←Back to structures

NC_055804.1__YP_010102929.1__KNU62_gp15__00015

Bact-Vir

NC_055804.1__YP_010102929.1__KNU62_gp15__00015

Identity

Accession:
NC_055804 ↗
Kingdom:
phage

Quality

83.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Stackebrandtviridae› Wizardvirus› Gordonia_phage_Bakery

TaxID: 2591205

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 239-366
PDB
Domain cluster: rep: MT771343.1__QOC56016.1__SEA_CLOWN_18__00018__D229-350
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04233.20 best Phage_Mu_F 32.4 1.90e-07 51.6% 44.6%
D2 medium residues 1-104
PDB
D3 medium residues 496-615_718-728
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2rrdA00 1.10.150.80 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › HRDC domain 0.51 31.0 3.48e-01 94.7% 78.2%
2xmoA02 1.10.246.180 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.51 30.0 3.58e-01 90.1% 88.4%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3791227 4009.1.1.0 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.58 32.0 4.06e-01 88.5% 91.0%
D4 medium residues 616-717
PDB
Domain cluster: rep: MW862982.1__QWY81909.1__SEA_SICARIUS2_4__00004__D502-582
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ukfA00 3.90.70.20 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.68 61.0 4.93e-01 98.0% 68.6%
4q8gA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.64 57.0 3.92e-01 97.1% 65.7%
1rerA01 2.60.98.10 Mainly Beta › Sandwich › Tick-borne Encephalitis virus Glycoprotein; domain 1 › Tick-borne Encephalitis virus Glycoprotein, domain 1 0.62 43.0 4.06e-01 72.5% 99.2%
1qexA03 2.60.40.1680 Mainly Beta › Sandwich › Immunoglobulin-like › 4-oxalocrotonate tautomerase-like 0.59 48.0 4.64e-01 87.3% 97.4%
5yzzC00 2.40.330.10 Mainly Beta › Beta Barrel › At1g16640 B3 domain › DNA-binding pseudobarrel domain 0.58 40.0 3.94e-01 71.6% 88.3%
1zq1A01 2.30.30.520 Mainly Beta › Roll › SH3 type barrels. › 0.57 39.0 4.37e-01 75.5% 92.2%
1iwlA00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.57 40.0 3.40e-01 74.5% 85.9%
4qv2A02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.57 41.0 3.98e-01 77.5% 91.5%
3q39B02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.56 42.0 4.15e-01 79.4% 97.3%
2o6cA00 2.60.40.2480 Mainly Beta › Sandwich › Immunoglobulin-like › Periplasmic metal-binding protein Tp34-type 0.56 42.0 3.68e-01 79.4% 86.7%
6j0qA02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.56 42.0 4.13e-01 79.4% 97.2%
2xzlA02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.56 41.0 4.61e-01 79.4% 100.0%
5ay6A01 2.60.98.20 Mainly Beta › Sandwich › Tick-borne Encephalitis virus Glycoprotein; domain 1 › Flagellar hook protein FlgE 0.56 39.0 3.36e-01 73.5% 97.1%
3hlkA01 2.60.40.2240 Mainly Beta › Sandwich › Immunoglobulin-like › Acyl-CoA thioester hydrolase/BAAT N-terminal domain 0.55 41.0 3.78e-01 78.4% 84.4%
2gk6A02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.55 41.0 4.49e-01 78.4% 100.0%
1yloE02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.54 39.0 4.21e-01 74.5% 100.0%
7ylrA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.53 40.0 3.97e-01 79.4% 100.0%
1ylnA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 37.0 3.63e-01 74.5% 65.8%
6lofA00 2.40.155.10 Mainly Beta › Beta Barrel › Green Fluorescent Protein › Green fluorescent protein 0.52 38.0 3.30e-01 76.5% 75.3%
5yjlD01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 37.0 3.39e-01 74.5% 81.7%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.52 42.0 4.05e-01 89.2% 96.6%
1h7zA00 2.60.90.10 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Adenovirus pIV-related, attachment domain 0.52 38.0 3.11e-01 76.5% 93.2%
2eixA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.52 40.0 4.01e-01 82.4% 94.3%
1vl7A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 33.0 3.05e-01 71.6% 48.1%
3ijfX00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.51 37.0 3.53e-01 97.1% 63.4%
6euaA01 3.90.215.10 Alpha Beta › Alpha-Beta Complex › Gamma Fibrinogen; Chain A, domain 1 › Gamma Fibrinogen, chain A, domain 1 0.51 42.0 3.85e-01 92.2% 95.0%
2oseA00 2.40.100.10 Mainly Beta › Beta Barrel › Cyclophilin › Cyclophilin-like 0.51 36.0 2.97e-01 74.5% 97.9%
4ic5A02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.51 34.0 3.41e-01 78.4% 67.3%
