74.4%
2b0hA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.70 51.0 4.13e-01 80.6% 41.4%
6t0bc01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 50.0 4.70e-01 77.4% 64.1%
5h5mA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.70 60.0 4.79e-01 100.0% 85.4%
3zdmB00 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 0.69 51.0 5.57e-01 98.4% 96.0%
4dnnA00 1.20.5.4010 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.69 48.0 5.14e-01 75.8% 92.0%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.69 51.0 5.12e-01 82.3% 80.0%
3wd6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.68 55.0 4.47e-01 90.3% 76.3%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.68 51.0 5.14e-01 82.3% 86.9%
4asvA00 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 49.0 4.50e-01 98.4% 60.8%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.66 50.0 4.84e-01 83.9% 81.7%
5uh5D02 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.66 55.0 4.25e-01 91.9% 78.3%
3sllA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.66 46.0 4.69e-01 75.8% 85.2%
1osnC00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.65 54.0 3.57e-01 100.0% 26.8%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.65 48.0 4.53e-01 95.2% 65.3%
3eslA01 1.20.58.2070 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 54.0 5.10e-01 100.0% 76.0%
7ymiD01 1.20.85.10 Mainly Alpha › Up-down Bundle › Photosynthetic Reaction Center, subunit M; domain 1 › Photosystem II protein D1-like 0.65 55.0 4.04e-01 100.0% 77.8%
3g64A02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.64 46.0 4.70e-01 77.4% 86.4%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.64 54.0 4.45e-01 96.8% 80.3%
1fx8A00 1.20.1080.10 Mainly Alpha › Up-down Bundle › Glycerol uptake facilitator protein › Glycerol uptake facilitator protein. 0.62 53.0 3.62e-01 100.0% 73.2%
4wczA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.62 44.0 4.63e-01 77.4% 92.6%
5c9gA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.61 43.0 4.49e-01 77.4% 87.7%
5xtck00 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 50.0 4.42e-01 95.2% 67.0%
2cr7A01 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.61 43.0 4.33e-01 95.2% 74.6%
5kjpA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.61 43.0 4.43e-01 77.4% 87.9%
3nivC02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.61 47.0 3.88e-01 88.7% 88.7%
4od8D00 6.10.140.1880 Special › Helix non-globular › Helix Hairpins › 0.60 42.0 4.45e-01 95.2% 92.2%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 53.0 4.50e-01 100.0% 94.1%
4k08A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.60 51.0 3.97e-01 98.4% 85.4%
3qxzA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.60 42.0 4.28e-01 77.4% 88.3%
2hw5A02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.59 44.0 4.60e-01 83.9% 93.0%
3k3oA02 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 50.0 4.60e-01 100.0% 83.3%
1yozA00 1.10.3200.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af0941 › AF0941-like 0.58 51.0 4.23e-01 100.0% 70.8%
4exjA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.58 48.0 3.97e-01 96.8% 68.6%
4jfcA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.58 41.0 4.23e-01 77.4% 91.1%
3swxA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.57 41.0 4.17e-01 77.4% 87.9%
4og1A02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.57 40.0 4.07e-01 75.8% 86.2%
4mouC02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.57 40.0 4.08e-01 75.8% 82.5%
3bemB00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.57 49.0 3.44e-01 98.4% 70.8%
7zmgL01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 45.0 4.29e-01 95.2% 81.2%
4jvyB00 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.56 46.0 3.40e-01 98.4% 94.2%
4bpxD00 1.20.930.80 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.56 47.0 3.29e-01 96.8% 39.9%
3juiA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.55 48.0 3.48e-01 96.8% 73.6%
4jwvA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.55 39.0 4.02e-01 77.4% 87.9%
3p5jB02 1.10.20.120 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › 0.55 47.0 4.08e-01 95.2% 90.6%
3alfA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.54 48.0 3.13e-01 100.0% 24.8%
2itbB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.53 43.0 3.20e-01 100.0% 65.2%
3zhiA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.50 36.0 3.46e-01 77.4% 74.0%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4942387 632.7.1.66 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › DUF2304 0.82 55.0 4.47e-01 71.0% 39.1%
3273048 633.1.1.1 ↗ alpha bundles › Bromodomain-like › Bromodomain › Bromodomain › Bromodomain 0.79 57.0 3.99e-01 77.4% 26.1%
5016035 7011.1.1.5 ↗ alpha bundles › RodA transmembrane domain › RodA transmembrane domain › RodA transmembrane domain › O_anti_polymase 0.76 56.0 3.48e-01 79.0% 14.2%
4644846 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 0.75 55.0 4.61e-01 77.4% 49.0%
3743177 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.74 64.0 4.86e-01 96.8% 50.3%
