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NC_019925.1__YP_007237418.1__G379_gp123__00096

Bact-Vir

NC_019925.1__YP_007237418.1__G379_gp123__00096

Identity

Accession:
NC_019925 ↗
Kingdom:
phage

Quality

83.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Ackermannviridae› Limestonevirus› Dickeya_phage_vB-DsoM-LIMEstone1

TaxID: 2678590

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 3-85
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF24200.2 best DUF7425 127.2 3.80e-37 100.0% 89.5%
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2xc8A00 2.60.40.2980 Mainly Beta › Sandwich › Immunoglobulin-like › 0.70 46.0 4.01e-01 78.3% 46.3%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.67 51.0 5.31e-01 84.3% 89.5%
1vwxS02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.66 50.0 5.22e-01 84.3% 90.8%
2vqpA01 2.70.20.30 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › HRSV-S2 matrix protein, N-terminal domain 0.65 46.0 4.13e-01 75.9% 89.2%
3lb6C01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 38.0 3.75e-01 75.9% 54.5%
4a18X01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.64 46.0 4.71e-01 74.7% 83.5%
2i1sA00 3.10.290.30 Alpha Beta › Roll › Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A › MM3350-like 0.63 54.0 4.22e-01 94.0% 96.6%
5jgfA02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.63 45.0 3.80e-01 74.7% 75.9%
2c4xA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.63 44.0 3.55e-01 72.3% 59.6%
3e0jB00 3.90.1030.20 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain 0.60 41.0 3.46e-01 98.8% 41.3%
3dzmB00 2.40.160.70 Mainly Beta › Beta Barrel › Porin › outer membrane protein from Thermus thermophilus HB27. 0.60 42.0 3.23e-01 74.7% 100.0%
4h3wA02 2.60.120.1260 Mainly Beta › Sandwich › Jelly Rolls › 0.59 42.0 3.43e-01 74.7% 40.1%
1qj8A00 2.40.160.20 Mainly Beta › Beta Barrel › Porin › 0.58 41.0 3.48e-01 74.7% 97.3%
1b66A00 3.30.479.10 Alpha Beta › 2-Layer Sandwich › Tetrahydropterin Synthase; Chain A › 6-pyruvoyl tetrahydropterin synthase/QueD 0.58 52.0 4.36e-01 97.6% 99.3%
3vtiA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 48.0 4.59e-01 91.6% 93.8%
6igbA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.57 41.0 2.69e-01 75.9% 100.0%
7vhqU01 3.30.479.30 Alpha Beta › 2-Layer Sandwich › Tetrahydropterin Synthase; Chain A › Band 7 domain 0.57 47.0 4.30e-01 90.4% 91.8%
1r5tA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.56 39.0 3.38e-01 74.7% 44.0%
6euaA01 3.90.215.10 Alpha Beta › Alpha-Beta Complex › Gamma Fibrinogen; Chain A, domain 1 › Gamma Fibrinogen, chain A, domain 1 0.56 35.0 2.95e-01 74.7% 38.1%
2o62A02 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.56 39.0 3.37e-01 73.5% 92.0%
2vpjA00 2.120.10.80 Mainly Beta › 6 Propeller › Neuraminidase › Kelch-type beta propeller 0.55 39.0 2.73e-01 74.7% 100.0%
3ef2A02 3.30.460.70 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › 0.53 37.0 3.13e-01 72.3% 73.2%
3lq6A02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.52 37.0 3.37e-01 74.7% 58.8%
1wr2A01 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.52 37.0 3.05e-01 75.9% 50.3%
1nnnA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.51 39.0 3.56e-01 95.2% 57.9%
5ixgA00 2.40.128.110 Mainly Beta › Beta Barrel › Lipocalin › Lipid/polyisoprenoid-binding, YceI-like 0.51 36.0 2.95e-01 73.5% 75.0%
5u81A01 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.51 35.0 2.58e-01 72.3% 88.0%
1jpdX01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.50 40.0 3.88e-01 92.8% 75.8%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3498264 219.1.1.53 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Vasohibin 0.75 56.0 3.86e-01 78.3% 34.5%
3227513 3115.1.1.3 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › NRF 0.73 52.0 4.86e-01 75.9% 65.7%
3712543 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.71 47.0 4.30e-01 73.5% 53.3%
4937773 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.71 47.0 5.42e-01 72.3% 96.6%
3598520 75.1.1.0 ↗ beta barrels › Cyclophilin-like › Cyclophilin-like › Cyclophilin-like 0.70 51.0 3.72e-01 75.9% 98.2%
5065436 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.70 47.0 5.32e-01 74.7% 90.6%
4983090 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.69 53.0 5.43e-01 81.9% 84.8%
1442393 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.69 52.0 4.82e-01 83.1% 62.4%
4967222 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.69 48.0 5.40e-01 72.3% 100.0%
4939739 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.68 47.0 5.38e-01 71.1% 100.0%
4990637 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.68 53.0 5.38e-01 85.5% 84.3%
4969863 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.68 52.0 5.42e-01 84.3% 90.7%
4128974 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.68 52.0 5.33e-01 83.1% 90.0%
