←Back to structures

NC_054443.1__YP_010051534.1__KDW73_gp62__00062

Bact-Vir

NC_054443.1__YP_010051534.1__KDW73_gp62__00062

Identity

Accession:
NC_054443 ↗
Kingdom:
phage

Quality

81.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Avocadovirus› Mycobacterium_phage_Avocado

TaxID: 2024302

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 4-48
PDB
Domain cluster: rep: KM591905.1__AIT13468.1__PBI_RONRAYGUN_55__00055__D3-47
D2 high residues 55-97
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7lt2A01 3.30.460.90 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › 0.66 54.0 3.47e-01 100.0% 63.3%
2azpA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.63 54.0 3.66e-01 100.0% 27.3%
3ednA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.61 51.0 3.67e-01 100.0% 37.3%
3ejxA02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.60 50.0 3.57e-01 100.0% 29.9%
2zkmX01 2.30.29.240 Mainly Beta › Roll › PH-domain like › 0.59 41.0 2.59e-01 74.4% 20.9%
5ha4A02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.58 47.0 3.46e-01 100.0% 31.6%
6hoxA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.58 44.0 2.78e-01 95.3% 15.9%
5w8mA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.57 41.0 2.76e-01 81.4% 85.7%
2ej9A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.57 41.0 2.78e-01 81.4% 31.9%
4rs6A01 3.30.1120.30 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › POLO box domain 0.57 47.0 3.54e-01 100.0% 53.4%
1b69A00 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.56 36.0 3.20e-01 72.1% 39.1%
2lojA01 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.56 39.0 4.04e-01 93.0% 84.6%
5oomJ01 3.30.1550.10 Alpha Beta › 2-Layer Sandwich › Ribosomal protein L11, N-terminal domain › Ribosomal protein L11/L12, N-terminal domain 0.55 41.0 3.56e-01 81.4% 97.0%
1afcA00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.55 45.0 3.25e-01 95.3% 68.5%
3f0zA01 3.30.310.260 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.54 41.0 3.24e-01 93.0% 44.6%
3v0aB03 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.54 40.0 2.66e-01 93.0% 18.0%
6z46V01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.53 45.0 3.01e-01 100.0% 26.4%
2avwD01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.53 42.0 3.04e-01 93.0% 45.4%
5kcoA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.53 36.0 3.41e-01 74.4% 89.8%
2zylA01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.53 39.0 2.92e-01 100.0% 28.1%
2x8fA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.53 40.0 2.51e-01 93.0% 98.5%
8f66A01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.53 44.0 2.87e-01 100.0% 25.2%
1g3pA01 2.30.27.10 Mainly Beta › Roll › Phage FD Coat Protein, Membrane penetration domain › Phage FD Coat Protein,Membrane penetration domain 0.52 42.0 3.52e-01 100.0% 54.5%
1iruI00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.52 42.0 2.77e-01 100.0% 21.4%
2im9A02 2.30.260.10 Mainly Beta › Roll › putative xylanase like fold › putative xylanase like domain 0.51 38.0 2.67e-01 76.7% 35.4%
5gxuB01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.51 40.0 3.07e-01 97.7% 50.8%
4csqA00 2.30.29.190 Mainly Beta › Roll › PH-domain like › 0.51 37.0 2.96e-01 88.4% 35.4%
1inlC02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.51 38.0 3.54e-01 90.7% 78.1%
7lxuE01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.51 43.0 2.80e-01 100.0% 24.8%
2x9aA00 2.30.27.10 Mainly Beta › Roll › Phage FD Coat Protein, Membrane penetration domain › Phage FD Coat Protein,Membrane penetration domain 0.51 41.0 3.82e-01 100.0% 80.3%
4wksC02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.51 41.0 3.57e-01 100.0% 94.7%
2fdbN00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.51 39.0 2.91e-01 100.0% 35.1%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4962176 4312.1.1.3 ↗ a+b two layers › RelE-like › RelE-like › RelE-like › ParE_toxin 0.71 59.0 4.98e-01 100.0% 66.3%
5041236 375.13.1.1 ↗ few secondary structure elements › Rubredoxin-like › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Toprim_C_rpt 0.70 48.0 4.41e-01 72.1% 63.6%