6y43A01 3.90.215.10 Alpha Beta › Alpha-Beta Complex › Gamma Fibrinogen; Chain A, domain 1 › Gamma Fibrinogen, chain A, domain 1 0.51 42.0 3.78e-01 93.1% 92.5%
5hmaA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.50 34.0 3.38e-01 78.4% 66.3%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
7384 219.1.1.21 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C58 0.68 61.0 4.93e-01 98.0% 68.6%
3167972 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.65 58.0 3.37e-01 97.1% 29.6%
4969694 4200.1.1.0 ↗ beta barrels › YmcC-like › YmcC-like › YmcC-like 0.65 45.0 3.75e-01 70.6% 97.6%
2491145 219.1.1.50 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH_1 0.65 58.0 3.67e-01 97.1% 48.5%
3854230 269.1.1.1 ↗ a+b complex topology › Fibrinogen C-terminal domain-like › Fibrinogen C-terminal domain-like › Fibrinogen C-terminal domain-like › Fibrinogen_C 0.59 49.0 3.47e-01 92.2% 61.5%
3210796 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.59 52.0 3.48e-01 97.1% 66.6%
4930890 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.59 42.0 4.82e-01 77.5% 100.0%
4278307 71.1.1.2 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolA 0.58 41.0 3.35e-01 72.5% 77.4%
4366483 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.58 46.0 4.94e-01 95.1% 100.0%
3526900 269.1.1.0 ↗ a+b complex topology › Fibrinogen C-terminal domain-like › Fibrinogen C-terminal domain-like › Fibrinogen C-terminal domain-like 0.58 48.0 3.32e-01 93.1% 52.5%
3359187 4.1.1.351 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_ISE2 0.57 42.0 3.49e-01 77.5% 60.0%
3280641 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.57 41.0 4.16e-01 76.5% 76.0%
4373556 4252.1.1.0 ↗ beta barrels › AttH-like › AttH-like › AttH-like 0.57 43.0 3.52e-01 80.4% 97.9%
3774692 4.1.1.31 ↗ beta barrels › SH3 › SH3 › SH3 › Spin-Ssty 0.57 41.0 4.55e-01 96.1% 98.8%
3789028 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.56 49.0 3.32e-01 97.1% 75.2%
4012136 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.56 46.0 3.21e-01 95.1% 77.4%
1558582 5092.1.1.6 ↗ beta sandwiches › Domain in virus attachment proteins › Domain in virus attachment proteins › Domain in virus attachment proteins › Fiber_head_BAdV-4 0.56 42.0 4.06e-01 81.4% 70.4%
3358389 1.1.11.1 ↗ beta barrels › cradle loop barrel › RIFT-related › Type II restriction endonuclease effector domain › B3 0.55 40.0 3.84e-01 73.5% 82.5%
3691533 10.1.1.41 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › GH43_C2 0.55 48.0 3.60e-01 98.0% 83.4%
3710913 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 43.0 4.08e-01 84.3% 90.0%
3207356 10.1.1.22 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › DUF1349 0.54 47.0 3.82e-01 98.0% 92.0%
2866962 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.54 38.0 3.77e-01 76.5% 69.4%
4999024 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.54 38.0 3.11e-01 72.5% 89.1%
4004549 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.53 41.0 4.16e-01 81.4% 100.0%
5049240 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.53 41.0 4.15e-01 83.3% 98.1%
3552831 1.1.7.41 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › UPF1_1B_dom 0.53 44.0 4.36e-01 88.2% 100.0%
2455725 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.53 41.0 4.15e-01 83.3% 94.3%
5055679 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 33.0 3.72e-01 72.5% 88.6%
4387111 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.53 39.0 4.36e-01 78.4% 100.0%
3280271 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.53 40.0 3.93e-01 82.4% 89.6%
4030625 219.1.1.97 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CEPT76_peptidase 0.53 47.0 3.62e-01 98.0% 68.7%
3218512 214.1.1.0 ↗ a+b two layers › SH2 › SH2 › SH2 0.52 40.0 4.03e-01 82.4% 97.1%
3611195 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.52 41.0 4.03e-01 85.3% 94.5%
3299228 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.52 40.0 3.66e-01 84.3% 72.9%
3255969 2004.1.1.174 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Elong_Iki1 0.51 38.0 2.86e-01 79.4% 86.0%
4658432 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.51 35.0 3.23e-01 76.5% 54.1%
3913637 4.1.1.31 ↗ beta barrels › SH3 › SH3 › SH3 › Spin-Ssty 0.51 35.0 3.75e-01 75.5% 82.2%
3972868 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.51 39.0 3.94e-01 82.4% 98.0%
3396115 11.1.1.53 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DOMON 0.50 41.0 3.62e-01 90.2% 90.3%