3345090 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.68 51.0 4.75e-01 84.3% 63.0%
5067865 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.67 51.0 5.46e-01 83.1% 95.7%
4942818 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.67 49.0 4.14e-01 77.1% 53.6%
3834402 5.1.4.550 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Kelch_FKB95 0.67 47.0 3.14e-01 73.5% 99.1%
4648475 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.67 46.0 5.20e-01 71.1% 100.0%
4951473 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.66 47.0 5.22e-01 74.7% 98.4%
4952910 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.66 46.0 4.38e-01 73.5% 95.0%
2106285 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.66 50.0 4.62e-01 83.1% 63.0%
1867336 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.66 46.0 5.03e-01 77.1% 96.8%
2512518 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.66 49.0 4.66e-01 83.1% 66.3%
3551719 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.65 46.0 4.87e-01 74.7% 86.7%
5030993 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.65 49.0 5.05e-01 83.1% 85.0%
3979798 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.65 52.0 4.75e-01 86.7% 89.1%
4084879 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.65 51.0 5.10e-01 85.5% 88.2%
3821141 5.1.4.550 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Kelch_FKB95 0.65 47.0 3.19e-01 75.9% 99.3%
5074648 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.65 51.0 5.31e-01 97.6% 93.3%
3508212 3115.1.1.6 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › DUF4494 0.65 47.0 5.00e-01 78.3% 90.0%
3892842 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.64 47.0 5.21e-01 78.3% 100.0%
2831852 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.64 49.0 4.65e-01 84.3% 67.3%
2741079 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.64 46.0 4.87e-01 74.7% 93.0%
2106284 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.64 45.0 4.92e-01 73.5% 95.5%
2527501 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.64 50.0 4.70e-01 97.6% 68.3%
1442666 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.63 45.0 4.59e-01 74.7% 81.5%
4013514 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.63 50.0 4.69e-01 97.6% 68.6%
4996552 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.62 52.0 5.17e-01 100.0% 89.4%
3516909 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.61 44.0 3.55e-01 78.3% 60.6%
4330212 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.60 45.0 4.05e-01 79.5% 59.1%
5009745 302.4.1.1 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › Hydant_A_C 0.60 44.0 4.00e-01 79.5% 56.5%
4325944 3767.1.1.0 ↗ a+b two layers › Giardia Dicer N-terminal domain › Giardia Dicer N-terminal domain › Giardia Dicer N-terminal domain 0.60 51.0 4.45e-01 95.2% 78.5%
3593508 3333.1.1.0 ↗ a+b two layers › Barrel domain in dedicator of cytokinesis protein 9 › Barrel domain in dedicator of cytokinesis protein 9 › Barrel domain in dedicator of cytokinesis protein 9 0.60 51.0 4.27e-01 95.2% 95.9%
3508713 382.1.1.25 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › YjeJ 0.59 51.0 4.55e-01 100.0% 67.5%
5068178 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.58 43.0 4.19e-01 80.7% 70.5%
4028467 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.58 48.0 3.32e-01 90.4% 62.9%
4556330 299.1.1.1 ↗ a+b complex topology › YbaK/ProRS associated domain › YbaK/ProRS associated domain › YbaK/ProRS associated domain › tRNA_edit 0.57 52.0 4.17e-01 100.0% 93.8%
3744119 868.1.1.3 ↗ a+b complex topology › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › Med20 0.57 47.0 3.61e-01 90.4% 92.2%
4332626 3532.1.1.0 ↗ alpha arrays › RNA-binding domain of telomerase › RNA-binding domain of telomerase › RNA-binding domain of telomerase 0.56 49.0 2.97e-01 100.0% 18.3%
4023069 219.1.1.93 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › DUF6540 0.56 48.0 4.19e-01 98.8% 85.8%
3731305 219.1.1.93 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › DUF6540 0.56 48.0 4.28e-01 98.8% 82.4%
5003848 221.11.1.0 ↗ a+b two layers › beta-Grasp › beta-grasp fold domain in probable beta-lactamase › beta-grasp fold domain in probable beta-lactamase 0.55 36.0 3.69e-01 74.7% 68.8%
3928044 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 39.0 3.06e-01 75.9% 53.2%
3195739 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.53 46.0 4.04e-01 98.8% 80.0%
3265857 299.1.1.0 ↗ a+b complex topology › YbaK/ProRS associated domain › YbaK/ProRS associated domain › YbaK/ProRS associated domain 0.53 46.0 4.18e-01 95.2% 77.3%
2629709 4252.1.1.3 ↗ beta barrels › AttH-like › AttH-like › AttH-like › DA_C 0.53 37.0 2.84e-01 74.7% 66.8%
4864681 327.5.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C 0.52 40.0 3.98e-01 95.2% 81.4%
3300916 5.1.4.231 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › FBA_3 0.51 45.0 3.10e-01 100.0% 100.0%