5051746 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.73 53.0 4.84e-01 77.4% 58.7%
3486312 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.73 50.0 4.08e-01 72.6% 38.7%
3671293 509.1.1.12 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PF25972 0.72 53.0 5.16e-01 98.4% 70.0%
3802502 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.72 53.0 5.27e-01 100.0% 75.4%
3737309 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.71 52.0 5.17e-01 100.0% 75.4%
3809254 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.71 51.0 5.06e-01 100.0% 73.8%
3725377 192.15.1.44 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › DUF6604 0.70 52.0 4.51e-01 77.4% 60.0%
3340051 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.70 51.0 4.74e-01 96.8% 61.3%
3419853 192.29.1.19 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Cornichon 0.70 61.0 4.70e-01 100.0% 63.4%
4873586 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 0.70 50.0 4.71e-01 75.8% 67.6%
3380124 109.4.1.1266 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Arm, ARM_PUB 0.69 53.0 3.33e-01 85.5% 16.7%
4419476 4958.1.1.1 ↗ a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 0.69 58.0 4.15e-01 91.9% 63.4%
3678102 109.4.1.213 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › FancD2 0.69 59.0 3.15e-01 96.8% 9.9%
4953762 5073.1.2.0 ↗ alpha bundles › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain-related › Copper efflux ATPase transmembrane domain 0.68 57.0 4.09e-01 100.0% 36.6%
3818805 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.67 50.0 5.00e-01 100.0% 76.9%
3858904 3285.1.1.16 ↗ alpha duplicates or obligate multimers › Alix V domain › Alix V domain › Alix V domain › MBOAT 0.67 58.0 4.22e-01 100.0% 83.9%
5054079 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.67 52.0 4.90e-01 88.7% 72.5%
4384067 632.7.1.37 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › LETM1_RBD 0.67 48.0 3.98e-01 79.0% 42.7%
3814902 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.66 52.0 4.85e-01 100.0% 69.3%
None — 0.66 54.0 3.87e-01 95.2% 38.5%
5031241 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.65 56.0 5.24e-01 100.0% 81.2%
3727634 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.65 55.0 5.30e-01 95.2% 91.4%
3728552 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.64 54.0 4.56e-01 100.0% 80.9%
3931480 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.64 55.0 4.92e-01 100.0% 75.6%
4978135 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.64 55.0 4.19e-01 96.8% 46.2%
3690916 604.5.1.51 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PF27980 0.64 54.0 5.13e-01 100.0% 100.0%
3787094 601.1.1.142 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Peptidase_S64, PF30502 0.64 55.0 3.96e-01 96.8% 91.7%
3812703 3758.1.1.7 ↗ alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins › BPS1 0.64 54.0 3.77e-01 100.0% 68.6%
3612098 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 54.0 3.59e-01 100.0% 28.8%
3391570 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.62 55.0 3.83e-01 100.0% 39.0%
4988250 3745.1.1.1 ↗ alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex 0.62 52.0 3.40e-01 100.0% 67.8%
4090129 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.62 51.0 3.29e-01 98.4% 70.3%
5065508 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.61 54.0 4.63e-01 98.4% 75.0%
5030299 633.16.1.0 ↗ alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like 0.61 53.0 4.90e-01 98.4% 88.7%
3725615 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.61 52.0 4.84e-01 100.0% 82.5%
4291115 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.60 48.0 4.53e-01 95.2% 83.7%
3366101 5001.1.1.28 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Per1 0.59 48.0 3.17e-01 93.5% 30.9%
3463192 109.4.1.1261 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1, PPR_2, PPR_long 0.59 42.0 3.66e-01 100.0% 48.0%
3290817 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.59 50.0 3.95e-01 100.0% 72.9%
2992201 6171.1.1.1 ↗ alpha bundles › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › JHD 0.58 50.0 4.21e-01 100.0% 63.6%
5043291 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.58 50.0 4.64e-01 96.8% 100.0%
3663996 109.4.1.1260 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, PPR_long 0.58 44.0 2.73e-01 100.0% 12.4%
4986745 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 46.0 3.38e-01 90.3% 43.2%
4882418 208.1.1.55 ↗ beta duplicates or obligate multimers › Single-stranded left-handed beta-helix › Trimeric LpxA-like enzymes › Trimeric LpxA-like enzymes › Oxidored_q2 0.56 49.0 4.39e-01 100.0% 71.6%
3886706 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.55 45.0 4.30e-01 100.0% 87.5%
5057229 371.1.1.0 ↗ few secondary structure elements › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 0.55 45.0 3.73e-01 96.8% 69.2%
3386456 3718.1.1.0 ↗ alpha bundles › Flagellar protein fliT › Flagellar protein fliT › Flagellar protein fliT 0.53 42.0 4.01e-01 95.2% 86.3%