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NC_070884.1__YP_010661393.1__PP935_gp008__00008

Bact-Vir

NC_070884.1__YP_010661393.1__PP935_gp008__00008

Identity

Accession:
NC_070884 ↗
Kingdom:
phage

Quality

87.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Trinifflemingvirus› Rhizobium_phage_RHph_N34

TaxID: 2509586

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 2-66
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1btkA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 46.0 3.48e-01 100.0% 35.6%
7vbnL01 3.30.160.190 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › atu1810 like domain 0.56 50.0 4.40e-01 100.0% 69.5%
3imoC00 3.30.920.70 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › 0.55 42.0 3.66e-01 86.2% 87.9%
3lxqA01 3.30.1120.80 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.52 33.0 2.98e-01 89.2% 42.4%
4lwoB02 2.70.160.11 Mainly Beta › Distorted Sandwich › Hnrnp arginine n-methyltransferase1 › Hnrnp arginine n-methyltransferase1 0.52 43.0 3.24e-01 100.0% 96.2%
3g16B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 36.0 2.83e-01 76.9% 37.5%
2je2A00 3.50.70.20 Alpha Beta › 3-Layer(bba) Sandwich › Chalcone isomerase › Cytochrome P460 0.50 38.0 3.00e-01 86.2% 68.8%
2ljuA01 3.30.160.190 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › atu1810 like domain 0.50 44.0 4.26e-01 100.0% 89.3%
4nkbA01 3.30.1120.120 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.50 39.0 3.32e-01 98.5% 50.0%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5077745 243.6.1.9 ↗ a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain › TGT_C2 0.62 44.0 4.20e-01 76.9% 92.5%
5054847 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.59 46.0 3.75e-01 100.0% 45.0%
3390587 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.56 38.0 4.00e-01 78.5% 78.3%
3785535 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.54 47.0 3.80e-01 100.0% 73.8%
5002722 223.1.1.23 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_2 0.53 42.0 3.22e-01 100.0% 34.7%
3215615 11.1.1.532 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C6 0.52 37.0 3.22e-01 76.9% 56.4%
3248470 3468.1.1.0 ↗ a+b two layers › HLTF protein HIRAN domain › HLTF protein HIRAN domain › HLTF protein HIRAN domain 0.51 43.0 3.64e-01 100.0% 70.0%
D2 high residues 73-146
PDB
Domain cluster: representative
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3iayA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.59 44.0 3.23e-01 81.1% 83.1%
2hgsA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.57 37.0 3.20e-01 100.0% 44.1%
3es1A01 2.20.70.150 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.56 27.0 3.53e-01 81.1% 86.5%
2ychA02 3.30.1490.300 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.56 34.0 3.63e-01 82.4% 73.3%
4hstB02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.55 41.0 4.22e-01 78.4% 89.7%
1fm2B03 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.52 37.0 3.91e-01 77.0% 90.9%
1cp9B02 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 38.0 3.90e-01 89.2% 82.2%
3vpyA00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.51 44.0 3.62e-01 100.0% 81.4%
1dw9A02 3.30.1160.10 Alpha Beta › 2-Layer Sandwich › Cyanate Lyase; Chain: A, domain 2 › Cyanate lyase, C-terminal domain 0.51 34.0 3.55e-01 91.9% 75.0%
4wksC02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.50 37.0 3.71e-01 79.7% 89.3%
5ib9A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.50 39.0 2.74e-01 89.2% 70.2%
4fdtB00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.50 39.0 2.51e-01 86.5% 88.1%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3368695 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.60 45.0 2.87e-01 81.1% 45.9%
3294964 3256.1.1.0 ↗ a+b two layers › DUF2233 N-terminal domain › DUF2233 N-terminal domain › DUF2233 N-terminal domain 0.57 22.0 3.16e-01 97.3% 100.0%
3558197 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.55 44.0 3.12e-01 89.2% 72.7%
4012111 812.2.1.0 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain 0.55 37.0 3.93e-01 91.9% 81.0%
4449325 387.1.1.24 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related › Toxin_35 0.55 32.0 3.83e-01 81.1% 93.3%
4059788 387.1.1.24 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related › Toxin_35 0.55 34.0 3.59e-01 86.5% 70.8%
4973231 304.48.1.20 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Thg1 0.54 42.0 3.04e-01 89.2% 86.7%
4778855 210.1.2.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain › Penicil_amidase 0.53 39.0 2.78e-01 82.4% 24.2%
3972135 205.1.1.71 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4_7, Fer4_11 0.53 43.0 3.32e-01 91.9% 78.9%
7696 812.2.1.1 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain › Cyanate_lyase 0.51 34.0 3.52e-01 91.9% 72.9%
4980065 210.1.2.0 ↗ a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain 0.51 41.0 2.40e-01 89.2% 34.1%
3810414 812.2.1.1 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain › Cyanate_lyase 0.51 34.0 3.35e-01 91.9% 63.7%
4262649 812.2.1.1 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain › Cyanate_lyase 0.51 34.0 3.34e-01 91.9% 63.7%
3195985 3447.1.1.9 ↗ alpha bundles › Isoprenylcysteine carboxyl methyltransferase (ICMT) › Isoprenylcysteine carboxyl methyltransferase (ICMT) › Isoprenylcysteine carboxyl methyltransferase (ICMT) › ERG4_ERG24, DUF1295 0.51 35.0 2.60e-01 82.4% 27.9%