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NC_009814.1__YP_001468823.1__LiPP35_gp39__00039

Bact-Vir

NC_009814.1__YP_001468823.1__LiPP35_gp39__00039

Identity

Accession:
NC_009814 ↗
Kingdom:
phage

Quality

90.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Listeria_phage_P35

TaxID: 330398

Cluster

View cluster (2 members)

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 5-68
PDB
Domain cluster: rep: OP328423.1__UXQ87803.1__X__00059__D23-94
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1s5jA03 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.59 53.0 3.96e-01 100.0% 74.5%
4kbmB01 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.58 43.0 4.64e-01 93.8% 94.5%
2zzeA03 2.40.30.130 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.58 38.0 3.33e-01 95.3% 44.9%
6fndA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.58 41.0 2.98e-01 76.6% 42.5%
2qv6B02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.57 50.0 4.10e-01 100.0% 77.9%
1df0A02 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.57 45.0 3.99e-01 100.0% 59.8%
3tupA02 3.30.70.380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain 0.56 48.0 4.24e-01 96.9% 90.6%
2qz8A02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.56 49.0 4.59e-01 100.0% 85.2%
6f2mA02 2.40.30.290 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.56 39.0 3.57e-01 95.3% 55.2%
2o3iA01 3.40.1610.10 Alpha Beta › 3-Layer(aba) Sandwich › CV3147-like fold › CV3147-like domain 0.54 42.0 2.95e-01 89.1% 97.5%
3n01A00 3.30.70.2470 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Protein-tyrosine phosphatase receptor IA-2 ectodomain 0.54 46.0 4.26e-01 100.0% 100.0%
4f3nA00 3.40.50.12710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 41.0 2.57e-01 100.0% 14.4%
4j6oA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.52 42.0 2.86e-01 90.6% 83.1%
2ej9A02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.51 35.0 3.76e-01 95.3% 91.8%
1mt1B00 3.50.20.10 Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Pyruvoyl-Dependent Histidine Decarboxylase, subunit B 0.51 37.0 3.19e-01 100.0% 45.5%
2qu8A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 40.0 2.94e-01 89.1% 60.3%
6bogA02 2.30.30.930 Mainly Beta › Roll › SH3 type barrels. › 0.51 40.0 4.16e-01 100.0% 96.7%
4e4tA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.51 41.0 2.92e-01 90.6% 37.6%
2qggA01 2.40.30.60 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › RimM 0.50 41.0 3.67e-01 100.0% 62.4%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3589722 11.1.4.36 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SpaA 0.66 55.0 4.37e-01 100.0% 45.4%
5040562 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.62 41.0 3.68e-01 96.9% 48.9%
4131077 304.24.1.3 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_III 0.60 52.0 5.01e-01 100.0% 92.0%
4936051 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 46.0 4.93e-01 98.4% 100.0%
3837995 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 42.0 4.51e-01 98.4% 89.1%
3626212 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.59 42.0 3.19e-01 75.0% 82.6%
4322439 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.59 38.0 3.18e-01 95.3% 38.2%
4481026 4.1.1.407 ↗ beta barrels › SH3 › SH3 › SH3 › PF29661 0.58 45.0 4.64e-01 96.9% 90.0%
3284595 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 43.0 4.50e-01 95.3% 86.2%
3964666 4.1.1.137 ↗ beta barrels › SH3 › SH3 › SH3 › PcrA_UvrD_tudor 0.58 42.0 4.30e-01 95.3% 81.7%
3950193 4.1.1.137 ↗ beta barrels › SH3 › SH3 › SH3 › PcrA_UvrD_tudor 0.58 42.0 4.51e-01 95.3% 92.5%
4938828 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 41.0 4.22e-01 95.3% 80.0%
3290852 304.48.1.10 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › IMS 0.58 51.0 3.99e-01 100.0% 70.7%
4946447 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 40.0 3.59e-01 98.4% 52.2%
3588979 4.1.1.137 ↗ beta barrels › SH3 › SH3 › SH3 › PcrA_UvrD_tudor 0.57 41.0 4.29e-01 95.3% 83.1%
4124092 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.56 42.0 4.14e-01 98.4% 74.3%
4939058 3457.1.1.3 ↗ alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Arc_PepC_II 0.54 43.0 2.97e-01 92.2% 33.6%
4958814 3457.1.1.3 ↗ alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Arc_PepC_II 0.54 42.0 2.94e-01 92.2% 30.8%
3531239 304.151.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain of receptor-type protein tyrosine phosphatase › Ferredoxin-like domain of receptor-type protein tyrosine phosphatase › Receptor_IA-2 0.54 46.0 4.13e-01 100.0% 91.6%
4074297 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.53 38.0 3.22e-01 100.0% 43.5%
4586058 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.52 34.0 2.90e-01 92.2% 40.0%
3514191 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 37.0 3.26e-01 100.0% 49.0%
5076995 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.52 36.0 3.40e-01 100.0% 58.7%
4199730 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.51 46.0 3.87e-01 100.0% 64.8%
3954716 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.50 39.0 3.17e-01 90.6% 97.9%
D2 high residues 71-142
PDB
Domain cluster: rep: SRR1747040_scaffold_2_curated_closed_complete_prodigal-single.1__X__X__00031__D2-73
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4e6zA02 3.40.1350.100 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.76 51.0 4.72e-01 100.0% 56.2%
2vseA02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.58 50.0 4.11e-01 100.0% 99.3%
4n0rA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.56 43.0 2.87e-01 84.7% 37.7%
3pieC05 2.170.260.40 Mainly Beta › Beta Complex › paz domain › 0.54 40.0 3.09e-01 79.2% 68.3%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.53 40.0 3.73e-01 100.0% 62.5%
4zg5A00 3.40.1210.10 Alpha Beta › 3-Layer(aba) Sandwich › Stationary-phase Survival Protein Sure Homolog; Chain: A, › Survival protein SurE-like phosphatase/nucleotidase 0.53 39.0 2.76e-01 80.6% 59.5%
3x1lB02 3.30.1040.70 Alpha Beta › 2-Layer Sandwich › Carboxypeptidase Inhibitor; Chain A › 0.52 31.0 3.25e-01 100.0% 65.1%
5dn8A03 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.52 36.0 3.65e-01 73.6% 100.0%
3sy6A02 2.60.40.2630 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 44.0 3.63e-01 100.0% 55.1%
2h92A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 39.0 2.96e-01 90.3% 80.1%
4jgjA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 40.0 3.63e-01 100.0% 62.7%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3924546 214.1.1.0 ↗ a+b two layers › SH2 › SH2 › SH2 0.67 37.0 3.06e-01 93.1% 30.8%
3839740 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.59 55.0 4.33e-01 100.0% 97.9%
3307237 807.1.1.0 ↗ a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) 0.57 33.0 3.78e-01 84.7% 82.0%
4963691 304.128.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.53 46.0 4.28e-01 95.8% 86.7%
3214011 1.1.7.9 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.52 33.0 2.91e-01 91.7% 40.9%
3273589 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.52 43.0 2.99e-01 98.6% 69.3%
4027502 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 38.0 3.96e-01 90.3% 84.6%
3236050 214.1.1.0 ↗ a+b two layers › SH2 › SH2 › SH2 0.51 33.0 2.90e-01 90.3% 43.6%
3593320 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.50 45.0 4.28e-01 100.0% 92.9%
3711194 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.50 45.0 4.11e-01 100.0% 82.1%
3217172 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.50 43.0 3.46e-01 97.2% 98.6%