←Back to structures

NC_048751.1__YP_009843758.1__HWC07_gp077__00077

Bact-Vir

NC_048751.1__YP_009843758.1__HWC07_gp077__00077

Identity

Accession:
NC_048751 ↗
Kingdom:
phage

Quality

74.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Lietduovirus› Pantoea_phage_vB_PagM_LIET2

TaxID: 2508071

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 9-56
PDB
Domain cluster: representative
CATH (14)
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 0.76 60.0 6.14e-01 100.0% 93.5%
4v19I01 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.73 53.0 5.06e-01 97.9% 66.7%
1vw4G00 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.73 54.0 5.27e-01 100.0% 72.7%
2hvfA00 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.72 52.0 5.12e-01 97.9% 73.1%
7tg5A01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.66 56.0 4.35e-01 100.0% 43.0%
2atzA00 3.90.920.20 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › HP0184-like 0.60 50.0 3.53e-01 100.0% 43.2%
1y7xA01 2.30.30.550 Mainly Beta › Roll › SH3 type barrels. › Major Vault Protein repeat 0.59 45.0 4.60e-01 100.0% 85.1%
3f83A03 2.60.40.2040 Mainly Beta › Sandwich › Immunoglobulin-like › CFA/I fimbrial subunit E, pilin domain 0.58 49.0 3.51e-01 100.0% 57.9%
4ie5A01 2.60.120.590 Mainly Beta › Sandwich › Jelly Rolls › Alpha-ketoglutarate-dependent dioxygenase AlkB-like 0.57 47.0 2.97e-01 93.8% 73.9%
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%
6uf3A00 3.40.630.190 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › LCP protein 0.54 43.0 2.87e-01 100.0% 22.0%
3pe0A03 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.54 44.0 4.13e-01 100.0% 78.1%
6f0cA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.54 38.0 2.30e-01 79.2% 15.4%
3l9aX01 3.30.720.180 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.50 38.0 3.36e-01 85.4% 81.3%
ECOD (50)
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 0.79 69.0 6.63e-01 100.0% 85.5%
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 6.58e-01 100.0% 81.7%
5009 4076.3.1.2 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › YqbF 0.76 60.0 6.02e-01 100.0% 87.8%
4988095 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.75 65.0 6.42e-01 97.9% 94.0%
3977412 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.75 65.0 6.47e-01 97.9% 98.0%
3788443 4076.1.1.1 ↗ a+b two layers › L9 N-domain-like › L9 N-domain-like › L9 N-domain-like › Ribosomal_L9_N 0.73 54.0 5.37e-01 100.0% 78.0%
5083883 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.73 57.0 5.85e-01 100.0% 93.3%
4956454 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.70 55.0 5.36e-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 58.0 5.16e-01 100.0% 64.3%
4927873 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.69 58.0 5.39e-01 100.0% 75.0%
3266009 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 0.69 53.0 5.12e-01 100.0% 74.5%
5010674 4076.3.1.11 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PF25865 0.69 52.0 5.09e-01 100.0% 74.5%
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 0.68 55.0 5.63e-01 100.0% 100.0%
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 0.68 54.0 5.18e-01 100.0% 78.2%
3705471 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 0.68 54.0 5.18e-01 100.0% 78.2%
4967982 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.67 53.0 5.45e-01 95.8% 97.7%
5033467 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.66 54.0 5.50e-01 100.0% 95.8%
4928679 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.66 53.0 5.26e-01 100.0% 88.0%
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 0.65 50.0 5.17e-01 100.0% 97.8%
4031645 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.64 54.0 5.36e-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 0.64 50.0 5.02e-01 100.0% 88.0%
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 0.64 50.0 5.07e-01 100.0% 91.7%
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 0.64 50.0 4.73e-01 100.0% 71.7%
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 0.63 51.0 5.12e-01 95.8% 96.0%
5036149 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.62 50.0 5.11e-01 100.0% 100.0%
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 0.62 49.0 5.00e-01 100.0% 100.0%
4814642 11.1.4.36 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SpaA 0.62 52.0 4.38e-01 100.0% 56.8%
4083057 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.62 47.0 4.75e-01 100.0% 88.0%
3601818 10.34.1.0 ↗ beta sandwiches › jelly-roll › Protein CLP1 jelly-roll domain › Protein CLP1 jelly-roll domain 0.61 51.0 4.40e-01 100.0% 58.7%
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 0.61 50.0 3.18e-01 100.0% 21.1%
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 0.60 47.0 4.80e-01 95.8% 93.3%
4593896 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.60 46.0 4.75e-01 97.9% 97.8%
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 46.0 4.67e-01 97.9% 97.8%
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 0.59 45.0 4.57e-01 100.0% 89.8%
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 0.59 46.0 4.65e-01 100.0% 88.0%
4934987 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.58 44.0 4.55e-01 97.9% 97.8%
4012562 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.56 44.0 2.68e-01 93.8% 34.7%
4536596 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.56 43.0 4.40e-01 100.0% 95.8%
4491021 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.56 45.0 3.65e-01 95.8% 47.6%
3643305 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.55 42.0 3.31e-01 100.0% 77.8%
3515342 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.54 42.0 2.62e-01 91.7% 44.4%
3806748 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.54 42.0 2.63e-01 91.7% 47.5%
4397359 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.52 41.0 2.53e-01 91.7% 43.4%
4887359 275.1.1.4 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › RNA_pol_Rpb1_5 0.52 36.0 3.12e-01 72.9% 50.0%
3454403 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.52 40.0 2.48e-01 91.7% 44.6%
3458617 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.52 39.0 2.51e-01 91.7% 50.2%
3458496 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.51 38.0 2.36e-01 89.6% 24.0%
4895981 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.51 36.0 3.13e-01 72.9% 50.0%
3330406 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.51 41.0 3.91e-01 93.8% 96.7%
3994204 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.50 39.0 2.43e-01 100.0% 25.7%