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NC_048767.1__YP_009845945.1__HWC23_gp11__00011

Bact-Vir

NC_048767.1__YP_009845945.1__HWC23_gp11__00011

Identity

Accession:
NC_048767 ↗
Kingdom:
phage

Quality

92.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Dibbivirus› Pantoea_phage_vB_PagM_PSKM

TaxID: 2588094

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 2-49
PDB
Domain cluster: rep: NC_048751.1__YP_009843758.1__HWC07_gp077__00077__D9-56
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2hjqA01 3.40.5.20 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › YqbF domain 0.80 65.0 6.59e-01 100.0% 93.5%
4fsdA02 3.40.5.100 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.77 68.0 5.62e-01 100.0% 57.0%
2hvfA00 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.74 54.0 5.35e-01 100.0% 75.0%
2cjsA01 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.64 54.0 3.88e-01 100.0% 80.4%
7tg5A01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.64 54.0 4.17e-01 100.0% 43.0%
4y6iA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 50.0 4.16e-01 100.0% 80.6%
2atzA00 3.90.920.20 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › HP0184-like 0.60 50.0 3.52e-01 100.0% 43.2%
2q1zB02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.59 49.0 4.01e-01 100.0% 49.5%
2qswA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.58 47.0 3.99e-01 100.0% 82.2%
3btxA00 2.60.120.590 Mainly Beta › Sandwich › Jelly Rolls › Alpha-ketoglutarate-dependent dioxygenase AlkB-like 0.56 47.0 3.18e-01 100.0% 34.3%
3upuA03 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.56 46.0 3.44e-01 97.9% 93.9%
3pe0A03 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.55 45.0 4.21e-01 100.0% 78.1%
6f0cA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.54 40.0 2.41e-01 83.3% 15.1%
6vtmB00 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.54 40.0 3.32e-01 81.2% 69.8%
3sftA00 3.40.50.180 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Methylesterase CheB, C-terminal domain 0.51 37.0 2.62e-01 81.2% 90.5%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4952672 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 75.0 7.18e-01 100.0% 85.5%
5009 4076.3.1.2 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › YqbF 0.80 65.0 6.46e-01 100.0% 87.8%
3977412 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.80 73.0 7.27e-01 100.0% 100.0%
5023430 3529.1.1.0 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain 0.79 71.0 6.57e-01 100.0% 81.7%
4988095 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.77 67.0 6.66e-01 100.0% 96.0%
5083883 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.74 58.0 5.93e-01 100.0% 93.3%
5010674 4076.3.1.11 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PF25865 0.71 53.0 5.19e-01 100.0% 74.5%
3703797 3529.1.1.0 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain 0.70 56.0 5.39e-01 100.0% 78.2%
5000438 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.70 56.0 5.07e-01 100.0% 64.3%
3251095 3529.1.1.1 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Vault 0.67 53.0 5.02e-01 100.0% 71.7%
5033467 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.66 55.0 5.57e-01 100.0% 97.9%
4932061 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.66 52.0 5.34e-01 97.9% 97.8%
4814642 11.1.4.36 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SpaA 0.64 54.0 4.56e-01 100.0% 56.8%
5035097 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.64 49.0 5.05e-01 97.9% 95.6%
4057802 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.63 49.0 5.04e-01 97.9% 95.6%
4031645 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.63 52.0 5.17e-01 100.0% 96.0%
4939553 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.63 50.0 4.95e-01 100.0% 88.0%
4536596 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.63 50.0 5.04e-01 100.0% 93.8%
4460255 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.62 49.0 4.91e-01 100.0% 88.0%
4419456 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.62 48.0 4.82e-01 100.0% 89.8%
5016388 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.62 50.0 4.33e-01 100.0% 88.2%
5068408 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.61 48.0 4.91e-01 97.9% 95.6%
4032281 268.2.1.1 ↗ a+b two layers › Sterol carrier protein-like › LytR-Cps2A-Psr (LCP) enzymes › LytR-Cps2A-Psr (LCP) enzymes › LytR_cpsA_psr 0.60 50.0 3.18e-01 100.0% 20.7%
5001806 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.60 46.0 4.62e-01 97.9% 89.6%
5038458 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.60 47.0 4.72e-01 93.8% 94.0%
4593896 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.60 44.0 4.55e-01 97.9% 93.3%
4280403 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.59 45.0 4.64e-01 95.8% 95.6%
4970994 10.34.1.0 ↗ beta sandwiches › jelly-roll › Protein CLP1 jelly-roll domain › Protein CLP1 jelly-roll domain 0.57 44.0 3.98e-01 100.0% 58.7%
4934987 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.56 44.0 4.46e-01 95.8% 97.8%
5036149 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.56 42.0 4.33e-01 100.0% 97.8%
4948343 304.4.1.82 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › DUF3303 0.55 44.0 3.85e-01 100.0% 93.2%
3806748 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.54 43.0 2.67e-01 93.8% 48.5%
4624820 2004.1.1.53 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Adenylsucc_synt 0.53 42.0 2.45e-01 100.0% 12.8%
3957920 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.50 36.0 2.26e-01 79.2% 89.0%