3410503 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 46.0 3.37e-01 76.7% 31.5%
5028087 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.64 53.0 4.00e-01 100.0% 87.0%
4048173 286.1.1.1 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › DAP_epimerase 0.63 54.0 3.95e-01 100.0% 36.7%
5041234 375.13.1.1 ↗ few secondary structure elements › Rubredoxin-like › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Toprim_C_rpt 0.63 47.0 4.29e-01 86.0% 60.0%
4444380 286.1.1.1 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › DAP_epimerase 0.62 53.0 3.67e-01 100.0% 27.7%
4991900 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.62 43.0 2.53e-01 74.4% 12.2%
4166163 314.1.1.12 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › LplA-B_cat 0.62 46.0 3.01e-01 83.7% 33.2%
5041229 375.13.1.0 ↗ few secondary structure elements › Rubredoxin-like › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Mycobacterium tuberculosis Topoisomerase I C-terminal domain 0.61 43.0 3.89e-01 76.7% 61.7%
3444338 10.1.1.35 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_3 0.60 42.0 2.60e-01 76.7% 14.0%
4417898 286.1.1.1 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › DAP_epimerase 0.59 49.0 3.47e-01 100.0% 27.9%
3702975 3556.1.1.0 ↗ a+b two layers › Uncharacterized Protein Rru_A0810 › Uncharacterized Protein Rru_A0810 › Uncharacterized Protein Rru_A0810 0.59 44.0 3.50e-01 83.7% 64.9%
4369844 286.1.1.1 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › DAP_epimerase 0.59 49.0 3.41e-01 100.0% 27.0%
2512825 10.1.1.25 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Toxin_R_bind_N 0.58 44.0 2.79e-01 95.3% 16.4%
1889033 2004.1.1.203 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › UvrD_C_2 0.57 45.0 2.86e-01 95.3% 37.4%
184803 6029.1.1.1 ↗ beta meanders › Hemin uptake protein hemP › Hemin uptake protein hemP › Hemin uptake protein hemP › hemP 0.56 39.0 3.54e-01 93.0% 52.4%
5029254 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.56 48.0 3.12e-01 100.0% 26.0%
4196255 10.1.1.25 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Toxin_R_bind_N 0.55 41.0 2.71e-01 93.0% 18.0%
3277860 4.1.1.368 ↗ beta barrels › SH3 › SH3 › SH3 › DUF3097_N 0.54 40.0 3.62e-01 86.0% 58.5%
3218150 5.1.1.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 4-bladed 0.54 39.0 2.72e-01 88.4% 33.8%
5030401 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.54 40.0 3.02e-01 90.7% 45.9%
3722971 239.3.1.1 ↗ beta barrels › Ribosomal protein L25-like › FAS1 domain › FAS1 domain › Fasciclin 0.54 42.0 3.03e-01 100.0% 64.8%
3884178 4184.1.1.0 ↗ beta barrels › MFPT repeat › MFPT repeat › MFPT repeat 0.54 40.0 3.54e-01 88.4% 53.3%
4255854 4294.1.1.8 ↗ few secondary structure elements › Trm112p-like › Trm112p-like › Trm112p-like › PF27112 0.53 39.0 3.77e-01 79.1% 72.0%
4073557 241.2.1.1 ↗ a+b two layers › Type III secretory system chaperone-like › Frataxin-like › Frataxin-like › Frataxin_Cyay 0.53 38.0 3.08e-01 83.7% 70.0%
4167904 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.52 44.0 2.87e-01 100.0% 23.4%
3214383 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.52 37.0 3.98e-01 95.3% 97.1%
3786489 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 39.0 2.41e-01 95.3% 18.9%
5051444 3504.3.1.1 ↗ beta barrels › MutM N-terminal domain-like › Fibrinogen binding protein N-terminal domain › Fibrinogen binding protein N-terminal domain › NFACT_N 0.52 43.0 3.03e-01 100.0% 29.0%
3929257 220.4.1.0 ↗ beta barrels › PH domain-like › second barrel domain in viral glycoproteins › second barrel domain in viral glycoproteins 0.51 40.0 3.42e-01 93.0% 83.7%
3384153 206.1.1.20 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.51 42.0 2.70e-01 100.0% 31.2%
4024411 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.51 36.0 3.37e-01 95.3% 58.2%
3602243 331.1.1.25 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › DUF1894 0.50 36.0 3.09e-01 81.4% 90.6%
5065765 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.50 42.0 2.77e-01 100.0% 24.1%