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NC_070764.1__YP_010649096.1__PP304_gp052__00052

Bact-Vir

NC_070764.1__YP_010649096.1__PP304_gp052__00052

Identity

Accession:
NC_070764 ↗
Kingdom:
phage

Quality

73.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Godonkavirus› Gordonia_phage_Phendrix

TaxID: 2593335

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 51-163
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4htgA03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.64 43.0 4.95e-01 90.3% 97.5%
3f6gA02 3.30.160.340 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.61 35.0 4.42e-01 83.2% 100.0%
3eqvA02 3.30.450.330 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.61 40.0 3.85e-01 92.0% 57.1%
2z5bA00 3.30.230.100 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.60 32.0 3.09e-01 90.3% 44.1%
4bs9A05 3.30.160.660 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.60 42.0 4.23e-01 92.9% 71.9%
2ywqA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.60 39.0 4.25e-01 92.9% 84.1%
7vd7A01 3.10.450.530 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Ribonuclease toxin, BrnT, of type II toxin-antitoxin system 0.57 29.0 3.22e-01 71.7% 57.6%
4dkwA00 3.30.420.280 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.57 31.0 2.62e-01 76.1% 28.9%
1g5hA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.55 48.0 3.59e-01 99.1% 37.4%
2w9jA00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.55 28.0 3.33e-01 85.0% 71.8%
4ojdH01 2.60.98.60 Mainly Beta › Sandwich › Tick-borne Encephalitis virus Glycoprotein; domain 1 › Cell-cell fusogen EFF/AFF, domain 1 0.55 38.0 3.33e-01 85.8% 48.2%
3l4gC04 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.54 45.0 3.45e-01 100.0% 38.0%
1b7yA00 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.54 44.0 3.39e-01 93.8% 38.5%
6canA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 42.0 3.12e-01 86.7% 68.2%
4icwA00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.51 42.0 4.07e-01 89.4% 86.2%
1so7A00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.51 41.0 2.92e-01 87.6% 29.9%
1d5rA02 2.60.40.1110 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 42.0 3.99e-01 91.2% 84.2%
2obdA02 3.15.10.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Bactericidal permeability-increasing protein; domain 1 0.50 41.0 3.48e-01 87.6% 66.7%
3zqsA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.50 36.0 3.95e-01 90.3% 95.5%
2r55A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.50 44.0 3.58e-01 95.6% 87.5%
3oyyA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.50 27.0 3.46e-01 79.6% 90.9%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3304792 2484.1.1.110 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MULE 0.70 40.0 3.79e-01 85.0% 46.7%
3166896 2484.1.1.10 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.69 55.0 3.79e-01 85.0% 40.3%
3411385 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 40.0 3.40e-01 84.1% 36.8%
3940149 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.64 40.0 4.45e-01 92.0% 78.9%
4054729 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.64 41.0 4.82e-01 91.2% 97.3%
4638787 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.63 43.0 5.01e-01 94.7% 100.0%
4508852 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.62 54.0 5.41e-01 95.6% 94.8%
4010500 7503.1.1.24 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › PF25851 0.62 50.0 4.55e-01 87.6% 89.0%
3600093 241.15.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.62 54.0 5.08e-01 94.7% 94.8%
3951048 331.4.1.17 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › ResB 0.61 39.0 3.86e-01 96.5% 60.0%
4030017 837.1.1.0 ↗ a+b two layers › Ribosomal protein S16 › Ribosomal protein S16 › Ribosomal protein S16 0.61 33.0 3.90e-01 79.6% 77.3%
3194095 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.61 44.0 4.79e-01 93.8% 90.5%
4954298 504.1.1.0 ↗ a+b two layers › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB 0.60 38.0 4.07e-01 89.4% 74.7%
4011588 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.59 39.0 4.65e-01 92.0% 100.0%
3223921 2484.1.1.259 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF26742 0.59 36.0 3.99e-01 77.0% 75.6%
3927366 2484.1.1.4 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.59 36.0 3.34e-01 81.4% 46.0%
3988064 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.58 35.0 4.28e-01 87.6% 97.1%
3370322 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.58 39.0 4.31e-01 94.7% 87.8%
3924083 2484.1.1.204 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27046, PF27073 0.58 34.0 3.04e-01 79.6% 38.2%
5061259 330.2.1.1 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › Ribosomal_S30AE 0.58 45.0 4.74e-01 99.1% 93.0%
3710326 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.58 39.0 4.36e-01 91.2% 90.6%
3730653 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.57 34.0 4.18e-01 86.7% 97.1%
3267746 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.57 39.0 4.39e-01 89.4% 94.1%
3445028 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.56 39.0 4.43e-01 87.6% 100.0%
3487306 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.56 46.0 4.18e-01 88.5% 93.5%
3517477 2484.1.1.230 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27073 0.56 34.0 3.53e-01 80.5% 62.9%
3436776 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.56 35.0 3.73e-01 90.3% 71.0%
3782867 11.2.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2 0.56 46.0 4.45e-01 89.4% 90.0%
3801624 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.55 36.0 3.84e-01 92.9% 76.0%
3836543 11.2.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2 0.55 46.0 4.02e-01 91.2% 77.1%
3255230 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.54 45.0 3.98e-01 89.4% 92.7%
3843423 2484.5.1.3 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH_2 0.54 34.0 3.27e-01 77.0% 53.1%
3621725 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.54 45.0 4.29e-01 88.5% 91.5%
3707085 5.1.2.33 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › BNR_3 0.54 47.0 3.80e-01 96.5% 50.5%
5054267 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.54 37.0 2.88e-01 89.4% 32.7%
3940017 5.1.3.6 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1 0.53 36.0 2.67e-01 75.2% 26.7%
3259407 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 37.0 4.14e-01 92.0% 95.3%
3846016 11.2.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › PI3K_C2 0.53 44.0 3.87e-01 88.5% 84.8%
3929756 2484.5.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH 0.52 33.0 3.63e-01 81.4% 80.0%
3561019 2484.5.1.3 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH_2 0.52 33.0 3.18e-01 79.6% 53.8%
3995220 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 38.0 3.40e-01 77.0% 88.7%
3352475 330.3.1.0 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like 0.52 34.0 3.93e-01 88.5% 100.0%
3864913 218.1.1.2 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › Enolase_N 0.51 40.0 3.64e-01 84.1% 88.4%
3596524 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 38.0 4.15e-01 84.1% 94.7%
3891207 11.2.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2 0.50 41.0 4.05e-01 89.4% 83.2%
3309019 5.1.3.67 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_1 0.50 40.0 2.91e-01 85.8% 47.8%
3210750 223.2.1.48 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › FNIP_N, Longin_2 0.50 42.0 3.93e-01 92.9% 94.5%