←Back to structures

NC_006565.1__YP_164641.1__LP65_gp006__00006

Bact-Vir

NC_006565.1__YP_164641.1__LP65_gp006__00006

Identity

Accession:
NC_006565 ↗
Kingdom:
phage

Quality

79.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Herelleviridae› Salchichonvirus› Lactobacillus_phage_LP65

TaxID: 2892344

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 2-70
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF24024.2 best DUF7336 25.7 1.00e-05 91.3% 56.7%
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4y6iA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 53.0 4.64e-01 88.4% 90.3%
2ww4A02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.65 51.0 4.22e-01 84.1% 91.6%
1p1lA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 51.0 4.56e-01 88.4% 90.2%
3ahpA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 52.0 4.51e-01 88.4% 87.7%
4e98C00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 50.0 4.40e-01 87.0% 88.6%
7o4xA01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 46.0 4.17e-01 88.4% 87.9%
2cqpA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.59 43.0 3.84e-01 78.3% 81.6%
2byeA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.58 44.0 3.90e-01 87.0% 55.4%
2cuiA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 43.0 3.74e-01 88.4% 50.9%
1burS00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.56 46.0 3.82e-01 91.3% 58.5%
2d9oA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 39.0 3.60e-01 79.7% 82.0%
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 0.54 39.0 3.80e-01 79.7% 90.1%
3p96A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.53 39.0 3.76e-01 82.6% 96.4%
6w6vE01 3.30.70.3250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribonuclease P, Pop5 subunit 0.53 40.0 3.22e-01 87.0% 76.1%
1uenA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 39.0 3.35e-01 87.0% 46.4%
2hfqA00 3.10.510.10 Alpha Beta › Roll › NE1680-like fold › NE1680-like 0.52 41.0 3.86e-01 87.0% 76.5%
3hrpA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 33.0 3.00e-01 84.1% 46.3%
5fc9A00 2.60.40.420 Mainly Beta › Sandwich › Immunoglobulin-like › Cupredoxins - blue copper proteins 0.52 34.0 3.08e-01 81.2% 48.4%
1vw4U00 3.30.1390.20 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L30/L7 0.51 40.0 3.81e-01 87.0% 76.8%
3bv8A00 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.51 40.0 3.84e-01 89.9% 76.5%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3721982 304.14.1.0 ↗ a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) 0.72 54.0 4.86e-01 79.7% 97.9%
3994441 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.64 50.0 4.22e-01 92.8% 50.0%
3170073 11.1.1.470 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Psg1 0.63 50.0 3.65e-01 87.0% 33.0%
3732370 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.61 46.0 4.79e-01 84.1% 96.7%
3457076 317.1.1.1 ↗ a+b two layers › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › IF4E 0.60 45.0 3.35e-01 84.1% 46.4%
3713749 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.59 49.0 3.65e-01 91.3% 46.8%
5025566 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.59 43.0 4.72e-01 78.3% 100.0%
4949196 304.117.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC 0.58 44.0 4.70e-01 82.6% 100.0%
4972750 304.12.1.17 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 › GYD 0.57 46.0 4.18e-01 89.9% 94.7%
3787525 871.1.1.1 ↗ a+b two layers › SSo0622-like (Pfam 02676) › SSo0622-like (Pfam 02676) › SSo0622-like (Pfam 02676) › TYW3 0.56 46.0 3.33e-01 95.7% 72.0%
5082628 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 0.56 40.0 3.63e-01 76.8% 100.0%
3355743 317.1.1.1 ↗ a+b two layers › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › IF4E 0.56 42.0 3.26e-01 82.6% 36.4%
4929350 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.56 42.0 4.08e-01 82.6% 100.0%
3199216 10.32.1.203 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.55 41.0 3.24e-01 82.6% 81.2%
5067536 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.55 43.0 4.04e-01 88.4% 97.8%
3595913 317.1.1.0 ↗ a+b two layers › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase 0.55 41.0 3.11e-01 84.1% 32.4%
5006766 304.163.1.0 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.55 41.0 4.28e-01 81.2% 100.0%
3284390 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.54 42.0 3.80e-01 89.9% 85.7%
3958827 205.1.1.0 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin 0.54 40.0 4.11e-01 82.6% 100.0%
3668999 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.54 39.0 3.95e-01 79.7% 100.0%
5028429 304.120.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI 0.54 40.0 3.83e-01 84.1% 100.0%
3562823 2004.1.1.130 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NACHT 0.53 39.0 2.83e-01 84.1% 86.4%
4027198 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.52 39.0 3.60e-01 87.0% 79.0%
3484942 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.51 41.0 3.58e-01 87.0% 58.1%
3596319 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.51 38.0 2.99e-01 82.6% 37.3%